Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold77
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: 1619719
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 197531 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:1748 original size:23 final size:23
Alignment explanation
Indices: 1721--1765 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1711 AGGTTGACTT
1721 CCATTGTTCTCGAGAACAATAGA
1 CCATTGTTCTCGAGAACAATAGA
1744 CCATTGTTCTCGAGAACAATAG
1 CCATTGTTCTCGAGAACAATAG
1766 CTCTATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (23 bp):
CCATTGTTCTCGAGAACAATAGA
Found at i:1923 original size:2 final size:2
Alignment explanation
Indices: 1916--1941 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1906 TTTCTCTTTA
1916 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
1942 CTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1992 original size:1 final size:1
Alignment explanation
Indices: 1959--1984 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1949 TTATTTCCAC
1959 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1985 GAGAAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3517 original size:200 final size:200
Alignment explanation
Indices: 3174--3573 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
3164 CACCCCCACT
3174 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT
1 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT
3239 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT
66 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT
3304 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG
131 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG
3369 TGTAA
196 TGTAA
3374 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT
1 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT
3439 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT
66 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT
3504 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG
131 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG
3569 TGTAA
196 TGTAA
3574 ACGTATATAT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.41
Consensus pattern (200 bp):
TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT
AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT
GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG
TGTAA
Found at i:8184 original size:14 final size:13
Alignment explanation
Indices: 8165--8196 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
8155 ATGTATAGTT
8165 TTTTTTTGCTATAA
1 TTTTTTTGCTAT-A
8179 TTTTTTTGCTATA
1 TTTTTTTGCTATA
8192 TTTTT
1 TTTTT
8197 CTTTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTTTGCTATA
Found at i:14446 original size:166 final size:166
Alignment explanation
Indices: 14155--14581 Score: 766
Period size: 166 Copynumber: 2.6 Consensus size: 166
14145 NNNNNNATTT
14155 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
*
14220 GGTTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG
66 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG
14285 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG
131 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG
* * *
14321 TTACAATTTAGAATCTTCACTATGTATACAAGCTTATGTGTAAATATTGGCATTTCTGGTGCAGT
1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
* *
14386 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTGAACCCC
66 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAA-TTTGAACCCC
*
14450 GCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTT
130 GCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG
14487 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
14552 GGTTCTTGAGAAGAAGATTTTTAAAGACAT
66 GGTTCTTGAGAAGAAGATTTTTAAA-ACAT
14582 GCACCCTATA
Statistics
Matches: 249, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
165 16 0.06
166 229 0.92
167 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (166 bp):
TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT
GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG
CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG
Found at i:14755 original size:4 final size:4
Alignment explanation
Indices: 14746--14791 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
14736 AAAGTTTACA
* *
14746 GACG GACG GACA GACA GACG GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
14792 AACGGGTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.30, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:14760 original size:12 final size:12
Alignment explanation
Indices: 14743--14796 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
14733 TGAAAAGTTT
14743 ACAGACGGACGG
1 ACAGACGGACGG
*
14755 ACAGACAGACGG
1 ACAGACGGACGG
*
14767 ACGGACGGACGG
1 ACAGACGGACGG
*
14779 ACGGAC-GACGG
1 ACAGACGGACGG
14790 ACA-ACGG
1 ACAGACGG
14797 GTGATCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 2 0.05
11 8 0.22
12 27 0.73
ACGTcount: A:0.33, C:0.26, G:0.41, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:19448 original size:2 final size:2
Alignment explanation
Indices: 19441--19501 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
19431 TCCAGTTCAT
19441 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
19483 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
19502 CACCTGTCAC
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22071 original size:44 final size:44
Alignment explanation
Indices: 21996--22914 Score: 1245
Period size: 44 Copynumber: 20.8 Consensus size: 44
21986 GATCAAGGTG
* ***
21996 CATGCTTATGCTTTATAACCATACAAAGATCCCATCCAATGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * * *
22040 CATCCTTTTGCGTTATAATCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22084 CATGCTTATGCTTTATAACCATATAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * * ***
22128 CATGCTTATGTTTTTTAACCATACAAAGATCCCATCCAATGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* **
22172 CATGCTTATGCTTTATAACCATATAGAGATCCCATCCAGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22216 CATGCTTTTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22260 CATGCTTATGCGTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22304 CATGCTTTTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22348 CATGCTTATGTTTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * * *
22392 CATGCTTATGTTTTATAACCATACAGATATCCCATCTGGAGGGT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* **
22436 CATGCTTATG-TGTTATAACCATATAGAGATCCCATCCAGTGGTT
1 CATGCTTATGCT-TTATAACCATACAGAGATCCCATCTGGTGGTT
* *
22480 CATGCTTTTGCTTTATAACCATACAGAGATCCAATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * * * *
22524 CATGCTTATGCATTATAATCATTCAAAGATCCCATCTGGTTGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * *
22568 CATGCTTTTGCTTTATAATCATACAGAGATCCCATCTGGTGGTC
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22612 CATGCTTGTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * *
22656 CATGCTTTTGCTTTATATTAACTATACAAAGATCCCATCTGGTGGTT
1 CATGCTTATGC-TT-TA-TAACCATACAGAGATCCCATCTGGTGGTT
*
22703 CCTGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* * * *
22747 CATGCTTTTGCTTTATATTAACTATACAAAGATCCCATCTGATGGTT
1 CATGCTTATGC-TT-TA-TAACCATACAGAGATCCCATCTGGTGGTT
* * *
22794 CCTGCTTATTCTTTATAACCATACAAAGATCCCATCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
* *
22838 CCTGCTTATGCTTTATAACCATACAGAGATCCCTTCTGGTGGTT
1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
*
22882 CATGCTT-T--TTCT-TAACCATACAAAGATCCCATC
1 CATGCTTATGCTT-TATAACCATACAGAGATCCCATC
22915 AGGCATCTGG
Statistics
Matches: 778, Mismatches: 88, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
41 21 0.03
42 1 0.00
43 2 0.00
44 667 0.86
45 9 0.01
46 8 0.01
47 70 0.09
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (44 bp):
CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT
Found at i:29460 original size:40 final size:40
Alignment explanation
Indices: 29416--29493 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
29406 CTTAATGATA
*
29416 ATAGTGTAAACCTAAACAGTTTCTATATTGAAATTTTATC
1 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTATC
29456 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTA
1 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTA
29494 GGCAGATCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (40 bp):
ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTATC
Found at i:30627 original size:10 final size:10
Alignment explanation
Indices: 30599--30630 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
30589 ATACACAGTT
*
30599 TATCACAAAA
1 TATCACAATA
30609 TATCACAATA
1 TATCACAATA
30619 TATCACAATA
1 TATCACAATA
30629 TA
1 TA
30631 CATACTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (10 bp):
TATCACAATA
Found at i:30810 original size:6 final size:6
Alignment explanation
Indices: 30799--30842 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
30789 TGCTATACCC
30799 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TCGGCG TC
30843 CGGACCTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.06
6 32 0.89
7 2 0.06
ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18
Consensus pattern (6 bp):
TCGGCG
Found at i:31189 original size:19 final size:19
Alignment explanation
Indices: 31167--31206 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31157 TTTCGGATGC
* *
31167 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
31186 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
31205 TG
1 TG
31207 TTGCGGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:31197 original size:177 final size:176
Alignment explanation
Indices: 30985--31497 Score: 688
Period size: 177 Copynumber: 2.9 Consensus size: 176
30975 CTAAATTTTA
* * *
30985 GATGCTGGAGGAGTTTAAGGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG
1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG
* *
31050 CAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATAC
66 CAATATCTAAGTTACTACTGGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATAC
* * *
31115 TGATGCACCAGACAGGCTTGAGTGCTGAATCTAAGCTATAGGTTTCG
130 TGATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG
* *
31162 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCGGGTGCCCATTGATAG
1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG
* * *
31227 CAATATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTTATGATAC
66 CAATATCTAAGTTACTACTGGTCCT-ACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATAC
* *
31292 TGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCG
130 TGATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG
** * *** *
31339 GATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAGATAAAGTTTTTGAAACAGGTGCCCTCTG
1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGG-T---TAAAGTTTTTGTTGCAGGTGCCCTTTG
* * * * *
31404 AT-G-ATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTA
62 ATAGCA--ATATCTAAGTTACTACTGGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTA
31467 TGATACTGATGCACCTGACAGGCTTGAATGC
124 TGATACTGATGCACCTGACAGGCTTGAATGC
31498 ATAGTCTGGT
Statistics
Matches: 295, Mismatches: 33, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
176 1 0.00
177 190 0.64
178 1 0.00
179 1 0.00
180 1 0.00
181 100 0.34
182 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (176 bp):
GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG
CAATATCTAAGTTACTACTGGTCCTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACT
GATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG
Found at i:32187 original size:20 final size:20
