Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:1938833 original size:10 final size:12
Alignment explanation
Indices: 1938782--1938844 Score: 81
Period size: 12 Copynumber: 5.0 Consensus size: 12
1938772 TTTATATTTT
1938782 TATATATTTAAA
1 TATATATTTAAA
*
1938794 TATTATATTTATA
1 TA-TATATTTAAA
*
1938807 TCTATATTTAAA
1 TATATATTTAAA
1938819 TATATATTTAAA
1 TATATATTTAAA
1938831 TATAAATATTTAAA
1 TAT--ATATTTAAA
1938845 AAATAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
12 25 0.57
13 10 0.23
14 9 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:1938864 original size:21 final size:21
Alignment explanation
Indices: 1938827--1938868 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1938817 AATATATATT
*
1938827 TAAATATAAATATTTAAAAAA
1 TAAATATAAATAATTAAAAAA
1938848 TAAA-ATAATATAATTAAAAAA
1 TAAATATAA-ATAATTAAAAAA
1938869 ATATAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATATAAATAATTAAAAAA
Found at i:1939284 original size:23 final size:24
Alignment explanation
Indices: 1939248--1939293 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1939238 AGCTGTCTAA
1939248 ATATTAAGATTTATATT-TTAAAT
1 ATATTAAGATTTATATTATTAAAT
*
1939271 ATATTAA-ATATTATTTTATTAAA
1 ATATTAAGAT-TTATATTATTAAA
1939294 ATAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATTAAGATTTATATTATTAAAT
Found at i:1939866 original size:2 final size:2
Alignment explanation
Indices: 1939859--1939896 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1939849 TAGGCTTGAA
1939859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1939897 CAAAATCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1941783 original size:3 final size:3
Alignment explanation
Indices: 1941775--1941817 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
1941765 TCAATCTCCT
1941775 ATA ATA ATA ATA ATA ATA AT- ATAA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A
1941818 AGCCCTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1946219 original size:23 final size:22
Alignment explanation
Indices: 1946165--1946217 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 22
1946155 ACTTTTTAAT
1946165 ATTTTTCAACAATATTATAAAAA
1 ATTTTT-AACAATATTATAAAAA
1946188 ATTATTTAACTAATATTTATAAAAA
1 ATT-TTTAAC-AATA-TTATAAAAA
1946213 ATTTT
1 ATTTT
1946218 AAATTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.22
24 9 0.33
25 12 0.44
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTTAACAATATTATAAAAA
Found at i:1946643 original size:26 final size:26
Alignment explanation
Indices: 1946576--1946649 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
1946566 TTAAGTTCAT
*
1946576 TTATTTA-A-TAAAAA-TAAATTTAA
1 TTATTTATATTAAAAATTAAATTTGA
**
1946599 TT-TTTATACTT-AATTTTAAATTTGA
1 TTATTTATA-TTAAAAATTAAATTTGA
1946624 TTATTTATATTAAAAATTAAATTTGA
1 TTATTTATATTAAAAATTAAATTTGA
1946650 ATTTGAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.10
23 3 0.08
24 2 0.05
25 13 0.32
26 18 0.45
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (26 bp):
TTATTTATATTAAAAATTAAATTTGA
Found at i:1949440 original size:15 final size:15
Alignment explanation
Indices: 1949420--1949468 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1949410 TAAAAAGTTA
1949420 AAAAACTCAAACTCG
1 AAAAACTCAAACTCG
* *
1949435 AAAAACCCAAACTTG
1 AAAAACTCAAACTCG
*
1949450 AAATAACTTAAACTC-
1 AAA-AACTCAAACTCG
1949465 AAAA
1 AAAA
1949469 TAGTCTGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 1 0.04
15 19 0.68
16 8 0.29
ACGTcount: A:0.57, C:0.22, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAAACTCAAACTCG
Found at i:1949510 original size:15 final size:16
Alignment explanation
Indices: 1949476--1949521 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1949466 AAATAGTCTG
1949476 AACCCGAAAGAACCTA
1 AACCCGAAAGAACCTA
*
1949492 AACCCGAAA-AACTTA
1 AACCCGAAAGAACCTA
1949507 AACCC-AAGAGAACCT
1 AACCCGAA-AGAACCT
1949522 GAACTTGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.50, C:0.30, G:0.11, T:0.09
Consensus pattern (16 bp):
