Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1599
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: 1324113
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 103357 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:900926 original size:2 final size:2
Alignment explanation
Indices: 900919--900964 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
900909 TTAAAATACA
*
900919 TC TC TC TC TC TG 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
900961 TC TC
1 TC TC
900965 GTATTGGGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:903578 original size:15 final size:16
Alignment explanation
Indices: 903558--903599 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
903548 TAGATCACAA
*
903558 AAAGAA-AAAAAAATG
1 AAAGAAGAAAAAAAAG
903573 AAAGAAGAAAAAAAAG
1 AAAGAAGAAAAAAAAG
903589 -AAGAAGAAAAA
1 AAAGAAGAAAAA
903600 TTCCACTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAGAAGAAAAAAAAG
Found at i:903582 original size:18 final size:16
Alignment explanation
Indices: 903559--903599 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
903549 AGATCACAAA
903559 AAGAAAAAAAAATGAAAG
1 AAGAAAAAAAAA-G-AAG
903577 AAG-AAAAAAAAGAAG
1 AAGAAAAAAAAAGAAG
903592 AAGAAAAA
1 AAGAAAAA
903600 TTCCACTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 5 0.23
17 8 0.36
18 3 0.14
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAGAAAAAAAAAGAAG
Found at i:913104 original size:4 final size:4
Alignment explanation
Indices: 913095--913182 Score: 176
Period size: 4 Copynumber: 22.0 Consensus size: 4
913085 ATACAAAAAA
913095 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
913143 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
913183 CTATTGACAG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:917605 original size:2 final size:2
Alignment explanation
Indices: 917598--917638 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
917588 GCAGTTTTCT
917598 GA GA GA GA GA GA GA 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 GA GA GA GA GA GA GA G
917639 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:918026 original size:2 final size:2
Alignment explanation
Indices: 918019--918052 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
918009 NNNNNNNNNN
918019 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
918053 GGTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:919192 original size:16 final size:16
Alignment explanation
Indices: 919171--919207 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
919161 TTTTTCTTTA
919171 ATTTTAGATT-TTGATT
1 ATTTTAGATTATT-ATT
919187 ATTTTAGATTATTATT
1 ATTTTAGATTATTATT
919203 ATTTT
1 ATTTT
919208 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (16 bp):
ATTTTAGATTATTATT
Found at i:923772 original size:21 final size:21
Alignment explanation
Indices: 923746--923787 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
923736 TCGATCCATA
923746 TGTCTATGAATCTCTCTATCC
1 TGTCTATGAATCTCTCTATCC
923767 TGTCTATGAATCTCTCTATCC
1 TGTCTATGAATCTCTCTATCC
923788 CTTCTCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.43
Consensus pattern (21 bp):
TGTCTATGAATCTCTCTATCC
Found at i:928184 original size:36 final size:36
Alignment explanation
Indices: 928135--928405 Score: 260
Period size: 36 Copynumber: 7.5 Consensus size: 36
928125 CAGAGGAACA
* *
928135 TCATGATGATGGGGATCATGAGAACCCACGGGGACG
1 TCATGATGGTGGGGATCATGAGAACCCACAGGGACG
*
928171 TCATGATGGTGGGGATCACGAGAACCCACAGGGACG
1 TCATGATGGTGGGGATCATGAGAACCCACAGGGACG
* *
928207 TCATGATGGTGGGGATCATGAGAACCCACGGGGACA
1 TCATGATGGTGGGGATCATGAGAACCCACAGGGACG
* * * *
928243 TCATGATGGTGGGGATTATGAGATCCCACAGGAACA
1 TCATGATGGTGGGGATCATGAGAACCCACAGGGACG
* * * * * * *
928279 TCATGATGGTGGGGGTCAGGAG-TCTTCACCGGTATG
1 TCATGATGGTGGGGATCATGAGAAC-CCACAGGGACG
* * * *
928315 TCGTGGTGGTGGGGATTATGAG-ACCCTACAGGAACG
1 TCATGATGGTGGGGATCATGAGAACCC-ACAGGGACG
* * * * * *
928351 TCATGATGGTGGGGGTCAGGAG-TCTTCACCGGCACG
1 TCATGATGGTGGGGATCATGAGAAC-CCACAGGGACG
928387 TCATGATGGTGGGGATCAT
1 TCATGATGGTGGGGATCAT
928406 CATGCTTTGC
Statistics
Matches: 193, Mismatches: 39, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
35 3 0.02
36 189 0.98
37 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (36 bp):
TCATGATGGTGGGGATCATGAGAACCCACAGGGACG
Found at i:928442 original size:15 final size:15
Alignment explanation
Indices: 928422--928450 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
928412 TTGCTGGTAT
928422 ATCGTGATGATGAGG
1 ATCGTGATGATGAGG
928437 ATCGTGATGATGAG
1 ATCGTGATGATGAG
928451 AATGTCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (15 bp):
ATCGTGATGATGAGG
Found at i:928848 original size:60 final size:60
Alignment explanation
Indices: 928775--928976 Score: 341
Period size: 60 Copynumber: 3.4 Consensus size: 60
928765 CTAACACCCT
928775 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCG
1 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCG
*
928835 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCTACTCG
1 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCG
* * * * *
928895 GTATACCACTCGCAGAACCAGTTCCCACTGGGAAGCCTGCGAAATTACCACCTGCACCCG
1 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCG
*
928955 GTATACCACTTGCAGAACCAGT
1 GTATACCACTCGCAGAACCAGT
928977 TCCTATTGGG
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 134 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (60 bp):
GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCG
Found at i:929000 original size:60 final size:60
Alignment explanation
Indices: 928769--929005 Score: 242
Period size: 60 Copynumber: 4.0 Consensus size: 60
928759 ACTCCTCTAA
* * * * * * * *
928769 CACCCTGTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTC
1 CACCCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAACCTCCAAAATTACCACCTG
* * * * * * *
928829 CACTCGGTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACA-CTT
1 CACCCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAACCTCCAAAATTACCACCTG
* * * *
928888 CTACTCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAGCCTGCGAAATTACCACCTG
1 C-ACCCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAACCTCCAAAATTACCACCTG
* * * **
928949 CACCCGGTATACCACTTGCAGAACCAGTTCCTATTGGGAAATTTCCAAAATTACCAC
1 CACCCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAACCTCCAAAATTACCAC
929006 TTAATGGTCC
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
59 2 0.01
60 154 0.97
61 3 0.02
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (60 bp):
CACCCGGTATACCACTCGCAGAACCAGTTCCCACTGGGAAACCTCCAAAATTACCACCTG
Found at i:929000 original size:120 final size:120
Alignment explanation
Indices: 928775--929007 Score: 331
Period size: 120 Copynumber: 1.9 Consensus size: 120
928765 CTAACACCCT
* *
928775 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCCACTCGGTATA
1 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACCTCCACCCGGTATA
* * *
928840 CCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACTTCTACTCG
66 CCACTCGCAGAACCAGTGCCCACTGGGAAACCTCCAAAATTAACACTTCTACTCG
* * *
928895 GTATACCACTCGCAGAACCAGTTCCCACTGGGAAGCCTGCGAAATTACCACCTGCACCCGGTATA
1 GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACCTCCACCCGGTATA
* * * * ** *
928960 CCACTTGCAGAACCAGTTCCTATTGGGAAATTTCCAAAATTACCACTT
66 CCACTCGCAGAACCAGTGCCCACTGGGAAACCTCCAAAATTAACACTT
929008 AATGGTCCTT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (120 bp):
GTATACCACTCGCAGAACCAGTGCCCACTGGGAAGCCTGCGAAATTAACACCTCCACCCGGTATA
CCACTCGCAGAACCAGTGCCCACTGGGAAACCTCCAAAATTAACACTTCTACTCG
Found at i:937886 original size:2 final size:2
Alignment explanation
Indices: 937879--937927 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
937869 AAGTCCTACT
937879 GA 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 GA
937921 GA GA GA G
1 GA GA GA G
937928 TACTTTACCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:940268 original size:47 final size:49
Alignment explanation
Indices: 940208--940302 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 49
940198 TAGGCAATAA
*
940208 ATCAAATTGTAAATTTATAGGAATGCTA-A-AATGCCATGAATAAATCC
1 ATCAAATTGTAAATTTATAGGAATGATATATAATGCCATGAATAAATCC
* * *
940255 ATCAAATTTTAAATTTATAGGATTGATATATGATGCCATGAATAAATC
1 ATCAAATTGTAAATTTATAGGAATGATATATAATGCCATGAATAAATC
940303 GATTTTCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 25 0.60
48 1 0.02
49 16 0.38
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (49 bp):
ATCAAATTGTAAATTTATAGGAATGATATATAATGCCATGAATAAATCC
Found at i:947049 original size:42 final size:42
Alignment explanation
Indices: 946998--947239 Score: 226
Period size: 41 Copynumber: 5.7 Consensus size: 42
946988 ACATTTTTAT
* * *
946998 AATAAACGCGAAACTTTTGCGATATAACGCGTTAA-TTTTGCG
1 AATAAACGCGTAACTTTCGCGATATAACGCG-TAACTTTCGCG
* * * *
947040 AAGAAACGCGAAACTTTTGC-AAATAACGCGTAACTTTCGCG
1 AATAAACGCGTAACTTTCGCGATATAACGCGTAACTTTCGCG
* *
947081 AATAAACGCGTGACTTTCGCGA-ATAAACGCGAAACTTTCGCG
1 AATAAACGCGTAACTTTCGCGATAT-AACGCGTAACTTTCGCG
**
947123 ATATATTAACGCGTAACTTTCGCGATATAACGCGTATTTTTCGCG
1 A-ATA--AACGCGTAACTTTCGCGATATAACGCGTAACTTTCGCG
* ** *
947168 AATAAATGCGTAAC-TTCGCGA-ATAAACGCAAAACTTTTGCG
1 AATAAACGCGTAACTTTCGCGATAT-AACGCGTAACTTTCGCG
* *
947209 AATAAACGCGTTACATTCGCGA-ATTAACGCG
1 AATAAACGCGTAACTTTCGCGATA-TAACGCG
947240 AAACCATTAT
Statistics
Matches: 169, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
40 5 0.03
41 64 0.38
42 59 0.35
43 4 0.02
44 3 0.02
45 32 0.19
46 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
AATAAACGCGTAACTTTCGCGATATAACGCGTAACTTTCGCG
Found at i:947075 original size:62 final size:62
Alignment explanation
Indices: 947002--947243 Score: 233
Period size: 62 Copynumber: 3.8 Consensus size: 62
946992 TTTTATAATA
* * * *
947002 AACGCGAAACTTTTGCG-ATATAACGCGTTAATTTTGCGAAGAAACGCGAAACTTTTGCAAAT
1 AACGCGAAACTTTCGCGAATA-AACGCGTTAATTTCGCGAATAAACGCGAAACTTTCGCAAAT
* * *
947064 AACGCGTAACTTTCGCGAATAAACGCGTGACTTTCGCGAATAAACGCGAAACTTTCGCGATATAT
1 AACGCGAAACTTTCGCGAATAAACGCGTTAATTTCGCGAATAAACGCGAAACTTTCGC-A-A-A-
947129 T
62 T
* * * * *
947130 AACGCGTAACTTTCGCG-ATATAACGCG-TATTTTTCGCGAATAAATGCGTAAC-TTCGCGAAT
1 AACGCGAAACTTTCGCGAATA-AACGCGTTA-ATTTCGCGAATAAACGCGAAACTTTCGCAAAT
* * *
947191 AAACGCAAAACTTTTGCGAATAAACGCGTTACA-TTCGCGAATTAACGCGAAAC
1 -AACGCGAAACTTTCGCGAATAAACGCGTTA-ATTTCGCGAATAAACGCGAAAC
947244 CATTATATAA
Statistics
Matches: 150, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
61 1 0.01
62 85 0.57
63 10 0.07
64 1 0.01
65 10 0.07
66 43 0.29
