Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold198
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1589021
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.28
Warning! 220217 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1067786 original size:17 final size:17
Alignment explanation
Indices: 1067732--1067789 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1067722 CTGTAAACTT
1067732 GTTTGAAGCAGTGTGAC
1 GTTTGAAGCAGTGTGAC
* *
1067749 ATTTGAA-C--TGTAAAC
1 GTTTGAAGCAGTGT-GAC
1067764 TTGTTTGAAGCAGTGTGAC
1 --GTTTGAAGCAGTGTGAC
1067783 GTTTGAA
1 GTTTGAA
1067790 CTGTAAACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
14 3 0.10
15 2 0.06
16 1 0.03
17 19 0.61
18 1 0.03
19 2 0.06
20 3 0.10
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (17 bp):
GTTTGAAGCAGTGTGAC
Found at i:1067788 original size:34 final size:34
Alignment explanation
Indices: 1067574--1067798 Score: 181
Period size: 34 Copynumber: 6.3 Consensus size: 34
1067564 TAAAATCCTA
1067574 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
1 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
* * ** **
1067608 AATTGTAAACTTTTCTTTCTA-CTAGATGTG-TGTTATG
1 AACTGTAAAC--TTGTTTGAAGC-AG-TGTGACATT-TG
1067645 CAAACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
1 --AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
* * **
1067681 AACTGTAAACTT-TTCT--ACCTACTAGATTTCTATTATG
1 AACTGTAAACTTGTT-TGAAGC-AGT-G-TGAC-ATT-TG
1067718 CAAACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
1 --AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
*
1067754 AACTGTAAACTTGTTTGAAGCAGTGTGACGTTTG
1 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
1067788 AACTGTAAACT
1 AACTGTAAACT
1067799 GTTCTACTTT
Statistics
Matches: 150, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
32 2 0.01
33 4 0.03
34 67 0.45
35 3 0.02
36 21 0.14
37 21 0.14
38 3 0.02
39 23 0.15
40 4 0.03
41 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (34 bp):
AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG
Found at i:1068004 original size:23 final size:24
Alignment explanation
Indices: 1067978--1068035 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
1067968 TAGTGGTTCC
1067978 AGGTCAAGGTCAAAT-ACATAT-A
1 AGGTCAAGGTCAAATAACATATCA
*
1068000 TAGGTCAAGG-CCAATAACATATCA
1 -AGGTCAAGGTCAAATAACATATCA
*
1068024 AGCTCAAGGTCA
1 AGGTCAAGGTCA
1068036 TATGCATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 23 0.79
24 2 0.07
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (24 bp):
AGGTCAAGGTCAAATAACATATCA
Found at i:1075445 original size:21 final size:21
Alignment explanation
Indices: 1075421--1075509 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
1075411 GTGTTTTATG
* *
1075421 TATATGCAATAGTAATATCAT
1 TATATGCAGTAGTAACATCAT
*
1075442 TATATGCAGTGGTAACATCAT
1 TATATGCAGTAGTAACATCAT
*
1075463 TACATGCAGT-GCTAACATCAT
1 TATATGCAGTAG-TAACATCAT
* *
1075484 TATATGCAGTACTAAAATCAT
1 TATATGCAGTAGTAACATCAT
1075505 TATAT
1 TATAT
1075510 ACTATTATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.02
21 58 0.98
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
TATATGCAGTAGTAACATCAT
Found at i:1077528 original size:21 final size:21
Alignment explanation
Indices: 1077502--1077541 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1077492 AATGATGTAC
1077502 GTTAGCACTGCATATAATGAT
1 GTTAGCACTGCATATAATGAT
1077523 GTTAGCACTGCATATAATG
1 GTTAGCACTGCATATAATG
1077542 CTATTACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (21 bp):
GTTAGCACTGCATATAATGAT
Found at i:1081301 original size:68 final size:68
Alignment explanation
Indices: 1081218--1081351 Score: 214
Period size: 68 Copynumber: 2.0 Consensus size: 68
1081208 GATCATCTCC
* * * *
1081218 TTGTACATGATGCTCTCTTACCATTGTATTAAGATAATCCATTCTCTCTGTATGACTGATCACCT
1 TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT
1081283 CAT
66 CAT
* *
1081286 TTGTACATGATGCTCTGTTACCATTATATTAAGACAATCCATTCTTTCTGTAGGACTGATAACCT
1 TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT
1081351 C
66 C
1081352 CTTCGCTGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (68 bp):
TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT
CAT
Found at i:1081477 original size:21 final size:21
Alignment explanation
Indices: 1081453--1081527 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
1081443 AACTCTATTG
*
1081453 TACACCCCACAGGTAAATTTT
1 TACACCCCACAGGTAAATTTA
*
1081474 TACACCCCTA-AAGTAACA-TTA
1 TACACCCC-ACAGGTAA-ATTTA
*
1081495 TACACCCCACAGGTAAATTTC
1 TACACCCCACAGGTAAATTTA
*
1081516 TACACCCAACAG
1 TACACCCCACAG
1081528 CATCATTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.23
Consensus pattern (21 bp):
TACACCCCACAGGTAAATTTA
Found at i:1081512 original size:42 final size:41
Alignment explanation
Indices: 1081449--1081744 Score: 286
Period size: 42 Copynumber: 7.2 Consensus size: 41
1081439 CATCAACTCT
*
1081449 ATTGTACACCCCACAGGTAAATTTTTACACCCCTAA-AGTAAC
1 ATTGTACACCCCACAGGTAAA-TTGTACACCCC-AACAGTAAC
* * * *
1081491 ATTATACACCCCACAGGTAAATTTCTACA-CCCAACAGCATC
1 ATTGTACACCCCACAGGTAAA-TTGTACACCCCAACAGTAAC
* *
1081532 ATTGTACACCCCAC------ATTGTACACCCCAACAGCAAT
1 ATTGTACACCCCACAGGTAAATTGTACACCCCAACAGTAAC
* * *
1081567 ATTGTACATCTCACAGGTAATATTGTACACCCCAAAAGTAAC
1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC
**
1081609 ATTGTACATTCCACAGGTAACATTGTACACCCCAACAGTAAC
1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC
* *
1081651 ATTGTACACCCCACAGGTAACATTGTACACCCCAACAGCAAT
1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC
* * * * *
1081693 ATTGTACATCTCACAGGTAACATTGTAC-TCCCTACAGTTAAA
1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAG-TAAC
1081735 ATTGTACACC
1 ATTGTACACC
1081745 TCAACAGTAA
Statistics
Matches: 216, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
34 6 0.03
35 23 0.11
40 2 0.01
41 27 0.12
42 158 0.73
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.24
Consensus pattern (41 bp):
ATTGTACACCCCACAGGTAAATTGTACACCCCAACAGTAAC
Found at i:1081550 original size:14 final size:14
Alignment explanation
Indices: 1081531--1081558 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1081521 CCAACAGCAT
1081531 CATTGTACACCCCA
1 CATTGTACACCCCA
1081545 CATTGTACACCCCA
1 CATTGTACACCCCA
1081559 ACAGCAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21
Consensus pattern (14 bp):
CATTGTACACCCCA
Found at i:1081907 original size:21 final size:21
Alignment explanation
Indices: 1081544--1081938 Score: 268
Period size: 21 Copynumber: 18.6 Consensus size: 21
1081534 TGTACACCCC
*
1081544 ACATTGTACACCCCAACA-GCA
1 ACATTGTACACCCC-ACAGGTA
* * *
1081565 ATATTGTACATCTCACAGGTA
1 ACATTGTACACCCCACAGGTA
* * *
1081586 ATATTGTACACCCCAAAAGTA
1 ACATTGTACACCCCACAGGTA
**
1081607 ACATTGTACATTCCACAGGTA
1 ACATTGTACACCCCACAGGTA
1081628 ACATTGTACACCCCAACA-GTA
1 ACATTGTACACCCC-ACAGGTA
1081649 ACATTGTACACCCCACAGGTA
1 ACATTGTACACCCCACAGGTA
*
1081670 ACATTGTACACCCCAACA-GCA
1 ACATTGTACACCCC-ACAGGTA
* * *
1081691 ATATTGTACATCTCACAGGTA
1 ACATTGTACACCCCACAGGTA
* * *
1081712 ACATTGTACTCCCTACAGTTA
1 ACATTGTACACCCCACAGGTA
* *
1081733 AAATTGTACACCTCAACA-GTA
1 ACATTGTACACC-CCACAGGTA
* ***
1081754 ACGTTGTACACCTGGCAGGTA
1 ACATTGTACACCCCACAGGTA
* *
1081775 ATATTGTACTGTACACCCAACA-ATA
1 ACATTGTAC---AC-CCC-ACAGGTA
**
1081800 ACATTAAACACCCCACAGGTA
1 ACATTGTACACCCCACAGGTA
*
1081821 AAATTGTACACCCCAACA-GTA
1 ACATTGTACACCCC-ACAGGTA
* * *
1081842 ATATTATACATCCCACAGGTA
1 ACATTGTACACCCCACAGGTA
* * *
1081863 ACATTGTACGCCCTAACA-GCA
1 ACATTGTACACCC-CACAGGTA
* *
1081884 ATATTGTACATCCCACAGGTA
1 ACATTGTACACCCCACAGGTA
* * *
1081905 ATATTATACA-CCCAGTAGGTGA
1 ACATTGTACACCCCA-CAGGT-A
1081927 A-ATTGTACACCC
1 ACATTGTACACCC
1081939 TTCAGAGTGA
Statistics
Matches: 289, Mismatches: 65, Indels: 39
0.74 0.17 0.10
Matches are distributed among these distances:
20 24 0.08
21 230 0.80
22 22 0.08
24 2 0.01
25 9 0.03
26 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
ACATTGTACACCCCACAGGTA
Found at i:1081915 original size:151 final size:152
Alignment explanation
Indices: 1081632--1081916 Score: 398
Period size: 151 Copynumber: 1.9 Consensus size: 152
1081622 CAGGTAACAT
* ** * *
1081632 TGTACACCCCAACAGTAACATTGTACACCCCACAGGTAACATTGTACACCCCAACAGCAATATTG
1 TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA
* * * * *
1081697 TACATCTCACAGGTAACATTGTACTCCCTACAGTTAAAATTGTACACCTCAACAGTAACGTTGTA
66 TACATCCCACAGGTAACATTGTACGCCCTACAGTCAAAATTGTACACCTCAACAGTAACATTATA
1081762 CACCTGGCAGGTAATATTGTAC
131 CACCTGGCAGGTAATATTGTAC
*
1081784 TGTACA-CCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGTAATATTA
1 TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA
* *
1081848 TACATCCCACAGGTAACATTGTACGCCCTAACAG-CAATATTGTACATCC-C-ACAGGTAATATT
66 TACATCCCACAGGTAACATTGTACGCCCT-ACAGTCAAAATTGTACA-CCTCAACA-GTAACATT
1081910 ATACACC
128 ATACACC
1081917 CAGTAGGTGA
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
150 3 0.03
151 102 0.87
152 12 0.10
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (152 bp):
TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA
TACATCCCACAGGTAACATTGTACGCCCTACAGTCAAAATTGTACACCTCAACAGTAACATTATA
CACCTGGCAGGTAATATTGTAC
Found at i:1082203 original size:30 final size:32
Alignment explanation
Indices: 1082167--1082228 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
1082157 CTCAGTCTGA
1082167 ATCAGGTAATGTC-AGTGGGAC-A-ATTAATGC
1 ATCAGGTAATGTCAAG-GGGACAACATTAATGC
1082197 ATCAGGTAATGTCAAGGGGACAACATTAATGC
1 ATCAGGTAATGTCAAGGGGACAACATTAATGC
1082229 CCCTCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 18 0.62
31 3 0.10
32 8 0.28
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (32 bp):
ATCAGGTAATGTCAAGGGGACAACATTAATGC
Found at i:1083957 original size:31 final size:28
Alignment explanation
Indices: 1083919--1083994 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
1083909 TCAGTCAGAA
1083919 CAAACAATTAGTCCAATGGATAACAACCATT
1 CAAACAATTAGTCCAATGG---ACAACCATT
*
1083950 CAAACAATTAGTCCATTGGACAACCATT
1 CAAACAATTAGTCCAATGGACAACCATT
*
1083978 CAGAA-ATTTAGTCCAAT
1 CA-AACAATTAGTCCAAT
1083995 TAACTGTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 21 0.51
29 2 0.05
31 18 0.44
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (28 bp):
CAAACAATTAGTCCAATGGACAACCATT
Found at i:1084780 original size:38 final size:38
Alignment explanation
Indices: 1084710--1084784 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
1084700 CAGGAGTCAA
* * **
1084710 AGTGTATAAGTACCTTAAACTGAGACGTTTCTTCTCCT
1 AGTGAATAAATACCTTAAACTGAGACAATTCTTCTCCT
1084748 AGTGAATAAATACCTTAAACTCG-GACAATTCTTCTCC
1 AGTGAATAAATACCTTAAACT-GAGACAATTCTTCTCC
1084785 ATTCGTAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (38 bp):
AGTGAATAAATACCTTAAACTGAGACAATTCTTCTCCT
Found at i:1087421 original size:28 final size:28
Alignment explanation
Indices: 1087396--1088324 Score: 1615
Period size: 28 Copynumber: 33.2 Consensus size: 28
1087386 ACCTACAGGA
*
1087396 AGTGTACTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087424 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087452 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
* *
1087480 AGTGTACTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087508 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
* * *
1087536 AGTTTACTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087564 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087592 AGTGTAATATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087620 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087648 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087676 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087704 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087732 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
* *
1087760 AGTGTATTGTAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087788 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087816 AGTGTATTATAGTTTGTTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087844 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087872 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1087900 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087928 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087956 AGTGTAATATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1087984 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1088012 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088040 AGTGCATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088068 AGTGTAATATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1088096 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088124 AGTGTATTATACTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1088152 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088180 AGTGTATTATAGTTTGTTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088208 AGTGTACTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
*
1088236 AGTGTATTATAGTTTGGTACTTACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
1088264 AGTGTATTATAGTTTGGTACTGACAGTG
1 AGTGTATTATAGTTTGGTACTGACAGTG
* * *
1088292 AGTGTAGTATAGTTTGGTACTTACAGTA
1 AGTGTATTATAGTTTGGTACTGACAGTG
1088320 AGTGT
1 AGTGT
1088325 GTTGTAGACC
Statistics
Matches: 855, Mismatches: 46, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 855 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (28 bp):
AGTGTATTATAGTTTGGTACTGACAGTG
Found at i:1089260 original size:80 final size:80
Alignment explanation
Indices: 1089120--1089858 Score: 815
Period size: 80 Copynumber: 9.2 Consensus size: 80
1089110 GTTATGAAAA
* * * * * *
1089120 ACTTTTGTACAATGCATGTCCTCACAAGCTT-AGACGACTTACTTTTGTACAATGCGTGTCATCA
1 ACTTTTGTACAATGCGTGTCCTCACGAG-TTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA
*
1089184 TTTGTTTGGAGGACTT
65 TTGGTTTGGAGGACTT
* * * *
1089200 ACTTTCGTACAATGCGTGTCCTCACAAGTTGGGAGGACTTGCTTTTGTATGATGCCTGTCATCAT
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
* *
1089265 TGGTTGGGTGGACTT
66 TGGTTTGGAGGACTT
* * * *
1089280 ACTTTTGTACAATACATGTCCTCATGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAT
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
1089345 TGGTTTGGAGGACTT
66 TGGTTTGGAGGACTT
* ** * *
1089360 ACTTTCGTACAATGCAAGTCCTCACGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAA
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