Alignment explanation
Indices: 32164--32206 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
32154 TATGATAAAG
32164 TATTGTATGATATGAAACAA
1 TATTGTATGATATGAAACAA
* *
32184 TATTGTTTGATATGATACAA
1 TATTGTATGATATGAAACAA
32204 TAT
1 TAT
32207 GATATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGTATGATATGAAACAA
Found at i:32317 original size:28 final size:28
Alignment explanation
Indices: 32268--32321 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
32258 TCAATTTTTT
32268 TGATATTTTATGATATGATATTGTATCA
1 TGATATTTTATGATATGATATTGTATCA
32296 TGATATTGTTATG-TAT-AGTATTGTAT
1 TGATATT-TTATGATATGA-TATTGTAT
32322 ATTATGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 18 0.75
29 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (28 bp):
TGATATTTTATGATATGATATTGTATCA
Found at i:32482 original size:15 final size:15
Alignment explanation
Indices: 32449--32582 Score: 72
Period size: 15 Copynumber: 8.4 Consensus size: 15
32439 ATATTCTATA
* **
32449 ATATTGTATCATACA
1 ATATTGTATAATATG
32464 ATATTGTATAATATG
1 ATATTGTATAATATG
32479 ATATTGGTTTCAGTAATATAG
1 ATATT-G--T-A-TAATAT-G
* * *
32500 A-ATTATATCACATG
1 ATATTGTATAATATG
* *
32514 AAATTGTATTATATG
1 ATATTGTATAATATG
*
32529 ATATTGTAATATTATATA
1 ATATTGT-ATA--ATATG
* *
32547 ATATTGTATCATACG
1 ATATTGTATAATATG
*
32562 ATATTGTATGATATG
1 ATATTGTATAATATG
32577 ATATTG
1 ATATTG
32583 GTTTTTATGA
Statistics
Matches: 92, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
14 2 0.02
15 59 0.64
16 4 0.04
17 3 0.03
18 12 0.13
19 1 0.01
20 9 0.10
21 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:32528 original size:50 final size:47
Alignment explanation
Indices: 32466--32632 Score: 156
Period size: 50 Copynumber: 3.4 Consensus size: 47
32456 ATCATACAAT
*
32466 ATTGTATAATATGATATTGGTTTCAGTAATATAGAATTATATCACATGAA
1 ATTGTATTATATGATATTGGTTT-A-TAATATA-AATTATATCACATGAA
* * * * * *
32516 ATTGTATTATATGATATT-GTAATATTATATAATATTGTATCATACGAT
1 ATTGTATTATATGATATTGGT-TTATAATATAA-ATTATATCACATGAA
* * * *
32564 ATTGTATGATATGATATTGGTTTTTATGATATATTATCATATCACATGAA
1 ATTGTATTATATGATATTGG--TTTATAATATA-AATTATATCACATGAA
32614 ATTGTATTATATGATATTG
1 ATTGTATTATATGATATTG
32633 TTATATATTA
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.01
48 34 0.36
49 4 0.04
50 54 0.57
51 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (47 bp):
ATTGTATTATATGATATTGGTTTATAATATAAATTATATCACATGAA
Found at i:32543 original size:18 final size:18
Alignment explanation
Indices: 32520--32554 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32510 CATGAAATTG
*
32520 TATTATATGATATTGTAA
1 TATTATATAATATTGTAA
32538 TATTATATAATATTGTA
1 TATTATATAATATTGTA
32555 TCATACGATA
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:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TATTATATAATATTGTAA
Found at i:32551 original size:98 final size:98
Alignment explanation
Indices: 32432--32643 Score: 311
Period size: 98 Copynumber: 2.2 Consensus size: 98
32422 CTATGATACA
*
32432 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGG-TTTCAGTAA
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCA-TAA
*
32495 TATAGAATTATATCACATGAAATTGTATTATATG
65 TATAGAATCATATCACATGAAATTGTATTATATG
* * * *
32529 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTTTATGAT
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCATAAT
**
32594 ATATTATCATATCACATGAAATTGTATTATATG
66 ATAGAATCATATCACATGAAATTGTATTATATG
32627 ATATTGTTATATATTAT
1 ATATTG-TA-ATATTAT
32644 TGTGTCATAT
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
97 7 0.07
98 83 0.81
99 6 0.06
100 7 0.07
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (98 bp):
ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCATAAT
ATAGAATCATATCACATGAAATTGTATTATATG
Found at i:32632 original size:15 final size:15
Alignment explanation
Indices: 32511--32633 Score: 79
Period size: 15 Copynumber: 7.7 Consensus size: 15
32501 ATTATATCAC
*
32511 ATGAAATTGTATTAT
1 ATGATATTGTATTAT
32526 ATGATATTGTAATATTAT
1 ATGATATTG---TATTAT
* *
32544 ATAATATTGTATCAT
1 ATGATATTGTATTAT
* *
32559 ACGATATTGTATGAT
1 ATGATATTGTATTAT
*
32574 ATGATATTGGT-TTTT
1 ATGATATT-GTATTAT
32589 ATGATATAT-TATCATAT
1 ATGATAT-TGTAT--TAT
*
32606 CACATGAAATTGTATTAT
1 ---ATGATATTGTATTAT
32624 ATGATATTGT
1 ATGATATTGT
32634 TATATATTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 1 0.01
15 51 0.61
16 3 0.04
17 2 0.02
18 17 0.20
19 1 0.01
20 9 0.11
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGATATTGTATTAT
Found at i:34630 original size:20 final size:20
Alignment explanation
Indices: 34605--34644 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34595 CACAACTACC
34605 CAAAGTCCAAGCTCTTGTTA
1 CAAAGTCCAAGCTCTTGTTA
34625 CAAAGTCCAAGCTCTTGTTA
1 CAAAGTCCAAGCTCTTGTTA
34645 AAATGGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
CAAAGTCCAAGCTCTTGTTA
Found at i:44464 original size:2 final size:2
Alignment explanation
Indices: 44457--44483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44447 TCCCCCGAAA
44457 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
44484 ATTAGTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61089 original size:37 final size:38
Alignment explanation
Indices: 61048--61122 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
61038 TACATAATAC
* * *
61048 CTCCAATATTGCAGTAGTTCAATGT-TAGATTCAGTAT
1 CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT
* *
61085 CTCCAACATTGTATTAGTTAAATGTATAAATTCAGTAT
1 CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT
61123 AGAAGGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 21 0.66
38 11 0.34
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (38 bp):
CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT
Found at i:67142 original size:12 final size:12
Alignment explanation
Indices: 67125--67170 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
67115 ACCGGTTTCA
*
67125 CCGTCTGTCTGT
1 CCGTCTGTCCGT
67137 CCGTCTGTCCGT
1 CCGTCTGTCCGT
*
67149 CCGTCAGTCCGT
1 CCGTCTGTCCGT
*
67161 CTGTCTGTCC
1 CCGTCTGTCC
67171 CACTTCAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.39, G:0.24, T:0.35
Consensus pattern (12 bp):
CCGTCTGTCCGT
Found at i:83564 original size:34 final size:34
Alignment explanation
Indices: 83526--83592 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
83516 TTGTACACAT
* *
83526 GTACATGTATGTGCAGAGAGGTGGATAGTATATA
1 GTACATGTATGTGCAGAGAAGTGGATAATATATA
**
83560 GTACATGTATGTGTGGAGAAGTGGATAATATAT
1 GTACATGTATGTGCAGAGAAGTGGATAATATAT
83593 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (34 bp):
GTACATGTATGTGCAGAGAAGTGGATAATATATA
Found at i:83778 original size:31 final size:31
Alignment explanation
Indices: 83743--83821 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
83733 CATGAAGGAG
* *
83743 TGGATAGTGTATTCATGTATTTGTGGAGGTA
1 TGGATAGTGTATACATGTATTTCTGGAGGTA
* * *
83774 TGGATAGTTTATACATATATTTCTGGAGGTT
1 TGGATAGTGTATACATGTATTTCTGGAGGTA
*
83805 TGGATAGTGTATGCATG
1 TGGATAGTGTATACATG
83822 CATGTGTAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (31 bp):
TGGATAGTGTATACATGTATTTCTGGAGGTA
Found at i:84008 original size:65 final size:65
Alignment explanation
Indices: 83933--84288 Score: 397
Period size: 67 Copynumber: 5.3 Consensus size: 65
83923 TCTGGTGGTA
* * * * * *
83933 TGGATAGTGTATATATGCATATGTAAAGGGAATGAATAGTTCATAAATATGTGTATATATAGGGT
1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTATATAGGGT
* * * * *
83998 TGGATAGTGTATACATATATATGTAGAGGGAATGGATAGTTCATAAATACATGTGTATAAAAAGG
1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTAT--ATAGG
84063 GT
64 GT
* * * * *
84065 TGGGTAGTGTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATATATGTGTATATAGA
1 TGGATAGTGTATACATGTATATGCAAAGG--GAATGGATAGTTCATAAATATATGTGTATATAGG
84130 GT
64 GT
* * *
84132 TGGATAGTGTATACATGCATATGAAAAGGGAATGGATAGTTCATATTAAATACATGTGTATATAG
1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTC--A-TAAATATATGTGTATATAG
84197 GGT
63 GGT
* * * * * *
84200 TGGGTAGTTTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATATTTGTGTATATAGG
1 TGGATAGTGTATACATGTATATGCAAAGG--GAATGGATAGTTCATAAATATATGTGTATATAGG
84265 GT
64 GT
*
84267 TGGGTAGTGTATACATGTATAT
1 TGGATAGTGTATACATGTATAT
84289 ATATATATAT
Statistics
Matches: 245, Mismatches: 37, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
65 61 0.25
67 102 0.42
68 45 0.18
69 26 0.11
70 11 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (65 bp):
TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTATATAGGGT
Found at i:84250 original size:135 final size:133
Alignment explanation
Indices: 83968--84288 Score: 500
Period size: 135 Copynumber: 2.4 Consensus size: 133
83958 AAGGGAATGA
* * * * *
83968 ATAGTTCATAAATATGTGTATATATAGGGTTGGATAGTGTATACATATATATGTAGAGGGAATGG
1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG
84033 ATAGTTCATAAATACATGTGTATAAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTA
66 ATAGTTCATAAATACATGTGTAT-AAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTA
84098 TTGG
130 TTGG
* *
84102 ATAGTTCATAAATATATGTGTATATAGAGTTGGATAGTGTATACATGCATATGAAAAGGGAATGG
1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG
* *
84167 ATAGTTCATATTAAATACATGTGTAT-ATAGGGTTGGGTAGTTTATACATGTATATACAAAGGTC
66 ATAGTTC--A-TAAATACATGTGTATAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTC
84231 TATTGG
128 TATTGG
* *
84237 ATAGTTCATAAATATTTGTGTATATAGGGTTGGGTAGTGTATACATGTATAT
1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATAT
84289 ATATATATAT
Statistics
Matches: 171, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
134 65 0.38
135 90 0.53
136 1 0.01
137 15 0.09
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (133 bp):
ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG
ATAGTTCATAAATACATGTGTATAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTAT
TGG
Found at i:84326 original size:108 final size:108
Alignment explanation
Indices: 84190--84396 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 108
84180 AATACATGTG
* * * * *
84190 TATATAGGGTTGGGTAGTTTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATAT-T-
1 TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGG--GAATGGATAGTTCATAAATATGTG
* * *
84253 TGTGTATATAGGGTTGGGTAGTGTATACATGTATATATATATATA
64 TGTATATATAGGGTTGGATAGCGTATACATGTATATATATATATA
* * ** *
84298 TATATAGGGTTGGATCGTGTAGAGATGTATATGTAGAGGGAATGGATAGTTCATAAATATGTGTG
1 TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGGGAATGGATAGTTCATAAATATGTGTG
84363 TATATATAGGGTTGGATAGCGTATACATGTATAT
66 TATATATAGGGTTGGATAGCGTATACATGTATAT
84397 GTAGAGGGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 19 0.23
107 1 0.01
108 64 0.76
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (108 bp):
TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGGGAATGGATAGTTCATAAATATGTGTG
TATATATAGGGTTGGATAGCGTATACATGTATATATATATATA
Found at i:84369 original size:67 final size:64
Alignment explanation
Indices: 84296--84513 Score: 339
Period size: 63 Copynumber: 3.4 Consensus size: 64
84286 TATATATATA
* * * *
84296 TATATATAGGGTTGGATCGTGTAGAGATGTATATGTAGAGGGAATGGATAGTTCATAAATATGTG
1 TATATATAGGATTGGATAGTGTA-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATA--TG
84361 TG
63 TG
* *
84363 TATATATAGGGTTGGATAGCGTATACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG
1 TATATATAGGATTGGATAGTGTA-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG
84428 TATATATAGGATTGGATAGTGT-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG
1 TATATATAGGATTGGATAGTGTAACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG