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (62 bp):
AACGCGAAACTTTCGCGAATAAACGCGTTAATTTCGCGAATAAACGCGAAACTTTCGCAAAT
Found at i:947140 original size:24 final size:21
Alignment explanation
Indices: 946998--947239 Score: 233
Period size: 21 Copynumber: 11.5 Consensus size: 21
946988 ACATTTTTAT
* *
946998 AATAAACGCGAAACTTTTGCG
1 AATAAACGCGTAACTTTCGCG
*
947019 -ATATAACGCGTTAA-TTTTGCG
1 AATA-AACGCG-TAACTTTCGCG
* * * *
947040 AAGAAACGCGAAACTTTTGCA
1 AATAAACGCGTAACTTTCGCG
947061 AAT-AACGCGTAACTTTCGCG
1 AATAAACGCGTAACTTTCGCG
*
947081 AATAAACGCGTGACTTTCGCG
1 AATAAACGCGTAACTTTCGCG
*
947102 AATAAACGCGAAACTTTCGCG
1 AATAAACGCGTAACTTTCGCG
947123 ATATATTAACGCGTAACTTTCGCG
1 A-ATA--AACGCGTAACTTTCGCG
**
947147 -ATATAACGCGTATTTTTCGCG
1 AATA-AACGCGTAACTTTCGCG
*
947168 AATAAATGCGTAAC-TTCGCG
1 AATAAACGCGTAACTTTCGCG
** *
947188 AATAAACGCAAAACTTTTGCG
1 AATAAACGCGTAACTTTCGCG
* *
947209 AATAAACGCGTTACATTCGCG
1 AATAAACGCGTAACTTTCGCG
*
947230 AATTAACGCG
1 AATAAACGCG
947240 AAACCATTAT
Statistics
Matches: 184, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
20 39 0.21
21 116 0.63
22 13 0.07
24 16 0.09
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
AATAAACGCGTAACTTTCGCG
Found at i:947230 original size:128 final size:128
Alignment explanation
Indices: 947002--947243 Score: 326
Period size: 128 Copynumber: 1.9 Consensus size: 128
946992 TTTTATAATA
* *
947002 AACGCGAAACTTTTGCGATATAACGCGTTAATTTTGCGAAGAAACGCGAAACTTTTGCAAATAAC
1 AACGCGAAACTTTCGCGATATAACGCGTTAATTTTGCGAAGAAACGCGAAACTTTCGCAAATAAC
** *
947067 GCGTAACTTTCGCGAATAAACGCGTGACTTTCGCGAATAAACGCGAAACTTTCGCGATATATT
66 GCAAAACTTTCGCGAATAAACGCGTGACATTCGCGAATAAACGCGAAACTTTCGCGATATATT
* * * * * *
947130 AACGCGTAACTTTCGCGATATAACGCG-TATTTTTCGCGAATAAATGCGTAAC-TTCGCGAATAA
1 AACGCGAAACTTTCGCGATATAACGCGTTAATTTT-GCGAAGAAACGCGAAACTTTCGCAAAT-A
* * *
947193 ACGCAAAACTTTTGCGAATAAACGCGTTACATTCGCGAATTAACGCGAAAC
64 ACGCAAAACTTTCGCGAATAAACGCGTGACATTCGCGAATAAACGCGAAAC
947244 CATTATATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
127 13 0.13
128 85 0.87
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (128 bp):
AACGCGAAACTTTCGCGATATAACGCGTTAATTTTGCGAAGAAACGCGAAACTTTCGCAAATAAC
GCAAAACTTTCGCGAATAAACGCGTGACATTCGCGAATAAACGCGAAACTTTCGCGATATATT
Found at i:947814 original size:15 final size:16
Alignment explanation
Indices: 947794--947823 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
947784 TTTTAATTCG
947794 AATTAAAAT-TGTTGT
1 AATTAAAATATGTTGT
947809 AATTAAAATATGTTG
1 AATTAAAATATGTTG
947824 CTGCCTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
AATTAAAATATGTTGT
Found at i:948115 original size:21 final size:21
Alignment explanation
Indices: 948049--948204 Score: 112
Period size: 21 Copynumber: 7.6 Consensus size: 21
948039 CGCAATTATT
*
948049 CGCGTTTATTCGCGATAGTAA
1 CGCGTTTATTCGCGAAAGTAA
* **
948070 CACG-TTATATCGCCG-AAGTTT
1 CGCGTTTAT-TCG-CGAAAGTAA
*
948091 CGCGTTTATTCGTGAAAGTAA
1 CGCGTTTATTCGCGAAAGTAA
*
948112 CGCG---A-TAGCGAAAGTAA
1 CGCGTTTATTCGCGAAAGTAA
* *
948129 CGCGTACTA-TCGCGAAAGGT-T
1 CGCGT-TTATTCGCGAAA-GTAA
*
948150 CGCGTTTATTCGCGAAAGTTA
1 CGCGTTTATTCGCGAAAGTAA
* *
948171 CGCGTTTATTCACGAAAGTTA
1 CGCGTTTATTCGCGAAAGTAA
*
948192 CGCCTTTATTCGC
1 CGCGTTTATTCGC
948205 AAAACTAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
17 14 0.13
18 1 0.01
20 9 0.08
21 75 0.70
22 8 0.07
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
CGCGTTTATTCGCGAAAGTAA
Found at i:948466 original size:11 final size:11
Alignment explanation
Indices: 948450--948478 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
948440 GCTTGTTAAA
948450 AAAAAAAAACG
1 AAAAAAAAACG
948461 AAAAAAAAACG
1 AAAAAAAAACG
948472 AAAAAAA
1 AAAAAAA
948479 CCCCAAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACG
Found at i:951685 original size:2 final size:2
Alignment explanation
Indices: 951680--951735 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
951670 CAATATGTGT
951680 GA 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 GA
951722 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
951736 TTAATGCAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:965360 original size:21 final size:21
Alignment explanation
Indices: 965344--965566 Score: 175
Period size: 21 Copynumber: 10.6 Consensus size: 21
965334 TATTTCGCAA
965344 TTATTCGCGAAAGTTTCGCGT
1 TTATTCGCGAAAGTTTCGCGT
** *
965365 TTATTCGCGAAAGTAACACG-
1 TTATTCGCGAAAGTTTCGCGT
*
965385 TTATATCGAGAAAGTTTCGCGT
1 TTAT-TCGCGAAAGTTTCGCGT
* **
965407 TTATTCGTGAAAGTAACGCGT
1 TTATTCGCGAAAGTTTCGCGT
* *
965428 ACTA-TCGCGAAAGGTTCGCGT
1 -TTATTCGCGAAAGTTTCGCGT
* *
965449 TTATTCGCCAAAGTTTCGCCT
1 TTATTCGCGAAAGTTTCGCGT
* * **
965470 TTATTCGCAAAACTAACGCGT
1 TTATTCGCGAAAGTTTCGCGT
*
965491 TATATT-GCGAAAGTTTCGTGT
1 T-TATTCGCGAAAGTTTCGCGT
**** *
965512 TTATTCGCGAAACAAACGC-C
1 TTATTCGCGAAAGTTTCGCGT
*
965532 TCATATCGCGAAAGTTTCGCGT
1 TTAT-TCGCGAAAGTTTCGCGT
*
965554 TTTTTCGCGAAAG
1 TTATTCGCGAAAG
965567 AAATATTTTT
Statistics
Matches: 151, Mismatches: 43, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
20 13 0.09
21 126 0.83
22 12 0.08
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (21 bp):
TTATTCGCGAAAGTTTCGCGT
Found at i:965824 original size:17 final size:17
Alignment explanation
Indices: 965802--965839 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
965792 TTTGCTTGTT
*
965802 AAAAAAATAAC-AAAACA
1 AAAAAAAGAACGAAAA-A
965819 AAAAAAAGAACGAAAAA
1 AAAAAAAGAACGAAAAA
965836 AAAA
1 AAAA
965840 TGTCGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAACGAAAAA
Found at i:973036 original size:9 final size:9
Alignment explanation
Indices: 973022--973065 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
973012 CAACAAATTA
973022 AAATTAACC
1 AAATTAACC
973031 AAATTAA-C
1 AAATTAACC
*
973039 AAATTGACC
1 AAATTAACC
*
973048 TAATTAA-C
1 AAATTAACC
973056 AAATTAACC
1 AAATTAACC
973065 A
1 A
973066 CACCATCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (9 bp):
AAATTAACC
Found at i:973043 original size:8 final size:8
Alignment explanation
Indices: 973013--973063 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
973003 CTGGGTGGTC
973013 AACAAATT
1 AACAAATT
973021 -A-AAATT
1 AACAAATT
973027 AACCAAATT
1 AA-CAAATT
973036 AACAAATT
1 AACAAATT
* *
973044 GACCTAATT
1 -AACAAATT
973053 AACAAATT
1 AACAAATT
973061 AAC
1 AAC
973064 CACACCATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 15 0.43
9 13 0.37
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (8 bp):
AACAAATT
Found at i:973052 original size:17 final size:17
Alignment explanation
Indices: 973022--973065 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
973012 CAACAAATTA
973022 AAATTAACCAAATTAAC
1 AAATTAACCAAATTAAC
* *
973039 AAATTGACCTAATTAAC
1 AAATTAACCAAATTAAC
973056 AAATTAACCA
1 AAATTAACCA
973066 CACCATCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATTAACCAAATTAAC
Found at i:988260 original size:24 final size:24
Alignment explanation
Indices: 988223--988332 Score: 68
Period size: 24 Copynumber: 4.7 Consensus size: 24
988213 CACGTAAAAA
* * *
988223 ATCAGTACTCAAGGTCCTGTACAG
1 ATCAGTAATTAAGGTCCTATACAG
988247 ATCAGTAATTAAGGTCCCATATACAG
1 ATCAGTAATTAAGGT-CC-TATACAG
** * *
988273 ATCAACAATTAA----CTGTAAAG
1 ATCAGTAATTAAGGTCCTATACAG
* *
988293 ATCAGTAATTAAAGTCCTATA-TG
1 ATCAGTAATTAAGGTCCTATACAG
*
988316 AACCAGTAATTAAGGTC
1 -ATCAGTAATTAAGGTC
988333 ATGTTTAGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
20 15 0.23
21 1 0.02
23 1 0.02
24 31 0.47
25 2 0.03
26 16 0.24
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (24 bp):
ATCAGTAATTAAGGTCCTATACAG
Found at i:988500 original size:24 final size:24
Alignment explanation
Indices: 988468--988530 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
988458 GTAAAGTCTA
988468 ATACAAATCAGTAAATAAGGTCCC
1 ATACAAATCAGTAAATAAGGTCCC
* *
988492 ATACAAATCAGTAATTAAGGTCCT
1 ATACAAATCAGTAAATAAGGTCCC
988516 ATACAAATCAGTAAA
1 ATACAAATCAGTAAA
988531 GGTCCTGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (24 bp):
ATACAAATCAGTAAATAAGGTCCC
Found at i:1001976 original size:23 final size:23
Alignment explanation
Indices: 1001946--1002000 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
1001936 TAGCATTTTA
*
1001946 TTGACCTTTATGACAGGATTCCC
1 TTGACCTTCATGACAGGATTCCC
*
1001969 TTGACCTTCATGACAGGATTTCC
1 TTGACCTTCATGACAGGATTCCC
1001992 TTGACCTTC
1 TTGACCTTC
1002001 TTGATGTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (23 bp):
TTGACCTTCATGACAGGATTCCC
Found at i:1002341 original size:13 final size:13
Alignment explanation
Indices: 1002323--1002474 Score: 164
Period size: 13 Copynumber: 11.2 Consensus size: 13
1002313 ATCAATGTTA
1002323 TGTGTTGATGCAG
1 TGTGTTGATGCAG
1002336 TGTGTTGATGC-G
1 TGTGTTGATGCAG
*
1002348 TTGTGTTAATGCAGTGCCTG
1 -TGTG-T--TG-A-TG-CAG
1002368 TGTGTTGATGCAG
1 TGTGTTGATGCAG
*
1002381 TGTGTTGATGAAG
1 TGTGTTGATGCAG
*
1002394 TGTGTTAATGCAG
1 TGTGTTGATGCAG
1002407 TGTGTTGATG-AGG
1 TGTGTTGATGCA-G
1002420 TGTGTTGATGCAG
1 TGTGTTGATGCAG
* * *
1002433 TGTTTTAATGCAA
1 TGTGTTGATGCAG
1002446 TGTGTTGATGCAG
1 TGTGTTGATGCAG
1002459 TGTGTTGATGCAG
1 TGTGTTGATGCAG
1002472 TGT
1 TGT
1002475 TGATGATATA
Statistics
Matches: 118, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
12 2 0.02
13 97 0.82
14 4 0.03
15 1 0.01
16 4 0.03
17 1 0.01
18 3 0.03
19 5 0.04
20 1 0.01
ACGTcount: A:0.17, C:0.07, G:0.36, T:0.40
Consensus pattern (13 bp):
TGTGTTGATGCAG
Found at i:1002371 original size:32 final size:32
Alignment explanation
Indices: 1002335--1002395 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1002325 TGTTGATGCA
*
1002335 GTGTGTTGATGC-GTTGTGTTAATGCAGTGCCT
1 GTGTGTTGATGCAG-TGTGTTAATGAAGTGCCT
*
1002367 GTGTGTTGATGCAGTGTGTTGATGAAGTG
1 GTGTGTTGATGCAGTGTGTTAATGAAGTG
1002396 TGTTAATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.39
Consensus pattern (32 bp):
GTGTGTTGATGCAGTGTGTTAATGAAGTGCCT
Found at i:1002410 original size:39 final size:39
Alignment explanation
Indices: 1002323--1002474 Score: 191
Period size: 39 Copynumber: 3.7 Consensus size: 39
1002313 ATCAATGTTA
1002323 TGTGTTGATGCAGTGTGTTGATGC-GTTGTGTTAATGCAGTGCCTG
1 TGTGTTGATGCAGTGTGTTGATGCAG-TGTGTTAATGCA------G
*
1002368 TGTGTTGATGCAGTGTGTTGATGAAGTGTGTTAATGCAG
1 TGTGTTGATGCAGTGTGTTGATGCAGTGTGTTAATGCAG
* *
1002407 TGTGTTGATG-AGGTGTGTTGATGCAGTGTTTTAATGCAA
1 TGTGTTGATGCA-GTGTGTTGATGCAGTGTGTTAATGCAG
1002446 TGTGTTGATGCAGTGTGTTGATGCAGTGT
1 TGTGTTGATGCAGTGTGTTGATGCAGTGT
1002475 TGATGATATA
Statistics