1089425 TGGTTTGGAGGACTT
66 TGGTTTGGAGGACTT
** * *
1089440 ACTTTCATACAATGCGTGTCCTCACGAGTTTGGAGGACTTACTTTTGTATGATGCCTGTCATCAT
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
1089505 TGG-TTGGAAGGACTT
66 TGGTTTGG-AGGACTT
* * * * * * * ** * **
1089520 ACTTTTGTACGATGTGTGTCATCATTG-GTTTGGAGGACTTACATTTGTACAATGTGTCTCCGCA
1 ACTTTTGTACAATGCGTGTCCTCA-CGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA
*** * *
1089584 AAAGTTGGGAGGACCT
65 TTGGTTTGGAGGACTT
* *
1089600 ACTTTCGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCATGTCATCAT
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
1089665 TGGTTTGGAGGACTT
66 TGGTTTGGAGGACTT
* * * * ** * * *
1089680 ACTTTTGTACGATGTGTCTCCTCAAGAGTTGGGAGGACTTACTTTCATACAATGCATGTCCTCA-
1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
* *
1089744 CGAATTTGGAGGACTT
66 TG-GTTTGGAGGACTT
* * * * * *
1089760 ACTTTTGTACAATGTGTGTCATCATTG-GTTTGGAGGACTTACTTTTTTA-GATGCGTGTCATCA
1 ACTTTTGTACAATGCGTGTCCTCA-CGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA
*
1089823 TTGATTTGGAGGACTT
65 TTGGTTTGGAGGACTT
*
1089839 ACTTTTGTACGATGCGTGTC
1 ACTTTTGTACAATGCGTGTC
1089859 ATCATTGGCT
Statistics
Matches: 561, Mismatches: 90, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
79 50 0.09
80 506 0.90
81 5 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (80 bp):
ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT
TGGTTTGGAGGACTT
Found at i:1089359 original size:120 final size:119
Alignment explanation
Indices: 1089120--1089862 Score: 731
Period size: 120 Copynumber: 6.2 Consensus size: 119
1089110 GTTATGAAAA
* * * * *
1089120 ACTTTTGTACAATGCATGTCCTCACAAGCTT-AGACGACTTACTTTTGTACAATGCGTGTCATCA
1 ACTTTCGTACAATGCATGTCATCACGAG-TTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA
* * *
1089184 TTTGTTTGGAGGACTTACTTTCGTACAATGCGTGTCCTCACAAGTTGGGAGGACTT
65 TTGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT
* * ** * * * * * *
1089240 GCTTTTGTATGATGCCTGTCATCATTG-GTTGGGTGGACTTACTTTTGTACAATACATGTCCTCA
1 ACTTTCGTACAATGCATGTCATCA-CGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA
* ** * * * *
1089304 -TGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCATTGGTTTGGAGGACTT
65 TTG-GTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT
* * ** * *
1089360 ACTTTCGTACAATGCAAGTCCTCACGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAA
1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT
** * *
1089425 TGGTTTGGAGGACTTACTTTCATACAATGCGTGTCCTCACGAGTTTGGAGGACTT
66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAG-GTTGGGAGGACTT
* ** * * * * *
1089480 ACTTTTGTATGATGCCTGTCATCATTG-GTTGGAAGGACTTACTTTTGTACGATGTGTGTCATCA
1 ACTTTCGTACAATGCATGTCATCA-CGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA
* * * * * *
1089544 TTGGTTTGGAGGACTTACATTTGTACAATGTGTCTCCGCAAAAGTTGGGAGGACCT
65 TTGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTC-AAGGTTGGGAGGACTT
* * * *
1089600 ACTTTCGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCATGTCATCAT
1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT
* * *
1089665 TGGTTTGGAGGACTTACTTTTGTACGATGTGTCTCCTCAAGAGTTGGGAGGACTT
66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAG-GTTGGGAGGACTT
* * * * *
1089720 ACTTTCATACAATGCATGTCCTCACGAATTTGGAGGACTTACTTTTGTACAATGTGTGTCATCAT
1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT
* * * * * *
1089785 TGGTTTGGAGGACTTACTTTTTTA-GATGCGTGTCATCATTGATTTGGAGGACTT
66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT
* * *
1089839 ACTTTTGTACGATGCGTGTCATCA
1 ACTTTCGTACAATGCATGTCATCA
1089863 TTGGCTTTGA
Statistics
Matches: 511, Mismatches: 101, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
119 49 0.10
120 458 0.90
121 4 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (119 bp):
ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT
TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAGGTTGGGAGGACTT
Found at i:1089864 original size:40 final size:40
Alignment explanation
Indices: 1089155--1089878 Score: 590
Period size: 40 Copynumber: 18.1 Consensus size: 40
1089145 AAGCTTAGAC
1089155 GACTTACTTTTGTACAATGCGTGTCATCATTTG-TTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCA-TTGATTTGGAG
* * ** *
1089195 GACTTACTTTCGTACAATGCGTGTCCTCA-CAAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
* ** * * * *
1089235 GACTTGCTTTTGTATGATGCCTGTCATCATTGGTTGGGTG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* * * *
1089275 GACTTACTTTTGTACAATACATGTCCTCA-TGAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
** * *
1089315 GACTTACTTTTGTATGATGCCTGTCATCATTGGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* ** * * *
1089355 GACTTACTTTCGTACAATGCAAGTCCTCA-CGAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
** * * *
1089395 GACTTACTTTTGTATGATGCCTGTCATCAATGGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
** * *
1089435 GACTTACTTTCATACAATGCGTGTCCTCA-CGAGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
** * *
1089475 GACTTACTTTTGTATGATGCCTGTCATCATTG-GTTGGAAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGG-AG
* * *
1089515 GACTTACTTTTGTACGATGTGTGTCATCATTGGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* * * ** ** *
1089555 GACTTACATTTGTACAATGTGTCTCCGCA-AAAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
* * * * *
1089595 GACCTACTTTCGTACAATGCGTGTCCTCA-CGAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
* * *
1089635 GACTTACTTTTGTACGATGCATGTCATCATTGGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* * * * * *
1089675 GACTTACTTTTGTACGATGTGTCTCCTCA-AGAGTTGGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG
** * * *
1089715 GACTTACTTTCATACAATGCATGTCCTCA-CGAATTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTG-ATTTGGAG
* *
1089755 GACTTACTTTTGTACAATGTGTGTCATCATTGGTTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* *
1089795 GACTTACTTTTTTA-GATGCGTGTCATCATTGATTTGGAG
1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
* *
1089834 GACTTACTTTTGTACGATGCGTGTCATCATTGGCTTT-GAG
1 GACTTACTTTTGTACAATGCGTGTCATCATT-GATTTGGAG
1089874 GACTT
1 GACTT
1089879 GGCTAACTGT
Statistics
Matches: 545, Mismatches: 121, Indels: 36
0.78 0.17 0.05
Matches are distributed among these distances:
39 44 0.08
40 486 0.89
41 15 0.03
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (40 bp):
GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG
Found at i:1091964 original size:34 final size:34
Alignment explanation
Indices: 1091902--1092057 Score: 249
Period size: 34 Copynumber: 4.6 Consensus size: 34
1091892 ACCCTGGCTG
* *
1091902 TTTATGTGTGGCAGCCTCACTATATAACCTCGCTA
1 TTTATGTGTGGCAACC-CTCTATATAACCTCGCTA
1091937 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA
1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA
*
1091971 TTTATGTGTGGCAACCCTCTATATAACCTTGCTA
1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA
* * *
1092005 TTTATGTGTGGCAACCCTCAAAATAACCTCGCTT
1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA
1092039 TTTATGTGTGGCAACCCTC
1 TTTATGTGTGGCAACCCTC
1092058 AAAATAACTA
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
34 99 0.87
35 15 0.13
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (34 bp):
TTTATGTGTGGCAACCCTCTATATAACCTCGCTA
Found at i:1092536 original size:42 final size:42
Alignment explanation
Indices: 1092473--1093030 Score: 753
Period size: 42 Copynumber: 13.0 Consensus size: 42
1092463 CAACCGTTTT
*
1092473 CTAACATTG-CTGTACAGTTGCCCACACTAACAGGCCCACTTC
1 CTAACATTGACT-TACAGTTGCCCACACTAACAGGCCCACTCC
* * *
1092515 CTAACACTGACTTACATTTGCCCACACTAACAGACCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
* *
1092557 CTAACATTGACTTACAGTTGCCAACACTAACAGGCTCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
1092599 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC
1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCC
1092641 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC
1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCC
* **
1092683 CTAACACTGACTTACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGG-------CCCACTCC
* * *
1092732 CTTACACTGACTTACAGTTGCCAACACTAACAGGCCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
*
1092774 CTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
1092816 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
* **
1092858 CTAACACTGACTTACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGG-------CCCACTCC
* * *
1092907 CTTACACTGACTTACAGTTGCCAACACTAACAGGCCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
*
1092949 CTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
*
1092991 CTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT
1093031 TACAATGACA
Statistics
Matches: 465, Mismatches: 34, Indels: 34
0.87 0.06 0.06
Matches are distributed among these distances:
41 2 0.00
42 382 0.82
43 3 0.01
49 78 0.17
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (42 bp):
CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC
Found at i:1092790 original size:175 final size:175
Alignment explanation
Indices: 1092473--1093030 Score: 938
Period size: 175 Copynumber: 3.2 Consensus size: 175
1092463 CAACCGTTTT
* *
1092473 CTAACATTG-CTGTACAGTTGCCCACACTAACAGGCCCACTTCCTAACACTGACTTACATTTGCC
1 CTAACATTGACT-TACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC
** * * *
1092537 CACACTAACA-G---A---CCCACTCCCTAACATTGACTTACAGTTGCCAACACTAACAGGCTCA
65 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA
*
1092595 CTCCCTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC
130 CTCCCTAACATTGACTTACAGTTGCCCA-CACTAACAGACCCACTCC
1092641 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC
1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC
1092705 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA
65 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA
1092770 CTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
130 CTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
1092816 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT
1092881 GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC
66 GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC
1092946 TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
131 TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
*
1092991 CTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT
1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT
1093031 TACAATGACA
Statistics
Matches: 370, Mismatches: 9, Indels: 15
0.94 0.02 0.04
Matches are distributed among these distances:
167 3 0.01
168 63 0.17
169 3 0.01
172 1 0.00
175 294 0.79
176 6 0.02
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (175 bp):
CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT
GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC
TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC
Found at i:1092853 original size:217 final size:211
Alignment explanation
Indices: 1092485--1093030 Score: 799
Period size: 217 Copynumber: 2.5 Consensus size: 211
1092475 AACATTGCTG
* * *
1092485 TACAGTTGCCCACACTAACAGGCCCACTTCCTAACACTGACTTACATTTGCCCACACTAACAGAC
1 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC
* *
1092550 CCACTCCCTAACATTGACTTACAGTTGCCAACACTAACAGGCTCACTCCCTAACATTGACTTACA
66 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTGACTTACA
*
1092615 GTTGCCACCACTAACAGGCCCACTCCCTAACATTGACTTACAGTTGCCACCACTAACAGG-CCCA
131 GTTGCCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAACAGGCCCCA
1092679 CTCCCTAACACTGACT
196 CTCCCTAACACTGACT
** * *
1092695 TACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACT
1 TACAGTTGCCAACACTAACAGG-------CCCACTCCCTAACACTGACTTACAGTTGCCCACACT
* *
1092760 AACAGGCCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCCCTAACATTG
59 AACAGACCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTG
**
1092825 ACTTACAGTTGCC-CACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCTGCACTAAC
124 ACTTACAGTTGCCAC-CACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAAC
*
1092889 AGGCCCACTTCCCACTCCCTTACACTGACT
188 AGG----C--CCCACTCCCTAACACTGACT
*
1092919 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGAC
1 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC
*
1092984 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT
66 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT
1093031 TACAATGACA
Statistics
Matches: 299, Mismatches: 22, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
210 20 0.07
216 1 0.00
217 239 0.80
224 39 0.13
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (211 bp):
TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC
CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTGACTTACA
GTTGCCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAACAGGCCCCA
CTCCCTAACACTGACT
Found at i:1098088 original size:27 final size:27
Alignment explanation
Indices: 1098058--1098327 Score: 163
Period size: 27 Copynumber: 10.3 Consensus size: 27
1098048 CCAATTACAC
1098058 TGTCATATA-ATGCTGTCACTGACACAG
1 TGTCATA-ACATGCTGTCACTGACACAG
* ** *
1098085 TGTCACAATGTGTTGTCACTGACACAG
1 TGTCATAACATGCTGTCACTGACACAG
* ** *
1098112 TGTCACAATGTGCTGTCACTGACACAT
1 TGTCATAACATGCTGTCACTGACACAG
* *
1098139 TGTCA-CACTGTGCTGTCACTG--ACAG
1 TGTCATAAC-ATGCTGTCACTGACACAG
* * *
1098164 TATCATAACCTGCGGT-ATCTG--ACAG
1 TGTCATAACATGCTGTCA-CTGACACAG
*
1098189 TTTCATAA-ACTGCTGTCACTGACA-A-
1 TGTCATAACA-TGCTGTCACTGACACAG
* *
1098214 TGTCACAATC-TGCTGTTACTGACACCA-
1 TGTCATAA-CATGCTGTCACTGACA-CAG
* **
1098241 TGTCAGAACATGCTGTCACTGACATGG
1 TGTCATAACATGCTGTCACTGACACAG
* *
1098268 TGTCAGAACATGTTGTCACTG--ACAG
1 TGTCATAACATGCTGTCACTGACACAG
* * * *
1098293 TGTAATAACTTGCTGTCACTGAAACAA
1 TGTCATAACATGCTGTCACTGACACAG
1098320 TGTCATAA
1 TGTCATAA
1098328 ATTGAAAGTG
Statistics
Matches: 196, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.01
25 72 0.37
26 7 0.04
27 116 0.59
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (27 bp):
TGTCATAACATGCTGTCACTGACACAG
Found at i:1102336 original size:9 final size:9
Alignment explanation
Indices: 1102322--1102346 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1102312 AGAATTCTGG
1102322 ATATTTAGA
1 ATATTTAGA
1102331 ATATTTAGA
1 ATATTTAGA
1102340 ATATTTA
1 ATATTTA
1102347 AATCTTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
ATATTTAGA
Found at i:1103052 original size:22 final size:21
Alignment explanation