84491 TATATATAGGATTGGATAGTGTA
1 TATATATAGGATTGGATAGTGTA
84514 TGAATGGATA
Statistics
Matches: 143, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
63 63 0.44
65 24 0.17
67 56 0.39
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (64 bp):
TATATATAGGATTGGATAGTGTAACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG
Found at i:84545 original size:48 final size:49
Alignment explanation
Indices: 84467--84563 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
84457 TATGTAGAGG
*
84467 GAATGGATAGGTCATAAATATGTGT-ATATATAGGATTGGATAGTGTAT
1 GAATGGATAGGTCATAAATATATGTAATATATAGGATTGGATAGTGTAT
*
84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTA
1 GAATGGATAGGTCATAAATATATGT-AATATATAGGATTGGATAGTGTA
84564 CATGTATATG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 24 0.52
50 22 0.48
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (49 bp):
GAATGGATAGGTCATAAATATATGTAATATATAGGATTGGATAGTGTAT
Found at i:84559 original size:50 final size:48
Alignment explanation
Indices: 84467--84563 Score: 176
Period size: 50 Copynumber: 2.0 Consensus size: 48
84457 TATGTAGAGG
84467 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
1 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTA
1 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTA
84564 CATGTATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 15 0.32
49 2 0.04
50 30 0.64
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (48 bp):
GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
Found at i:84571 original size:243 final size:245
Alignment explanation
Indices: 84027--84637 Score: 651
Period size: 243 Copynumber: 2.5 Consensus size: 245
84017 TATGTAGAGG
* * * * ** *
84027 GAATGGATAGTTCATAAATACATGTGTATAAAAAGGGTTGGGTAGTGTATACATGTATATACAAA
1 GAATGGATAG-TCATAAATATATGTGTATATATAGGGTTGGATAGTG--TACATGTATATGTAGA
* * * *
84092 GGTCTATTGGATAGTTCATAAATATATGTG--TATATAGAGTTGGATAGTGTATACATGCATATG
63 GG--GAATGGATAGTTCATAAATAT-TGTGTATATATAGGGTTGGATAGTGTATACATGTATATG
* * * *
84155 AAAAGGGAATGGATAGTTCATATTAAATACATGTGTATATAGGGTTGGGTAGTTTATACATGTAT
125 AAAAGGGAATGGATAGGTCA-ATTAAATACATGTATATATAGGATTGGATAG-TTATACATGTAT
* * * * * * *
84220 ATACAAAGGTCTATTGGATAGTTCATAAATATTTGTGTATATAGGGTTGGGTAGTGTAT
188 ATACAAAGG-CGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
* * *
84279 -ACAT-G-TA-T-AT--ATATA--TATATATATAGGGTTGGATCGTGTAGAGATGTATATGTAGA
1 GA-ATGGATAGTCATAAATATATGTGTATATATAGGGTTGGATAGTGT--ACATGTATATGTAGA
* *
84335 GGGAATGGATAGTTCATAAATATGTGTGTATATATAGGGTTGGATAGCGTATACATGTATATGTA
63 GGGAATGGATAGTTCATAAATAT-TGTGTATATATAGGGTTGGATAGTGTATACATGTATATGAA
* ** * **
84400 GAGGGAATGGATAGGTC-A-TAAATATGTGTATATATAGGATTGGATAG-TGTACATGTATATGT
127 AAGGGAATGGATAGGTCAATTAAATACATGTATATATAGGATTGGATAGTTATACATGTATATAC
*
84462 AGAGG-GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
192 AAAGGCGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
*
84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG
1 GAATGGATA-GTCATAAATATATGTGTATATATAGGGTTGGATAGTGTACATGTATATGTAGAGG
* *
84580 GAATGGATAGGTCATAAATA-TGTGTATATATAGGATTGGATAGTGTATACATGTATAT
65 GAATGGATAGTTCATAAATATTGTGTATATATAGGGTTGGATAGTGTATACATGTATAT
84638 ACAAAGGTCT
Statistics
Matches: 302, Mismatches: 42, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
236 43 0.14
237 2 0.01
238 18 0.06
240 25 0.08
241 63 0.21
243 117 0.39
245 25 0.08
247 2 0.01
248 1 0.00
250 2 0.01
251 2 0.01
252 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (245 bp):
GAATGGATAGTCATAAATATATGTGTATATATAGGGTTGGATAGTGTACATGTATATGTAGAGGG
AATGGATAGTTCATAAATATTGTGTATATATAGGGTTGGATAGTGTATACATGTATATGAAAAGG
GAATGGATAGGTCAATTAAATACATGTATATATAGGATTGGATAGTTATACATGTATATACAAAG
GCGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
Found at i:84600 original size:113 final size:111
Alignment explanation
Indices: 84404--84627 Score: 430
Period size: 113 Copynumber: 2.0 Consensus size: 111
84394 TATGTAGAGG
84404 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA
1 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA
84469 ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
66 ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG
1 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG
84580 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
64 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
84628 ACATGTATAT
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
111 15 0.14
112 2 0.02
113 94 0.85
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (111 bp):
GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA
ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT
Found at i:84623 original size:63 final size:66
Alignment explanation
Indices: 84515--84637 Score: 216
Period size: 63 Copynumber: 1.9 Consensus size: 66
84505 GATAGTGTAT
84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTG-TACATGTATATGTAGAG
1 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGATACATGTATATGTAGAG
84579 G
66 G
84580 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTATACATGTATAT
1 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTG-ATACATGTATAT
84638 ACAAAGGTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
63 28 0.50
64 2 0.04
65 26 0.46
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (66 bp):
GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGATACATGTATATGTAGAG
G
Found at i:85800 original size:35 final size:35
Alignment explanation
Indices: 85761--85962 Score: 181
Period size: 35 Copynumber: 5.5 Consensus size: 35
85751 TTATGTCAAA
*
85761 GTAAGTGATACAGACCCTGTGTCTGTCATGTCCAT
1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT
* * *
85796 GTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTACCAGGGGG
1 GTAAGTGATGCAGACC--CT-G-TGTC-TG-TCATGT-CCA----T
** * *
85842 GTAAGTGATGCAGACCAAGTGGT-TGCCATGTTCAT
1 GTAAGTGATGCAGACCCTGT-GTCTGTCATGTCCAT
* *
85877 GTAAGTGCTGCAGACCCTGTGTCTGTCATGTCCAA
1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT
* *
85912 GTAAGTGATACAGACCCTGTGTCTGTCATGTTCAT
1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT
85947 GTAAGTGATGCAGACC
1 GTAAGTGATGCAGACC
85963 AAGTGGTTGT
Statistics
Matches: 133, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.02
35 87 0.65
37 1 0.01
38 1 0.01
39 5 0.04
40 7 0.05
41 8 0.06
42 4 0.03
43 2 0.02
46 16 0.12
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (35 bp):
GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT
Found at i:86093 original size:151 final size:149
Alignment explanation
Indices: 85752--86040 Score: 456
Period size: 151 Copynumber: 1.9 Consensus size: 149
85742 CAGTCCTTGT
*
85752 TATGTCAAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG
1 TATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG
* * **
85817 GTTGCCATGTTCATGTACCAGGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTAAG
66 GTTGCCATGTTCATGTACCA-GGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAG
* *
85882 TGCTGCAGACCCTGTGTCTG
130 TGCTACAGACCCTGTGTCTA
*
85902 TCATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTTCATGTAAGTGATGCAGACCAAGT
1 T-ATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGT
* *
85967 GGTTG-TATGTTCATGTACC-GGGGGTAAGTGATGCAGACCAAGTGGTTGTCATCTCCAAATAAG
65 GGTTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAG
86030 TGCTACAGACC
130 TGCTACAGACC
86041 AAGTTGATGT
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
148 49 0.38
150 14 0.11
151 66 0.51
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (149 bp):
TATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG
GTTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGT
GCTACAGACCCTGTGTCTA
Found at i:86110 original size:151 final size:150
Alignment explanation
Indices: 85753--86113 Score: 401
Period size: 151 Copynumber: 2.4 Consensus size: 150
85743 AGTCCTTGTT
* ** **
85753 ATGTCAAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTGG
1 ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG
* * **
85818 TTGCCATGTTCATGTACCAGGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTAAGT
66 TTGCCATGTTCATGTACCA-GGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGT
* *
85883 GCTGCAGACCCTGTGTCTGTC
130 GCTACAGACCCTGTGTCTATC
** * **
85904 ATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTTCATGTAAGTGATGCAGACCAAGTGG
1 ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG
* *
85969 TTG-TATGTTCATGTACC-GGGGGTAAGTGATGCAGACCAAGTGGTTGTCATCTCCAAATAAGTG
66 TTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGTG
*
86032 CTACAGACCAAGTTGATGT-TAAT-
131 CTACAGACC---CTG-TGTCT-ATC
* * * *
86055 ATGTCCAAGTAAGTGTTCCAGACCAAGTG-CTTGTCATGTCCAACAT-TGTGCTGCAGACC
1 ATGTCCAAGTAAGTGATACAGACCAAGTGTC-TGTCATGTCC-ACATAAGTGATGCAGACC
86114 TTGTGTTTTT
Statistics
Matches: 183, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
148 49 0.27
150 14 0.08
151 114 0.62
152 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (150 bp):
ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG
TTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGTG
CTACAGACCCTGTGTCTATC
Found at i:86158 original size:69 final size:69
Alignment explanation
Indices: 86000--86221 Score: 239
Period size: 69 Copynumber: 3.1 Consensus size: 69
85990 GTAAGTGATG
* * *
86000 CAGACCAAGTGGTTGTCATCTCCAAATAAGTGCTACAGACCAAGTTGATGTTAATATGTCCAAGT
1 CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACC---TTG-TGTTATTATGTCCAAGT
*
86065 AAGTGTTC
62 ATGTGTTC
* * *
86073 CAGACCAAGTGCTTGTCATGTCCAACAT-TGTGCTGCAGACCTTGTGTTTTTATGTCCAAGTATG
1 CAGACCAAGTGGTTGTCATGTCCAA-ATATGTGCTACAGACCTTGTGTTATTATGTCCAAGTATG
86137 TGTTC
65 TGTTC
* * * ** * *
86142 CAGACCAAGTGGTTGTCATGCCCAAGTATGTGCTACACACCAAGTGGTTGTCATGTCCAAGTATG
1 CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACCTTGT-GTTATTATGTCCAAGTATG
* *
86207 TGCTG
65 TGTTC
86212 CAGACCAAGT
1 CAGACCAAGT
86222 TGATGTTGTG
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
68 1 0.01
69 58 0.45
70 33 0.26
73 34 0.27
74 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (69 bp):
CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACCTTGTGTTATTATGTCCAAGTATGT
GTTC
Found at i:86235 original size:35 final size:35
Alignment explanation
Indices: 85852--86221 Score: 210
Period size: 35 Copynumber: 10.3 Consensus size: 35
85842 GTAAGTGATG
* * * * *
85852 CAGACCAAGTGGTTGCCATGTTCATGTAAGTGCTG
1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
** * *
85887 CAGACCCTGT-GTCTGTCATGTCCAAGTAAGTGATA
1 CAGACCAAGTGGT-TGTCATGTCCAAGTATGTGCTA
** * * * * *
85922 CAGACCCTGT-GTCTGTCATGTTCATGTAAGTGATG
1 CAGACCAAGTGGT-TGTCATGTCCAAGTATGTGCTA
** * * *
85957 CAGACCAAGTGGTTGTATGTTCATGTACCGGGGGTAAGTGATG
1 CAGACCAAGT-G--GT-TG-TCATGT-CC--AAGTATGTGCTA
* * *
86000 CAGACCAAGTGGTTGTCATCTCCAAATAAGTGCTA
1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
* * * *
86035 CAGACCAAGTTGATGTTAAT-ATGTCCAAGTAAGTGTTC
1 CAGACCAAG-TG--GTT-GTCATGTCCAAGTATGTGCTA
* * *
86073 CAGACCAAGTGCTTGTCATGTCCAA-CATTGTGCTG
1 CAGACCAAGTGGTTGTCATGTCCAAGTA-TGTGCTA
** * * * *
86108 CAGACCTTGT-GTTTTTATGTCCAAGTATGTGTTC
1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
*
86142 CAGACCAAGTGGTTGTCATGCCCAAGTATGTGCTA
1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
* *
86177 CACACCAAGTGGTTGTCATGTCCAAGTATGTGCTG
1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
86212 CAGACCAAGT
1 CAGACCAAGT
86222 TGATGTTGTG
Statistics
Matches: 266, Mismatches: 52, Indels: 34
0.76 0.15 0.10
Matches are distributed among these distances:
34 28 0.11
35 164 0.62
36 2 0.01
37 4 0.02
38 31 0.12
39 7 0.03
40 8 0.03