Matches: 100, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
38 1 0.01
39 62 0.62
40 1 0.01
45 35 0.35
46 1 0.01
ACGTcount: A:0.17, C:0.07, G:0.36, T:0.40
Consensus pattern (39 bp):
TGTGTTGATGCAGTGTGTTGATGCAGTGTGTTAATGCAG
Found at i:1043432 original size:61 final size:61
Alignment explanation
Indices: 1043360--1043481 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
1043350 CTTAATTATT
* * * *
1043360 TTTCAATTAAATGATAACTTTTA-CTGGTATATATATACAAAATACATGCATAAATGAGAAC
1 TTTCAACTAAATGATAACCTTTAGC-AGTACATATATACAAAATACATGCATAAATGAGAAC
*
1043421 TTTCAACTAAATGATAACCTTTAGCAGTACATATATACAAAATACATGCATATATGAGAAC
1 TTTCAACTAAATGATAACCTTTAGCAGTACATATATACAAAATACATGCATAAATGAGAAC
1043482 ATATTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 54 0.98
62 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (61 bp):
TTTCAACTAAATGATAACCTTTAGCAGTACATATATACAAAATACATGCATAAATGAGAAC
Found at i:1043782 original size:15 final size:15
Alignment explanation
Indices: 1043762--1043792 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1043752 TGTTGTTTCT
*
1043762 TTATATATTTATAAG
1 TTATATATTTACAAG
1043777 TTATATATTTACAAG
1 TTATATATTTACAAG
1043792 T
1 T
1043793 AACAACGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (15 bp):
TTATATATTTACAAG
Found at i:1047304 original size:18 final size:18
Alignment explanation
Indices: 1047281--1047315 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1047271 TCCTCACGAA
*
1047281 AAATTTATATTGAAATTC
1 AAATTTATACTGAAATTC
1047299 AAATTTATACTGAAATT
1 AAATTTATACTGAAATT
1047316 TAAAAGAAAT
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:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATTTATACTGAAATTC
Found at i:1053687 original size:16 final size:15
Alignment explanation
Indices: 1053658--1053695 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1053648 GATCACATTT
1053658 TGTCTGTCGTCCGTC
1 TGTCTGTCGTCCGTC
1053673 TGTCTGTCTGTCCGTC
1 TGTCTGTC-GTCCGTC
*
1053689 TATCTGT
1 TGTCTGT
1053696 AAACTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.03, C:0.29, G:0.24, T:0.45
Consensus pattern (15 bp):
TGTCTGTCGTCCGTC
Found at i:1054143 original size:166 final size:166
Alignment explanation
Indices: 1053869--1054715 Score: 1299
Period size: 166 Copynumber: 5.1 Consensus size: 166
1053859 AGAAATTTTC
1053869 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
1053934 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACGATGGGGGGT
66 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
* *
1053999 CAAAGTTTTACATAGGAATATACAGAGTTAATCTTT
131 CAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1054035 AAAAATCTTCTTCTCATGAACCATAAAACCAGGAACGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1054100 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGT
66 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
1054165 CGAAA-TTTAACATAGGAATATATAGAGTAAATCTTT
131 C-AAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1054201 AAATATCTCCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1054266 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGG
66 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGG
* *
1054331 TCAAAATTTTACATAGGAATATACAGAGTAAATCTTT
130 TCAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
1054368 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * * **
1054433 TAGTGTAGATTC-ATTGTTGTTAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGAAGG
66 TAGTGTAGATTCTAAT-TTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
1054497 TCGAAGTTTTACGTAGGAATATATAGAGTAAATCTTT
130 TCAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * * *
1054534 AAAAATCTTCTTCTCA-GAAAC-TAATCAGCCAGGTAAGCTGAAACTTATGTGGAAGCGTCCTCA
1 AAAAATCTTCTTCTCATGAACCATAA-GA-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * * *
1054597 GGTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
* *
1054662 GTCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTT
129 GTCAAAGTTTTACATAGGAATATATA-GAGTAAATCTTT
1054700 AAAAATCTTCTTCTCA
1 AAAAATCTTCTTCTCA
1054716 GAAACTAATC
Statistics
Matches: 625, Mismatches: 48, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
164 3 0.00
165 5 0.01
166 464 0.74
167 153 0.24
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1054483 original size:333 final size:332
Alignment explanation
Indices: 1053869--1054715 Score: 1335
Period size: 333 Copynumber: 2.5 Consensus size: 332
1053859 AGAAATTTTC
1053869 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1053934 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACGATGGGGGGT
66 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGT
*
1053999 CAAAGTTTTACATAGGAATATACAGAGTTAATCTTTAAAAATCTTCTTCTCATGAACCATAAAAC
131 CAAAGTTTTACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAAAC
* * *
1054064 CAGGAACGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCTAATTTGTGAAATTCAT
196 CAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGGTAGTGTAGATTCTAATTTGTGAAAATCAT
* *
1054129 GACCCCCGGGGGTAGGGTGGGGCCACAATTGG-GGGTCGAAATTTAACATAGGAATATATAGAGT
261 GACCCCCGAGGGTAGGGTGGGGCCACAA-TGGAAGGTCGAAATTTAACATAGGAATATATAGAGT
1054193 AAATCTTT
325 AAATCTTT
* *
1054201 AAATATCTCCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1054266 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGG
66 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAAT-GGGGGG
* *
1054331 TCAAAATTTTACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGA
130 TCAAAGTTTTACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAAA
* *
1054396 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGGTAGTGTAGATTC-ATTGTTGTTAAAATC
195 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGGTAGTGTAGATTCTAAT-TTGTGAAAATC
* * *
1054460 ATGACCCCCGAGGGTAGGGTGGGGCCACAATGGAAGGTCGAAGTTTTACGTAGGAATATATAGAG
259 ATGACCCCCGAGGGTAGGGTGGGGCCACAATGGAAGGTCGAAATTTAACATAGGAATATATAGAG
1054525 TAAATCTTT
324 TAAATCTTT
* * * * *
1054534 AAAAATCTTCTTCTCA-GAAAC-TAATCAGCCAGGTAAGCTGAAACTTATGTGGAAGCGTCCTCA
1 AAAAATCTTCTTCTCATGAACCATAA-GA-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * * * *
1054597 GGTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGG
* * *
1054662 GTCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCA
129 GTCAAAGTTTTACATAGGAATATACA-GAGTAAATCTTTAAAAATCTTCTTCTCA
1054716 GAAACTAATC
Statistics
Matches: 476, Mismatches: 33, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
331 3 0.01
332 183 0.38
333 290 0.61
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (332 bp):
AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGT
CAAAGTTTTACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAAAC
CAGGAAAGCTGAAACTTGTGTGGAAGCATCATCAGGTAGTGTAGATTCTAATTTGTGAAAATCAT
GACCCCCGAGGGTAGGGTGGGGCCACAATGGAAGGTCGAAATTTAACATAGGAATATATAGAGTA
AATCTTT
Found at i:1056885 original size:27 final size:27
Alignment explanation
Indices: 1056854--1056908 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1056844 CCAAGTCCAG
1056854 GAAAGTAATTGTTTTAATTGCTTTACT
1 GAAAGTAATTGTTTTAATTGCTTTACT
1056881 GAAAGTAATTGTTTTAATTGCTTTACT
1 GAAAGTAATTGTTTTAATTGCTTTACT
1056908 G
1 G
1056909 GGCGGGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (27 bp):
GAAAGTAATTGTTTTAATTGCTTTACT
Found at i:1057654 original size:1 final size:1
Alignment explanation
Indices: 1057650--1057682 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1057640 GAAGGGTTAG
1057650 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1057683 GCCTCCCCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1060879 original size:2 final size:2
Alignment explanation
Indices: 1060872--1060936 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1060862 ATTTAAAATG
1060872 GA 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 GA
1060914 GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
1060937 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1062677 original size:15 final size:16
Alignment explanation
Indices: 1062645--1062682 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1062635 GGATTTCAGT
1062645 AATATTTGAGGGCATC
1 AATATTTGAGGGCATC
1062661 AA-ATTTCGAGGGC-TC
1 AATATTT-GAGGGCATC
1062676 AATATTT
1 AATATTT
1062683 TTAGCAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (16 bp):
AATATTTGAGGGCATC
Found at i:1063633 original size:2 final size:2
Alignment explanation
Indices: 1063626--1063686 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1063616 TTAAAGGTCA
1063626 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
1063668 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1063687 CTCACACCGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1064074 original size:29 final size:29
Alignment explanation
Indices: 1064032--1064091 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1064022 AACGATTTTT
*
1064032 ATTTTTATTCAAGACTATTAATGATACAC
1 ATTTTTATTCAAGACTATTAATGAAACAC
1064061 ATTTTTATTCAAGACTATTAATGAAACAC
1 ATTTTTATTCAAGACTATTAATGAAACAC
1064090 AT
1 AT
1064092 AAATGACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTTTATTCAAGACTATTAATGAAACAC
Found at i:1065760 original size:29 final size:29
Alignment explanation
Indices: 1065718--1065777 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1065708 AACGATTTTT
*
1065718 ATTTTTATTCAAGACTATTAATGATACAC
1 ATTTTTATTCAAGACTATTAATGAAACAC
1065747 ATTTTTATTCAAGACTATTAATGAAACAC
1 ATTTTTATTCAAGACTATTAATGAAACAC
1065776 AT
1 AT
1065778 AAATGACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTTTATTCAAGACTATTAATGAAACAC
Found at i:1067396 original size:21 final size:21
Alignment explanation
Indices: 1067370--1067539 Score: 164
Period size: 21 Copynumber: 8.1 Consensus size: 21
1067360 TTTTTTTTTT
* *
1067370 ATCTCGTAATTACTAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
*
1067391 ATCTCGTTACTAC-ATGAAAAG
1 ATCTCGTTATTACGA-GAAAAG
* ** **
1067412 ATCTCGTTATAACGAGTTATT
1 ATCTCGTTATTACGAGAAAAG
1067433 ATCTCGTTATTACGA-AAAAG
1 ATCTCGTTATTACGAGAAAAG
*
1067453 ATCCCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
* * **
1067474 ATCTCGTTGTTACGAGTTAATT
1 ATCTCGTTATTACGAG-AAAAG
*
1067496 ATCTTGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
* *
1067517 ATCTCGTTATTAGGAGAGAAG
1 ATCTCGTTATTACGAGAAAAG
1067538 AT
1 AT
1067540 TTATATAAAA
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.14
21 85 0.72
22 17 0.14
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (21 bp):
ATCTCGTTATTACGAGAAAAG
Found at i:1067472 original size:62 final size:64
Alignment explanation
Indices: 1067368--1067539 Score: 233