AACCCGAAAGAACCTA
Found at i:1949733 original size:22 final size:22
Alignment explanation
Indices: 1949708--1949749 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1949698 ATAGTAATTC
1949708 ATCAAAAAGTAAATTATATCTT
1 ATCAAAAAGTAAATTATATCTT
**
1949730 ATCAAAGGGTAAATTATATC
1 ATCAAAAAGTAAATTATATC
1949750 ATGAGCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCAAAAAGTAAATTATATCTT
Found at i:1952520 original size:2 final size:2
Alignment explanation
Indices: 1952509--1952548 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1952499 ACAATGACTT
1952509 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1952549 GCACACACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1952759 original size:4 final size:4
Alignment explanation
Indices: 1952750--1952784 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1952740 ATCACATCTC
1952750 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1952785 TGAAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1953111 original size:20 final size:20
Alignment explanation
Indices: 1953086--1953126 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1953076 AAATTATAGA
1953086 AAGGTTCAGAAATCTTTTTT
1 AAGGTTCAGAAATCTTTTTT
1953106 AAGGTTCAGAAATCTTTTTT
1 AAGGTTCAGAAATCTTTTTT
1953126 A
1 A
1953127 CAATAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (20 bp):
AAGGTTCAGAAATCTTTTTT
Found at i:1955466 original size:15 final size:16
Alignment explanation
Indices: 1955442--1955477 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1955432 TAAAATTTGC
1955442 TTTGTACACAAT-TGA
1 TTTGTACACAATATGA
*
1955457 TTTGTTCACAATATGA
1 TTTGTACACAATATGA
1955473 TTTGT
1 TTTGT
1955478 GAAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (16 bp):
TTTGTACACAATATGA
Found at i:1956020 original size:33 final size:33
Alignment explanation
Indices: 1955983--1956049 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1955973 TTCAACGATC
1955983 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1956016 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1956049 T
1 T
1956050 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1956021 original size:13 final size:13
Alignment explanation
Indices: 1956003--1956027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1955993 CATAAAATGT
1956003 TGTATCGATACAA
1 TGTATCGATACAA
1956016 TGTATCGATACA
1 TGTATCGATACA
1956028 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1956110 original size:13 final size:13
Alignment explanation
Indices: 1956092--1956116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1956082 ATTACTCACA
1956092 TGTATCGATACAT
1 TGTATCGATACAT
1956105 TGTATCGATACA
1 TGTATCGATACA
1956117 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1956181 original size:52 final size:52
Alignment explanation
Indices: 1956125--1956245 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1956115 CACTGATCTT
*
1956125 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1956177 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1956229 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1956246 ATAAAATTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1959393 original size:37 final size:36
Alignment explanation
Indices: 1959323--1959445 Score: 121
Period size: 37 Copynumber: 3.5 Consensus size: 36
1959313 ACGACAATCG
***
1959323 GTAAGAATAGTGATTTTTGTTTCGATTTGTGCCACCA
1 GTAAGAATAGTGATTTTTGTTTCGACCCGTGCCA-CA
*
1959360 GTAAGAATAGTGATTTTTGTTTCGACCCATGCCA-A
1 GTAAGAATAGTGATTTTTGTTTCGACCCGTGCCACA
* *
1959395 G---G-ATAGTGGTTTTTGTTTCGACCCGTGCCACGG
1 GTAAGAATAGTGATTTTTGTTTCGACCCGTGCCAC-A
* *
1959428 GTAAAAATAGTGGTTTTT
1 GTAAGAATAGTGATTTTT
1959446 ATTCCAACCT
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
31 26 0.36
32 1 0.01
33 1 0.01
35 2 0.03
37 42 0.58
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (36 bp):
GTAAGAATAGTGATTTTTGTTTCGACCCGTGCCACA
Found at i:1959401 original size:31 final size:31
Alignment explanation