41 1 0.00
42 1 0.00
43 20 0.08
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (35 bp):
CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA
Found at i:89750 original size:26 final size:26
Alignment explanation
Indices: 89730--89975 Score: 177
Period size: 26 Copynumber: 9.7 Consensus size: 26
89720 CATCCGTTTC
*
89730 GATACATTTTATCATTTATCCTGTTT
1 GATACATTTTATCATTTATCCTGTTG
* * *
89756 GATACATTTTATCATTAATTCTATTG
1 GATACATTTTATCATTTATCCTGTTG
* *
89782 GATACATTTTATTATTCATCCTGTTG
1 GATACATTTTATCATTTATCCTGTTG
**
89808 GATAGTTTTTATCATTTATCCTGTTG
1 GATACATTTTATCATTTATCCTGTTG
** *
89834 GATAC-TTTTGA-CATTTATTAT-TTT
1 GATACATTTT-ATCATTTATCCTGTTG
* *
89858 GATACATTTTATCA---ATCATGTTT
1 GATACATTTTATCATTTATCCTGTTG
* * * *
89881 GTTACATTATATCATTCA-CACGGTTG
1 GATACATTTTATCATTTATC-CTGTTG
* * * *
89907 GATAC-TTTTTTGAATTTATCCTATTA
1 GATACATTTTAT-CATTTATCCTGTTG
* * *
89933 GATACATTTCATGATTTATAAC-GTTG
1 GATACATTTTATCATTTAT-CCTGTTG
89959 GATACATTTTATCATTT
1 GATACATTTTATCATTT
89976 GATTGTATGA
Statistics
Matches: 170, Mismatches: 38, Indels: 24
0.73 0.16 0.10
Matches are distributed among these distances:
22 4 0.02
23 15 0.09
24 8 0.05
25 23 0.14
26 114 0.67
27 6 0.04
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (26 bp):
GATACATTTTATCATTTATCCTGTTG
Found at i:91011 original size:15 final size:15
Alignment explanation
Indices: 91001--91033 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
90991 TATGATATTG
91001 TATCATATGATACAA
1 TATCATATGATACAA
91016 TATCATATGATACAA
1 TATCATATGATACAA
91031 TAT
1 TAT
91034 TGTATCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (15 bp):
TATCATATGATACAA
Found at i:91114 original size:20 final size:20
Alignment explanation
Indices: 91091--91130 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
91081 TTTTCTTTTC
* *
91091 ATATTATACAATATCATATA
1 ATATGATACAATAGCATATA
*
91111 ATATGGTACAATAGCATATA
1 ATATGATACAATAGCATATA
91131 TAATGTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (20 bp):
ATATGATACAATAGCATATA
Found at i:98226 original size:165 final size:164
Alignment explanation
Indices: 97825--98281 Score: 442
Period size: 165 Copynumber: 2.8 Consensus size: 164
97815 GTGAATATGC
* * ** * * *
97825 AAAATAAGCAAAGTTGTCATTTAATAAAAAGCTGACATCCAATTGGTACAAAAAAAATACCCCAA
1 AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTAC-AAAAATATATCCCAA
* * **
97890 CGTATGGCATATCTAAACAAATA--GTGTTAGAATTTCAAGCATCTGCAATGAATTGTTGCTATG
65 CGTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGAACAGTTGCTATG
* * * * *
97953 AAATTTGTGTCGAAAATTTGTTTAAAACTTATGCT
130 AAATCTGCGACGAAAATTTCTTTAAAACTTAAGCT
* * * * * ** *
97988 AGAAATAAACAAAGTTGTCATTTCACAGGAAGTTGACATCTGATAGGTACAGAAATGGATCCCAC
1 A-AAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAA
* * * * **
98053 CATATGGCATGCCTAAACAAACAGTGTGTTAAAACTTCAAGCATCTGTGAT-ACACAGTTGCTGA
65 CGTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGA-ACAGTTGCT-A
*
98117 -GAAATCCT-CGAC-AAAATTTCTTTGAAAATTTAAGCT
128 TGAAAT-CTGCGACGAAAATTTCTTT-AAAACTTAAGCT
* *
98153 GAAAATAAACAAAGTTGTCATTTAACAGGAAGCTGAAATCCGATTGGTACAAAAATATATCCAAA
1 -AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAA
* * * *
98218 TGTATGGCATATGTCTAAACAAATAGTGTGTTAATATTTTAAGCATCTG-AGATGAATAGTTGCT
65 CGTATGGC--ATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCA-ATGAACAGTTGCT
98282 TGGAAAAATG
Statistics
Matches: 232, Mismatches: 50, Indels: 20
0.77 0.17 0.07
Matches are distributed among these distances:
163 29 0.12
164 50 0.22
165 105 0.45
166 3 0.01
167 44 0.19
168 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (164 bp):
AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAAC
GTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGAACAGTTGCTATGA
AATCTGCGACGAAAATTTCTTTAAAACTTAAGCT
Found at i:100988 original size:18 final size:17
Alignment explanation
Indices: 100962--101018 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
100952 CATCAGATCA
100962 TCGTCATCATCATCTTCT
1 TCGTCATCATCATC-TCT
*
100980 TCTTCATCAT-A-CTCT
1 TCGTCATCATCATCTCT
100995 TCGTCATCATCATCCTCT
1 TCGTCATCATCAT-CTCT
101013 TCGTCA
1 TCGTCA
101019 AGAATTGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 1 0.03
18 19 0.56
ACGTcount: A:0.18, C:0.35, G:0.05, T:0.42
Consensus pattern (17 bp):
TCGTCATCATCATCTCT
Found at i:102428 original size:21 final size:21
Alignment explanation
Indices: 102404--102459 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
102394 AATTGAAGTA
102404 ATCAACTGAGGAGCAGAGCTG
1 ATCAACTGAGGAGCAGAGCTG
* ***
102425 ATCAGCTGAGGAATGGAGCTG
1 ATCAACTGAGGAGCAGAGCTG
102446 ATCAACTGAGGAGC
1 ATCAACTGAGGAGC
102460 TGTGTTGACT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16
Consensus pattern (21 bp):
ATCAACTGAGGAGCAGAGCTG
Found at i:105385 original size:66 final size:66
Alignment explanation
Indices: 105279--105416 Score: 197
Period size: 66 Copynumber: 2.1 Consensus size: 66
105269 GGGGAGACTC
* * ** *
105279 ATTTTCTGGAACTGATTGACATTTATCATTGATGTTCCACTTAAT-ATTTTTATCCTTAACAAAA
1 ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGA-TTTTATCCCTAACAAAA
105343 AT
65 AT
*
105345 ATTTTCTGCAACTGATTGACATTTATTATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA
1 ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA
105410 T
66 T
*
105411 GTTTTC
1 ATTTTC
105417 CCTCATCAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (66 bp):
ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA
T
Found at i:116085 original size:2 final size:2
Alignment explanation
Indices: 116078--116130 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
116068 CGTGTTACCG
116078 CT CT CT CT CT CT CT CT CT CT CT C- CAT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT
116120 CT CT CT CT CT C
1 CT CT CT CT CT C
116131 ATTATTTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:116755 original size:2 final size:2
Alignment explanation
Indices: 116748--116797 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
116738 TGTCCATGCA
*
116748 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
116790 CT CT CT CT
1 CT CT CT CT
116798 GGCACAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:117683 original size:125 final size:125
Alignment explanation
Indices: 117458--117685 Score: 402
Period size: 125 Copynumber: 1.8 Consensus size: 125
117448 NNNNNNNNNN
* *
117458 TAACAGTTGAAATTGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGATAATG
1 TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG
117523 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG
66 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG
*
117583 TAACAGTTGAAATCGACACCCCGAGGAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG
1 TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG
** *
117648 GTTTTCTCGGGGTGTCAATTTCAACTGTTATCCTCCCA
66 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCA
117686 AACAGGCACT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 97 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (125 bp):
TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG
GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG
Found at i:125964 original size:12 final size:13
Alignment explanation
Indices: 125941--125972 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
125931 GATCCTGCGC
125941 TACATATGAGTAA
1 TACATATGAGTAA
125954 TACAT-TGAGTAA
1 TACATATGAGTAA
125966 TACATAT
1 TACATAT
125973 CAACAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (13 bp):
TACATATGAGTAA
Found at i:142401 original size:2 final size:2
Alignment explanation
Indices: 142394--142430 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
142384 TGTATTAAAC
142394 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
142431 CAAGCACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:155366 original size:2 final size:2
Alignment explanation
Indices: 155359--155414 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
155349 CGAATTAAAA
155359 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
155401 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
155415 CATTTTTAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:160582 original size:31 final size:31
Alignment explanation
Indices: 160541--160990 Score: 519
Period size: 31 Copynumber: 16.1 Consensus size: 31
160531 CGCGCTAACA
160541 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
160572 CATAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160595 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160626 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160657 CACAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160680 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160711 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160742 CACAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
160765 CACAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160796 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
160827 CATAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
160850 CACAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160881 CACAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160904 CACAACACGCCGTCGCGCTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
160927 CACAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160958 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
160989 CA
1 CA
160991 AGTTTCACAG
Statistics
Matches: 373, Mismatches: 6, Indels: 80
0.81 0.01 0.17
Matches are distributed among these distances:
23 126 0.34
25 5 0.01
26 5 0.01
28 5 0.01
29 5 0.01
31 227 0.61
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14
Consensus pattern (31 bp):
CACAACACGCCGTCGCGCTAACGCAACTTTG
Found at i:160612 original size:54 final size:55
Alignment explanation
Indices: 160530--160979 Score: 418
Period size: 54 Copynumber: 8.2 Consensus size: 55
160520 AAACGAGACA
*
160530 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCG
1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG
160584 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG
1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG
160638 TCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG
1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG
160692 TCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG
1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG
160754 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCG
1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG
*
160808 TCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG
1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG
160862 TCGCGCTAACACAACTTTGCACAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG
1 TCGCGCT-A-ACAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG
160916 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCG
1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG
160970 TCGCGCTAAC
1 TCGCGCTAAC
160980 GCAACTTTGC
Statistics
Matches: 358, Mismatches: 4, Indels: 68
0.83 0.01 0.16
Matches are distributed among these distances:
46 21 0.06
48 1 0.00
49 1 0.00
51 1 0.00
52 2 0.01
53 1 0.00
54 255 0.71
55 1 0.00
56 4 0.01
57 3 0.01
59 3 0.01
60 3 0.01
62 62 0.17
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14
Consensus pattern (55 bp):
TCGCGCTAACAATCACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG
Found at i:160684 original size:85 final size:85
Alignment explanation
Indices: 160541--160990 Score: 808
Period size: 85 Copynumber: 5.4 Consensus size: 85
160531 CGCGCTAACA
*