Period size: 62 Copynumber: 2.7 Consensus size: 64
1067358 TTTTTTTTTT
* * *
1067368 TTATCTCGTAATTACTAGAAAAGATCTCGTTACTAC-ATGAAAAGATCTCGTTATAACGAGTT-A
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGA-GAAAAGATCTCGTTATAACGAGTTAA
* * *
1067431 TTATCTCGTTATTACGA-AAAAGATCCCGTTATTACGAGAAAAGATCTCGTTGTTACGAGTTAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATCTCGTTATAACGAGTTAA
* * *
1067494 TTATCTTGTTATTACGAGAAAAGATCTCGTTATTAGGAGAGAAGAT
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGAT
1067540 TTATATAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
62 38 0.40
63 33 0.34
64 25 0.26
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (64 bp):
TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATCTCGTTATAACGAGTTAA
Found at i:1067478 original size:41 final size:42
Alignment explanation
Indices: 1067370--1067539 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 42
1067360 TTTTTTTTTT
* * *
1067370 ATCTCGTAATTACTAGAAAAGATCTCGTTACTAC-ATGAAAAG
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGA-GAAAAG
* ** **
1067412 ATCTCGTTATAACGAGTTATTATCTCGTTATTACGA-AAAAG
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAG
* * * **
1067453 ATCCCGTTATTACGAGAAAAGATCTCGTTGTTACGAGTTAATT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAG-AAAAG
* * *
1067496 ATCTTGTTATTACGAGAAAAGATCTCGTTATTAGGAGAGAAG
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAG
1067538 AT
1 AT
1067540 TTATATAAAA
Statistics
Matches: 99, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
41 34 0.34
42 29 0.29
43 36 0.36
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (42 bp):
ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAG
Found at i:1068586 original size:21 final size:21
Alignment explanation
Indices: 1068508--1068722 Score: 191
Period size: 21 Copynumber: 10.2 Consensus size: 21
1068498 CATTTTATAT
* *
1068508 AGATCTGTTCTCGTAACAACG
1 AGATCTTTTCTCGTAATAACG
* * *
1068529 AGCTCTTTTTTCGTGATAACG
1 AGATCTTTTCTCGTAATAACG
* **
1068550 AGATGATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
* *
1068572 AGATCTTTTCTCGTACTTACG
1 AGATCTTTTCTCGTAATAACG
* *
1068593 AAACCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* *
1068614 AGATCTTTTCTGGTAATAATG
1 AGATCTTTTCTCGTAATAACG
*
1068635 AGATTTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* * * *
1068656 AAATAATTAAT-TCATAATAACG
1 AGAT-CTT-TTCTCGTAATAACG
* *
1068678 AGATC-TTTATCGTAATAATG
1 AGATCTTTTCTCGTAATAACG
*
1068698 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
1068719 AGAT
1 AGAT
1068723 AAAAATATTT
Statistics
Matches: 150, Mismatches: 39, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
19 1 0.01
20 15 0.10
21 102 0.68
22 31 0.21
23 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATAACG
Found at i:1072762 original size:131 final size:131
Alignment explanation
Indices: 1072514--1072768 Score: 307
Period size: 131 Copynumber: 1.9 Consensus size: 131
1072504 CTTTGACAGT
* * * *
1072514 AGTTCTTATGACATCACCGCTTTAGTATATTGCGGGTCACTTTATGATTTTTCAGATTAGTAGTA
1 AGTTCTTATGACATCACCGCTTAAGTATATTGCGGGTCACTTTATGATTTTTCAAATCACTAG--
* * * * *
1072579 AGCTAAATACATGAAGCACAAACATTTCAGACAAAAATGATTATTCTGATATTGATTCGTTAATT
64 AGCTAAATACATGAAGCAAAAACAATTCAGACAAAAATAATAATTCTAATATTGATTCGTTAATT
1072644 ATA
129 ATA
** * *
1072647 AGTTCTTATGATGTCACCGCTTAAGTATATATTGCGGGTCACTTTCTGGTTTTTCAAATCACT-G
1 AGTTCTTATGACATCACCGCTTAAG--TATATTGCGGGTCACTTTATGATTTTTCAAATCACTAG
* ** *
1072711 -GCTAAATACATGAAGCAAAAATAATTCTTACAAAAATAATAATTTTAATATTGATTCG
64 AGCTAAATACATGAAGCAAAAACAATTCAGACAAAAATAATAATTCTAATATTGATTCG
1072769 ATATACTTTA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
131 49 0.48
133 22 0.21
134 1 0.01
135 31 0.30
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (131 bp):
AGTTCTTATGACATCACCGCTTAAGTATATTGCGGGTCACTTTATGATTTTTCAAATCACTAGAG
CTAAATACATGAAGCAAAAACAATTCAGACAAAAATAATAATTCTAATATTGATTCGTTAATTAT
A
Found at i:1080144 original size:8 final size:7
Alignment explanation
Indices: 1080119--1080265 Score: 68
Period size: 8 Copynumber: 19.4 Consensus size: 7
1080109 GCCTTTAGGT
1080119 CGAAGATG
1 CGAAG-TG
1080127 CGAGAGTG
1 CGA-AGTG
1080135 CGAAGTTG
1 CGAAG-TG
1080143 CGAAG-G
1 CGAAGTG
1080149 CGAAAGTG
1 CG-AAGTG
*
1080157 CGAGAATG
1 CGA-AGTG
*
1080165 CGACG-G
1 CGAAGTG
*
1080171 CGAAGGAG
1 CGAA-GTG
1080179 CGAAAGTG
1 CG-AAGTG
1080187 CGAAGATG
1 CGAAG-TG
*
1080195 CGACG-G
1 CGAAGTG
*
1080201 CGAAGCG
1 CGAAGTG
1080208 CGAAGTTG
1 CGAAG-TG
*
1080216 CGATG-G
1 CGAAGTG
1080222 CGAAAGTG
1 CG-AAGTG
1080230 CGAAGGTG
1 CGAA-GTG
*
1080238 CGAAGNGAG
1 CGAA--GTG
1080247 CGAAAGTG
1 CG-AAGTG
1080255 CGAAGATG
1 CGAAG-TG
1080263 CGA
1 CGA
1080266 CGGCTCAGCA
Statistics
Matches: 109, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
6 15 0.14
7 23 0.21
8 61 0.56
9 8 0.07
10 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.42, T:0.10
Consensus pattern (7 bp):
CGAAGTG
Found at i:1080161 original size:30 final size:30
Alignment explanation
Indices: 1080125--1080205 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
1080115 AGGTCGAAGA
1080125 TGCGAGAGTGCGAAGTTGCGAA-G-GCGAAAG
1 TGCGAGAGTGCGAAG--GCGAAGGAGCGAAAG
* *
1080155 TGCGAGAATGCGACGGCGAAGGAGCGAAAG
1 TGCGAGAGTGCGAAGGCGAAGGAGCGAAAG
*
1080185 TGCGA-AGATGCGACGGCGAAG
1 TGCGAGAG-TGCGAAGGCGAAG
1080206 CGCGAAGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 38 0.84
ACGTcount: A:0.31, C:0.16, G:0.43, T:0.10
Consensus pattern (30 bp):
TGCGAGAGTGCGAAGGCGAAGGAGCGAAAG
Found at i:1080166 original size:22 final size:22
Alignment explanation
Indices: 1080141--1080259 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
1080131 AGTGCGAAGT
*
1080141 TGCGAAGGCGAAAGTGCGAGAA-
1 TGCGAAGGCGAAAGAGCGA-AAG
* *
1080163 TGCGACGGCGAAGGAGCGAAAG
1 TGCGAAGGCGAAAGAGCGAAAG
*
1080185 TGCGAAGATGCG-ACG-GCG-AAG
1 TGCGAAG--GCGAAAGAGCGAAAG
* *
1080206 CGCGAAGTTGCG-ATG-GCGAAAG
1 TGCGAAG--GCGAAAGAGCGAAAG
*
1080228 TGCGAAGGTGCGAAGNGAGCGAAAG
1 TGCGAA-G-GCGAA-AGAGCGAAAG
1080253 TGCGAAG
1 TGCGAAG
1080260 ATGCGACGGC
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
21 20 0.25
22 37 0.47
23 4 0.05
24 5 0.06
25 13 0.16
ACGTcount: A:0.31, C:0.16, G:0.43, T:0.09
Consensus pattern (22 bp):
TGCGAAGGCGAAAGAGCGAAAG
Found at i:1080211 original size:21 final size:22
Alignment explanation
Indices: 1080178--1080303 Score: 94
Period size: 21 Copynumber: 5.7 Consensus size: 22
1080168 CGGCGAAGGA
*
1080178 GCGAAAGTGCGAAGATGCGACG
1 GCGAAAGCGCGAAGATGCGACG
* *
1080200 GCG-AAGCGCGAAGTTGCGATG
1 GCGAAAGCGCGAAGATGCGACG
* * *
1080221 GCGAAAGTGCGAAGGTGCGAAGNG
1 GCGAAAGCGCGAAGATGCG-A-CG
*
1080245 AGCGAAAGTGCGAAGATGCGACG
1 -GCGAAAGCGCGAAGATGCGACG
** * *
1080268 GC-TCAGCACGAAGATGCGATG
1 GCGAAAGCGCGAAGATGCGACG
* *
1080289 GCAAAAGTGCGAAGA
1 GCGAAAGCGCGAAGA
1080304 CGAAGGAGCG
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 34 0.41
22 26 0.32
23 2 0.02
24 2 0.02
25 18 0.22
ACGTcount: A:0.32, C:0.17, G:0.40, T:0.10
Consensus pattern (22 bp):
GCGAAAGCGCGAAGATGCGACG
Found at i:1080255 original size:68 final size:67
Alignment explanation
Indices: 1080170--1080314 Score: 213
Period size: 68 Copynumber: 2.2 Consensus size: 67
1080160 GAATGCGACG
* * *
1080170 GCGAAGGAGCGAAAGTGCGAAGATGCGACGGCGAAGCGCGAAGTTGCGATGGCGAAAGTGCGAAG
1 GCGAAGGAGCGAAAGTGCGAAGATGCGACGGCGAAGCACGAAGATGCGATGGCAAAAGTGCGAAG
1080235 GT
66 GT
**
1080237 GCGAAGNGAGCGAAAGTGCGAAGATGCGACGGCTCAGCACGAAGATGCGATGGCAAAAGTGCGAA
1 GCGAAG-GAGCGAAAGTGCGAAGATGCGACGGCGAAGCACGAAGATGCGATGGCAAAAGTGCGAA
1080302 -G-
65 GGT
*
1080303 ACGAAGGAGCGA
1 GCGAAGGAGCGA
1080315 TACTACTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 6 0.08
66 5 0.07
67 7 0.10
68 53 0.75
ACGTcount: A:0.32, C:0.17, G:0.41, T:0.09
Consensus pattern (67 bp):
GCGAAGGAGCGAAAGTGCGAAGATGCGACGGCGAAGCACGAAGATGCGATGGCAAAAGTGCGAAG
GT
Found at i:1080346 original size:14 final size:14
Alignment explanation
Indices: 1080329--1080384 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1080319 ACTATCGCTC
1080329 CTTCGC-CTTCGCAA
1 CTTCGCACTTCGC-A
1080343 CTTCGCACTCTCGC-
1 CTTCGCACT-TCGCA
1080357 CTTCGCAACTTCGCA
1 CTTCGC-ACTTCGCA
1080372 CTTTCGC-CTTCGC
1 C-TTCGCACTTCGC
1080385 CTTTTTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 22 0.59
15 6 0.16
16 9 0.24
ACGTcount: A:0.11, C:0.45, G:0.14, T:0.30
Consensus pattern (14 bp):
CTTCGCACTTCGCA
Found at i:1080356 original size:22 final size:22
Alignment explanation
Indices: 1080331--1080384 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1080321 TATCGCTCCT
1080331 TCGCCTTCGCAACTTCGCACTC
1 TCGCCTTCGCAACTTCGCACTC
*
1080353 TCGCCTTCGCAACTTCGCACTT
1 TCGCCTTCGCAACTTCGCACTC
1080375 TCGCCTTCGC
1 TCGCCTTCGC
1080385 CTTTTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.44, G:0.15, T:0.30
Consensus pattern (22 bp):
TCGCCTTCGCAACTTCGCACTC
Found at i:1080377 original size:8 final size:7
Alignment explanation
Indices: 1080329--1080384 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
1080319 ACTATCGCTC
1080329 CTTCGC-
1 CTTCGCA
1080335 CTTCGCAA
1 CTTCGC-A
1080343 CTTCGCA
1 CTTCGCA
1080350 CTCTCGC-
1 CT-TCGCA
1080357 CTTCGCAA
1 CTTCGC-A
1080365 CTTCGCA
1 CTTCGCA
1080372 CTTTCGC-
1 C-TTCGCA
1080379 CTTCGC
1 CTTCGC
1080385 CTTTTTTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 15 0.34
7 8 0.18
8 21 0.48
ACGTcount: A:0.11, C:0.45, G:0.14, T:0.30
Consensus pattern (7 bp):
CTTCGCA
Found at i:1086397 original size:22 final size:22
Alignment explanation
Indices: 1086369--1086430 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1086359 TTATAAAAAG
1086369 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAAAGTGCGAAGAT
* *
1086391 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCGAAGAT
* *
1086413 GCGATGGCGAAGGTGCGA
1 GCGAAGGCGAAAGTGCGA
1086431 TATTGGTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.45, T:0.11
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCGAAGAT
Found at i:1086462 original size:8 final size:7
Alignment explanation
Indices: 1086445--1086561 Score: 73
Period size: 8 Copynumber: 16.1 Consensus size: 7
1086435 GGTATCGCTT
1086445 CTTCGC-
1 CTTCGCA
1086451 CTTCGCAA
1 CTTCGC-A
1086459 CTTCGCA
1 CTTCGCA
1086466 CTTTCGC-
1 C-TTCGCA
1086473 CTTCGCA
1 CTTCGCA
*
1086480 TCTTCGCG
1 -CTTCGCA
1086488 CTTCGC-
1 CTTCGCA
*
1086494 CGTCGCA
1 CTTCGCA
1086501 TCTTCGCA
1 -CTTCGCA
*
1086509 CTTTCGCTC
1 C-TTCGC-A
1086518 CTTCGC-
1 CTTCGCA
*
1086524 CGTCGCA
1 CTTCGCA
1086531 CTTTCGC-
1 C-TTCGCA
*
1086538 CGTCGCAA
1 CTTCGC-A
1086546 CTTCGCA
1 CTTCGCA
1086553 CTCTCGCA