Indices: 1959366--1959424 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1959356 ACCAGTAAGA
1959366 ATAGTGATTTTTGTTTCGACCCATGCCAAGG
1 ATAGTGATTTTTGTTTCGACCCATGCCAAGG
* *
1959397 ATAGTGGTTTTTGTTTCGACCCGTGCCA
1 ATAGTGATTTTTGTTTCGACCCATGCCA
1959425 CGGGTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (31 bp):
ATAGTGATTTTTGTTTCGACCCATGCCAAGG
Found at i:1960676 original size:16 final size:16
Alignment explanation
Indices: 1960626--1960681 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1960616 AATAGACTCG
**
1960626 AACTCGAATAAGCCCG
1 AACTCGAATAAGCCTA
** *
1960642 AACAGGAATAA-ACTCA
1 AACTCGAATAAGCCT-A
1960658 AACTCGAATAAGCCTA
1 AACTCGAATAAGCCTA
1960674 AACTCGAA
1 AACTCGAA
1960682 AGAACCTGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.90
17 2 0.07
ACGTcount: A:0.46, C:0.25, G:0.14, T:0.14
Consensus pattern (16 bp):
AACTCGAATAAGCCTA
Found at i:1961552 original size:2 final size:2
Alignment explanation
Indices: 1961545--1961574 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1961535 GAGATCAAAG
1961545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1961575 GTAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1964576 original size:76 final size:80
Alignment explanation
Indices: 1964424--1964689 Score: 211
Period size: 80 Copynumber: 3.4 Consensus size: 80
1964414 AACACTAAAA
* *** * *
1964424 ATCTTTGGGGATACTCCAACCCCATCATCTTTGAGAGGATACTCCAACCTCATTTCTACTTTCAA
1 ATCTTTGGGGATACTCCAACCCCAACATCTAAAAGAGGATACTACAACCCCATTTCTACTTTCAA
1964489 AACATCGAATTTTTC
66 AACATCGAATTTTTC
* *
1964504 ATCTTTGGGGA-ACTCCAACCCCAACATC-AAAAG-GGGTACTACAACCCCATTT-T-GTTTCTA
1 ATCTTTGGGGATACTCCAACCCCAACATCTAAAAGAGGATACTACAACCCCATTTCTACTTTC-A
**
1964564 AAACATTTAATTTTTC
65 AAACATCGAATTTTTC
* * ** * * ** * * ** * *
1964580 ATTTTTGTGGATACTATAACCCTACCATCTCCAAGGGGATACTCCAACCTTATTTTTATTTTCAA
1 ATCTTTGGGGATACTCCAACCCCAACATCTAAAAGAGGATACTACAACCCCATTTCTACTTTCAA
* *
1964645 AACA-CTAAATTTTTT
66 AACATC-GAATTTTTC
* * *
1964660 ATCTCTGGGGATACTCCAACTCCACCATCT
1 ATCTTTGGGGATACTCCAACCCCAACATCT
1964690 CTAAGGGATA
Statistics
Matches: 146, Mismatches: 33, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
75 4 0.03
76 25 0.17
77 29 0.20
78 5 0.03
79 31 0.21
80 48 0.33
81 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (80 bp):
ATCTTTGGGGATACTCCAACCCCAACATCTAAAAGAGGATACTACAACCCCATTTCTACTTTCAA
AACATCGAATTTTTC
Found at i:1972576 original size:24 final size:24
Alignment explanation
Indices: 1972549--1972603 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
1972539 TTAATGTTCA
1972549 TTTAATA-AAATAATAATTTTTA-AG
1 TTTAATATAAA-AAT-ATTTTTATAG
*
1972573 TTTAATTATAAAAATATTTTTATAT
1 TTTAA-TATAAAAATATTTTTATAG
1972598 TTTAAT
1 TTTAAT
1972604 TTTTAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAATATAAAAATATTTTTATAG
Found at i:1977734 original size:28 final size:29
Alignment explanation
Indices: 1977702--1977786 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 29
1977692 ATATAATTAT
1977702 ATTTAAAATATTTTATAT-TTATATAAAA
1 ATTTAAAATATTTTATATATTATATAAAA
* * *
1977730 TTTTAATATATTAATAATTAATATTATATAAAA
1 ATTTAAAATATT--TTA-T-ATATTATATAAAA
1977763 ATTTAAAATA-TTTATATATTATAT
1 ATTTAAAATATTTTATATATTATAT
1977787 TATTTTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 19 0.41
29 1 0.02
30 4 0.09
31 1 0.02
32 3 0.07
33 18 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTAAAATATTTTATATATTATATAAAA
Found at i:1977746 original size:19 final size:20
Alignment explanation
Indices: 1977705--1977780 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 20
1977695 TAATTATATT
*
1977705 TAAAATATTTTATATTTATA
1 TAAAATATTTAATATTTATA
1977725 TAAAAT-TTTAATA--TAT-
1 TAAAATATTTAATATTTATA
*
1977741 T--AATAATTAATA-TTATA
1 TAAAATATTTAATATTTATA
1977758 TAAAA-ATTTAAAATATTTATA
1 TAAAATATTT--AATATTTATA
1977779 TA
1 TA
1977781 TTATATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.07
15 6 0.13
16 4 0.09
17 4 0.09
18 3 0.07
19 8 0.18
20 10 0.22