160541 CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAACACACAACACGCC
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
*
160606 GTCGCGCTAACGCAACTTTG
66 GTCGCGCTAACACAACTTTG
160626 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
*
160691 GTCGCGCTAACGCAACTTTG
66 GTCGCGCTAACACAACTTTG
160711 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
160776 GTCGCGCTAACACAACTTTG
66 GTCGCGCTAACACAACTTTG
*
160796 CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAACACACAACACGCC
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
160861 GTCGCGCTAACACAACTTTG
66 GTCGCGCTAACACAACTTTG
160881 CACAACACGCCGTCGCGCTAA--C-A-----CACAACACGCCGTCGCGCTAACACACAACACGCC
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
160938 GTCGCGCTAACACAACTTTG
66 GTCGCGCTAACACAACTTTG
160958 CACAACACGCCGTCGCGCTAACGCAACTTTGCA
1 CACAACACGCCGTCGCGCTAACGCAACTTTGCA
160991 AGTTTCACAG
Statistics
Matches: 353, Mismatches: 4, Indels: 16
0.95 0.01 0.04
Matches are distributed among these distances:
77 74 0.21
79 1 0.00
80 1 0.00
82 1 0.00
83 1 0.00
85 275 0.78
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14
Consensus pattern (85 bp):
CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC
GTCGCGCTAACACAACTTTG
Found at i:160685 original size:23 final size:23
Alignment explanation
Indices: 160657--160701 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
160647 CGCAACTTTG
160657 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160680 CACAACACGCCGTCGCGCTAAC
1 CACAACACGCCGTCGCGCTAAC
160702 GCAACTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.44, G:0.18, T:0.09
Consensus pattern (23 bp):
CACAACACGCCGTCGCGCTAACA
Found at i:160791 original size:21 final size:23
Alignment explanation
Indices: 160742--160789 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
160732 CGCAACTTTG
160742 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160765 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160788 CA
1 CA
160790 ACTTTGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08
Consensus pattern (23 bp):
CACAACACGCCGTCGCGCTAACA
Found at i:160850 original size:16 final size:16
Alignment explanation
Indices: 160768--160850 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 16
160758 GCTAACACAC
160768 AACACGCCGTCGCGCT
1 AACACGCCGTCGCGCT
** * * *
160784 AACACAACTTTGCAC-
1 AACACGCCGTCGCGCT
160799 AACACGCCGTCGCGCT
1 AACACGCCGTCGCGCT
* ** * * *
160815 AACGCAACTTTGC-AT
1 AACACGCCGTCGCGCT
160830 AACACGCCGTCGCGCT
1 AACACGCCGTCGCGCT
160846 AACAC
1 AACAC
160851 ACAACACGCC
Statistics
Matches: 43, Mismatches: 22, Indels: 4
0.62 0.32 0.06
Matches are distributed among these distances:
15 19 0.44
16 24 0.56
ACGTcount: A:0.28, C:0.39, G:0.18, T:0.16
Consensus pattern (16 bp):
AACACGCCGTCGCGCT
Found at i:160875 original size:21 final size:23
Alignment explanation
Indices: 160830--160951 Score: 102
Period size: 23 Copynumber: 5.0 Consensus size: 23
160820 AACTTTGCAT
160830 AACACGCCGTCGCGCTAACACAC
1 AACACGCCGTCGCGCTAACACAC
160853 AACACGCCGTCGCGCTAACACAAC
1 AACACGCCGTCGCGCTAACAC-AC
** * * **
160877 TTTGCACAACACGCCGTCGCGCTA-ACACAC
1 --AACAC-GC-CGTCG-CGC-TAACACA--C
160907 AACACGCCGTCGCGCTAACACAC
1 AACACGCCGTCGCGCTAACACAC
160930 AACACGCCGTCGCGCTAACACA
1 AACACGCCGTCGCGCTAACACA
160952 ACTTTGCACA
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
23 44 0.57
24 3 0.04
25 6 0.08
26 7 0.09
27 2 0.03
28 8 0.10
29 5 0.06
30 2 0.03
ACGTcount: A:0.30, C:0.42, G:0.17, T:0.11
Consensus pattern (23 bp):
AACACGCCGTCGCGCTAACACAC
Found at i:160922 original size:77 final size:77
Alignment explanation
Indices: 160830--160979 Score: 300
Period size: 77 Copynumber: 1.9 Consensus size: 77
160820 AACTTTGCAT
160830 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC
1 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC
160895 GCGCTAACACAC
66 GCGCTAACACAC
160907 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC
1 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC
160972 GCGCTAAC
66 GCGCTAAC
160980 GCAACTTTGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.29, C:0.41, G:0.17, T:0.12
Consensus pattern (77 bp):
AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC
GCGCTAACACAC
Found at i:160953 original size:21 final size:23
Alignment explanation
Indices: 160881--160951 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
160871 CACAACTTTG
160881 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160904 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160927 CACAACACGCCGTCGCGCTAACA
1 CACAACACGCCGTCGCGCTAACA
160950 CA
1 CA
160952 ACTTTGCACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08
Consensus pattern (23 bp):
CACAACACGCCGTCGCGCTAACA
Found at i:161958 original size:31 final size:31
Alignment explanation
Indices: 161920--162026 Score: 149
Period size: 31 Copynumber: 3.7 Consensus size: 31
161910 GGACACGTGT
161920 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
161951 GTTAGCGCGACGGCGTGTTGT-----G-T--
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
*
161974 GTTAGCGCGACGGCGTGTTATGCAAAGTTGC
1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
162005 GTTAGCGCGACGGCGTGTTGTG
1 GTTAGCGCGACGGCGTGTTGTG
162027 TGTTAGCGCG
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
23 20 0.30
25 1 0.02
26 1 0.02
28 1 0.02
29 1 0.02
31 42 0.64
ACGTcount: A:0.14, C:0.19, G:0.40, T:0.27
Consensus pattern (31 bp):
GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC
Found at i:161992 original size:54 final size:54
Alignment explanation
Indices: 161916--162037 Score: 235
Period size: 54 Copynumber: 2.3 Consensus size: 54
161906 TTCCGGACAC
*
161916 GTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTT
1 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT
161970 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT
1 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT
162024 GTGTGTTAGCGCGA
1 GTGTGTTAGCGCGA
162038 TGTCTCGTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.14, C:0.18, G:0.40, T:0.28
Consensus pattern (54 bp):
GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT
Found at i:173903 original size:102 final size:102
Alignment explanation
Indices: 173797--174020 Score: 396
Period size: 102 Copynumber: 2.2 Consensus size: 102
173787 CAGAAAGGGG
*
173797 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACATTAGACCTCTATCTCCCTCAGA
1 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA
173862 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA
66 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA
** *
173899 AAGAAAAAGAAGAAGAAAGGAGATGAGACTGAAGATGAAGACACTAGACCTTTATCTCCCTCAGA
1 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA
173964 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA
66 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA
*
174001 AAGAAAAAGAAG-GGAAAGGA
1 AAGAAAAAGAAGAAGAAAGGA
174021 TGAAGAGAGG
Statistics
Matches: 117, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 7 0.06
102 110 0.94
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (102 bp):
AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA
GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA
Found at i:174217 original size:27 final size:27
Alignment explanation
Indices: 174157--174226 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
174147 TTCAAAGAAA
* *
174157 AAGAAGAAGAA-AA-AGAAGGAAGGTG
1 AAGAAGAAGAAGAAGAGGAGGAAGATG
*
174182 AAGAAGAAGAAGAGGAGGAGGAAGATG
1 AAGAAGAAGAAGAAGAGGAGGAAGATG
* *
174209 ATGATGAAGAAGAAGAGG
1 AAGAAGAAGAAGAAGAGG
174227 TGTGTTCATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 11 0.30
26 1 0.03
27 25 0.68
ACGTcount: A:0.54, C:0.00, G:0.40, T:0.06
Consensus pattern (27 bp):
AAGAAGAAGAAGAAGAGGAGGAAGATG
Found at i:174935 original size:32 final size:32
Alignment explanation
Indices: 174894--175007 Score: 219
Period size: 32 Copynumber: 3.6 Consensus size: 32
174884 TGTTTTATTG
174894 ATGATACAGTTTACATATGATACAGTGTATAT
1 ATGATACAGTTTACATATGATACAGTGTATAT
174926 ATGATACAGTTTACATATGATACAGTGTATAT
1 ATGATACAGTTTACATATGATACAGTGTATAT
174958 ATGATACAGTTTACATATGATACAGTGTATAT
1 ATGATACAGTTTACATATGATACAGTGTATAT
*
174990 ATGATACAGTTTATATAT
1 ATGATACAGTTTACATAT
175008 ATGATAAGTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 81 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (32 bp):
ATGATACAGTTTACATATGATACAGTGTATAT
Found at i:175019 original size:16 final size:16
Alignment explanation
Indices: 174894--175007 Score: 174
Period size: 16 Copynumber: 7.1 Consensus size: 16
174884 TGTTTTATTG
*
174894 ATGATACAGTTTACAT
1 ATGATACAGTTTATAT
*
174910 ATGATACAGTGTATAT
1 ATGATACAGTTTATAT
*
174926 ATGATACAGTTTACAT
1 ATGATACAGTTTATAT
*
174942 ATGATACAGTGTATAT
1 ATGATACAGTTTATAT
*
174958 ATGATACAGTTTACAT
1 ATGATACAGTTTATAT
*
174974 ATGATACAGTGTATAT
1 ATGATACAGTTTATAT
174990 ATGATACAGTTTATAT
1 ATGATACAGTTTATAT
175006 AT
1 AT
175008 ATGATAAGTT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 87 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (16 bp):
ATGATACAGTTTATAT
Found at i:195409 original size:183 final size:181
Alignment explanation
Indices: 195075--195623 Score: 473
Period size: 178 Copynumber: 2.9 Consensus size: 181
195065 AGCTGTTGAA
* * ** * * * * * **
195075 CTCGCAGAATATTGCATAAAGGGTGCACCTATTGTAGGAGTAACTCCTCCTTCAGTTTTCAAGAT
1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT
* * * * * *
195140 AGGAGAAAGTTGTTGTTTTGAAGATCAACTGTACATACATGTATATTAGAGATATGCATATTTCA
66 A-G-G-AA--TGTTGTTTTGCAGATCAA-AGTATATACA--TATATCAGAGATATGCATATTACT
195205 TGGATTTTGATTTTTGATAATTTATGGGAAAAAATTAATACCAGCTGTTGAACTTT-GT-TATTT
123 TGGATTTTGA-TTTTGATAATTTAT--G-AAAAA-T-ATACCAGCTGTTGAACTTTCGTCT-TTT
195268 T
181 T
* * * *
195269 CTCGCAGATTATTGCATATAGGGCACCCCTATAGTAATAATAACCCCTCCTACAGTTTTCAAGGA
1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAA-GA
* *
195334 TATGAA-GTTGTTTTGCAGATC-AA-T-TATACATATATCAGAGATATGCATATTACTTGGGTTT
65 TAGGAATGTTGTTTTGCAGATCAAAGTATATACATATATCAGAGATATGCATATTACTTGGATTT
* * * *
195395 TAGATTTTGATAATTCATGAAAAATATACCTGTTATTGAA-TTTCGTCTTTTT
130 T-GATTTTGATAATTTATGAAAAATATACCAGCTGTTGAACTTTCGTCTTTTT
* ** * ** * *
195447 CTCGCAGACTATTGTATACAGGGTTCCCCTATTGTGCGGATAACTCCTCCCACAGTTTTCAAGAT
1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT
* * *
195512 AGGAAGTTGTTGTTTTGCATATCAAATGTACATATACATGTATCAGAGATATGCATATGACTTGG
66 AGGAA--TGTTGTTTTGCAGATCAAA-GT--ATATACATATATCAGAGATATGCATATTACTTGG
* * *
195577 ATTTTGATTTTTATGAAATTATGAAAAATATACCAGCTGTTAAACTT
126 ATTTTGATTTTGAT-AATTTATGAAAAATATACCAGCTGTTGAACTT
195624 AGCAATGTTC
Statistics
Matches: 293, Mismatches: 47, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
177 10 0.03
178 68 0.23
179 2 0.01
180 19 0.06
181 3 0.01
183 42 0.14
184 2 0.01
185 13 0.04
186 59 0.20
187 2 0.01
188 1 0.00
189 14 0.05
192 2 0.01
193 1 0.00
194 51 0.17
195 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (181 bp):
CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT
AGGAATGTTGTTTTGCAGATCAAAGTATATACATATATCAGAGATATGCATATTACTTGGATTTT
GATTTTGATAATTTATGAAAAATATACCAGCTGTTGAACTTTCGTCTTTTT
Found at i:196030 original size:1 final size:1
Alignment explanation
Indices: 196024--196058 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
196014 CAAAATACGT
* *
196024 GGGGGGGGGGGGGGGGGGGGTGGGGGCGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
196059 ATGGACACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.94, T:0.03
Consensus pattern (1 bp):
G
Found at i:202897 original size:2 final size:2