1 CT-TCGCA
1086561 C
1 C
1086562 CTCGACCTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
6 25 0.28
7 15 0.17
8 48 0.54
9 1 0.01
ACGTcount: A:0.09, C:0.44, G:0.17, T:0.30
Consensus pattern (7 bp):
CTTCGCA
Found at i:1086462 original size:14 final size:13
Alignment explanation
Indices: 1086445--1086561 Score: 65
Period size: 14 Copynumber: 8.1 Consensus size: 13
1086435 GGTATCGCTT
1086445 CTTCGCCTTCGCAA
1 CTTCGCCTTCGC-A
1086459 CTTCGCACTTTCGC-
1 CTTCGC-C-TTCGCA
*
1086473 CTTCGCATCTTCGCG
1 CTTCGC--CTTCGCA
*
1086488 CTTCGCCGTCGCA
1 CTTCGCCTTCGCA
*
1086501 TCTTCGCACTTTCGCTC
1 -CTTCGC-C-TTCGC-A
*
1086518 CTTCGCCGTCGCA
1 CTTCGCCTTCGCA
*
1086531 CTTTCGCCGTCGCAA
1 C-TTCGCCTTCGC-A
1086546 CTTCGCACTCTCGCA
1 CTTCGC-CT-TCGCA
1086561 C
1 C
1086562 CTCGACCTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.07
14 43 0.52
15 15 0.18
16 19 0.23
ACGTcount: A:0.09, C:0.44, G:0.17, T:0.30
Consensus pattern (13 bp):
CTTCGCCTTCGCA
Found at i:1086471 original size:22 final size:22
Alignment explanation
Indices: 1086446--1086559 Score: 126
Period size: 22 Copynumber: 5.2 Consensus size: 22
1086436 GTATCGCTTC
1086446 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCTTCGCAACTTCGCACT
* *
1086468 TTCGCCTTCGCATCTTCGCGC-
1 TTCGCCTTCGCAACTTCGCACT
* *
1086489 TTCGCCGTCGCATCTTCGCACT
1 TTCGCCTTCGCAACTTCGCACT
*
1086511 TTCGCTCCTTCGC--CGTCGCACT
1 TTCG--CCTTCGCAACTTCGCACT
*
1086533 TTCGCCGTCGCAACTTCGCACT
1 TTCGCCTTCGCAACTTCGCACT
*
1086555 CTCGC
1 TTCGC
1086560 ACCTCGACCT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
20 6 0.08
21 19 0.24
22 47 0.60
24 6 0.08
ACGTcount: A:0.09, C:0.43, G:0.18, T:0.31
Consensus pattern (22 bp):
TTCGCCTTCGCAACTTCGCACT
Found at i:1088301 original size:16 final size:16
Alignment explanation
Indices: 1088280--1088310 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1088270 TAAAAAGTTT
*
1088280 ACAGACGGACGGACGG
1 ACAGACAGACGGACGG
1088296 ACAGACAGACGGACG
1 ACAGACAGACGGACG
1088311 ACGGACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00
Consensus pattern (16 bp):
ACAGACAGACGGACGG
Found at i:1093043 original size:166 final size:166
Alignment explanation
Indices: 1092233--1094306 Score: 2416
Period size: 166 Copynumber: 12.6 Consensus size: 166
1092223 TAGTCTTTAA
* * * * * *
1092233 AAAGATTTTCTCTATAAATTCCTAAGTAAAAATTCATCCCCC-ATTGTGGCCTCACCCTA-CCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
* * * * * * * ** ** * **
1092296 -TGGACTATTATTTAAACAAACCTGAATCTATA-TGATCTGGGGATGCTTTCACTCAAATTTG-G
66 GGGGACCATGATTTGAACAAACTTGAATCTACACT-ACCTAAGGATGCTCCCATTTTAATTTGAG
* * *
1092358 GTTTCCTGGCCTAATAG-TTTTGAGAAGAAGACTTTT
130 CTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * * * *
1092394 AAAGATTTT-TGCTATA-A-----A--TAAAAATTTAT-CCCCTATTGTGGCCCCGCCCGACCCC
1 AAAGATTTTCT-CTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCC
* * * * * ** ****
1092449 CAGGGACCATGATTTGAACAAACTTGAATCTACATTATCTGAGGATGGTTACACGCCAATTTGAG
65 CGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAG
* ** * **
1092514 CTTTCTTGGCCAAATAGTTTTT-AAAAGAA-ATCTTAAA
130 CTTTCCTGGCCTGATAGTTTTTGAGAAGAAGAT-TT-TT
** * * * *
1092551 AAAGATTTTCTCTATATATTCCTATAAAAAAAGTT-ATCACACAATTGTGGCCCCAT-CCTACCT
1 AAAGATTTTCTCTATATATTCCTAT-GTAAAACTTGATCCCCCAATTGTGGCCCC-TCCCTACCC
* * * * * **
1092614 CCTGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTGA
64 CCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGA
1092679 GCTTTCCTGGCC---TAGTTTTTGAGAAGAAGATTTTT
129 GCTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * * *
1092714 AAAGATTTTCTCTATATATTCCTTTGTAAAAATTGATCCCCAAATTGTGGCCCCACCCTA-CCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
* * * * *
1092778 GGGGACTATGATTTGAATAAACCTAAATCTACACTACCCAAGGATGCTCCCATTTTAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
*
1092843 TTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
131 TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * *
1092879 CATGATTTTCTTTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
* * * *
1092944 AGGGACCAT-ATTCTAAACAAACTTGAATTTACACTACCCAAGGATGCTCCCATTTTAATTTGAG
66 GGGGACCATGATT-TGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAG
*
1093008 CTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
130 CTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * *
1093045 CATGATTTTCTTTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
* * * *
1093110 AGGGACCAT-ATTCTAAACAAACTTGAATTTACACTACCTAAGGATGCTCCCTTTTTAATTTGAG
66 GGGGACCATGATT-TGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAG
* *
1093174 CTTTTCTGGCCTGATAGTTTTTGAGAAGAAGAGTTTT
130 CTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
*
1093211 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
** ** * **
1093276 GGGGACCATGATTTGAACAAACTTGAATCTACACTGTCTTGGGATGCTCCCACTCAAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
* *
1093341 TTTCCTGGCCTAAAAGTTTTTGAGAAGAAGATTTTT
131 TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
*
1093377 AAAGATTTTTTAAAGATTTGCTCTATATATTCC--TGTTAAACTTGATCCCCCAATTGTGGCCCC
1 AAAGA-----T-----TTT-CTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCC
* * * *
1093440 ACCCTACCCCCGGGGTCCATGATCTGAACAAACTTAAATCTACACTACCTAAGGATGCTCCCATT
55 TCCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATT
*
1093505 TTAATTTGAGCTTTCCTGGCCTGATAGTTTTTGAAAAGAAGATTTTT
120 TTAATTTGAGCTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * * *
1093552 AAAGATTTTCTCTTTATATTCCTATGTAAAACTTGATCCCCAAATTGTGGTCCCTCCCTACCCCT
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
* * * *
1093617 GGAGACCATGATTTGAACAAACTTTAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
*
1093682 TTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
131 TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* *
1093718 AAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
** ** * * **
1093783 GGGGACCATGATTTGAACAAACTTGAATCTACACTGTCTTGGGATGCTTCCACTCAAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
**
1093848 TTTCCTGGCCAAATAGTTTTTGAGAAGAAGATTTTT
131 TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* *
1093884 AAAGATTTTCTCTATATATTCCTATGTAAAACTCGATCCCCCAATTGTGGCCCCACCCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
*
1093949 GGGGACCATGATTTGAACAAACTTAAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
66 GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
* *
1094014 TTTTCTGGCCTGATAGTTTTTGAAAAGAAGATTTTT
131 TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * * * *
1094050 AAAGATTTTCTCTATATATTCCTATATAAAAAGTT-ATCACACAATTGTGGCCCCAT-CCTACCT
1 AAAGATTTTCTCTATATATTCCTATGT-AAAACTTGATCCCCCAATTGTGGCCCC-TCCCTACCC
* * * * * **
1094113 CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTGA
64 CCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGA
*
1094178 GCTTTCCT-GCC--CTAGTTTTTGAGAAGAAGA-TTTT
129 GCTTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
* * * *
1094212 AAAGATTTTCTCTATATATTCCTTTGTAAAAATTGATCCCCAAATTGTGGCCCCTCGCTACCCCC
1 AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
*
1094277 CGGGACCATGATTTGAACAAACTTGAATCT
66 GGGGACCATGATTTGAACAAACTTGAATCT
1094307 GAAAAATACC
Statistics
Matches: 1679, Mismatches: 186, Indels: 95
0.86 0.09 0.05
Matches are distributed among these distances:
152 4 0.00
153 24 0.01
154 4 0.00
155 50 0.03
156 24 0.01
157 18 0.01
158 2 0.00
160 2 0.00
161 21 0.01
162 152 0.09
163 70 0.04
164 20 0.01
165 89 0.05
166 1040 0.62
167 8 0.00
170 1 0.00
171 1 0.00
175 133 0.08
176 3 0.00
177 13 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (166 bp):
AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCTCCCTACCCCC
GGGGACCATGATTTGAACAAACTTGAATCTACACTACCTAAGGATGCTCCCATTTTAATTTGAGC
TTTCCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT
Found at i:1096803 original size:12 final size:12
Alignment explanation
Indices: 1096786--1096870 Score: 134
Period size: 12 Copynumber: 7.1 Consensus size: 12
1096776 AAACAATGTT
1096786 TGACTATATATA
1 TGACTATATATA
1096798 TGACTATATATA
1 TGACTATATATA
*
1096810 TGACTGTATATA
1 TGACTATATATA
1096822 TGACTATATATA
1 TGACTATATATA
*
1096834 TGACTACATATA
1 TGACTATATATA
*
1096846 TGACTACATATA
1 TGACTATATATA
*
1096858 TGACTATACATA
1 TGACTATATATA
1096870 T
1 T
1096871 ATTAACCTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 68 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (12 bp):
TGACTATATATA
Found at i:1105657 original size:24 final size:23
Alignment explanation
Indices: 1105630--1105683 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1105620 TCCATACGTG
*
1105630 ATCAGGGGCCGCTCTACAATCCCA
1 ATCAGGGGCAGCT-TACAATCCCA
*
1105654 ATCAGGGGGCAGCTTATAATCCCA
1 ATCA-GGGGCAGCTTACAATCCCA
1105678 ATCAGG
1 ATCAGG
1105684 TATACCGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 17 0.63
25 8 0.30
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (23 bp):
ATCAGGGGCAGCTTACAATCCCA
Found at i:1106831 original size:14 final size:14
Alignment explanation
Indices: 1106812--1106862 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
1106802 ATTCAACTAC
1106812 TTTATTACATTACA
1 TTTATTACATTACA
1106826 TTTATTACAATT-CA
1 TTTATTAC-ATTACA
*
1106840 CTTATTACATTACA
1 TTTATTACATTACA
1106854 TTTATTACA
1 TTTATTACA
1106863 ACTACGTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTATTACATTACA
Found at i:1114015 original size:19 final size:19
Alignment explanation
Indices: 1113991--1114044 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1113981 CACTTTAAAT
1113991 TTATATCCCATTTGGGCTA
1 TTATATCCCATTTGGGCTA
* ****
1114010 TTATATCCAAGACAGGCTA
1 TTATATCCCATTTGGGCTA
1114029 TTATATCCCATTTGGG
1 TTATATCCCATTTGGG
1114045 AGATTGGTCC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (19 bp):
TTATATCCCATTTGGGCTA
Found at i:1115137 original size:2 final size:2
Alignment explanation
Indices: 1115130--1115171 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1115120 ATTTTATGAT
1115130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1115172 GCTCTTATCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1119348 original size:2 final size:2
Alignment explanation
Indices: 1119341--1119372 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1119331 TGCAGTCTTG
1119341 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
1119373 CATAGCTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1120747 original size:1 final size:1
Alignment explanation
Indices: 1120741--1120765 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1120731 AAATATGCCT