Indices: 1103012--1103052 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1103002 TTTGTAACAA
*
1103012 GTAAAAATAAACAGTAAACTT
1 GTAAAAATAAACAGCAAACTT
*
1103033 GTAAAAATATACATGCAAAC
1 GTAAAAATAAACA-GCAAAC
1103053 CTTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (21 bp):
GTAAAAATAAACAGCAAACTT
Found at i:1106741 original size:38 final size:38
Alignment explanation
Indices: 1106723--1107513 Score: 1564
Period size: 38 Copynumber: 20.8 Consensus size: 38
1106713 AAGCATACCT
*
1106723 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCT
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106761 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106799 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106837 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106875 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106913 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106951 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1106989 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107027 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107065 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107103 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107141 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107179 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107217 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107255 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107293 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107331 CAACAATAGAGTGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAG-GTACAGTTATTTATCAAGACTACATCC
1107370 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107408 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107446 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
1107484 CAACAATAGAGGTACAGTTATTTATCAAGA
1 CAACAATAGAGGTACAGTTATTTATCAAGA
1107514 TGTTGTGTAC
Statistics
Matches: 751, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
38 713 0.95
39 38 0.05
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (38 bp):
CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC
Found at i:1114887 original size:44 final size:44
Alignment explanation
Indices: 1114824--1114914 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
1114814 AAAATCAATG
1114824 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT
1 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT
*
1114868 TATTTTTATGGCTCACCCTACCAAAATATCATCAATACTGTGAT
1 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT
1114912 TAT
1 TAT
1114915 CAAATATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (44 bp):
TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT
Found at i:1118824 original size:35 final size:35
Alignment explanation
Indices: 1118778--1118884 Score: 187
Period size: 35 Copynumber: 3.1 Consensus size: 35
1118768 AAATCTTATA
*
1118778 GTGAATCACAATCAGTACTGTACATATATTTGTTT
1 GTGAATCACAATCAGTACTGTACATACATTTGTTT
*
1118813 GTGAATCACAATCAGTACTGTACATACATTTGTTA
1 GTGAATCACAATCAGTACTGTACATACATTTGTTT
*
1118848 GTGAATCAAAATCAGTACTGTACATACATTTGTTT
1 GTGAATCACAATCAGTACTGTACATACATTTGTTT
1118883 GT
1 GT
1118885 TTCAAGCCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (35 bp):
GTGAATCACAATCAGTACTGTACATACATTTGTTT
Found at i:1127094 original size:61 final size:61
Alignment explanation
Indices: 1127025--1127599 Score: 745
Period size: 61 Copynumber: 9.4 Consensus size: 61
1127015 GTCTGTGTGT
* *
1127025 GGGTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC
* * * *
1127086 GGGTTGGATACGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTAAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC
* * *
1127147 GGGTTGGATGCGTCACAGTTTGTTTGTGTATTTGTTTGGTTGTCT--GTGAATGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC
* * * *
1127208 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCT--GTGAGTGTTTATGAGT
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC
* * * *
1127269 GGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC
* * *
1127330 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC
* * *
1127391 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC
* * *
1127452 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCT--GTGAGTGTTTATGAGT
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC
* * *
1127513 GGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTGAGC
1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC
1127574 GGGTTGGATGCGTCACGGTTTGTTTG
1 GGGTTGGATGCGTCACGGTTTGTTTG
1127600 GTTGTCTGTG
Statistics
Matches: 466, Mismatches: 40, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
59 1 0.00
60 2 0.00
61 460 0.99
62 2 0.00
63 1 0.00
ACGTcount: A:0.11, C:0.09, G:0.37, T:0.44
Consensus pattern (61 bp):
GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC
Found at i:1127333 original size:183 final size:183
Alignment explanation
Indices: 1127025--1127599 Score: 823
Period size: 183 Copynumber: 3.1 Consensus size: 183
1127015 GTCTGTGTGT
* * *
1127025 GGGTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACG-GA-TGTTTGTGAGCGG
1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCT--GTGAGTGTTTGTGAGCGG
* * * *
1127088 GTTGGATACGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACG-GATGTTTGTAAGCGGGTT
64 GTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAG-TGTTTGTGAGCGGGTT
* * *
1127152 GGATGCGTCACAGTTTGTTTGTGTATTTGTTTGGTTGTCTGTGAATGTTTGTGAGC
128 GGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC
* * * *
1127208 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGAGTGTTTATGAGTGGAT
1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT
*
1127273 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGCGGGTTGGA
66 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA
* * *
1127338 TACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC
131 TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC
**
1127391 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGCGGGT
1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT
* * * * * *
1127456 TGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGAGTGTTTATGAGTGGATTGGA
66 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA
* * * *
1127521 TGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAGC
131 TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC
*
1127574 GGGTTGGATGCGTCACGGTTTGTTTG
1 GGGTTGGATACGTCACGGTTTGTTTG
1127600 GTTGTCTGTG
Statistics
Matches: 350, Mismatches: 39, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
181 1 0.00
182 2 0.01
183 346 0.99
184 1 0.00
ACGTcount: A:0.11, C:0.09, G:0.37, T:0.44
Consensus pattern (183 bp):
GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT
TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA
TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC
Found at i:1127622 original size:161 final size:153
Alignment explanation
Indices: 1127445--1127741 Score: 416
Period size: 161 Copynumber: 1.9 Consensus size: 153
1127435 AATGAGTGTT
*
1127445 TGTGAGCGGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGT-GAGTGTTTAT
1 TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGA-TGTTTAT
* *
1127509 GAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAGC
65 GAGCGGATTGGATGCGTCAC-G---G--T-T-TGTTTGTTTGGTTGTCTACGGATGTTTGTGAGC
1127574 GGGTTGGATGCGTCACGGTTTGTTTGGTTGTC
122 GGGTTGGATGCGTCACGGTTTGTTTGGTTGTC
* * * *
1127606 TGTGAGTGGATTGGATGCGTCATGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGGATGTTTGTG
1 TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGATGTTTATG
* * *
1127671 AGCGGGTTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTATGGATTTTTGTGAGCGGGTTGGAT
66 AGCGGATTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTACGGATGTTTGTGAGCGGGTTGGAT
1127736 GCGTCA
131 GCGTCA
1127742 GAACGCCTAC
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
153 45 0.36
154 1 0.01
155 1 0.01
157 1 0.01
160 1 0.01
161 74 0.59
162 2 0.02
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.44
Consensus pattern (153 bp):
TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGATGTTTATG
AGCGGATTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTACGGATGTTTGTGAGCGGGTTGGAT
GCGTCACGGTTTGTTTGGTTGTC
Found at i:1127717 original size:100 final size:100
Alignment explanation
Indices: 1127508--1127699 Score: 339
Period size: 100 Copynumber: 1.9 Consensus size: 100
1127498 TGAGTGTTTA
*
1127508 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAG
1 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG
1127573 CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG
66 CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG
* * **
1127608 TGAGTGGATTGGATGCGTCATGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGGATGTTTGTGAG
1 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG
1127673 CGGGTTGGATGCGTCACGGTTTGTTTG
66 CGGGTTGGATGCGTCACGGTTTGTTTG
1127700 TTTGGTTGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.09, C:0.09, G:0.39, T:0.43
Consensus pattern (100 bp):
TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG
CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG
Found at i:1127722 original size:53 final size:53
Alignment explanation
Indices: 1127541--1127741 Score: 186
Period size: 53 Copynumber: 3.9 Consensus size: 53
1127531 TCTGTTTGTG
* *
1127541 TGTTTGTTTGGTTGTGTACGGATGTTTGTGAGCGGGTTGGATGCGTCAC-G--
1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT
* * *** ** ** *
1127591 -GTTTGTTTGGTTGTCTGT-GAGTGGATTG-GATGCGTCATGG-TTTGT--TTGTG
1 TGTTTGTTTGGTTGTCTATGGA-T-GTTTGTGA-GCGGGTTGGATGCGTCACGGTT
*
1127641 TGTTTGTTTGGTTGTCTGTGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT
1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT
*
1127694 TGTTTGTTTGGTTGTCTATGGATTTTTGTGAGCGGGTTGGATGCGTCA
1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCA
1127742 GAACGCCTAC
Statistics
Matches: 118, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
48 3 0.03
49 21 0.18
50 20 0.17
51 24 0.20
52 2 0.02
53 48 0.41
ACGTcount: A:0.09, C:0.08, G:0.38, T:0.44
Consensus pattern (53 bp):
TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT
Found at i:1132089 original size:21 final size:21
Alignment explanation
Indices: 1131923--1132076 Score: 263
Period size: 21 Copynumber: 7.3 Consensus size: 21
1131913 GAATAAACTA
1131923 TAAAGTACCATCATGTAATGT
1 TAAAGTACCATCATGTAATGT
*
1131944 TAAAGTACCATCATGCAATGT
1 TAAAGTACCATCATGTAATGT
*
1131965 TGAAGTACCATCATGTAATGT
1 TAAAGTACCATCATGTAATGT
*
1131986 TAAAGTACCATCACGTAATGT
1 TAAAGTACCATCATGTAATGT
*
1132007 TGAAGTACCATCATGTAATGT
1 TAAAGTACCATCATGTAATGT
1132028 TAAAGTACCATCATGTAATGT
1 TAAAGTACCATCATGTAATGT
*
1132049 TGAAGTACCATCATGTAATGT
1 TAAAGTACCATCATGTAATGT
1132070 TAAAGTA
1 TAAAGTA
1132077 TAATCATATA
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 123 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (21 bp):
TAAAGTACCATCATGTAATGT
Found at i:1140039 original size:20 final size:20
Alignment explanation
Indices: 1139993--1140063 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1139983 ATTGTATTTG
*
1139993 ATCACATAATACAATATCAT
1 ATCATATAATACAATATCAT
**
1140013 AAAATATAATACAATAT-AGT
1 ATCATATAATACAATATCA-T
1140033 ATCATAT--TACAATATCAT
1 ATCATATAATACAATATCAT
* *
1140051 ATTACATAATACA
1 ATCATATAATACA
1140064 TCATAACACT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
18 14 0.35
19 2 0.05
20 24 0.60
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.32
Consensus pattern (20 bp):
ATCATATAATACAATATCAT
Found at i:1140050 original size:13 final size:13
Alignment explanation
Indices: 1140032--1140056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140022 TACAATATAG
1140032 TATCATATTACAA
1 TATCATATTACAA
1140045 TATCATATTACA
1 TATCATATTACA
1140057 TAATACATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TATCATATTACAA
Found at i:1140310 original size:15 final size:15
Alignment explanation
Indices: 1140292--1140415 Score: 83
Period size: 15 Copynumber: 7.7 Consensus size: 15
1140282 TAAAATGAAT
1140292 TACAATATCATATAA
1 TACAATATCATATAA
*
1140307 TACAATTTCATTTGATATGA
1 TACAATATCA--T-ATA--A
1140327 TA-ATATATCATATAA
1 TACA-ATATCATATAA
1140342 -ACCAATATCATATCAA
1 TA-CAATATCATAT-AA
* *
1140358 -ACAATATCGTATGA
1 TACAATATCATATAA
*
1140372 TACAATATTATATAATA
1 TACAATATCATAT-A-A
1140389 TTACAATATCATATAA
1 -TACAATATCATATAA
*
1140405 TACAATTTCAT
1 TACAATATCAT
1140416 GTGATATAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
14 2 0.02
15 49 0.56
16 5 0.06
17 6 0.07
18 16 0.18
19 1 0.01
20 8 0.09
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (15 bp):
TACAATATCATATAA
Found at i:1140348 original size:50 final size:49
Alignment explanation
Indices: 1140294--1140494 Score: 164
Period size: 50 Copynumber: 4.1 Consensus size: 49
1140284 AAATGAATTA
* *
1140294 CAATATCATATAATACAATTTCATTTGATATGATAATATATCATATAAAC
1 CAATATCATATAATACAATTTCATATGATATAATAATATAT-ATATAAAC
* * * * *
1140344 CAATATCATATCAA-ACAATATCGTATGATACAATATTATATA-ATATTA-
1 CAATATCATAT-AATACAATTTCATATGATATAATAATATATATATA-AAC
* **
1140392 CAATATCATATAATACAATTTCATGTGATATAATTCTATATA-ACTGAAAC
1 CAATATCATATAATACAATTTCATATGATATAATAATATATATA-T-AAAC
* * * * *
1140442 CAATATCATATTATACAATATT-GTATGATACAATATTATAGA-ATAAA-
1 CAATATCATATAATACAAT-TTCATATGATATAATAATATATATATAAAC
1140489 CAATAT
1 CAATAT
1140495 TGTATCATAG
Statistics
Matches: 123, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
47 8 0.07
48 40 0.33
49 5 0.04
50 66 0.54
51 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (49 bp):
CAATATCATATAATACAATTTCATATGATATAATAATATATATATAAAC
Found at i:1140395 original size:18 final size:18
Alignment explanation
Indices: 1140372--1140406 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1140362 TATCGTATGA
*
1140372 TACAATATTATATAATAT
1 TACAATATCATATAATAT
1140390 TACAATATCATATAATA
1 TACAATATCATATAATA
1140407 CAATTTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TACAATATCATATAATAT
Found at i:1140401 original size:98 final size:98
Alignment explanation
Indices: 1140290--1140494 Score: 290
Period size: 98 Copynumber: 2.1 Consensus size: 98
1140280 AATAAAATGA
* *
1140290 ATTACAATATCATATAATACAATTTCATTTGATATGATAATATATCATA-T-AAACCAATATCAT
1 ATTACAATATCATATAATACAATTTCATGTGATATAATAATATAT-A-ACTGAAACCAATATCAT
*
1140353 ATCAAACAATATCGTATGATACAATATTATATAAT
64 ATCAAACAATATCGTATGATACAATATTATAGAAT