Alignment explanation
Indices: 202892--202957 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
202882 TATGTGATAA
202892 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
202934 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
202958 ACACACACAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:202962 original size:2 final size:2
Alignment explanation
Indices: 202957--202984 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
202947 CTCTCTCTCT
202957 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
202985 TCATTTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:205071 original size:21 final size:21
Alignment explanation
Indices: 205047--205094 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
205037 TTGTACTTAT
*
205047 TACTTACTTGTTGATTT-TTAA
1 TACTTACTAGTT-ATTTATTAA
205068 TACTTACTAGTTATTTATTAA
1 TACTTACTAGTTATTTATTAA
*
205089 TTCTTA
1 TACTTA
205095 ATACTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (21 bp):
TACTTACTAGTTATTTATTAA
Found at i:205071 original size:28 final size:28
Alignment explanation
Indices: 205040--205105 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
205030 TTCTTGCTTG
* * * *
205040 TACTTATTACTTACTTGTTGATTTTTAA
1 TACTTACTACTTACTTATTAATTCTTAA
* *
205068 TACTTACTAGTTATTTATTAATTCTTAA
1 TACTTACTACTTACTTATTAATTCTTAA
205096 TACTTACTAC
1 TACTTACTAC
205106 CTATTACTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (28 bp):
TACTTACTACTTACTTATTAATTCTTAA
Found at i:205101 original size:49 final size:49
Alignment explanation
Indices: 205042--205229 Score: 157
Period size: 49 Copynumber: 3.9 Consensus size: 49
205032 CTTGCTTGTA
* *
205042 CTTATTACTTACTTGTTGATT-TTTAATACTTACTAGTTATTTATTAATT
1 CTTAATACTTACTTGTT-ATTACTTAATACTTACTAGTTATTTATTAATT
*** * * * *
205091 CTTAATACTTACTACCTATTACTTAATACTTGCTTGTTAATTGTTAAATT
1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATT-AATT
* * * * * *
205141 -TTATTTCTTAATTGTTATTACTTATTATTTACTGGTTATTTATTAATT
1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATTAATT
* ** * *
205189 CTTAATACTTATTTGTT-TTACTTGTTATTTTCTAGTTATTT
1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTT
205230 CTAATTTCAT
Statistics
Matches: 109, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 28 0.26
49 77 0.71
50 4 0.04
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (49 bp):
CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATTAATT
Found at i:206818 original size:39 final size:41
Alignment explanation
Indices: 206738--206818 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
206728 AAAAAATAAG
* *
206738 TCATTACAATTAAGAAATAAGTCAATATGTCCTTCCAGGGC
1 TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC
*
206779 TCATAACAATTAAGAAGTAAGTC-A-ATGTCCTCCCAGGGC
1 TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC
206818 T
1 T
206819 TCCGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.41
40 1 0.03
41 21 0.57
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (41 bp):
TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC
Found at i:219818 original size:4 final size:4
Alignment explanation
Indices: 219809--219885 Score: 73
Period size: 4 Copynumber: 19.2 Consensus size: 4
219799 TAACAATGAA
* * * * *
219809 AGAG AGAG AGAG AGAG AGAG AGAG AGAG ACAG ACAG ACAG ACAG ACAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * *
219857 ACAG ACAG ACAG AGAG AGAC AGAG AGAG A
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG A
219886 ATGATTGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.51, C:0.12, G:0.38, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:219884 original size:12 final size:12
Alignment explanation
Indices: 219809--219885 Score: 82
Period size: 12 Copynumber: 6.2 Consensus size: 12
219799 TAACAATGAA
*
219809 AGAGAGAGAGAG
1 AGAGACAGAGAG
*
219821 AGAGAGAGAGAG
1 AGAGACAGAGAG
*
219833 AGAGACAGACAG
1 AGAGACAGAGAG
* *
219845 ACAGACAGACAG
1 AGAGACAGAGAG
*
219857 ACAGACAGACAGAG
1 AGAGACAG--AGAG
219871 AGAGACAGAGAG
1 AGAGACAGAGAG
219883 AGA
1 AGA
219886 ATGATTGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
12 48 0.83
14 10 0.17
ACGTcount: A:0.51, C:0.12, G:0.38, T:0.00
Consensus pattern (12 bp):
AGAGACAGAGAG
Found at i:224302 original size:21 final size:21
Alignment explanation
Indices: 224276--224328 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
224266 TCATTAATCT
224276 TTTGGGTCATAAAAATATTTA
1 TTTGGGTCATAAAAATATTTA
224297 TTTGGGTCATAAAAATATTTA
1 TTTGGGTCATAAAAATATTTA
224318 TTTGGGTCATA
1 TTTGGGTCATA
224329 TGAGAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTGGGTCATAAAAATATTTA
Found at i:225445 original size:22 final size:22
Alignment explanation
Indices: 225415--225462 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
225405 TCTTCAGTTA
*
225415 GTCAT-AAATTAATCT-TTTGG
1 GTCATAAAAATAATCTATTTGG
* *
225435 GTCATAAAAATATTTTATTTGG
1 GTCATAAAAATAATCTATTTGG
225457 GTCATA
1 GTCATA
225463 TGAGAATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 11 0.48
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (22 bp):
GTCATAAAAATAATCTATTTGG
Found at i:227305 original size:181 final size:180
Alignment explanation
Indices: 226699--227834 Score: 2058
Period size: 180 Copynumber: 6.3 Consensus size: 180
226689 GGCTGCCAAA
* *
226699 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCC
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
226764 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAA-TTCATGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTC-TGA
226828 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
226879 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCC
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
226944 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
227009 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
**
227059 AGATTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
227124 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTCTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A
227189 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* * *
227240 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCATTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
* *
227305 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
227370 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* *
227420 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
227485 GATCAATTGTACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A
227550 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* *
227601 AGAGTACCCTCATTGTATGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
227666 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
*
227731 AAAAATACCAGCTTTTGAACTTAGTCATATTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
227781 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGAAAGTT
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTT
227835 TGAACTGAAG
Statistics
Matches: 926, Mismatches: 27, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
180 576 0.62
181 350 0.38
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:227372 original size:361 final size:360
Alignment explanation
Indices: 226699--227994 Score: 2135
Period size: 361 Copynumber: 3.5 Consensus size: 360
226689 GGCTGCCAAA
* *
226699 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCC
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
226764 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAA-TTCATGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTC-TGA
226828 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
*
226893 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCCGATCAATTGTACAT
195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
226958 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT
260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT
227023 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
**
227059 AGATTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
227124 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTCTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A
227189 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
* * *
227254 TTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCATTTGCAGATCAATTGTACAT
195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
* *
227319 ATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTATGAAAAAAATACCAGCTT
260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT
227384 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* *
227420 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
*
227485 GATCAATTGTACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A
*
227550 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGAGTACCCTCATT
130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
*
227615 GTATGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT
227680 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT
260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT
*
227745 TTGAACTTAGTCATATTTTGGCAAAATATTGCATAT
325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
227781 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGAAAGTTTGAACTGAAGT
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGT----A----G----GAAG-
*
227846 TTGAATTGAAAAGCTGGAACTTTTGCCGATCAATTGTACATATATCAGAGGTGTGCATATTGCTA
53 TTG---T-------T----CTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTA
* *
227911 GGATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCATTCTTTGGCAA
104 GGATTTTGATTTCTGATAATTTCTGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAA
227976 AATATTGCATATAGGGTAC
169 AATATTGCATATAGGGTAC
227995 ACCATTTCAC
Statistics
Matches: 875, Mismatches: 32, Indels: 31
0.93 0.03 0.03
Matches are distributed among these distances:
360 119 0.14
361 620 0.71
365 1 0.00
369 1 0.00
373 4 0.00
374 3 0.00
377 1 0.00
384 1 0.00
387 57 0.07
388 68 0.08
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (360 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTG
TACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACATA
TATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTTT
TGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:236809 original size:11 final size:11
Alignment explanation
Indices: 236793--236818 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
236783 AAAGATTAAT
236793 GTGATAATTGG
1 GTGATAATTGG
236804 GTGATAATTGG
1 GTGATAATTGG
236815 GTGA
1 GTGA
236819 AATGTCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (11 bp):
GTGATAATTGG
Found at i:243652 original size:13 final size:13
Alignment explanation
Indices: 243634--243659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243624 CTTCTTTGCG
243634 GGAGTAACTGAGC
1 GGAGTAACTGAGC
243647 GGAGTAACTGAGC
1 GGAGTAACTGAGC
243660 ATTTTATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
GGAGTAACTGAGC
Found at i:245392 original size:30 final size:30
Alignment explanation
Indices: 245356--245417 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
245346 AGATTTATAA
245356 ATAAAAAACATGTACACTGTACATGTACCT
1 ATAAAAAACATGTACACTGTACATGTACCT
245386 ATAAAAAACATGTACACTGTACATGTACCT
1 ATAAAAAACATGTACACTGTACATGTACCT
245416 AT
1 AT
245418 CAGCTTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (30 bp):
ATAAAAAACATGTACACTGTACATGTACCT
Found at i:255850 original size:16 final size:16
Alignment explanation
Indices: 255814--255861 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
255804 GATCGGGGTT
* *
255814 TCTCTCTCCTCTCCCCT