1120741 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1120766 TGCCCGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1127055 original size:20 final size:20
Alignment explanation
Indices: 1127030--1127067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1127020 ATTATTAATT
1127030 TGAAAATC-ATTCTTATTGAG
1 TGAAAATCTATT-TTATTGAG
1127050 TGAAAATCTATTTTATTG
1 TGAAAATCTATTTTATTG
1127068 GCCTATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
TGAAAATCTATTTTATTGAG
Found at i:1137641 original size:2 final size:2
Alignment explanation
Indices: 1137636--1137681 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1137626 TTCCTTTTAT
1137636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1137678 TA TA
1 TA TA
1137682 AAATGGGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1137874 original size:49 final size:49
Alignment explanation
Indices: 1137810--1137947 Score: 197
Period size: 49 Copynumber: 2.8 Consensus size: 49
1137800 CTTAATAAAG
*
1137810 TAATGCAACTTAATTCAAAGAGTGAAGCCACATACTT-AACAATTACAAA
1 TAATGCAACTAAATTCAAAGAGTGAAGCCACATACTTAAAC-ATTACAAA
*
1137859 TAATGAAACTAAATTCAAAGAGTGAAGCCACATACTTAAACATTACAAA
1 TAATGCAACTAAATTCAAAGAGTGAAGCCACATACTTAAACATTACAAA
* * * * *
1137908 TAATGCGACTGAATTTAATGAGTGAAGCCACAAACTTAAA
1 TAATGCAACTAAATTCAAAGAGTGAAGCCACATACTTAAA
1137948 AAATATAAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 77 0.96
50 3 0.04
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (49 bp):
TAATGCAACTAAATTCAAAGAGTGAAGCCACATACTTAAACATTACAAA
Found at i:1138171 original size:2 final size:2
Alignment explanation
Indices: 1138164--1138193 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1138154 GATAACTATA
1138164 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
1138194 CGAGCGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1139573 original size:204 final size:204
Alignment explanation
Indices: 1139033--1139642 Score: 1095
Period size: 204 Copynumber: 3.0 Consensus size: 204
1139023 ATCGAGTAGT
1139033 AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACCGGTTTAATGGATGTCCT
1 AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACCGGTTTAATGGATGTCCT
1139098 AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
66 AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
**
1139163 GGTTGTGGTATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
131 GGTTGTCATATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
1139228 TAAAGAAAC
196 TAAAGAAAC
*
1139237 AAAGCACTTGCCCCCACACAGTTGGCA-----TCTAAGAACATGAACCGGTTTAATGGATGTCTT
1 AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACCGGTTTAATGGATGTCCT
* *
1139297 AGAAAGATAAGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
66 AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
*
1139362 GGTTGTCATATACATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
131 GGTTGTCATATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
1139427 TAAAGAAAC
196 TAAAGAAAC
**
1139436 AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACTTGTTTAATGGATGTCCT
1 AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACCGGTTTAATGGATGTCCT
*
1139501 AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATTTAAACATAATAATGCAATGCC
66 AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
*
1139566 GGTTGTCATATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTAGATTGAAAA
131 GGTTGTCATATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
1139631 TAAAGAAAC
196 TAAAGAAAC
1139640 AAA
1 AAA
1139643 CATACATGCT
Statistics
Matches: 387, Mismatches: 14, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
199 193 0.50
204 194 0.50
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (204 bp):
AAAGCACTTGCCCCCACACAGTTGGCATCCTTTCTAAGAACATGAACCGGTTTAATGGATGTCCT
AGAAACATAGGGTAAAGACAGCAAGGGAAAGTACTGGGTAGATCTAAACATAATAATGCAATGCC
GGTTGTCATATGCATAGAAGTCACGTCATTTTCTTTGATTTTCCAGGGGGTGGGTGGATTGAAAA
TAAAGAAAC
Found at i:1142119 original size:2 final size:2
Alignment explanation
Indices: 1142112--1142166 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1142102 AACATTGTAC
1142112 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
1142154 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1142167 TTTTCCTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1145114 original size:2 final size:2
Alignment explanation
Indices: 1145107--1145152 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1145097 AACCATAAGA
1145107 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1145149 CT CT
1 CT CT
1145153 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1145342 original size:2 final size:2
Alignment explanation
Indices: 1145330--1145360 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1145320 ATCATTCATN
*
1145330 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1145361 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1145489 original size:210 final size:209
Alignment explanation
Indices: 1145120--1145538 Score: 793
Period size: 210 Copynumber: 2.0 Consensus size: 209
1145110 TCTCTCTCTC
* *
1145120 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATACATGTATATATATCTCTTT
1 TCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATACATGTATATATATCTCTTT
*
1145185 GCACACTTGCATATTTGTAATATTCGTCAATGCAAACAGACAATGAAAATTTTATTTTCACAATA
66 GCACACTTGCATATTTGTAATATTCGTCAATGCAAACAGACAATGAAAATATTATTTTCACAATA
*
1145250 TTTTGACCACGCTCTTTCAATGCAATTAGTCTTTCAATGATGATGTTTATCAAAACGATGTTGCA
131 TTTTGACCACGCTCTTTCAATGCAATTAGTCTTTCAATGATGATGGTTATCAAAACGATGTTGCA
1145315 TTCAAATCATTCAT
196 TTCAAATCATTCAT
1145329 NTCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATACATGTATATATATCTCTT
1 -TCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATACATGTATATATATCTCTT
1145394 TGCACACTTGCATATTTGTAATATTCGTCAATGCAAACAGACAATGAAAATATTATTTTCACAAT
65 TGCACACTTGCATATTTGTAATATTCGTCAATGCAAACAGACAATGAAAATATTATTTTCACAAT
1145459 ATTTTGACCACGCTCTTTCAATGCAATTAGTCTTTCAATGATGATGGTTATCAAAACGATGTTGC
130 ATTTTGACCACGCTCTTTCAATGCAATTAGTCTTTCAATGATGATGGTTATCAAAACGATGTTGC
1145524 ATTCAAATCATTCAT
195 ATTCAAATCATTCAT
1145539 AAATAGGCCT
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 205 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (209 bp):
TCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATACATGTATATATATCTCTTT
GCACACTTGCATATTTGTAATATTCGTCAATGCAAACAGACAATGAAAATATTATTTTCACAATA
TTTTGACCACGCTCTTTCAATGCAATTAGTCTTTCAATGATGATGGTTATCAAAACGATGTTGCA
TTCAAATCATTCAT
Found at i:1146664 original size:21 final size:21
Alignment explanation
Indices: 1146639--1146690 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1146629 GATCTGCCAC
1146639 CACTTGTCAGATAATTATG-T
1 CACTTGTCAGATAATTATGTT
1146659 CGACTTGTCAGATAATTATGTT
1 C-ACTTGTCAGATAATTATGTT
1146681 CACTTGTCAG
1 CACTTGTCAG
1146691 TTCTTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
CACTTGTCAGATAATTATGTT
Found at i:1146834 original size:21 final size:21
Alignment explanation
Indices: 1146810--1146929 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 21
1146800 CGTTATAAGG
*
1146810 ATCTGACAAGTCGACATAATC
1 ATCTGACAAGTCGACATAATT
*** * *
1146831 ATCTTTTAAGTCGATAAAATT
1 ATCTGACAAGTCGACATAATT
* *
1146852 ATTTGACAAAGTCGAAATAATT
1 ATCTGAC-AAGTCGACATAATT
* * *
1146874 ATTTGACAAGACGACATAA-C
1 ATCTGACAAGTCGACATAATT
* *
1146894 ATCTGACAAGTCAACATCATT
1 ATCTGACAAGTCGACATAATT
*
1146915 ATCTGGCAAGTCGAC
1 ATCTGACAAGTCGAC
1146930 TTACAATATG
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.20
21 41 0.55
22 19 0.25
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (21 bp):
ATCTGACAAGTCGACATAATT
Found at i:1146865 original size:22 final size:22
Alignment explanation
Indices: 1146838--1146882 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146828 ATCATCTTTT
1146838 AAGTCGATAA-AATTATTTGACA
1 AAGTCGA-AATAATTATTTGACA
1146860 AAGTCGAAATAATTATTTGACA
1 AAGTCGAAATAATTATTTGACA
1146882 A
1 A
1146883 GACGACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (22 bp):
AAGTCGAAATAATTATTTGACA
Found at i:1146991 original size:21 final size:21
Alignment explanation
Indices: 1146967--1147060 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 21
1146957 ATCTGCCACC
*
1146967 ACTTGTCAGATAATTATGTTA
1 ACTTGTCAGATAATTATGTCA
* * * * *
1146988 ACTTCTCATATGATAATGTCG
1 ACTTGTCAGATAATTATGTCA
*
1147009 ACTTGTCAGATATTTATGTCA
1 ACTTGTCAGATAATTATGTCA
* ** **
1147030 ACTTTTCAGATCTTTATGTTG
1 ACTTGTCAGATAATTATGTCA
1147051 ACTTGTCAGA
1 ACTTGTCAGA
1147061 AAATAACCAA
Statistics
Matches: 56, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCA
Found at i:1147026 original size:42 final size:42
Alignment explanation
Indices: 1146967--1147060 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1146957 ATCTGCCACC
* * *
1146967 ACTTGTCAGATAATTATGTTAACTTCTCATATGATAATGTCG
1 ACTTGTCAGATAATTATGTCAACTTCTCAGATCATAATGTCG
* * * * *
1147009 ACTTGTCAGATATTTATGTCAACTTTTCAGATCTTTATGTTG
1 ACTTGTCAGATAATTATGTCAACTTCTCAGATCATAATGTCG
1147051 ACTTGTCAGA
1 ACTTGTCAGA
1147061 AAATAACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTCAACTTCTCAGATCATAATGTCG
Found at i:1147184 original size:21 final size:21
Alignment explanation
Indices: 1147160--1147278 Score: 105
Period size: 21 Copynumber: 5.7 Consensus size: 21
1147150 ATAAGTCGAA
* *
1147160 ATAAATATCTGAAAAGTTTAC
1 ATAAATATCTGACAAGTTAAC
**
1147181 AT-AATCATCTGACAAGTCGAC
1 ATAAAT-ATCTGACAAGTTAAC
*
1147202 ATAAAGATCTGACAAGTTAAC
1 ATAAATATCTGACAAGTTAAC
* * **
1147223 ATAATTATCTGTCAAGTCGAC
1 ATAAATATCTGACAAGTTAAC
* *
1147244 ATAAAGATCGGACAAGTTAAC
1 ATAAATATCTGACAAGTTAAC
* *
1147265 ATTATTATCTGACA
1 ATAAATATCTGACA
1147279 GAAAAAATAA
Statistics
Matches: 75, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.04
21 70 0.93
22 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (21 bp):
ATAAATATCTGACAAGTTAAC
Found at i:1147212 original size:42 final size:42
Alignment explanation
Indices: 1147152--1147278 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
1147142 TATTTCATAT
* * * * *
1147152 AAGTCGAAATAAATATCTGAAAAGTTTACATAATCATCTGAC
1 AAGTCGACATAAAGATCTGACAAGTTAACATAATTATCTGAC
*
1147194 AAGTCGACATAAAGATCTGACAAGTTAACATAATTATCTGTC
1 AAGTCGACATAAAGATCTGACAAGTTAACATAATTATCTGAC
* *
1147236 AAGTCGACATAAAGATCGGACAAGTTAACATTATTATCTGAC
1 AAGTCGACATAAAGATCTGACAAGTTAACATAATTATCTGAC
1147278 A
1 A
1147279 GAAAAAATAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (42 bp):
AAGTCGACATAAAGATCTGACAAGTTAACATAATTATCTGAC
Found at i:1147359 original size:21 final size:21
Alignment explanation