**
1140388 ATTACAATATCATATAATACAATTTCATGTGATATAATTCTATATAACTGAAACCAATATCATAT
1 ATTACAATATCATATAATACAATTTCATGTGATATAATAATATATAACTGAAACCAATATCATAT
* * *
1140453 TATACAATATTGTATGATACAATATTATAGAAT
66 CAAACAATATCGTATGATACAATATTATAGAAT
*
1140486 A-AACAATAT
1 ATTACAATAT
1140495 TGTATCATAG
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
96 1 0.01
97 9 0.09
98 86 0.90
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (98 bp):
ATTACAATATCATATAATACAATTTCATGTGATATAATAATATATAACTGAAACCAATATCATAT
CAAACAATATCGTATGATACAATATTATAGAAT
Found at i:1140638 original size:18 final size:18
Alignment explanation
Indices: 1140615--1140649 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1140605 ATACAATACT
1140615 ATACATAA-CAATATCATG
1 ATACATAATC-ATATCATG
1140633 ATACATAATCATATCAT
1 ATACATAATCATATCAT
1140650 AAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (18 bp):
ATACATAATCATATCATG
Found at i:1140740 original size:20 final size:20
Alignment explanation
Indices: 1140715--1140767 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1140705 ACATGATATC
1140715 ATATTGTATCATATCAAACA
1 ATATTGTATCATATCAAACA
* *
1140735 ATATTGTTTCATATCATACA
1 ATATTGTATCATATCAAACA
1140755 ATACTT-TATCATA
1 ATA-TTGTATCATA
1140768 GGAATCATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (20 bp):
ATATTGTATCATATCAAACA
Found at i:1141794 original size:176 final size:177
Alignment explanation
Indices: 1141424--1142221 Score: 941
Period size: 177 Copynumber: 4.5 Consensus size: 177
1141414 ACCAGACTAT
* * * * *
1141424 GCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGGAAGTCTGGTGAAGTA
1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT
* ***
1141489 AGGACAAGTAATAACTAAGAT-AT-CATCATCAGAGGGCACCTGTTTCAAAAACTTTATCTAACC
66 AGGACCAGTAATAACTAAGATAATGC-T-ATCAGAGGGCACCTGCAACAAAAAC--T-T-TAACC
**
1141552 AGCTCTTAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA
125 AGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA
*
1141605 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATACAAGTTTGGTGAAGTT
1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT
1141670 AGGACCAGTAATAACTAAGATTAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC
66 AGGACCAGTAATAACTAAGA-TAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC
* *
1141733 TAAAAACCTTAACCTCTTCCAGCATCCGAAACCTATTGCTCAGATTCA
130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA
* *
1141781 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAAGTTTGGTGAAGTT
1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT
* * * * *
1141846 AGGACCAGTAGTAACTTAGATATTGCTATCA-ATGGGCACCCGCAACAAAAACTTTAACCTGCTC
66 AGGACCAGTAATAACTAAGATAATGCTATCAGA-GGGCACCTGCAACAAAAACTTTAACCAGCTC
*
1141910 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCA
130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA
* * * * * *
1141958 GCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGGCACACCATCCATGCAAGTTAGGTGAAG-T
1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT
* * * * * * *
1142022 ACAGACCAGCAGTAACTAAGATACTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTC
66 A-GGACCAGTAATAACTAAGATAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC
* * ** * *
1142087 CAACAACCTTAACCTCCTCCAGCATCTGAAATTTA-GGACCCAGATTCA
130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTG-CTCAGATTCA
* * * * * * *
1142135 GCATCCAAGTCTT-TCAAGTCCATAAGTAGGTC--CAGATGCATCATCCATGCAAGTTTGGTGAA
1 GCATTCAAG-CTTGTCAGGTGCATCAGTA--TCATAAGACGCACCATCCATGCAAGTTTGGTGAA
* * * *
1142197 GATAGGACAAGTAATAGCTTAGATA
63 GTTAGGACCAGTAATAACTAAGATA
1142222 CAGGACCTGC
Statistics
Matches: 545, Mismatches: 60, Indels: 28
0.86 0.09 0.04
Matches are distributed among these distances:
175 3 0.01
176 143 0.26
177 287 0.53
178 6 0.01
179 2 0.00
180 22 0.04
181 78 0.14
182 1 0.00
183 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (177 bp):
GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT
AGGACCAGTAATAACTAAGATAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTCC
AAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA
Found at i:1141915 original size:19 final size:19
Alignment explanation
Indices: 1141891--1141930 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1141881 GCACCCGCAA
* *
1141891 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
1141910 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
1141929 CA
1 CA
1141931 GCATCCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:1146538 original size:21 final size:21
Alignment explanation
Indices: 1146513--1146563 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1146503 ATTTTCCTGA
*
1146513 TACACGCACGATC-CCGCACGT
1 TACACGAACGATCACC-CACGT
1146534 TACACGAACGATCACCCACGT
1 TACACGAACGATCACCCACGT
*
1146555 AACACGAAC
1 TACACGAAC
1146564 TATTTAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.39, G:0.16, T:0.12
Consensus pattern (21 bp):
TACACGAACGATCACCCACGT
Found at i:1146860 original size:21 final size:21
Alignment explanation
Indices: 1146805--1146863 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1146795 TTTGCACGTC
* *
1146805 CTCTCGCATACATTGCACAAG
1 CTCTCGCATTCGTTGCACAAG
* *
1146826 CCCTCGC-TTACGTTGCACGAG
1 CTCTCGCATT-CGTTGCACAAG
1146847 CTCTCGCATTCGTTGCA
1 CTCTCGCATTCGTTGCA
1146864 TACGTTTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.27
Consensus pattern (21 bp):
CTCTCGCATTCGTTGCACAAG
Found at i:1147641 original size:18 final size:18
Alignment explanation
Indices: 1147587--1147646 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1147577 TGTATTGTGT
1147587 TAATACAATATCATAATATA
1 TAATACAATATCAT-AT-TA
* **
1147607 TAAAACAATATGGTATTA
1 TAATACAATATCATATTA
*
1147625 TATTACAATATCATATTA
1 TAATACAATATCATATTA
1147643 -AATA
1 TAATA
1147647 ATACATCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 3 0.09
18 16 0.50
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
TAATACAATATCATATTA
Found at i:1147941 original size:15 final size:15
Alignment explanation
Indices: 1147807--1147992 Score: 65
Period size: 15 Copynumber: 11.5 Consensus size: 15
1147797 GATAAAGTAA
* *
1147807 AATATAATATAATAC
1 AATATCATATTATAC
*
1147822 AATATTATATTATAC
1 AATATCATATTATAC
1147837 ATATTGTATCATA--ATAC
1 A-A---TATCATATTATAC
*
1147854 AATAAT-ATATTTTAC
1 AAT-ATCATATTATAC
**
1147869 AATATCATACAATAC
1 AATATCATATTATAC
*
1147884 AATTTCATGTGATGTGATA-
1 AATATCA--T-AT-T-ATAC
1147903 ATATATCATATTATAAACC
1 A-ATATCATATTAT--A-C
*
1147922 AATATTATATTATAC
1 AATATCATATTATAC
* *
1147937 AATATCGTATGATAC
1 AATATCATATTATAC
* *
1147952 TATATTATATAATATAAC
1 AATATCATAT--TAT-AC
*
1147970 AGTATCATATTATAC
1 AATATCATATTATAC
*
1147985 AATTTCAT
1 AATATCAT
1147993 GTGATATAAT
Statistics
Matches: 126, Mismatches: 24, Indels: 42
0.66 0.12 0.22
Matches are distributed among these distances:
13 4 0.03
14 4 0.03
15 62 0.49
16 7 0.06
17 11 0.09
18 22 0.17
19 8 0.06
20 8 0.06
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (15 bp):
AATATCATATTATAC
Found at i:1147998 original size:48 final size:48
Alignment explanation
Indices: 1147895--1147998 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
1147885 ATTTCATGTG
* *
1147895 ATGTGATAATATATCATATTATAAACCAATATTATATTATACAATATC
1 ATGTGATAATATATCATATAATAAACCAATATCATATTATACAATATC
* * * * * *
1147943 GTATGATACTATATTATATAATATAA-CAGTATCATATTATACAATTTC
1 ATGTGATAATATATCATATAATA-AACCAATATCATATTATACAATATC
1147991 ATGTGATA
1 ATGTGATA
1147999 TAATTCTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (48 bp):
ATGTGATAATATATCATATAATAAACCAATATCATATTATACAATATC
Found at i:1149271 original size:177 final size:178
Alignment explanation
Indices: 1148966--1149882 Score: 1244
Period size: 177 Copynumber: 5.2 Consensus size: 178
1148956 TGTGACCTGT
* * * * * * **
1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT
1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT
* * * * * * * * *
1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA
65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTA
* * *** *
1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGC
129 ACTTAGATAT-ATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1149143 TCTAAAAACCTTAACCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
* * * * * * *
1149208 TGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATAA
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAA
* *
1149272 CTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
130 CTTAGATAT-ATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
* *
1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
* * *
1149449 TTAGTTAT-TGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGC
131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149496 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1149561 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
1149626 TTAGATAT-TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
*
1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
* *
1149803 TTAGATAT-TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGG
131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* *
1149850 TCCAACAACCTTAACCTCCTCCAGCATCTGAAA
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA
1149883 TTTAGGACTC
Statistics
Matches: 683, Mismatches: 52, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
174 1 0.00
175 3 0.00
176 148 0.22
177 531 0.78
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (178 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
Found at i:1149495 original size:19 final size:19
Alignment explanation
Indices: 1149471--1149512 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1149461 ATCAATGGGC
*
1149471 ACCTGCAACAAAAACTTTA
1 ACCTGCAACAAAAACCTTA
**
1149490 ACCTGCTCCAAAAACCTTA
1 ACCTGCAACAAAAACCTTA
1149509 ACCT
1 ACCT
1149513 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21
Consensus pattern (19 bp):
ACCTGCAACAAAAACCTTA
Found at i:1149517 original size:19 final size:19
Alignment explanation
Indices: 1149479--1149518 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1149469 GCACCTGCAA
* *
1149479 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
1149498 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
1149517 CA
1 CA
1149519 GCATCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:1149694 original size:19 final size:19
Alignment explanation
Indices: 1149656--1149695 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1149646 GCACCTGCAA
* *
1149656 CAAAAACTTTAACCAGCTC
1 CAAAAACCTTAACCACCTC
*
1149675 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCACCTC
1149694 CA
1 CA
1149696 GCATCCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.38, G:0.03, T:0.20
Consensus pattern (19 bp):
CAAAAACCTTAACCACCTC
Found at i:1149834 original size:354 final size:353
Alignment explanation
Indices: 1148966--1149877 Score: 1262
Period size: 353 Copynumber: 2.6 Consensus size: 353
1148956 TGTGACCTGT
* * * * * * **
1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT
1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT
* * * * * * ** * *
1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA
65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTA
* * *** * * *
1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGCTCTAAAAACCTTAA
129 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAA
* * * *
1149157 CCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTAT
192 CCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTAT
* * *
1149222 CATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTAGAACAAGTAATAACTAAGATATAATCAT
257 CATAAGACACACCATCCATGCAAGTCTGGTGAAGTTAGAACAAGCAATAACTAAGATAT-ATCAT
*
1149287 CAGAGGGCACCTGCAACAAAAACTTTAACCAGC
321 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
*
1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
* *
1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
1149514 CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA
196 CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA
* * * * *
1149579 AGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTTAGATAT-TGCTATCA
261 AGACACACCATCCATGCAAGTCTGGTGAAGTTA-GAACAAGCAATAACTAAGATATAT-C-ATCA
1149642 AAGGGCACCTGCAACAAAAACTTTAACCAGC
323 AAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
* *
1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTC
131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
1149868 CTCCAGCATC
196 CTCCAGCATC
1149878 TGAAATTTAG
Statistics
Matches: 494, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
351 2 0.00
352 7 0.01
353 291 0.59
354 194 0.39
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (353 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA
AGACACACCATCCATGCAAGTCTGGTGAAGTTAGAACAAGCAATAACTAAGATATATCATCAAAG
GGCACCTGCAACAAAAACTTTAACCAGC
Found at i:1149947 original size:354 final size:351
Alignment explanation
Indices: 1148966--1149986 Score: 1227
Period size: 353 Copynumber: 2.9 Consensus size: 351
1148956 TGTGACCTGT
* * * * * * **
1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT
1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT
* * * * * * ** * *
1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA
65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTA
* * *** * * *
1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGCTCTAAAAACCTTAA
129 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAA
* *
1149157 CCTCCTTCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTA
192 CCTCCTCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTA
* * *
1149221 TCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTAGAACAAGTAATAACTAAGATATAATCA
255 TCA-AAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATAT-ATCA
*
1149286 TCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
318 TCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
*
1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
* *
1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
*
1149514 CTCCAGCATCCAAAACCTATA-GCTCAGATTCAGCA-CTCAAGCCTGTCTGGTGCATCAGTATCA
196 CTCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATC-CAAGCCTGTCTGGTGCATCAGTATCA
* * * * *
1149577 TAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTTAGATAT-TGCTAT
258 -AAGACGCACCATCCATGCAAGTTTGGTGAAGTTA-GAACAAGCAATAACTAAGATATAT-C-AT
1149640 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC
319 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
* *
1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTC
131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
* * * * ** * *
1149868 CTCCAGCATCTGAAATTTAGGACTCAGATTCAGCATCCAAGTCTTTCAAGTCCATAAGTAGGTC-
196 CTCCAGCATCCGAAATATAGG-CTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTA--TCA
* * * * * * * *
1149932 CAGATGCATCATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA
258 AAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATA
1149987 CAGGACCTGC
Statistics
Matches: 579, Mismatches: 72, Indels: 32
0.85 0.11 0.05
Matches are distributed among these distances:
351 2 0.00
352 10 0.02
353 291 0.50
354 271 0.47
355 3 0.01
356 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (351 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
CTCCAGCATCCGAAATATAGGCTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTATCAAAG
ACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATATATCATCAAAGGG
CACCTGCAACAAAAACTTTAACCAGC
Found at i:1149985 original size:177 final size:174
Alignment explanation
Indices: 1148966--1149986 Score: 1119
Period size: 177 Copynumber: 5.8 Consensus size: 174
1148956 TGTGACCTGT
* * * * * * **
1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT
1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGT
* * * * * * *
1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA
63 CTGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAATA
* * *** *
1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGC
126 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1149143 TCTAAAAACCTTAACCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGTC
* * * * *
1149208 TGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATAA
64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAATAA
* *
1149272 CTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
127 CTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * *
1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGTC
* ** *
1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC
* * *
1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGC
128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149496 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCAC-CAAGCCTGTC
* *
1149561 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC
64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC
1149626 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCAC-CAAGCCTGTC
** *
1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC
64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC
* *
1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGG
128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * * *
1149850 TCCAACAACCTTAACCTCCTCCAGCATCTGAAA-TTTAGGACTCAGATTCAGCATCCAAGTCTTT
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACTATA-G-CTCAGATTCAGCA-CCAAGCCTGT
** * * * ** * *
1149914 CAAGTCCATAAGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAAGATA-GGACAAGTAAT
63 CTGGTGCATCAGTA--TCAAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAAT
*
1149977 AGCTTAGATA
125 AACTTAGATA
1149987 CAGGACCTGC
Statistics
Matches: 765, Mismatches: 67, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
174 1 0.00
175 6 0.01
176 150 0.20
177 603 0.79
178 3 0.00
179 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (174 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACTATAGCTCAGATTCAGCACCAAGCCTGTCTG
GTGCATCAGTATCAAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAACTTA
GATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
Found at i:1152888 original size:2 final size:2
Alignment explanation
Indices: 1152881--1152907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1152871 TGATCGTCAT
1152881 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1152908 TACTGGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1154712 original size:3 final size:3
Alignment explanation
Indices: 1154698--1154733 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1154688 TTTGTCGACT
* *
1154698 TTC TTT TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1154734 ATCCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1157752 original size:21 final size:22
Alignment explanation
Indices: 1157717--1157758 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1157707 ACTGTATAGC
* *
1157717 TGTCCGATGCTTGGT-AAATAT
1 TGTCCGATCCATGGTGAAATAT
1157738 TGTCCGATCCATGGTGAAATA
1 TGTCCGATCCATGGTGAAATA
1157759 GTTCAACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
TGTCCGATCCATGGTGAAATAT
Found at i:1162395 original size:166 final size:166
Alignment explanation
Indices: 1162220--1162538 Score: 437
Period size: 166 Copynumber: 1.9 Consensus size: 166
1162210 CAGGTTAAAG
* *
1162220 TTTTTGTTGCAGGTGTCCTCTGATAGCA-ATATCTAACTTACTGCTGGTCCAAACTTCACCAAAC
1 TTTTTGTTGCAGGTGCCCTCTGAT-G-ATATATCTAACTTACTACTGGTCCAAACTTCACCAAAC
* * *
1162284 TTGCATGGATGGT-GTCTTATGATACTGATGCACCAGACAGGCTTAAATGCTGAATCTGAGCTAT
64 TTGCATGGATGGTCGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCAT
1162348 AGG-CTTCGGATGCTGGATGAGGTTAAGGTTTTTTGAGC
129 AGGTCTTCGGA-GCTGGATGAGGTTAAGGTTTTTTGAGC
* * ** *
1162386 TTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTGGTCCTTACTTCATCAAACT
1 TTTTTGTTGCAGGTGCCCTCTGATGA-TATATCTAACTTACTACTGGTCCAAACTTCACCAAACT
* * *
1162451 TGCATGGATGGTGCGTCTCATGATAGTGATGCACCATACAGACTTGAATGCTGAATCTGAGCCAT
65 TGCATGGATGGT-CGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCAT
* *
1162516 AGGTTTTTGGAGCTGGATGAGGT
129 AGGTCTTCGGAGCTGGATGAGGT
1162539 GAAGATTAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
164 1 0.01
165 1 0.01
166 66 0.50
168 60 0.45
169 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (166 bp):
TTTTTGTTGCAGGTGCCCTCTGATGATATATCTAACTTACTACTGGTCCAAACTTCACCAAACTT
GCATGGATGGTCGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCATAG
GTCTTCGGAGCTGGATGAGGTTAAGGTTTTTTGAGC
Found at i:1165118 original size:171 final size:172
Alignment explanation
Indices: 1164700--1165151 Score: 773
Period size: 172 Copynumber: 2.6 Consensus size: 172
1164690 TCACACTTTT
1164700 TTGTAAGCGCTCTCATGCCTA-ATAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTAT
1 TTGTAAGCGCTCTCATGCCTACA-AATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTAT
** * *
1164764 ACCACTTTTACCTTGGTCAAGTTTGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGG
1164829 ACTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC
130 ACTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC
*
1164872 TTGTAAGCGCTCTCATGCCAACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* *
1164937 CCATTAATACCTTGGTCAAGTTCGAAAATCAGCGTTGGTCGATACTTTTTGTTGGAGTAATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGGA
**
1165002 CTTTGACCACAATAATGACT-TGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC
1165043 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
** *
1165108 CCACTAATACCTTGGTCAAGTTCCTAAATCAGCCTTGGTCGATA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA
1165152 GACTCGATAC
Statistics
Matches: 265, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 123 0.46
172 141 0.53
173 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGGA
CTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC
Found at i:1166627 original size:19 final size:20
Alignment explanation
Indices: 1166593--1166637 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1166583 CCGTGTCGCA
*
1166593 CCGTGGCCGCCTGTGTAACT
1 CCGTGGCCGACTGTGTAACT
*
1166613 CCGTGGCC-ACTGTGTTACT
1 CCGTGGCCGACTGTGTAACT
1166632 CCGTGG
1 CCGTGG
1166638 ATATCGTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.09, C:0.33, G:0.31, T:0.27
Consensus pattern (20 bp):
CCGTGGCCGACTGTGTAACT
Found at i:1168109 original size:2 final size:2
Alignment explanation
Indices: 1168104--1168148 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1168094 ACACTTTCAC
1168104 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1168146 AG A
1 AG A
1168149 TTTTACAACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1168480 original size:2 final size:2
Alignment explanation
Indices: 1168473--1168524 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1168463 ATACTGGTTT
1168473 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1168515 TC TC TC TC TC
1 TC TC TC TC TC
1168525 ATATGACGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1170144 original size:180 final size:180
Alignment explanation
Indices: 1169838--1170208 Score: 600
Period size: 180 Copynumber: 2.1 Consensus size: 180
1169828 TGGCGGCTGC
*
1169838 CATA-AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTT
1 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT
* * *
1169902 TCGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCAAGGATTTTGATTTCTGATAATTT
66 TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT
*
1169967 ATCAAAAAAATACCAGGTTTTGAACTTAGTCATTTTTTGGCAAAATATTG
131 ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG
*
1170017 CATATAGGGTACCCTCATTGTGCGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT
1 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT
* * *
1170082 TTGCAGATCAAATGTACTTATATCAGAGGTGTGCATAATGCTAGGATCTTGATTTCTGATAATTT
66 TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT
* * * * *
1170147 ATGAAAAAAATACTAGCTTTTGAACTTGGTCATTTTTTTGCAAAATGTTG
131 ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG
*
1170197 CATGTAGGGTAC
1 CATATAGGGTAC
1170209 TCCATTTCAC
Statistics
Matches: 176, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
179 4 0.02
180 172 0.98
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (180 bp):
CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT
TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT
ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG
Found at i:1173880 original size:38 final size:38
Alignment explanation
Indices: 1173822--1174639 Score: 1317
Period size: 38 Copynumber: 21.6 Consensus size: 38
1173812 TGAATGACTA
* *
1173822 AGCCCCATCCATCTCTTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1173860 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
*
1173898 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAGCACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
* * *
1173936 AGCCCCATCCAACACTTAAAGCAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
*
1173974 AGCCCCATCCAAC-CCTTAAAACAATTCCTGTAACACTG
1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG
1174012 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174050 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
*
1174088 AGCCTCATCCAAC-CCTTAAAACAAG-TCCTGTAACACTG
1 AGCCCCATCCAACTCC-TAAAAC-AGTTCCTGTAACACTG
*
1174126 AGCCCCATCCAAC-CCTTAAAACAGTTACTGTAACACTG
1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG
1174164 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174202 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
* * *
1174240 AGCCCAATCCAACTCCTAAAAAAGTTCCTGTAGCACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174278 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
**
1174316 AGCCTTATCCAAC-CCTTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG
* * *
1174354 AGCCCCATCCAACACTTAAAACAGTTCCTGTAACACTA
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174392 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
* * *
1174430 AGCCCCATCCAAC-ACTTAAGCAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
*
1174467 AGCCCCATCCAACTCCTAAAGCAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174505 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
* *
1174543 AGCTCCATCCAACTCTTAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
1174581 AGCCCCATCCAAC-CCTCAAAACAGTTCCTGTAACACTG
1 AGCCCCATCCAACTCCT-AAAACAGTTCCTGTAACACTG
*
1174619 AGCCCCATCCAACTCTTAAAA
1 AGCCCCATCCAACTCCTAAAA
1174640 TAGCTCTGTT
Statistics
Matches: 728, Mismatches: 41, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
37 43 0.06
38 676 0.93
39 9 0.01
ACGTcount: A:0.32, C:0.36, G:0.11, T:0.22
Consensus pattern (38 bp):
AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG
Found at i:1181047 original size:17 final size:17
Alignment explanation
Indices: 1181025--1181057 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1181015 TTTAAATTTT
*
1181025 TAATTTTAATTTAATAG
1 TAATTTTAATTGAATAG
1181042 TAATTTTAATTGAATA
1 TAATTTTAATTGAATA
1181058 AATTAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TAATTTTAATTGAATAG
Found at i:1190605 original size:2 final size:2
Alignment explanation
Indices: 1190598--1190639 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1190588 CCCCCTACCC
1190598 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1190640 CCCGGTACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1195121 original size:12 final size:12
Alignment explanation
Indices: 1195106--1195131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1195096 ATATATACAC
1195106 ATATATATTGCA
1 ATATATATTGCA
1195118 ATATATATTGCA
1 ATATATATTGCA
1195130 AT
1 AT
1195132 TAAGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATATATATTGCA
Found at i:1195683 original size:11 final size:11
Alignment explanation
Indices: 1195669--1195697 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1195659 AATTTTTTAA
1195669 TTTTTTA-TTT
1 TTTTTTATTTT
1195679 TTTTTTATTTT
1 TTTTTTATTTT
1195690 TTTTTTAT
1 TTTTTTAT
1195698 AAAAAGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:1195683 original size:17 final size:16
Alignment explanation
Indices: 1195661--1195695 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1195651 TTTTATATAA
1195661 TTTTTTAATTTTTTATT
1 TTTTTTAATTTTTT-TT
*
1195678 TTTTTTTATTTTTTTT
1 TTTTTTAATTTTTTTT
1195694 TT
1 TT
1195696 ATAAAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTAATTTTTTTT
Found at i:1195694 original size:10 final size:10
Alignment explanation
Indices: 1195669--1195694 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1195659 AATTTTTTAA
1195669 TTTTTTATTT
1 TTTTTTATTT
1195679 TTTTTTATTT
1 TTTTTTATTT
1195689 TTTTTT
1 TTTTTT
1195695 TATAAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1196916 original size:22 final size:22
Alignment explanation
Indices: 1196891--1197059 Score: 194
Period size: 22 Copynumber: 7.5 Consensus size: 22
1196881 TAGAATGTTT
*
1196891 ATTAAAGGACGGCTAGTATGTC
1 ATTAATGGACGGCTAGTATGTC