1 TCTCTCT-CTCTCTCCA
255831 TCTCTCTCTCTCTCCA
1 TCTCTCTCTCTCTCCA
255847 TCTCTCTCTCTCTCC
1 TCTCTCTCTCTCTCC
255862 TGGGAGGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.02, C:0.54, G:0.00, T:0.44
Consensus pattern (16 bp):
TCTCTCTCTCTCTCCA
Found at i:257929 original size:27 final size:27
Alignment explanation
Indices: 257899--257956 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
257889 CGAAATCCCG
257899 AGCGACCTTTCAAATACAAAGGTGACA
1 AGCGACCTTTCAAATACAAAGGTGACA
257926 AGCGACCTTTCAAATACAAAGGTGACA
1 AGCGACCTTTCAAATACAAAGGTGACA
257953 AGCG
1 AGCG
257957 TCACACGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (27 bp):
AGCGACCTTTCAAATACAAAGGTGACA
Found at i:267478 original size:25 final size:25
Alignment explanation
Indices: 267432--267479 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
267422 TTTGTATAAT
**
267432 ATATATTTAATAATATTTTATTTTA
1 ATATATTTAATAATATAATATTTTA
267457 ATAT-TTTATATAATATAATATTT
1 ATATATTTA-ATAATATAATATTT
267480 ATTGAGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATATTTAATAATATAATATTTTA
Found at i:278343 original size:2 final size:2
Alignment explanation
Indices: 278330--278368 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
278320 AGATAAAAGT
*
278330 TC TC TT TC TC TC TC TC 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 TC TC TC TC T
278369 GTATTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:284363 original size:32 final size:32
Alignment explanation
Indices: 284327--284455 Score: 240
Period size: 32 Copynumber: 4.0 Consensus size: 32
284317 TGCAGGAAAG
*
284327 ATACAAATAATTATAAGTTTGAACAGGTTTGT
1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
284359 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
284391 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
*
284423 ATACAAGTAATTATAAGTTTGTACAGGTTTGT
1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT
284455 A
1 A
284456 CCTGAGAGAC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (32 bp):
ATACAAGTAATTATAAGTTTGAACAGGTTTGT
Found at i:285568 original size:51 final size:51
Alignment explanation
Indices: 285512--285616 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
285502 AGTTCGGAAG
285512 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA
1 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA
285563 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA
1 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA
285614 CAT
1 CAT
285617 TTGAATTCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (51 bp):
CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA
Found at i:300386 original size:2 final size:2
Alignment explanation
Indices: 300379--300425 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
300369 NNNNNNNNNN
300379 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
300421 TA TA T
1 TA TA T
300426 GGTGTTTACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:304610 original size:33 final size:33
Alignment explanation
Indices: 304558--304678 Score: 136
Period size: 33 Copynumber: 3.7 Consensus size: 33
304548 AATGTAAACA
* * *
304558 TTGTAAAACGTACACTCGTAATTTACGTTAACG
1 TTGTAAAACATATATTCGTAATTTACGTTAACG
* ** *
304591 TTGTAAAATATATATTCGTAATAAAGGTTAACG
1 TTGTAAAACATATATTCGTAATTTACGTTAACG
* * *
304624 TTGTAAAACGA-ACAGTCGTAATTTACGTTAAAG
1 TTGTAAAAC-ATATATTCGTAATTTACGTTAACG
304657 TTGTAAAACATATATTCGTAAT
1 TTGTAAAACATATATTCGTAAT
304679 AAACGTCAAA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.01
33 68 0.97
34 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (33 bp):
TTGTAAAACATATATTCGTAATTTACGTTAACG
Found at i:304664 original size:66 final size:66
Alignment explanation
Indices: 304558--304681 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 66
304548 AATGTAAACA
* * *
304558 TTGTAAAACGTACACTCGTAATTTACGTTAACGTTGTAAAATATATATTCGTAATAAAGGTTAAC
1 TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAAGGTTAAC
304623 G
66 G
*
304624 TTGTAAAACGAACAGTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAA
1 TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAA
304682 CGTCAAAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (66 bp):
TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAAGGTTAAC
G
Found at i:305527 original size:14 final size:14
Alignment explanation
Indices: 305508--305534 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
305498 CTACACATAC
305508 AGCTTCCGGTCTGT
1 AGCTTCCGGTCTGT
305522 AGCTTCCGGTCTG
1 AGCTTCCGGTCTG
305535 AAAAAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.30, T:0.33
Consensus pattern (14 bp):
AGCTTCCGGTCTGT
Found at i:309301 original size:11 final size:11
Alignment explanation
Indices: 309280--309309 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
309270 TGCAAAAAAA
309280 AAAACAACAACC
1 AAAA-AACAACC
309292 AAAAAACAACC
1 AAAAAACAACC
309303 AAAAAAC
1 AAAAAAC
309310 CCCCCCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAACC
Found at i:314225 original size:31 final size:32
Alignment explanation
Indices: 314166--314261 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
314156 AAGTAACGTA
314166 CCCTACATGTAGACCTAATGATTACTATAGGT
1 CCCTACATGTAGACCTAATGATTACTATAGGT
* *
314198 CCCTACATGTAGGCCAAATG-TTACTATAGGT
1 CCCTACATGTAGACCTAATGATTACTATAGGT
*
314229 TCCTACATGTAGACCTAATGATTACTATAGGT
1 CCCTACATGTAGACCTAATGATTACTATAGGT
314261 C
1 C
314262 TTACAATTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 28 0.49
32 29 0.51
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (32 bp):
CCCTACATGTAGACCTAATGATTACTATAGGT
Found at i:314369 original size:32 final size:32
Alignment explanation
Indices: 314319--314864 Score: 729
Period size: 32 Copynumber: 16.9 Consensus size: 32
314309 TGAAGAGATT
*
314319 CATGTAGATCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314351 CATGCAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314383 CATGTAGACCTAATGATTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314415 CATGTAGACCTAATGATTACTATAGGT-CTTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
**
314446 CATGTAGACCTAATGATTACTATAGACCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* * **
314478 CATATAGATCTAATGATTACTATAGACCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* * *
314510 CATATAGATCTAATGATTACTATAGGCCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314542 CATGTAGACCTAATGATTACTATAGG-CCCCA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314573 CCATATAGACCTAATGATTACTATAGGTCCCTA
1 -CATGTAGACCTAATGATTACTATAGGTCCCTA
* *
314606 CATGTAGATCTAATGATTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
** ** *
314638 CATGTAGATATAATGATTACTATAGACCCCTG
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* *
314670 CATATAGATCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* *
314702 CATATAGACCTAATGATTACTATAGGCCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
314734 CATGTAGACCTAATGATTACTATANAAGTAACGTACCCTA
1 CATGTAGACCTAATGATTACTAT---AG----GT-CCCTA
314774 CATGTAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* * *
314806 CATGTAGGCCAAATG-TTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
314837 CATGTAGACCTAATGATTACTATAGGTC
1 CATGTAGACCTAATGATTACTATAGGTC
314865 TTACAATTAC
Statistics
Matches: 463, Mismatches: 39, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
31 60 0.13
32 364 0.79
33 6 0.01
35 2 0.00
37 2 0.00
39 1 0.00
40 28 0.06
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (32 bp):
CATGTAGACCTAATGATTACTATAGGTCCCTA
Found at i:314396 original size:64 final size:64
Alignment explanation
Indices: 314319--315303 Score: 1029
Period size: 64 Copynumber: 15.0 Consensus size: 64
314309 TGAAGAGATT
* *
314319 CATGTAGATCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* *
314383 CATGTAGACCTAATGATTACTATAGGTTCCTACATGTAGACCTAATGATTACTATAGGT-CTTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
** * * **
314446 CATGTAGACCTAATGATTACTATAGACCCCTACATATAGATCTAATGATTACTATAGACCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* * * *
314510 CATATAGATCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATAGG-CCCCA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* * *
314573 CCATATAGACCTAATGATTACTATAGGTCCCTACATGTAGATCTAATGATTACTATAGGTTCCTA
1 -CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
** ** * * *
314638 CATGTAGATATAATGATTACTATAGACCCCTGCATATAGATCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* *
314702 CATATAGACCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATANAAGTAACG
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT---AG----G
314767 TACCCTA
59 T-CCCTA
* * *
314774 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGGCCAAATG-TTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* * * *
314837 CATGTAGACCTAATGATTACTATAGGTCTTACAATTACATGTAGACCTACTGATAACTATAGGCC
1 CATGTAGACCTAATGATTACTATAGGTC---C--CTACATGTAGACCTAATGATTACTATAGGTC
*
314902 CCTGT
61 CCT-A
* * * * ** * * * *
314907 GATGTTGA---AGA-GATT-CATGTAGATCTAATGATTACTATAGGTCCCTACATGCA-GACCTA
1 CATGTAGACCTA-ATGATTAC-TATAGGTC-CCT-A-CA-TGTA-G-ACCTA-ATG-ATTA-CTA
* **
314966 -ATGATTACTA
55 TA-GGTCCCTA
* * *
314976 TAGGTCCCTACATGTAGACCTAATGATTACTATAGGTTCCTACATGTAGACCTAATGATTACTAT
1 CA--T--GT------AGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT
*
315041 AGGT-CTTA
56 AGGTCCCTA
** * *
315049 CATGTAGACCTAATGATTACTATAGACCCCTACATATAGACCTAATGATTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
* * *
315113 CATGTAGACCAAATGATTACTATAGGCCCCTACATATAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
315177 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
*
315241 CATGCAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCT
1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCT
315304 GTGATGTTGA
Statistics
Matches: 776, Mismatches: 98, Indels: 94
0.80 0.10 0.10
Matches are distributed among these distances:
63 142 0.18
64 460 0.59
65 4 0.01
66 5 0.01
67 14 0.02
68 21 0.03
69 18 0.02
70 13 0.02
71 11 0.01
72 48 0.06
73 4 0.01
74 6 0.01
75 5 0.01
76 4 0.01
77 1 0.00
78 3 0.00
79 3 0.00
80 1 0.00
81 2 0.00
82 10 0.01
83 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (64 bp):
CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA
Found at i:314587 original size:96 final size:95
Alignment explanation
Indices: 314323--315303 Score: 891
Period size: 96 Copynumber: 9.9 Consensus size: 95
314313 GAGATTCATG
* * * *
314323 TAGATCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTACATGT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT
* *
314388 AGACCTAATGATTACTATAGGTTCCTACATG
65 AGACCTAATGATTACTATAGGTCCCTACATA
* *
314419 TAGACCTAATGATTACTATAGGT-CTTACATGTAGACCTAATGATTACTATAGACCCCTACATAT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT
* **
314483 AGATCTAATGATTACTATAGACCCCTACATA
65 AGACCTAATGATTACTATAGGTCCCTACATA
* *
314514 TAGATCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATAGGCCCCACCATAT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCCA-CATAT
*
314579 AGACCTAATGATTACTATAGGTCCCTACATG
65 AGACCTAATGATTACTATAGGTCCCTACATA
* * ** * *
314610 TAGATCTAATGATTACTATAGGTTCCTACATGTAGATATAATGATTACTATAGACCCCTGCATAT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT
*
314675 AGATCTAATGATTACTATAGGTCCCTACATA
65 AGACCTAATGATTACTATAGGTCCCTACATA
*
314706 TAGACCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATANAAGTAACGTACC
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT---AG----G--CC
* * *
314771 CTACATGTAGACCTAATGATTACTATAGGTCCCTACATG
57 CCACATATAGACCTAATGATTACTATAGGTCCCTACATA