Indices: 1147327--1147468 Score: 142
Period size: 21 Copynumber: 6.8 Consensus size: 21
1147317 ATTCATATTG
1147327 TATGTCGACTTGTCAGATAAT
1 TATGTCGACTTGTCAGATAAT
* * * * *
1147348 GATGTTGTCTTGTCTGAT-GT
1 TATGTCGACTTGTCAGATAAT
* * * *
1147368 TTTTTCGTCTTGTCAAATAAT
1 TATGTCGACTTGTCAGATAAT
1147389 TATGTCGACTTGTCAGATAAT
1 TATGTCGACTTGTCAGATAAT
*
1147410 TATGTCGACTTGTCAAATAAT
1 TATGTCGACTTGTCAGATAAT
* *** *
1147431 TATATCGACTTAAAAGATGAT
1 TATGTCGACTTGTCAGATAAT
1147452 TATGTCGACTTGTCAGA
1 TATGTCGACTTGTCAGA
1147469 AAATATTATT
Statistics
Matches: 93, Mismatches: 27, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 13 0.14
21 80 0.86
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.41
Consensus pattern (21 bp):
TATGTCGACTTGTCAGATAAT
Found at i:1147592 original size:21 final size:20
Alignment explanation
Indices: 1147568--1147616 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1147558 TAAAGAACTG
1147568 ACAAGTGAACATAATTATCTA
1 ACAAGTG-ACATAATTATCTA
*
1147589 ACAAGTCGACATAATTATCTG
1 ACAAGT-GACATAATTATCTA
1147610 ACAAGTG
1 ACAAGTG
1147617 GTGGCAGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (20 bp):
ACAAGTGACATAATTATCTA
Found at i:1147707 original size:21 final size:21
Alignment explanation
Indices: 1147682--1147753 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
1147672 TTATTTTTTC
1147682 TGTCAGATAATTATGTTGACT
1 TGTCAGATAATTATGTTGACT
* **
1147703 TGTCAAATCTTTATGTTGACT
1 TGTCAGATAATTATGTTGACT
* **
1147724 TGTCAGATGATTATGTAAACT
1 TGTCAGATAATTATGTTGACT
1147745 TGTCAGATA
1 TGTCAGATA
1147754 GCAGTTAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (21 bp):
TGTCAGATAATTATGTTGACT
Found at i:1147843 original size:21 final size:21
Alignment explanation
Indices: 1147818--1147869 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1147808 ATGGTTATTT
1147818 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCAACATAAAGA
* *
1147839 TCTGACAAGTTAACATAAATA
1 TCTGACAAGTCAACATAAAGA
1147860 TCTGACAAGT
1 TCTGACAAGT
1147870 GGTGGCAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAAGA
Found at i:1151304 original size:55 final size:55
Alignment explanation
Indices: 1151220--1151329 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
1151210 CTTCGCTAAC
*
1151220 CCTTGGTTCGTGAGAAGCGGTGCGTATCAGAAACCCTTGGCTAGCGAAGATGGTT
1 CCTTGGTTCGTGAGAAGCGGTGCGGATCAGAAACCCTTGGCTAGCGAAGATGGTT
*
1151275 CCTTGGTTCGTGAGAAGCGGTGCGGATCAGAAACCCTTGGCTAGCGCAGATGGTT
1 CCTTGGTTCGTGAGAAGCGGTGCGGATCAGAAACCCTTGGCTAGCGAAGATGGTT
1151330 TGAATATAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (55 bp):
CCTTGGTTCGTGAGAAGCGGTGCGGATCAGAAACCCTTGGCTAGCGAAGATGGTT
Found at i:1154590 original size:11 final size:11
Alignment explanation
Indices: 1154573--1154630 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
1154563 AACCNNNAAA
1154573 AAAAAAAACAC
1 AAAAAAAACAC
*
1154584 CAAAAAAAC-C
1 AAAAAAAACAC
1154594 AAAACAAAACA-
1 AAAA-AAAACAC
1154605 AAAAAAAA-AC
1 AAAAAAAACAC
1154615 AAATAAAAA-AC
1 AAA-AAAAACAC
1154626 AAAAA
1 AAAAA
1154631 CACTTTCGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 1 0.02
10 13 0.32
11 27 0.66
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAC
Found at i:1154602 original size:22 final size:22
Alignment explanation
Indices: 1154572--1154630 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1154562 CAACCNNNAA
**
1154572 AAAAAAAAACACCAAAAAAACC
1 AAAAAAAAACAAAAAAAAAACC
*
1154594 AAAACAAAACAAAAAAAAAA-C
1 AAAAAAAAACAAAAAAAAAACC
1154615 AAATAAAAAACAAAAA
1 AAA-AAAAAACAAAAA
1154631 CACTTTCGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAAACC
Found at i:1156143 original size:2 final size:2
Alignment explanation
Indices: 1156136--1156171 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1156126 TTTTTGTTAT
1156136 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1156172 TAACATGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1159366 original size:12 final size:12
Alignment explanation
Indices: 1159351--1159375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1159341 CAAAGAACAG
1159351 ACCAAAAAAAAA
1 ACCAAAAAAAAA
1159363 ACCAAAAAAAAA
1 ACCAAAAAAAAA
1159375 A
1 A
1159376 AAACCTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
ACCAAAAAAAAA
Found at i:1161333 original size:30 final size:30
Alignment explanation
Indices: 1161297--1161357 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1161287 ACTTGTATAA
* *
1161297 GATTCAAGACTTGTTAAGGACCGAAGACTT
1 GATTCAAGACTTGTTAAGAACCAAAGACTT
1161327 GATTCAAGACTTGTTAAGAACCAAAGACTT
1 GATTCAAGACTTGTTAAGAACCAAAGACTT
1161357 G
1 G
1161358 TTTAAGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (30 bp):
GATTCAAGACTTGTTAAGAACCAAAGACTT
Found at i:1161355 original size:18 final size:18
Alignment explanation
Indices: 1161332--1161374 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1161322 GACTTGATTC
1161332 AAGACTTG-TTAAGAACCA
1 AAGACTTGTTTAAG-ACCA
*
1161350 AAGACTTGTTTAAGATCA
1 AAGACTTGTTTAAGACCA
1161368 AAGACTT
1 AAGACTT
1161375 ATATAGGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (18 bp):
AAGACTTGTTTAAGACCA
Found at i:1161384 original size:18 final size:18
Alignment explanation
Indices: 1161348--1161496 Score: 104
Period size: 18 Copynumber: 8.1 Consensus size: 18
1161338 TGTTAAGAAC
* *
1161348 CAAAGACTTGTTTAAGAT
1 CAAAGACTTGTATAGGAT
*
1161366 CAAAGACTTATATAGGAT
1 CAAAGACTTGTATAGGAT
* * *
1161384 CAAAGATTTAATTTAAATAGGAC
1 CAAAGA-CT--TGT--ATAGGAT
* * *
1161407 CAAGGAATTGTTTAGGAT
1 CAAAGACTTGTATAGGAT
* *
1161425 -AAACACTTGTATA-GAA
1 CAAAGACTTGTATAGGAT
*
1161441 CTAAGACTTGTATAGGAT
1 CAAAGACTTGTATAGGAT
*
1161459 CAAAGACTTGTATAGAAT
1 CAAAGACTTGTATAGGAT
* *
1161477 CAAAGATTTGTACAGGAT
1 CAAAGACTTGTATAGGAT
1161495 CA
1 CA
1161497 GAAACTTTTT
Statistics
Matches: 100, Mismatches: 24, Indels: 14
0.72 0.17 0.10
Matches are distributed among these distances:
16 2 0.02
17 20 0.20
18 61 0.61
19 1 0.01
20 2 0.02
21 2 0.02
22 1 0.01
23 11 0.11
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (18 bp):
CAAAGACTTGTATAGGAT
Found at i:1164442 original size:16 final size:17
Alignment explanation
Indices: 1164423--1164454 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1164413 GTGTAGAGAA
1164423 AGATA-AAAATAGATAG
1 AGATATAAAATAGATAG
1164439 AGATATAAAATAGATA
1 AGATATAAAATAGATA
1164455 CAGTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (17 bp):
AGATATAAAATAGATAG
Found at i:1164498 original size:2 final size:2
Alignment explanation
Indices: 1164491--1164526 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1164481 TTAAAAATTC
1164491 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
1164527 CGCGGGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1165109 original size:2 final size:2
Alignment explanation
Indices: 1165102--1165135 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1165092 TGTTTATTCT
1165102 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
1165136 AATTACAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1175662 original size:156 final size:156
Alignment explanation
Indices: 1175378--1175845 Score: 918
Period size: 156 Copynumber: 3.0 Consensus size: 156
1175368 CTACAAGTTC
1175378 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
1 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
1175443 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
66 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
1175508 GAGCCATCTCTAAACCTTGGTCCTCA
131 GAGCCATCTCTAAACCTTGGTCCTCA
1175534 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
1 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
1175599 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
66 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
1175664 GAGCCATCTCTAAACCTTGGTCCTCA
131 GAGCCATCTCTAAACCTTGGTCCTCA
*
1175690 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGATC
1 TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
*
1175755 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGTT
66 CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
1175820 GAGCCATCTCTAAACCTTGGTCCTCA
131 GAGCCATCTCTAAACCTTGGTCCTCA
1175846 AGTTATAATC
Statistics
Matches: 310, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 310 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (156 bp):
TATATCTCAAGCTCAGTCAGATTCTTTTGCCTCCTCGTCATTAGTCAATATTAAACCCCCGGGTC
CACTTGTCCAAACAACTCCTTATGATGTGTATAATGATCATCTTGTAGATTTAAATGACGGAGCT
GAGCCATCTCTAAACCTTGGTCCTCA
Found at i:1182319 original size:25 final size:25
Alignment explanation
Indices: 1182291--1182378 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
1182281 ACACTACTTG
1182291 TACCTCATTGTACATAAAATGCATA
1 TACCTCATTGTACATAAAATGCATA
* *
1182316 TACCTTGA-TGTTACAT-AAA--C-TG
1 TACC-TCATTG-TACATAAAATGCATA
* *
1182338 TA-CTCATTATACATACAATGCATA
1 TACCTCATTGTACATAAAATGCATA
*
1182362 AACCTCATTGTAACATA
1 TACCTCATTGT-ACATA
1182379 CAGCTTGTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 17
0.65 0.11 0.24
Matches are distributed among these distances:
20 7 0.15
21 4 0.09
22 3 0.07
23 2 0.04
24 2 0.04
25 16 0.35
26 12 0.26
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TACCTCATTGTACATAAAATGCATA
Found at i:1182378 original size:46 final size:47
Alignment explanation
Indices: 1182289--1182394 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 47
1182279 ATACACTACT
* * * *
1182289 TGTACCTCATTGTACATAAAATGCATATACCTTGATGTTACATAAAC
1 TGTACCTCATTATACATAAAATGCATAAACCTTCATGTAACATAAAC
* *
1182336 TGTA-CTCATTATACATACAATGCATAAACC-TCATTGTAACATACAGC
1 TGTACCTCATTATACATAAAATGCATAAACCTTCA-TGTAACATA-AAC
1182383 TTGTACCTCATT
1 -TGTACCTCATT
1182395 GTAACATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.04
46 31 0.63
47 6 0.12
48 4 0.08
49 6 0.12
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (47 bp):
TGTACCTCATTATACATAAAATGCATAAACCTTCATGTAACATAAAC
Found at i:1182380 original size:26 final size:24
Alignment explanation
Indices: 1182357--1182411 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1182347 TACATACAAT
1182357 GCATAAACCTCATTGTAACATACA
1 GCATAAACCTCATTGTAACATACA
* **
1182381 GCTTGTACCTCATTGTAACATATACA
1 GCATAAACCTCATTGTAAC--ATACA
1182407 GCATA
1 GCATA
1182412 TACATGGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 16 0.67
26 8 0.33
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (24 bp):
GCATAAACCTCATTGTAACATACA
Found at i:1182470 original size:26 final size:26
Alignment explanation
Indices: 1182441--1182510 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 26