1196913 ATTAATGGACGGCTAGTATGTC
1 ATTAATGGACGGCTAGTATGTC
* * * *
1196935 ATTGATGGACGGCTAGAAAGTTT
1 ATTAATGGACGGCTAGTATG-TC
1196958 ATTAATGGACGGCTAGTATGTC
1 ATTAATGGACGGCTAGTATGTC
* * *
1196980 ATTGATGGACGGCTAGAAAGTC
1 ATTAATGGACGGCTAGTATGTC
1197002 TATTAATGGACGGCTAGTATGTC
1 -ATTAATGGACGGCTAGTATGTC
* * * *
1197025 ATTGATGGACAGCTAGAAAGTC
1 ATTAATGGACGGCTAGTATGTC
*
1197047 TATTAAAGGACGG
1 -ATTAATGGACGG
1197060 TTTTTTTTTT
Statistics
Matches: 122, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
22 76 0.62
23 46 0.38
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (22 bp):
ATTAATGGACGGCTAGTATGTC
Found at i:1196967 original size:45 final size:45
Alignment explanation
Indices: 1196897--1197059 Score: 274
Period size: 45 Copynumber: 3.6 Consensus size: 45
1196887 GTTTATTAAA
* *
1196897 GGACGGCTAGTATGTC-ATTAATGGACGGCTAGTATGTCATTGAT
1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT
*
1196941 GGACGGCTAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGAT
1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT
1196986 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT
1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT
* *
1197031 GGACAGCTAGAAAGTCTATTAAAGGACGG
1 GGACGGCTAGAAAGTCTATTAATGGACGG
1197060 TTTTTTTTTT
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 13 0.12
45 99 0.88
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.28
Consensus pattern (45 bp):
GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT
Found at i:1196989 original size:67 final size:68
Alignment explanation
Indices: 1196881--1197018 Score: 215
Period size: 67 Copynumber: 2.0 Consensus size: 68
1196871 AGTATGTCGT
* * * *
1196881 TAGAATGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGTATGTC-ATTGATGGAC
1 TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC
1196945 GGC
66 GGC
* *
1196948 TAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGATGGACGGCTAGAAAGTCTATTAATGGAC
1 TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC
1197013 GGC
66 GGC
1197016 TAG
1 TAG
1197019 TATGTCATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
67 49 0.77
68 15 0.23
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (68 bp):
TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC
GGC
Found at i:1197033 original size:67 final size:67
Alignment explanation
Indices: 1196881--1197059 Score: 198
Period size: 67 Copynumber: 2.7 Consensus size: 67
1196871 AGTATGTCGT
* * * * * *
1196881 TAGAATGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGTATGTCATTGATGGACG
1 TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCATTAATGGACG
1196946 GC
66 GC
* *
1196948 TAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGATGGACGGCTAGAAAGTCTATTAATGGAC
1 TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTC-ATTAATGGAC
1197013 GGC
65 GGC
* * * * * * *
1197016 TAGTATG-TCATTGATGGACAGCTAGAAAGTCTATTAAAGGACGG
1 TAGAAAGTTCATTAATGGACGGCTAGTATGTC-ATTAATGGACGG
1197060 TTTTTTTTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
67 68 0.72
68 27 0.28
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30
Consensus pattern (67 bp):
TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCATTAATGGACG
GC
Found at i:1197248 original size:17 final size:17
Alignment explanation
Indices: 1197223--1197265 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1197213 TACTTTGCTT
1197223 CCAAAAAAAGAGAAAAAA
1 CCAAAAAAA-AGAAAAAA
*
1197241 CCAAAAAAAATAAAAAA
1 CCAAAAAAAAGAAAAAA
1197258 CCAAAAAA
1 CCAAAAAA
1197266 TAAATAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (17 bp):
CCAAAAAAAAGAAAAAA
Found at i:1197276 original size:14 final size:15
Alignment explanation
Indices: 1197235--1197282 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1197225 AAAAAAAGAG
1197235 AAAAAACCAAAAAAAAT
1 AAAAAACC--AAAAAAT
1197252 AAAAAACCAAAAAAT
1 AAAAAACCAAAAAAT
* *
1197267 AAATAA-CAAATAAT
1 AAAAAACCAAAAAAT
1197281 AA
1 AA
1197283 TACGAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 12 0.41
17 8 0.28
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAACCAAAAAAT
Found at i:1220405 original size:1 final size:1
Alignment explanation
Indices: 1220399--1220434 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
1220389 NNNNNNNNNN
1220399 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1220435 TTAAAGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1224008 original size:23 final size:18
Alignment explanation
Indices: 1223962--1223997 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1223952 TAAAGTGAAA
1223962 TACAAATACAAATATTTT
1 TACAAATACAAATATTTT
1223980 TACAAATACAAATATTTT
1 TACAAATACAAATATTTT
1223998 ATTGGCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
TACAAATACAAATATTTT
Found at i:1226300 original size:40 final size:39
Alignment explanation
Indices: 1226256--1226341 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
1226246 TACGGATCGA
* * *
1226256 AAACTGTAGTCAACGACGTTAATCTATATTTCACGTCTGT
1 AAACTATAGTCAACG-CGATAATCTATATTTCACATCTGT
* * *
1226296 AAACTATAGTTAACGTGATAATCTATGTTTCACATCTGT
1 AAACTATAGTCAACGCGATAATCTATATTTCACATCTGT
*
1226335 TAACTAT
1 AAACTAT
1226342 TATTGGTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 26 0.67
40 13 0.33
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (39 bp):
AAACTATAGTCAACGCGATAATCTATATTTCACATCTGT
Found at i:1227213 original size:2 final size:2
Alignment explanation
Indices: 1227206--1227257 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1227196 TTTGCCACCA
*
1227206 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1227248 TC TC TC TC TC
1 TC TC TC TC TC
1227258 ACACACACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1227312 original size:2 final size:2
Alignment explanation
Indices: 1227257--1227298 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1227247 CTCTCTCTCT
1227257 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1227299 ACCTTAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1227679 original size:12 final size:12
Alignment explanation
Indices: 1227662--1227714 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
1227652 CGCGTTCATC
1227662 TGTTGATGTTGT
1 TGTTGATGTTGT
1227674 TGTTGATGTTGT
1 TGTTGATGTTGT
1227686 TGTTGAT-TTGGT
1 TGTTGATGTT-GT
* * *
1227698 TGCTGTTGCTGT
1 TGTTGATGTTGT
1227710 TGTTG
1 TGTTG
1227715 TCCTAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 2 0.06
12 32 0.91
13 1 0.03
ACGTcount: A:0.06, C:0.04, G:0.34, T:0.57
Consensus pattern (12 bp):
TGTTGATGTTGT
Found at i:1227824 original size:24 final size:24
Alignment explanation
Indices: 1227779--1227825 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1227769 CTGCGCCGCC
*
1227779 TGCATCTGCATCATCTGCTGCTGT
1 TGCATCTGCATCACCTGCTGCTGT
*
1227803 TGCAT-TGCATTCACCTGTTGCTG
1 TGCATCTGCA-TCACCTGCTGCTG
1227826 ATACTGCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (24 bp):
TGCATCTGCATCACCTGCTGCTGT
Found at i:1228313 original size:63 final size:63
Alignment explanation
Indices: 1228214--1228343 Score: 242
Period size: 63 Copynumber: 2.1 Consensus size: 63
1228204 GTCGTTGTTT
*
1228214 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCTTAAC
1 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC
*
1228277 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGGACTGATCGTATTAATATCATAAC
1 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC
1228340 GTGT
1 GTGT
1228344 GTTCGAATAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (63 bp):
GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC
Found at i:1229442 original size:13 final size:13
Alignment explanation
Indices: 1229424--1229471 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
1229414 ATTTTGTTAC
1229424 ATAATTGAATATA
1 ATAATTGAATATA
**
1229437 ATAATTGAATGCA
1 ATAATTGAATATA
*
1229450 ATAATTGAATATG
1 ATAATTGAATATA
1229463 ATAATTGAA
1 ATAATTGAA
1229472 ATCCATATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.35
Consensus pattern (13 bp):
ATAATTGAATATA
Found at i:1230910 original size:2 final size:2
Alignment explanation
Indices: 1230892--1230948 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1230882 CATAAAATAA
*
1230892 TC TC TC TA TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1230933 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1230949 GATATATGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1231205 original size:36 final size:36
Alignment explanation
Indices: 1231159--1231338 Score: 360
Period size: 36 Copynumber: 5.0 Consensus size: 36
1231149 GGTCATCACC
1231159 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1231195 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1231231 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1231267 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1231303 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
1231339 GGATTGGTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 144 1.00
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (36 bp):
CAGACAGACAAACAAACAGTAGAATGGTAACTTACA
Found at i:1236392 original size:15 final size:16
Alignment explanation
Indices: 1236362--1236395 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1236352 AGATTTTTTA
1236362 ATTTCTATACCAGTAC
1 ATTTCTATACCAGTAC
*
1236378 ATTTCTA-AGCAGTAC
1 ATTTCTATACCAGTAC
1236393 ATT
1 ATT
1236396 GAGCTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (16 bp):
ATTTCTATACCAGTAC
Found at i:1243429 original size:22 final size:21
Alignment explanation
Indices: 1243391--1243556 Score: 113
Period size: 21 Copynumber: 7.6 Consensus size: 21
1243381 TTTTTGAGGT
*
1243391 ATTTTCTGATATCAGAAAATG
1 ATTTTTTGATATCAGAAAATG
* *
1243412 ATTTTTTGGTATCA-AGAATTCG
1 ATTTTTTGATATCAGA-AAAT-G
* *
1243434 AATTTCTGATATCAGAAAATG
1 ATTTTTTGATATCAGAAAATG
*
1243455 ATTTTTTGATATCAG--ACTCG
1 ATTTTTTGATATCAGAAAAT-G
* * *
1243475 AATTCTTGATATAAGAAAATACG
1 ATTTTTTGATATCAGAAAAT--G
*
1243498 ATCCATTTTCTGATATCAGAAATTCG
1 AT---TTTT-TGATATCAGAAAAT-G
* *
1243524 ATTTTTTTATCTCAGAAAATG
1 ATTTTTTGATATCAGAAAATG
1243545 ATTTTTTGATAT
1 ATTTTTTGATAT
1243557 TACAAATTCA
Statistics
Matches: 111, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
19 2 0.02
20 14 0.13
21 40 0.36
22 28 0.25
23 8 0.07
26 7 0.06
27 12 0.11
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
ATTTTTTGATATCAGAAAATG
Found at i:1243454 original size:43 final size:42
Alignment explanation
Indices: 1243393--1243556 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 42
1243383 TTTGAGGTAT
*
1243393 TTTCTGATATCAGAAAATGATTTTTTGGTATCAAGAATTCGAA
1 TTTCTGATATCAGAAAATGATTTTTTGATATC-AGAATTCGAA
*
1243436 TTTCTGATATCAGAAAATGATTTTTTGATATCAG-ACTCGAA
1 TTTCTGATATCAGAAAATGATTTTTTGATATCAGAATTCGAA
* *
1243477 -TTCTTGATATAAGAAAATACGATCCATTTTCTGATATCAGAAATTCGAT
1 TTTC-TGATATCAGAAAAT--GAT---TTTT-TGATATCAG-AATTCGAA
* * *
1243526 TTTTTTATCTCAGAAAATGATTTTTTGATAT
1 TTTCTGATATCAGAAAATGATTTTTTGATAT
1243557 TACAAATTCA
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
40 3 0.03
41 19 0.19
42 2 0.02
43 40 0.39
44 4 0.04
46 4 0.04
47 12 0.12
49 16 0.16
50 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (42 bp):
TTTCTGATATCAGAAAATGATTTTTTGATATCAGAATTCGAA
Found at i:1244085 original size:21 final size:22
Alignment explanation
Indices: 1244059--1244254 Score: 130
Period size: 22 Copynumber: 8.8 Consensus size: 22
1244049 TGTAGGTCTT
1244059 ATTTTCTGATATCAAAAAAT-G
1 ATTTTCTGATATCAAAAAATCG
* *
1244080 ATTTTCTGATATCAAGAATTCG
1 ATTTTCTGATATCAAAAAATCG
*
1244102 A-TTTCTTGATATCAAAAAATCA
1 ATTTTC-TGATATCAAAAAATCG
*
1244124 ACTTTAACTCTTGATATCAAAAAATCT
1 A-TTT---TC-TGATATCAAAAAATCG
* * * *
1244151 ATTTTGTAATATC-AGAAATCC
1 ATTTTCTGATATCAAAAAATCG
* ** * *
1244172 ATTTTTTTTTATCAAGAATTCG
1 ATTTTCTGATATCAAAAAATCG
* **
1244194 AATTAGTGATATCAAAAAAT-G
1 ATTTTCTGATATCAAAAAATCG
* * *
1244215 ATTTCCTGATATCACAAAATAG
1 ATTTTCTGATATCAAAAAATCG
*
1244237 ATTTTTTGATATCAAAAA
1 ATTTTCTGATATCAAAAA
1244255 TTATTTTTTT
Statistics
Matches: 137, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
21 55 0.40
22 57 0.42
23 1 0.01
24 2 0.01
26 3 0.02
27 19 0.14
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTTTCTGATATCAAAAAATCG
Found at i:1244121 original size:43 final size:43
Alignment explanation
Indices: 1244061--1244294 Score: 145
Period size: 43 Copynumber: 5.3 Consensus size: 43
1244051 TAGGTCTTAT
1244061 TTTC-TGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA
1 TTTCTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA
* * * *
1244103 TTTCTTGATATCAAAAAATCAACTTTAACTCTTGATATCAAAAAATCTA
1 TTTCTTGATATCAAAAAAT-GA-TTT---TC-TGATATCAAGAATTCGA
* * * * **
1244152 TTT-TGTAATATC-AGAAATCCATTTTTTTTTATCAAGAATTCGA
1 TTTCT-TGATATCAAAAAAT-GATTTTCTGATATCAAGAATTCGA
* ** * * *
1244195 ATTAGTGATATCAAAAAATGATTTCCTGATATCACA-AAATAGA
1 TTTCTTGATATCAAAAAATGATTTTCTGATATCA-AGAATTCGA
* * * **
1244238 TTTTTTGATATC-AAAAATTATTTTTTTGATATCAAGAATTTTA
1 TTTCTTGATATCAAAAAATGA-TTTTCTGATATCAAGAATTCGA
*
1244281 TTTTTTGATATCAA
1 TTTCTTGATATCAA
1244295 TTCGAATTAT
Statistics
Matches: 145, Mismatches: 33, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
42 12 0.08
43 85 0.59
44 9 0.06
45 3 0.02
47 3 0.02
48 10 0.07
49 23 0.16
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (43 bp):
TTTCTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA
Found at i:1244255 original size:21 final size:21
Alignment explanation
Indices: 1244200--1244294 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
1244190 TTCGAATTAG
**
1244200 TGATATCAAAAA-ATGATTTCC
1 TGATATCAAAAATA-GATTTTT
1244221 TGATATCACAAAATAGATTTTT
1 TGATATCA-AAAATAGATTTTT
*
1244243 TGATATCAAAAATTA-TTTTTT
1 TGATATCAAAAA-TAGATTTTT
* **
1244264 TGATATCAAGAATTTTATTTTT
1 TGATATCAA-AAATAGATTTTT
1244286 TGATATCAA
1 TGATATCAA
1244295 TTCGAATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
21 27 0.43
22 35 0.56
23 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (21 bp):
TGATATCAAAAATAGATTTTT
Found at i:1244263 original size:22 final size:21
Alignment explanation
Indices: 1244057--1244339 Score: 106
Period size: 21 Copynumber: 13.0 Consensus size: 21
1244047 TATGTAGGTC
* *
1244057 TTATTTTCTGATATCAAAAAA
1 TTATTTTTTGATATCAAAAAT
* * *
1244078 TGATTTTCTGATATCAAGAAT
1 TTATTTTTTGATATCAAAAAT
* *
1244099 TCGATTTCTTGATATCAAAAAAT
1 T-TATTTTTTGATATC-AAAAAT
**
1244122 CAACTTTAACTCTTGATATCAAAAAAT