* * * **
314810 TAGGCCAAATG-TTACTATAGGTTCCTACATGTAGACCTAATGATTACTATAGGTCTTACAATTA
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-C---C--CCA
* * * * ** *
314874 CATGTAGACCTACTGATAACTATAGGCCCCTGTGATG
60 CATATAGACCTAATGATTACTATAGGTCCCT-ACATA
* * * ** * * * *
314911 TTGA---AGA-GATT-CATGTAGATCTAATGATTACTATAGGTCCCTACATGCA-GACCTAATGA
1 TAGACCTA-ATGATTAC-TATAGGTC-CCT-A-CA-TGTA-G-ACCTA-ATG-ATTA-CT-AT-A
** *** * * *
314970 TTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTTCCTACATG
53 -GGCCCCA----CATA----TAGACCTAATGATTACTATAGGTCCCTACATA
* *
315022 TAGACCTAATGATTACTATAGGT-CTTACATGTAGACCTAATGATTACTATAGACCCCTACATAT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT
* *
315086 AGACCTAATGATTACTATAGGTTCCTACATG
65 AGACCTAATGATTACTATAGGTCCCTACATA
* * * * *
315117 TAGACCAAATGATTACTATAGGCCCCTACATATAGACCTAATGATTACTATAGGTCCCTACATGT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT
*
315182 AGACCTAATGATTACTATAGGTCCCTACATG
65 AGACCTAATGATTACTATAGGTCCCTACATA
* * *
315213 TAGACCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTACATGT
1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT
315278 AGACCTAATGATTACTATAGGTCCCT
65 AGACCTAATGATTACTATAGGTCCCT
315304 GTGATGTTGA
Statistics
Matches: 736, Mismatches: 98, Indels: 102
0.79 0.10 0.11
Matches are distributed among these distances:
94 3 0.00
95 134 0.18
96 369 0.50
97 3 0.00
98 4 0.01
99 13 0.02
100 33 0.04
101 6 0.01
102 3 0.00
103 42 0.06
104 47 0.06
105 10 0.01
106 8 0.01
107 7 0.01
108 5 0.01
109 5 0.01
110 1 0.00
111 7 0.01
112 24 0.03
113 1 0.00
114 10 0.01
115 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (95 bp):
TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCCACATATA
GACCTAATGATTACTATAGGTCCCTACATA
Found at i:314972 original size:32 final size:32
Alignment explanation
Indices: 314922--315303 Score: 649
Period size: 32 Copynumber: 12.0 Consensus size: 32
314912 TGAAGAGATT
*
314922 CATGTAGATCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314954 CATGCAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
314986 CATGTAGACCTAATGATTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
315018 CATGTAGACCTAATGATTACTATAGGT-CTTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
**
315049 CATGTAGACCTAATGATTACTATAGACCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* *
315081 CATATAGACCTAATGATTACTATAGGTTCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
* *
315113 CATGTAGACCAAATGATTACTATAGGCCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
315145 CATATAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
315177 CATGTAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
315209 CATGTAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
*
315241 CATGCAGACCTAATGATTACTATAGGTCCCTA
1 CATGTAGACCTAATGATTACTATAGGTCCCTA
315273 CATGTAGACCTAATGATTACTATAGGTCCCT
1 CATGTAGACCTAATGATTACTATAGGTCCCT
315304 GTGATGTTGA
Statistics
Matches: 327, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 28 0.09
32 299 0.91
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (32 bp):
CATGTAGACCTAATGATTACTATAGGTCCCTA
Found at i:315076 original size:18 final size:18
Alignment explanation
Indices: 315053--315105 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
315043 GTCTTACATG
315053 TAGACCTAATGATTACTA
1 TAGACCTAATGATTACTA
** *
315071 TAGACC-CCT-A-CA-TA
1 TAGACCTAATGATTACTA
315085 TAGACCTAATGATTACTA
1 TAGACCTAATGATTACTA
315103 TAG
1 TAG
315106 GTTCCTACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 8
0.64 0.15 0.21
Matches are distributed among these distances:
14 8 0.32
15 2 0.08
16 2 0.08
17 2 0.08
18 11 0.44
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (18 bp):
TAGACCTAATGATTACTA
Found at i:327327 original size:2 final size:2
Alignment explanation
Indices: 327320--327351 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
327310 ACCAGGCATA
327320 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
327352 GAGTAATTTC
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):
CT
Found at i:344662 original size:22 final size:22
Alignment explanation
Indices: 344634--344677 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
344624 GAGGTACGAG
344634 AGTGCGA-AGTTGCGACGGCGAA
1 AGTGCGAGAG-TGCGACGGCGAA
344656 AGTGCGAGAGTGCGACGGCGAA
1 AGTGCGAGAGTGCGACGGCGAA
344678 GGAGCAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.27, C:0.18, G:0.43, T:0.11
Consensus pattern (22 bp):
AGTGCGAGAGTGCGACGGCGAA
Found at i:344689 original size:22 final size:22
Alignment explanation
Indices: 344644--344692 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
344634 AGTGCGAAGT
* * *
344644 TGCGACGGCGAAAGTGCGAGAG
1 TGCGACGGCGAAAGAGCAAAAG
*
344666 TGCGACGGCGAAGGAGCAAAAG
1 TGCGACGGCGAAAGAGCAAAAG
344688 TGCGA
1 TGCGA
344693 AGATGCGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.43, T:0.08
Consensus pattern (22 bp):
TGCGACGGCGAAAGAGCAAAAG
Found at i:344738 original size:22 final size:21
Alignment explanation
Indices: 344685--344751 Score: 107
Period size: 21 Copynumber: 3.1 Consensus size: 21
344675 GAAGGAGCAA
*
344685 AAGTGCGAAGATGCGACGGCG
1 AAGTGCGAAGTTGCGACGGCG
*
344706 AAGCGCGAAGTTGCGACGGCG
1 AAGTGCGAAGTTGCGACGGCG
344727 AGAGTGCGAAGTTGCGACGGCG
1 A-AGTGCGAAGTTGCGACGGCG
344749 AAG
1 AAG
344752 AAGCGATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
21 22 0.52
22 20 0.48
ACGTcount: A:0.27, C:0.19, G:0.43, T:0.10
Consensus pattern (21 bp):
AAGTGCGAAGTTGCGACGGCG
Found at i:344757 original size:22 final size:22
Alignment explanation
Indices: 344689--344757 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
344679 GAGCAAAAGT
* *
344689 GCGAAGATGCGACGGCGAAG-C
1 GCGAAGTTGCGACGGCGAAGAA
*
344710 GCGAAGTTGCGACGGCG-AGAGT
1 GCGAAGTTGCGACGGCGAAGA-A
344732 GCGAAGTTGCGACGGCGAAGAA
1 GCGAAGTTGCGACGGCGAAGAA
344754 GCGA
1 GCGA
344758 TACTACTATC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.05
21 16 0.38
22 21 0.50
23 3 0.07
ACGTcount: A:0.28, C:0.20, G:0.43, T:0.09
Consensus pattern (22 bp):
GCGAAGTTGCGACGGCGAAGAA
Found at i:344791 original size:14 final size:14
Alignment explanation
Indices: 344766--344827 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
344756 GATACTACTA
344766 TCGCACTCTCGC-CT
1 TCGCACT-TCGCACT
344780 TCGCAACTTCGCACT
1 TCGC-ACTTCGCACT
344795 CTCGC-CTTCGCATCT
1 -TCGCACTTCGCA-CT
344810 TCGCACTTTCGC-CT
1 TCGCAC-TTCGCACT
344824 TCGC
1 TCGC
344828 CTTTTTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
14 25 0.60
15 8 0.19
16 9 0.21
ACGTcount: A:0.10, C:0.45, G:0.15, T:0.31
Consensus pattern (14 bp):
TCGCACTTCGCACT
Found at i:344794 original size:22 final size:22
Alignment explanation
Indices: 344766--344827 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
344756 GATACTACTA
344766 TCGCACTCTCGCCTTCGCAACT
1 TCGCACTCTCGCCTTCGCAACT
*
344788 TCGCACTCTCGCCTTCGCATCT
1 TCGCACTCTCGCCTTCGCAACT
*
344810 TCGCACTTTCGCCTTCGC
1 TCGCACTCTCGCCTTCGC
344828 CTTTTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.10, C:0.45, G:0.15, T:0.31
Consensus pattern (22 bp):
TCGCACTCTCGCCTTCGCAACT
Found at i:345530 original size:22 final size:22
Alignment explanation
Indices: 345501--345558 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
345491 TGCTATCAAA
345501 AAAG-GCGAAGGCGACAGTGCG
1 AAAGTGCGAAGGCGACAGTGCG
345522 AAAGTGCGAAGGCGACAGTGCG
1 AAAGTGCGAAGGCGACAGTGCG
*
345544 -AAGTTGCGAAAGCGA
1 AAAG-TGCGAAGGCGA
345559 GGGAGCGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 7 0.21
22 27 0.79
ACGTcount: A:0.34, C:0.17, G:0.40, T:0.09
Consensus pattern (22 bp):
AAAGTGCGAAGGCGACAGTGCG
Found at i:345597 original size:14 final size:15
Alignment explanation
Indices: 345575--345714 Score: 68
Period size: 14 Copynumber: 9.5 Consensus size: 15
345565 GATAGTAGTA
*
345575 TCGCTCCTTCGC-CT
1 TCGCACCTTCGCACT
345589 TCGCACCTTCGCACTT
1 TCGCACCTTCGCAC-T
345605 TCG--CCTTCGCATCT
1 TCGCACCTTCGCA-CT
* *
345619 TCGC-GCTTCGC-CG
1 TCGCACCTTCGCACT
* *
345632 TCGTATCTTCGCACTT
1 TCGCACCTTCGCAC-T
* *
345648 TCGCTCCTTCGC-CG
1 TCGCACCTTCGCACT
345662 TCGCA-CTCTCGCACTT
1 TCGCACCT-TCGCAC-T
345678 TCG--CCTTCGCAACT
1 TCGCACCTTCGC-ACT
345692 TCGCA-CTCTCGCATCT
1 TCGCACCT-TCGCA-CT
345708 TCG-ACCT
1 TCGCACCT
345715 AAAGGCGAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
13 6 0.06
14 45 0.46
15 19 0.20
16 27 0.28
ACGTcount: A:0.09, C:0.44, G:0.16, T:0.32
Consensus pattern (15 bp):
TCGCACCTTCGCACT
Found at i:345607 original size:22 final size:22
Alignment explanation
Indices: 345582--345710 Score: 99
Period size: 22 Copynumber: 5.8 Consensus size: 22
345572 GTATCGCTCC
*
345582 TTCGCCTTCGCACCTTCGCACT
1 TTCGCCTTCGCATCTTCGCACT
*
345604 TTCGCCTTCGCATCTTCGCGC-
1 TTCGCCTTCGCATCTTCGCACT
* *
345625 TTCGCCGTCGTATCTTCGCACT
1 TTCGCCTTCGCATCTTCGCACT
*
345647 TTCGCTCCTTCGC--CGTCGCACT
1 TTCG--CCTTCGCATCTTCGCACT
*
345669 CTCGCACTTTCGC--CTTCGCAAC-
1 TTCGC-C-TTCGCATCTTCGC-ACT
345691 TTCGCACTCTCGCATCTTCG
1 TTCGC-CT-TCGCATCTTCG
345711 ACCTAAAGGC
Statistics
Matches: 87, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.01
21 20 0.23
22 54 0.62
23 2 0.02
24 10 0.11
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.33
Consensus pattern (22 bp):
TTCGCCTTCGCATCTTCGCACT
Found at i:345660 original size:30 final size:30
Alignment explanation
Indices: 345624--345704 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
345614 CATCTTCGCG
*
345624 CTTCGCCGTCGTA-TCTTCGCACTTTCGCTC
1 CTTCGCCGTCGCACTC-TCGCACTTTCGCTC
345654 CTTCGCCGTCGCACTCTCGCACTTTCG--C
1 CTTCGCCGTCGCACTCTCGCACTTTCGCTC
*
345682 CTTCGCAACTTCGCACTCTCGCA
1 CTTCGC--CGTCGCACTCTCGCA
345705 TCTTCGACCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 7 0.15
30 37 0.80
31 2 0.04
ACGTcount: A:0.10, C:0.43, G:0.16, T:0.31
Consensus pattern (30 bp):
CTTCGCCGTCGCACTCTCGCACTTTCGCTC
Found at i:351047 original size:2 final size:2
Alignment explanation
Indices: 351034--351068 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
351024 NNNNNNNNNN
*
351034 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
351069 ATAAAATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:370552 original size:12 final size:12
Alignment explanation
Indices: 370535--370560 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
370525 TTTTTTGTAA
370535 AAAAAAAAAAAG
1 AAAAAAAAAAAG
370547 AAAAAAAAAAAG
1 AAAAAAAAAAAG
370559 AA
1 AA
370561 GAAGAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:370553 original size:15 final size:15
Alignment explanation
Indices: 370533--370563 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
370523 TTTTTTTTGT
370533 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
370548 AAAAAAAAAAGAAGA
1 AAAAAAAAAAAAAGA
370563 A
1 A
370564 GAAGTCATTT
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:380468 original size:12 final size:13
Alignment explanation
Indices: 380446--380474 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
380436 CATGGATAAA
380446 ATTATTAATCACT
1 ATTATTAATCACT
380459 ATTA-TAATCACT
1 ATTATTAATCACT
380471 ATTA
1 ATTA
380475 ATGGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATTAATCACT
Found at i:382736 original size:29 final size:31
Alignment explanation
Indices: 382685--382745 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
382675 CATTTATTTT
* *
382685 ATAATCATCTTATTGTATGGTATGAT-ACAA
1 ATAATCATCATATTATATGGTATGATGACAA
* *
382715 ATAAT-ATCATATTATATTGTATTATGACAA
1 ATAATCATCATATTATATGGTATGATGACAA
382745 A
1 A
382746 GCCAAAGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
ATAATCATCATATTATATGGTATGATGACAA
Done.