1182431 CTCATACTCT
* *
1182441 ATGTATATCATTGTAACATACACTGC
1 ATGTACATCATTATAACATACACTGC
* * *
1182467 ATGTACCTCATTATAATATACGCTGC
1 ATGTACATCATTATAACATACACTGC
*
1182493 AT-AAC-TCATTATAACATA
1 ATGTACATCATTATAACATA
1182511 AAGTACATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 12 0.32
25 2 0.05
26 23 0.62
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (26 bp):
ATGTACATCATTATAACATACACTGC
Found at i:1182623 original size:26 final size:26
Alignment explanation
Indices: 1182594--1182725 Score: 171
Period size: 26 Copynumber: 5.2 Consensus size: 26
1182584 CATAAACTGT
* * *
1182594 ATGTACCTCATTGTGACAAGTACTAC
1 ATGTGCCTCATTGTAACATGTACTAC
1182620 ATGTGCCTCATTGTAACATGTACTGA-
1 ATGTGCCTCATTGTAACATGTACT-AC
* *
1182646 ATGTGCCTTATTGTAACATGTACTGC
1 ATGTGCCTCATTGTAACATGTACTAC
* *
1182672 ATGTGCCTCATTGTAACGTGTACTGC
1 ATGTGCCTCATTGTAACATGTACTAC
1182698 ATGTGCCTCATTGTAACA--TACTAC
1 ATGTGCCTCATTGTAACATGTACTAC
1182722 ATGT
1 ATGT
1182726 ATGTTACCTT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
24 9 0.09
26 85 0.89
27 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (26 bp):
ATGTGCCTCATTGTAACATGTACTAC
Found at i:1182951 original size:2 final size:2
Alignment explanation
Indices: 1182862--1182933 Score: 65
Period size: 2 Copynumber: 36.5 Consensus size: 2
1182852 TTTTTTCTCT
* * * * *
1182862 GA GA GA GA GT GA GA CA GA GA GA CA GA GA GA GA CA CA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
1182904 AA G- GA GA GA GA CA GA AA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1182934 GGGGGGAAAG
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.01
Consensus pattern (2 bp):
GA
Found at i:1184039 original size:34 final size:36
Alignment explanation
Indices: 1183947--1184065 Score: 136
Period size: 34 Copynumber: 3.3 Consensus size: 36
1183937 TCAGTCCCGC
1183947 CCCTCTCTCAC-ACCCACTCTCGCTTCCCATTCTCAG
1 CCCTCTCTCACAACCCACTCTCGC-TCCCATTCTCAG
* * * *
1183983 CCCTCTTTTACATCCCACTCTCGCTCCCATTCTC-T
1 CCCTCTCTCACAACCCACTCTCGCTCCCATTCTCAG
*
1184018 CCC-CTCTCACAACCCACTCTCGCTCCTATTCTCACG
1 CCCTCTCTCACAACCCACTCTCGCTCCCATTCTCA-G
*
1184054 TCCCACTCTCAC
1 -CCCTCTCTCAC
1184066 CCTACGCTCT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
34 26 0.38
35 3 0.04
36 19 0.28
37 14 0.20
38 7 0.10
ACGTcount: A:0.14, C:0.52, G:0.04, T:0.29
Consensus pattern (36 bp):
CCCTCTCTCACAACCCACTCTCGCTCCCATTCTCAG
Found at i:1184114 original size:38 final size:36
Alignment explanation
Indices: 1184032--1184127 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 36
1184022 TCTCACAACC
1184032 CACTCTCGCTCCTATTCTCACGTCCCACTCTCACCCTA
1 CACTCTCGC-CCT-TTCTCACGTCCCACTCTCACCCTA
* *
1184070 CGCTCTCGCCCTTTCTCACG-CCCAACTCTCACACCATT
1 CACTCTCGCCCTTTCTCACGTCCC-ACTCTCAC-CC-TA
*
1184108 CACTCTCGCCCCTCTCTCAC
1 CACTCTCG-CCCTTTCTCAC
1184128 ACCCCCTCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
35 3 0.06
36 16 0.32
37 5 0.10
38 16 0.32
39 10 0.20
ACGTcount: A:0.15, C:0.52, G:0.06, T:0.27
Consensus pattern (36 bp):
CACTCTCGCCCTTTCTCACGTCCCACTCTCACCCTA
Found at i:1184207 original size:28 final size:28
Alignment explanation
Indices: 1184169--1184848 Score: 134
Period size: 28 Copynumber: 24.8 Consensus size: 28
1184159 TCACAGCCAA
1184169 CTCTCGCCCCTCTCTCACACCCCTCACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
*
1184197 CTCTCGCCCCTCTTTCACA-CCC-CACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * * *
1184223 TTCTCGCTCCTCT-T-A-AACCCTCGCT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * * * *
1184248 CTTTTGCCCCACTCTTACACCCCTTACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* ** * * *
1184276 CTCTCACAACACTCACACACTTGCC-C-CT
1 CTCTCGCCCCTCTCTCACAC--CCCTCACT
* ** ** * * **
1184304 CTCTCACACACCTAGCTTGC-TCGCTCTTTT
1 CTCTCGC-C-CCTCTCTCACACCCCTC-ACT
* *
1184334 CTCACGCCCCTCTCTCACGCCCCTCACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* *
1184362 TTCTCGCCCCTCTCT------CC-C-CG
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * **
1184382 CTCTCGCTCCTCTCTCACATCCAGCACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* ** * *
1184410 CTCTCACCAAATTCTCTCAAACTCCTCACT
1 CTCTCGCC--CCTCTCTCACACCCCTCACT
*
1184440 CTCTCGCCCCTCTCTCACACACC-CAGCT
1 CTCTCGCCCCTCTCTCACACCCCTCA-CT
* * * * **
1184468 CTTTCACCCCTTTCTCACGCCCCTTGCT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
*
1184496 CTCTCGCCCCTCTCTCACA---C-C-CG
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * * *
1184519 CTCTCGCTCCTCTCTCACATCCATCATT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * * *
1184547 CTCTCACCAAACTCTCTCAAACTCCTCACT
1 CTCTCGCC--CCTCTCTCACACCCCTCACT
* ** *
1184577 CTCTTGCCCCTCTCTCACACTTTCTCGCT
1 CTCTCGCCCCTCTCTCACAC-CCCTCACT
* * ** *
1184606 CCTCTCACACCCTTCGCTCTCTCA-CAATC-CA
1 -CTCTCGC-CCC-T--CTCTCACACCCCTCACT
* *
1184637 CACTCGTCCCC-CTCTCACACACCT-AGCT
1 CTCTCG-CCCCTCTCTCACACCCCTCA-CT
* * * * * *
1184665 CGCTCGCTCTTTTCCCACGCCCCTCACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * *
1184693 TTCTCGCCCCTCT-T-----TCC-C-CG
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * *
1184713 CTCTCGCTCCTCTCTCACATCCATCACT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
* * * *
1184741 CTCTCACCCAGCTCTCTCAAACTCCTCATT
1 CTCTCGCCC--CTCTCTCACACCCCTCACT
* *
1184771 CTCTCGCCCCTCTCTCACTCACCT-AGCT
1 CTCTCGCCCCTCTCTCACACCCCTCA-CT
* * * * *
1184799 CTTTCACCCCTTTCTCACGCCCCTCGCT
1 CTCTCGCCCCTCTCTCACACCCCTCACT
1184827 CTCTCGCCCCTCTCTCACACCC
1 CTCTCGCCCCTCTCTCACACCC
1184849 GCTCTCGCTT
Statistics
Matches: 445, Mismatches: 151, Indels: 112
0.63 0.21 0.16
Matches are distributed among these distances:
20 26 0.06
21 3 0.01
22 4 0.01
23 20 0.04
24 4 0.01
25 13 0.03
26 25 0.06
27 14 0.03
28 224 0.50
29 12 0.03
30 85 0.19
31 5 0.01
32 3 0.01
34 7 0.02
ACGTcount: A:0.13, C:0.52, G:0.06, T:0.29
Consensus pattern (28 bp):
CTCTCGCCCCTCTCTCACACCCCTCACT
Found at i:1184351 original size:13 final size:13
Alignment explanation
Indices: 1184333--1184377 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1184323 CTCGCTCTTT
1184333 TCTCACGCCCCTC
1 TCTCACGCCCCTC
1184346 TCTCACGCCCCTCAC
1 TCTCACGCCCCT--C
* *
1184361 TTTCTCGCCCCTC
1 TCTCACGCCCCTC
1184374 TCTC
1 TCTC
1184378 CCCGCTCTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.07, C:0.58, G:0.07, T:0.29
Consensus pattern (13 bp):
TCTCACGCCCCTC
Found at i:1184555 original size:137 final size:134
Alignment explanation
Indices: 1184340--1184596 Score: 415
Period size: 137 Copynumber: 1.9 Consensus size: 134
1184330 TTTTCTCACG
*
1184340 CCCCTCTCTCACGCCCCTCACTTTCTCGCCCCTCTCTCCCCGCTCTCGCTCCTCTCTCACATCCA
1 CCCCTCTCTCACGCCCCTCACTCTCTCGCCCCTCTCTCCCCGCTCTCGCTCCTCTCTCACATCCA
*
1184405 GCACTCTCTCACCAAATTCTCTCAAACTCCTCACTCTCTCGCCCCTCTCTCACACACCCAGCTCT
66 GCACTCTCTCACCAAACTCTCTCAAACTCCTCACTCTCTCGCCCCTCTCTCACACACCCAGCTCT
1184470 TTCA
131 TTCA
* **
1184474 CCCCTTTCTCACGCCCCTTGCTCTCTCGCCCCTCTCTCACACCCGCTCTCGCTCCTCTCTCACAT
1 CCCCTCTCTCACGCCCCTCACTCTCTCGCCCCTCTCT--C-CCCGCTCTCGCTCCTCTCTCACAT
* * *
1184539 CCATCATTCTCTCACCAAACTCTCTCAAACTCCTCACTCTCTTGCCCCTCTCTCACAC
63 CCAGCACTCTCTCACCAAACTCTCTCAAACTCCTCACTCTCTCGCCCCTCTCTCACAC
1184597 TTTCTCGCTC
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 33 0.29
136 1 0.01
137 78 0.70
ACGTcount: A:0.14, C:0.53, G:0.05, T:0.28
Consensus pattern (134 bp):
CCCCTCTCTCACGCCCCTCACTCTCTCGCCCCTCTCTCCCCGCTCTCGCTCCTCTCTCACATCCA
GCACTCTCTCACCAAACTCTCTCAAACTCCTCACTCTCTCGCCCCTCTCTCACACACCCAGCTCT
TTCA
Found at i:1184629 original size:17 final size:18
Alignment explanation
Indices: 1184586--1184631 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1184576 TCTCTTGCCC
**
1184586 CTCTCTCACACTTTCTCG
1 CTCTCTCACACCCTCTCG
1184604 CTCCTCTCACACCCT-TCG
1 CT-CTCTCACACCCTCTCG
1184622 CTCTCTCACA
1 CTCTCTCACA
1184632 ATCCACACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.13, C:0.50, G:0.04, T:0.33
Consensus pattern (18 bp):
CTCTCTCACACCCTCTCG
Found at i:1184886 original size:137 final size:132
Alignment explanation
Indices: 1184639--1184919 Score: 359
Period size: 134 Copynumber: 2.1 Consensus size: 132
1184629 ACAATCCACA
* * * *
1184639 CTCGTCCCC-CTCTCACACACCTAGCTCGCTCGCTCTTTTCCCACGCCCCTCACTTTCTCGCCCC
1 CTCG-CCCCTCTCTCACACACCTAGCTCGCTCACCCCTTTCCCACGCCCCTCACTCTCTCGCCCC
* *
1184703 TCTTTCCCCGCTCTCGCTCCTCTCTCACATCCATCACTCTCTCACCCAGCTCTCTCAAACTCCTC
65 TCTTACCCCGCTCTCGCTCCTCTCTCACATCCATCACTCTCTCACCCAACTCTCTCAAAC-CC-C
1184768 A-TTCT
128 ACTT-T
* ** * *
1184773 CTCGCCCCTCTCTCACTCACCTAGCTCTTTCACCCCTTTCTCACGCCCCTCGCTCTCTCGCCCCT
1 CTCGCCCCTCTCTCACACACCTAGCTCGCTCACCCCTTTCCCACGCCCCTCACTCTCTCGCCCCT
* *
1184838 CTCTCACACCCGCTCTCGCTTCTCTCTCACATCCATCATTCTCTCACCCAACTCTCTCAAACCCC
66 CT-T-AC-CCCGCTCTCGCTCCTCTCTCACATCCATCACTCTCTCACCCAACTCTCTCAAACCCC
1184903 ACTTT
128 ACTTT
*
1184908 CTCGCTCCTCTC
1 CTCGCCCCTCTC
1184920 ACAATCCTCG
Statistics
Matches: 128, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
133 4 0.03
134 53 0.41
135 15 0.12
136 5 0.04
137 51 0.40
ACGTcount: A:0.12, C:0.52, G:0.06, T:0.30
Consensus pattern (132 bp):
CTCGCCCCTCTCTCACACACCTAGCTCGCTCACCCCTTTCCCACGCCCCTCACTCTCTCGCCCCT
CTTACCCCGCTCTCGCTCCTCTCTCACATCCATCACTCTCTCACCCAACTCTCTCAAACCCCACT
TT
Found at i:1185070 original size:15 final size:13
Alignment explanation
Indices: 1185034--1185128 Score: 68
Period size: 13 Copynumber: 7.5 Consensus size: 13
1185024 CACCCTCTCG
1185034 CCCCTCTCTCACA
1 CCCCTCTCTCACA
1185047 CCCCTCTCTCACA
1 CCCCTCTCTCACA
* * *
1185060 CCCCTCACTCTCG
1 CCCCTCTCTCACA
* * *
1185073 CACCTCTTTCACG
1 CCCCTCTCTCACA
*
1185086 CTCCTCTCTCACA
1 CCCCTCTCTCACA
** * *
1185099 ATCCACTCT--CG
1 CCCCTCTCTCACA
*
1185110 TCCCTCTCTCACA
1 CCCCTCTCTCACA
1185123 CCCCTC
1 CCCCTC
1185129 GCTCTCTTGC
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 7 0.11
13 55 0.89
ACGTcount: A:0.14, C:0.57, G:0.03, T:0.26
Consensus pattern (13 bp):
CCCCTCTCTCACA
Found at i:1185134 original size:39 final size:38
Alignment explanation
Indices: 1185028--1185128 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 38
1185018 ACTCCTCACC
*
1185028 CTCTCGCCCCTCTCTCACACCCCTCTCTCACACCCCTCA
1 CTCTCG-CCCTCTCTCACACCCCTCTCTCACACACCTCA
* * * *
1185067 CTCTCGCACCTCTTTCACGCTCCTCTCTCACA-ATC-CA
1 CTCTCGC-CCTCTCTCACACCCCTCTCTCACACACCTCA
1185104 CTCTCGTCCCTCTCTCACACCCCTC
1 CTCTCG-CCCTCTCTCACACCCCTC
1185129 GCTCTCTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
37 22 0.42
38 3 0.06
39 27 0.52
ACGTcount: A:0.13, C:0.56, G:0.04, T:0.27
Consensus pattern (38 bp):
CTCTCGCCCTCTCTCACACCCCTCTCTCACACACCTCA
Done.