1 TTA-TTT---T-TTGATATC-AAAAAT
* * * *
1244149 CTATTTTGTAATATCAGAAAT
1 TTATTTTTTGATATCAAAAAT
** ** *
1244170 CCATTTTTTTTTATCAAGAAT
1 TTATTTTTTGATATCAAAAAT
* * ** *
1244191 TCGAATTAGTGATATCAAAAAA
1 T-TATTTTTTGATATCAAAAAT
* **
1244213 TGATTTCCTGATATCACAAAAT
1 TTATTTTTTGATATCA-AAAAT
**
1244235 AGATTTTTTGATATCAAAAA-
1 TTATTTTTTGATATCAAAAAT
*
1244255 TTATTTTTTTGATATCAAGAATT
1 TTA-TTTTTTGATATCAA-AAAT
1244278 TTATTTTTTGATATC---AAT
1 TTATTTTTTGATATCAAAAAT
* * * *
1244296 TCGAATTATTGATATCAAATAT
1 T-TATTTTTTGATATCAAAAAT
*
1244318 TTATTTTTTTATATCAGAAAAT
1 TTATTTTTTGATATCA-AAAAT
1244340 ACCTCAAAAA
Statistics
Matches: 197, Mismatches: 48, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
18 3 0.02
19 11 0.06
20 1 0.01
21 80 0.41
22 70 0.36
23 12 0.06
26 3 0.02
27 17 0.09
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43
Consensus pattern (21 bp):
TTATTTTTTGATATCAAAAAT
Found at i:1249394 original size:169 final size:166
Alignment explanation
Indices: 1248411--1250128 Score: 2368
Period size: 169 Copynumber: 10.2 Consensus size: 166
1248401 ATAGAATCAT
*
1248411 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTAAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-
* * *
1248476 TTAAC-ACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATG-TTTTCACAACTTTGA
65 TT--CGA---CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGA
*
1248539 ATCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
124 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1248582 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAATATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1248647 TCGA-CCCCCCATTGT-GCCCCACCCTACCCTCAGGGATCATGATTTTCACAACTTTGAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCC-CAGGGATCATGATTTTCACAACTTTGAATCTAC
* *
1248710 ACTGCCTGAGGATGCTTCCACACGAGTTTCAGCTTTC
130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1248747 CTGGCTGATAAG-TT-TGAGAAGAAGATTTTCAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
1248810 TCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTT--C-AC----AA
66 TCGA-----CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGAA
* *
1248868 TCTACACTGCCTGAGGATGCTTCCACACAAGTTTCAGCTCTC
125 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1248910 CTTGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--TATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-
* *
1248973 TTAAC-ACCCCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGA
65 TT--CGA---CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGA
* *
1249037 ATCTACACTGCCTGAGGATACTTCCACACAAGTTTCAGCTTTC
124 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1249080 CTGGCTGATTAGTTTCTGAGAAGAAGAATTTTGAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1249145 ACGA-CCCTCCATTGT-GCTCCACCCTACCCCAAGGGATCATGATTTTCACAACTTTGAATCTGC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCC-AGGGATCATGATTTTCACAACTTTGAATCTAC
*
1249208 ACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC
130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1249245 CTGGCTGATTAGTTTCTGAGAAGAAGA-TTTTAAAGATTTACTCTATATATAAATTCTTATGTAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--TATAT--ATTCCTATGTAA
* * * * * *
1249309 AAATTTGA-CCACCCATTGTGGCCCCACCCTACCCCTGGGAGTCATGAATTTAACAACTTTGAAT
62 AACTTCGACCCCCCCATTGTGGCCCCACCCTACCCCAGGGA-TCATGATTTTCACAACTTTGAAT
* *
1249373 CTACACTACCTGAGAATGCTTCCACACAAGTTTCAGTTTTC
126 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1249414 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
** *
1249479 TCGACCCCCCCCCCCATTGTGGCCTTACCCTACACCCAGGGATCATGAATTTCACAACTTTGAAT
66 TCGA----CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAAT
* *
1249544 CTACACTTCCTGAGGATGCTACCACACAAGTTTCAGCTTTC
126 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1249585 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * ** *
1249650 TTGACCCCCCCCCCTTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCT
66 TCGA--CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAATCT
1249715 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
128 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1249754 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * ** *
1249819 TTGACCCCCCCCCCTTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCT
66 TCGA--CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAATCT
1249884 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
128 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1249923 CTGGCTGATTACTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1249988 TCCA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGAATCTAC
1250052 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1250089 CTGGCT--TTCTGGTTCTGGAGAAGAAGATTTTTGAAA-ATTT
1 CTGGCTGATT-AGTTTCT-GAGAAGAAGATTTTT-AAAGATTT
1250129 CTCGAAATTT
Statistics
Matches: 1419, Mismatches: 84, Indels: 93
0.89 0.05 0.06
Matches are distributed among these distances:
163 167 0.12
164 47 0.03
165 210 0.15
166 151 0.11
167 6 0.00
168 36 0.03
169 437 0.31
170 127 0.09
171 213 0.15
172 25 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (166 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCCCATTGTGGCCCCACCCTACCCCAGGGATCATGATTTTCACAACTTTGAATCTACA
CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1249677 original size:340 final size:339
Alignment explanation
Indices: 1248411--1250128 Score: 2482
Period size: 340 Copynumber: 5.1 Consensus size: 339
1248401 ATAGAATCAT
*
1248411 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTAAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
** * * *
1248476 TTAACACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATG-TTTTCACAACTTTGAA
66 TCGAC-CCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAA
*
1248540 TCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
130 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
* *
1248605 AAGATTTTTAAATATTTACTCTATATATTCCTATGTAAAACTTCGA--CCCCCCATTGT-GCCCC
195 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCATTGTGGCCCC
*
1248667 ACCCTACCCTCAGGGA-TCATGATTTTCACAACTTTGAATCTACACTGCCTGAGGATGCTTCCAC
260 ACCCTACCC-CAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
*
1248731 ACGAGTTTCAGCTTTC
324 ACAAGTTTCAGCTTTC
* *
1248747 CTGGCTGATAAG-TT-TGAGAAGAAGATTTTCAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1248810 TCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTT--C-AC----AA
66 TCGA-CCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAA
* * *
1248868 TCTACACTGCCTGAGGATGCTTCCACACAAGTTTCAGCTCTCCTTGCTGATTAGTTTCTGAGAAG
130 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG
* *
1248933 AAGATTTTTAAAGATTTACTC--TATATTCCTATGTAAAACTTTAACACCCCCCCCCCAATGTGG
195 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT--GA--CCCCCCCCATTGTGG
* * *
1248996 CCTCACCCTACCCCCAGGGA-TCATGATTTTCACAACTTTGAATCTACACTGCCTGAGGATACTT
256 CCCCACCCTA-CCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTT
1249060 CCACACAAGTTTCAGCTTTC
320 CCACACAAGTTTCAGCTTTC
* *
1249080 CTGGCTGATTAGTTTCTGAGAAGAAGAATTTTGAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
1249145 ACGA-----CCCTCCATTGT-G-CTCCACCCTAC-CCCAAGGGATCATGATTTTCACAACTTTGA
66 TCGACCCCCCCCCCCATTGTGGCCT-CACCCTACACCC-AGGGATCATGATTTTCACAACTTTGA
* *
1249202 ATCTGCACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAA
129 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAA
* * *
1249267 GAAGA-TTTTAAAGATTTACTCTATATATAAATTCTTATGTAAAAATTTGA--CCACCCATTGTG
194 GAAGATTTTTAAAGATTTACTC--TATAT--ATTCCTATGTAAAACTTTGACCCCCCCCATTGTG
* * * *
1249329 GCCCCACCCTACCCCTGGGAGTCATGAATTTAACAACTTTGAATCTACACTACCTGAGAATGCTT
255 GCCCCACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTT
*
1249394 CCACACAAGTTTCAGTTTTC
320 CCACACAAGTTTCAGCTTTC
*
1249414 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
1249479 TCGACCCCCCCCCCCATTGTGGCCTTACCCTACACCCAGGGATCATGAATTTCACAACTTTGAAT
66 TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT
* *
1249544 CTACACTTCCTGAGGATGCTACCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA
131 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA
*
1249609 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCCCTTGTGGCCCC
196 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGA-CCCCCCCCATTGTGGCCCC
* * *
1249674 ACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA
260 ACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA
1249739 CAAGTTTCAGCTTTC
325 CAAGTTTCAGCTTTC
1249754 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * ** *
1249819 TTGA-CCCCCCCCCC-TTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAAT
66 TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT
*
1249882 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTACTTTCTGAGAAGA
131 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA
1249947 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TT--CCACCCCCCATTGTGGCCCC
196 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACC-CCCCCCATTGTGGCCCC
* * *
1250009 ACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA
260 ACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA
1250074 CAAGTTTCAGCTTTC
325 CAAGTTTCAGCTTTC
* *
1250089 CTGGCT--TTCTGGTTCTGGAGAAGAAGATTTTTGAAA-ATTT
1 CTGGCTGATT-AGTTTCT-GAGAAGAAGATTTTT-AAAGATTT
1250129 CTCGAAATTT
Statistics
Matches: 1253, Mismatches: 85, Indels: 89
0.88 0.06 0.06
Matches are distributed among these distances:
326 20 0.02
327 4 0.00
328 106 0.08
329 10 0.01
330 1 0.00
331 2 0.00
332 12 0.01
333 100 0.08
334 258 0.21
335 240 0.19
336 14 0.01
337 20 0.02
338 149 0.12
339 25 0.02
340 271 0.22
341 21 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (339 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT
CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA
AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCATTGTGGCCCCA
CCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACAC
AAGTTTCAGCTTTC
Found at i:1256061 original size:33 final size:32
Alignment explanation
Indices: 1255889--1256266 Score: 427
Period size: 32 Copynumber: 11.7 Consensus size: 32
1255879 ACACCATATA
* * * *
1255889 TTTACCTGAAGCAACTGTTTCTACAGCTGGGT
1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT
*
1255921 TTTACCTGAAGTAACTGTTCCTACACCTGATT
1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT
* ** * * *
1255953 TTTACCTGAAGAAACCATTCCTGCAACTAGTT
1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT
* * ***
1255985 TTTACCCGAAGAAACTGTTCCTACACCAT-ACA
1 TTTACCTGAAGTAACTGTTCCTACACC-TGGTT
*
1256017 TTTACCAGAAGTAACTGTTCCTACCACCTGGTT
1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT
1256050 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT
1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT
* *
1256083 TTTACCTGAAGTAACTGTTCCTGCACTTGGTT
1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT
* * ** * *
1256115 TTTACCTAAAGAAACCATTCCTGCAACTGGTT
1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT
* ***
1256147 TTTACCTGAAGAAACTGTTCCTACACCAT-ACA
1 TTTACCTGAAGTAACTGTTCCTACACC-TGGTT
1256179 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT
1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT
1256212 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT
1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT
1256245 TTTACCTGAAGTAACTGTTCCT
1 TTTACCTGAAGTAACTGTTCCT
1256267 NNNNNNNNNN
Statistics
Matches: 294, Mismatches: 46, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
32 175 0.60
33 119 0.40
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (32 bp):
TTTACCTGAAGTAACTGTTCCTACACCTGGTT
Found at i:1256160 original size:162 final size:162
Alignment explanation
Indices: 1255889--1256266 Score: 650
Period size: 162 Copynumber: 2.3 Consensus size: 162
1255879 ACACCATATA
* * * *
1255889 TTTACCTGAAGCAACTGTTTCTA-CAGCTGGGTTTTACCTGAAGTAACTGTTCCTACACCTGATT
1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT
*
1255953 TTTACCTGAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT
66 TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT
1256018 TTACCAGAAGTAACTGTTCCTACCACCTGGTT
131 TTACCAGAAGTAACTGTTCCTACCACCTGGTT
* * *
1256050 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTGCACTTGGTT
1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT
* *
1256115 TTTACCTAAAGAAACCATTCCTGCAACTGGTTTTTACCTGAAGAAACTGTTCCTACACCATACAT
66 TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT
*
1256180 TTACCTGAAGTAACTGTTCCTACCACCTGGTT
131 TTACCAGAAGTAACTGTTCCTACCACCTGGTT
1256212 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCT
1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCT
1256267 NNNNNNNNNN
Statistics
Matches: 205, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
161 21 0.10
162 184 0.90
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (162 bp):
TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT
TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT
TTACCAGAAGTAACTGTTCCTACCACCTGGTT
Found at i:1260595 original size:38 final size:38
Alignment explanation
Indices: 1260544--1260709 Score: 332
Period size: 38 Copynumber: 4.4 Consensus size: 38
1260534 NNNNNNNNNN
1260544 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1260582 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1260620 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1260658 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
1260696 AAGTCAACAGTCAT
1 AAGTCAACAGTCAT
1260710 TAACTAGATG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 128 1.00
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (38 bp):
AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG
Found at i:1275037 original size:28 final size:28
Alignment explanation
Indices: 1275012--1275187 Score: 262
Period size: 28 Copynumber: 6.3 Consensus size: 28
1275002 ACATTGTAAA
1275012 TATCGTTATCCTTAGTGTACAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
* *
1275040 TATTGTTATCCTTAGTGAACAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
* *
1275068 TATTGTTATCCTTAGTGTAAAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
* *
1275096 TATCGTAATCCTTAGTGAACAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
* *
1275124 TATCGTTATCTTTAGTATACAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
* *
1275152 TATCATTATCCTTAGTGTAAAGTGTAGC
1 TATCGTTATCCTTAGTGTACAGTGTAGC
1275180 TATCGTTA
1 TATCGTTA
1275188 GAGAATGGTA
Statistics
Matches: 131, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 131 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (28 bp):
TATCGTTATCCTTAGTGTACAGTGTAGC
Found at i:1276820 original size:2 final size:2
Alignment explanation
Indices: 1276813--1276852 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1276803 AGTGGATGAT
1276813 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1276853 ACTTTGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1282747 original size:34 final size:34
Alignment explanation
Indices: 1282683--1282748 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1282673 ACATGTGATG
* * *
1282683 CTATGCTCTGTGAATTTTGCTATGACATATGACA
1 CTATGCTCTGTGAATTATGCTAGGAAATATGACA
*
1282717 CTATGCTCTGTGAATTATGCTGGGAAATATGA
1 CTATGCTCTGTGAATTATGCTAGGAAATATGA
1282749 TGTGATGCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (34 bp):
CTATGCTCTGTGAATTATGCTAGGAAATATGACA
Found at i:1286740 original size:13 final size:13
Alignment explanation
Indices: 1286722--1286748 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1286712 TACGAGTAAA
1286722 AGAATCAAACAGG
1 AGAATCAAACAGG
1286735 AGAATCAAACAGG
1 AGAATCAAACAGG
1286748 A
1 A
1286749 TGTACTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.22, T:0.07
Consensus pattern (13 bp):
AGAATCAAACAGG
Found at i:1286773 original size:27 final size:28
Alignment explanation
Indices: 1286735--1286787 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
1286725 ATCAAACAGG
1286735 AGAATCAAACAGGATGT-ACTGTATGAA
1 AGAATCAAACAGGATGTAACTGTATGAA
1286762 AGAATCAAACAGGATGTAACTGTATG
1 AGAATCAAACAGGATGTAACTGTATG
1286788 TTAATGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (28 bp):
AGAATCAAACAGGATGTAACTGTATGAA
Found at i:1303157 original size:38 final size:38
Alignment explanation
Indices: 1303115--1303204 Score: 180
Period size: 38 Copynumber: 2.4 Consensus size: 38
1303105 AACAAGTCAC
1303115 TGATTACATCAACATTTTACAAATCTACATACAGAATA
1 TGATTACATCAACATTTTACAAATCTACATACAGAATA
1303153 TGATTACATCAACATTTTACAAATCTACATACAGAATA
1 TGATTACATCAACATTTTACAAATCTACATACAGAATA
1303191 TGATTACATCAACA
1 TGATTACATCAACA
1303205 AGTCTCTACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (38 bp):
TGATTACATCAACATTTTACAAATCTACATACAGAATA
Found at i:1303240 original size:20 final size:20
Alignment explanation
Indices: 1303191--1303481 Score: 127
Period size: 20 Copynumber: 14.7 Consensus size: 20
1303181 ATACAGAATA
1303191 TGATTACATCAACAAGTCTC
1 TGATTACATCAACAAGTCTC
*
1303211 ----TACTTCAACAAGTCTC
1 TGATTACATCAACAAGTCTC
1303227 TGATTACATCAACAAGTCTC
1 TGATTACATCAACAAGTCTC
* *
1303247 TGATTACATCAAC-ATTTTAC
1 TGATTACATCAACAAGTCT-C
** ** *
1303267 AAATATACAT--AC-AGAATA
1 TGAT-TACATCAACAAGTCTC
*
1303285 TGATTACATCAATAAGTCTC
1 TGATTACATCAACAAGTCTC
1303305 TGATTACATCACACTTTACAAG--TC
1 TGATTACAT--CA----ACAAGTCTC
* ** *
1303329 TGATTACATTAAC-AGAATA
1 TGATTACATCAACAAGTCTC
* ** *
1303348 TGATTACACCAGTAAGTCAC
1 TGATTACATCAACAAGTCTC
** * *
1303368 TGATGGCATTAACAAGTTTC
1 TGATTACATCAACAAGTCTC
** *
1303388 TGATGGCATTAACAAGTCTC
1 TGATTACATCAACAAGTCTC
*** * *
1303408 TGATGGTATTAACAAGTCTG
1 TGATTACATCAACAAGTCTC
** * *
1303428 TGATGCCATTAATAAGTCTC
1 TGATTACATCAACAAGTCTC
*
1303448 TGATTACATTAACAAGTCTC
1 TGATTACATCAACAAGTCTC
1303468 TGATTACATCAACA
1 TGATTACATCAACA
1303482 TTTTACAAAT
Statistics
Matches: 207, Mismatches: 46, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
16 15 0.07
17 7 0.03
18 4 0.02
19 18 0.09
20 140 0.68
21 5 0.02
22 3 0.01
24 11 0.05
26 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
TGATTACATCAACAAGTCTC
Found at i:1303302 original size:58 final size:62
Alignment explanation
Indices: 1303227--1303371 Score: 183
Period size: 58 Copynumber: 2.4 Consensus size: 62
1303217 AACAAGTCTC
* *
1303227 TGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAA-AT-A-TACA-T-ACAGAATA
1 TGATTACATCAATAAGTCTCTGATTACATC-ACACTTTACAAGATGATTACATTAACAGAATA
*
1303285 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATA
1 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAG-ATGATTACATTAACAGAATA
* * *
1303348 TGATTACACCAGTAAGTCACTGAT
1 TGATTACATCAATAAGTCTCTGAT
1303372 GGCATTAACA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
57 10 0.13
58 29 0.39
59 1 0.01
60 1 0.01
61 4 0.05
62 1 0.01
63 29 0.39
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (62 bp):
TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGATGATTACATTAACAGAATA
Found at i:1303411 original size:40 final size:40
Alignment explanation
Indices: 1303361--1303471 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 40
1303351 TTACACCAGT
* * *
1303361 AAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAAC
1 AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC
* * *
1303401 AAGTCTCTGATGGTATTAACAAGTCTGTGATGCCATTAAT
1 AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC
**
1303441 AAGTCTCTGATTACATTAACAAGTCTCTGAT
1 AAGTCTCTGATGGCATTAACAAGTCTCTGAT
1303472 TACATCAACA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (40 bp):
AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC
Found at i:1303530 original size:58 final size:60
Alignment explanation
Indices: 1303448--1303592 Score: 179
Period size: 63 Copynumber: 2.4 Consensus size: 60
1303438 AATAAGTCTC
* *
1303448 TGATTACATTAACAAGTCTCTGATTACATCAACATTTTACAAATC-TACA-T-ACAGAATA
1 TGATTACATCAATAAGTCTCTGATTACATC-ACATTTTACAAATCTTACATTAACAGAATA
* *
1303506 TGTTTACATCAATAAGTCTCTGATTACATCACATTTTACAAGTCTGATTACATTAACAGAATA
1 TGATTACATCAATAAGTCTCTGATTACATCACATTTTACAAATC---TTACATTAACAGAATA
* *
1303569 TGATTACATCAGTAAGTCACTGAT
1 TGATTACATCAATAAGTCTCTGAT
1303593 GGCATTAACA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
57 13 0.18
58 27 0.36
61 4 0.05
62 1 0.01
63 29 0.39
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (60 bp):
TGATTACATCAATAAGTCTCTGATTACATCACATTTTACAAATCTTACATTAACAGAATA
Found at i:1303603 original size:221 final size:221
Alignment explanation
Indices: 1303220--1303681 Score: 836
Period size: 221 Copynumber: 2.1 Consensus size: 221
1303210 CTACTTCAAC
1303220 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA
1 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA
1303285 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG
66 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG
*
1303350 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGGT
131 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT
1303415 ATTAACAAGTCTGTGATGCCATTAAT
196 ATTAACAAGTCTGTGATGCCATTAAT
* *
1303441 AAGTCTCTGATTACATTAACAAGTCTCTGATTACATCAACATTTTACAAATCTACATACAGAATA
1 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA
* *
1303506 TGTTTACATCAATAAGTCTCTGATTACATCACATTTTACAAGTCTGATTACATTAACAGAATATG
66 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG
* *
1303571 ATTACATCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTTTGATGAT
131 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT
*
1303636 ATTAACAAGTCTGTGATGGCATTAAT
196 ATTAACAAGTCTGTGATGCCATTAAT
*
1303662 -AGTCTCTGATTAAATCAACA
1 AAGTCTCTGATTACATCAACA
1303682 TTTTACAAGT
Statistics
Matches: 231, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
220 18 0.08
221 213 0.92
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (221 bp):
AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA
TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG
ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT
ATTAACAAGTCTGTGATGCCATTAAT
Found at i:1303605 original size:20 final size:20
Alignment explanation
Indices: 1303582--1303671 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
1303572 TTACATCAGT
*
1303582 AAGTCACTGATGGCATTAAC
1 AAGTCTCTGATGGCATTAAC
*
1303602 AAGTTTCTGATGGCATTAAC
1 AAGTCTCTGATGGCATTAAC
* **
1303622 AAGTCTTTGATGATATTAAC
1 AAGTCTCTGATGGCATTAAC
*
1303642 AAGTCTGTGATGGCATTAA-
1 AAGTCTCTGATGGCATTAAC
*
1303661 TAGTCTCTGAT
1 AAGTCTCTGAT
1303672 TAAATCAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 9 0.15
20 50 0.85
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
AAGTCTCTGATGGCATTAAC
Found at i:1303715 original size:45 final size:45
Alignment explanation
Indices: 1303663--1303751 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
1303653 GGCATTAATA
* *
1303663 GTCTCTGATTAAATCAACATTTTACAAGTCTTATTACATTAACAT
1 GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACAT
*
1303708 GTCTCTGATTACATCAACATTTCACAAGTCTGATTACATTAACA
1 GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACA
1303752 GAATTCACAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (45 bp):
GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACAT
Found at i:1303740 original size:25 final size:24
Alignment explanation
Indices: 1303666--1303751 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
1303656 ATTAATAGTC
*
1303666 TCTGATTAAATCAACATTTTACAAG
1 TCTGATTACATCAACA-TTTACAAG
* * *
1303691 TCTTATTACATTAACATGT-C---
1 TCTGATTACATCAACATTTACAAG
1303711 TCTGATTACATCAACATTTCACAAG
1 TCTGATTACATCAACATTT-ACAAG
*
1303736 TCTGATTACATTAACA
1 TCTGATTACATCAACA
1303752 GAATTCACAG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 16 0.33
22 1 0.02
23 1 0.02
24 2 0.04
25 28 0.58
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (24 bp):
TCTGATTACATCAACATTTACAAG
Found at i:1303758 original size:27 final size:25
Alignment explanation
Indices: 1303711--1303760 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1303701 TTAACATGTC
*
1303711 TCTGATTACATCAACATTTCACAAG
1 TCTGATTACATCAACAATTCACAAG
*
1303736 TCTGATTACATTAACAGAATTCACA
1 TCTGATTACATCAAC--AATTCACA
1303761 GTAAACTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
27 7 0.33
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (25 bp):
TCTGATTACATCAACAATTCACAAG
Found at i:1312616 original size:47 final size:47
Alignment explanation
Indices: 1312534--1312724 Score: 283
Period size: 47 Copynumber: 4.1 Consensus size: 47
1312524 TACATGTCCC
* * * * * *
1312534 AATGATTCCCTACTTTTGAGGGAATAGCTCTGAGTTTTAATGGTACA
1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
* * * *
1312581 ATTGATTTCTCACCTTTGAGAGAGTAGTTCCGAGTTTTGATGGTACA
1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
1312628 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
*
1312675 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGGTGGTACA
1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
1312722 AAT
1 AAT
1312725 CAGCCGGTTA
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 129 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (47 bp):
AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA
Found at i:1315249 original size:85 final size:85
Alignment explanation
Indices: 1315106--1315277 Score: 344
Period size: 85 Copynumber: 2.0 Consensus size: 85
1315096 GGCCACCGAC
1315106 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT
1 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT
1315171 AATACAAGTATAGTCAGTTT
66 AATACAAGTATAGTCAGTTT
1315191 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT
1 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT
1315256 AATACAAGTATAGTCAGTTT
66 AATACAAGTATAGTCAGTTT
1315276 GT
1 GT
1315278 CAGTCTCGGG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (85 bp):
GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT
AATACAAGTATAGTCAGTTT
Found at i:1315862 original size:33 final size:33
Alignment explanation
Indices: 1315775--1316060 Score: 493
Period size: 33 Copynumber: 8.7 Consensus size: 33
1315765 GCATGGTTAN
*
1315775 TACCATACATGTAATACAGTAAGGTGGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
* * *
1315808 TACCATACTTG-AACACCGTAAGGTAGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
*
1315840 TACCATACATGTAACACAGTAAGGTGGCATATG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
1315873 TACCATACATGTAACACAGTAAGGTGGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
*
1315906 TATCATACATGTAACACAGTAAGGTGGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
1315939 TACCATACATGTAACACAGTAAGGTGGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
*
1315972 TACCATACATGTAATACAGTAAGGTGGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
*
1316005 TACCATACATGTAACACAGTAAGGTAGCATAGG
1 TACCATACATGTAACACAGTAAGGTGGCATAGG
1316038 TACCATACATGTAACACAGTAAG
1 TACCATACATGTAACACAGTAAG
1316061 CAGCGACTTA
Statistics
Matches: 238, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
32 28 0.12
33 210 0.88
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (33 bp):
TACCATACATGTAACACAGTAAGGTGGCATAGG
Found at i:1317188 original size:166 final size:166
Alignment explanation
Indices: 1316749--1317375 Score: 911
Period size: 166 Copynumber: 3.8 Consensus size: 166
1316739 GTGAATATGC
* * * * * * *
1316749 AAAATAAGCAAAGTCGA-CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCAC
1 AAAATAAACAAAGTC-ATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC
*
1316813 AATATGGCATGCCTAAACAAATAGTGTGTTAAAAA-TTCAAGCATCTGCGATAAATAGCTGCTGA
65 AATATGACATGCCTAAACAAATAGTGTG-TAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
*
1316877 GAAATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-
129 GAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
1316914 AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTGACGTCCAATTGGTACAAAAATATGTCCCAC
1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC
* * * *
1316978 GATATGACATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
65 AATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
1317043 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
1317080 AAAATAAACAAAGTCATTATTTAACAAGAAGTTGACGTCCGACTGATACAAAAATATATCCCACA
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
* * * * * * *
1317145 ATATGGCAAGCCAAAACAAATAGTGTATTACAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
* *
1317210 AATCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
1317246 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAACTATATCCCACG
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
*
1317311 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
1317376 TAAATGCGAC
Statistics
Matches: 412, Mismatches: 45, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
163 1 0.00
164 6 0.01
165 141 0.34
166 263 0.64
167 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (166 bp):
AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
Done.