21 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATATTTAATATTTATA
Found at i:1977758 original size:33 final size:33
Alignment explanation
Indices: 1977708--1977789 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
1977698 TTATATTTAA
* * *
1977708 AATATTTTATATTTATATAAAATTTTAATATATT
1 AATATATTATA-TTATATAAAAATTTAAAATATT
1977742 AATA-ATTAATATTATATAAAAATTTAAAATATT
1 AATATATT-ATATTATATAAAAATTTAAAATATT
*
1977775 TATATATTATATTAT
1 AATATATTATATTAT
1977790 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 32 0.76
34 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATATTATATTATATAAAAATTTAAAATATT
Found at i:1977768 original size:18 final size:18
Alignment explanation
Indices: 1977705--1977768 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 18
1977695 TAATTATATT
*
1977705 TAAAATATTTTATATTTATA
1 TAAAA-ATTTAATA-TTATA
*
1977725 TAAAATTTTAATA-TAT-
1 TAAAAATTTAATATTATA
*
1977741 TAATAA-TTAATATTATA
1 TAAAAATTTAATATTATA
1977758 TAAAAATTTAA
1 TAAAAATTTAA
1977769 AATATTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 6 0.17
16 7 0.19
17 8 0.22
18 4 0.11
19 6 0.17
20 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAAATTTAATATTATA
Found at i:1978623 original size:2 final size:2
Alignment explanation
Indices: 1978616--1978719 Score: 75
Period size: 2 Copynumber: 51.5 Consensus size: 2
1978606 AAGAATATAA
* * * *
1978616 AG AG AG AG AG AA AG -G AG TAG AG AG AG AA AG AG AG AA AG AC AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG
** * * *
1978658 AG CC AA AG GG TAG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
1978701 AG AA AG AG AC AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1978720 AATAGCGAAA
Statistics
Matches: 77, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
1 1 0.01
2 73 0.95
3 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.42, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1988579 original size:20 final size:20
Alignment explanation
Indices: 1988504--1988579 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
1988494 TGTATTGATA
*
1988504 CAAAATGTATCGATATATAT
1 CAAAATGTATCGATACATAT
1988524 CAAAATGTATCGATACAATAT
1 CAAAATGTATCGATAC-ATAT
* * * *
1988545 -ACACTGTATTGATACATTT
1 CAAAATGTATCGATACATAT
1988564 CAAAATGTATCGATAC
1 CAAAATGTATCGATAC
1988580 TCTGAGCTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.07
20 39 0.85
21 4 0.09
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (20 bp):
CAAAATGTATCGATACATAT
Found at i:1990637 original size:19 final size:19
Alignment explanation
Indices: 1990613--1990650 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1990603 GCATAACTCA
1990613 TTCTCTAGGTTTTATATGT
1 TTCTCTAGGTTTTATATGT
1990632 TTCTCTAGGTTTTATATGT
1 TTCTCTAGGTTTTATATGT
1990651 CACAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (19 bp):
TTCTCTAGGTTTTATATGT
Found at i:1993754 original size:13 final size:13
Alignment explanation
Indices: 1993732--1993772 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1993722 CTGAAAAACC
*
1993732 AAAAATAGAAAAA
1 AAAAAGAGAAAAA
1993745 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
1993758 AAGAAAGA-AAAAA
1 AA-AAAGAGAAAAA
1993771 AA
1 AA
1993773 TGACTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:1993756 original size:12 final size:12
Alignment explanation
Indices: 1993732--1993772 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1993722 CTGAAAAACC
*
1993732 AAAAATAGA-AA
1 AAAAAAAGAGAA
1993743 AAAAAAAGAGAA
1 AAAAAAAGAGAA
1993755 AAAAAGAA-AGAA
1 AAAAA-AAGAGAA
1993767 AAAAAA
1 AAAAAA
1993773 TGACTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 9 0.33
12 16 0.59
13 2 0.07
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:1994760 original size:58 final size:56
Alignment explanation
Indices: 1994652--1994903 Score: 211
Period size: 58 Copynumber: 4.4 Consensus size: 56
1994642 CTGGGTATCG
* * * * *
1994652 TTTAGGTCATTTTTCATGATCTAAGGACTTTTATTCAA-TTT-TGCACATGTTAAGGTCA
1 TTTAGGTCATTTTCCATGATCT-AGGAATTTGATGCAATTTTATG-A-ATGTT-GGGTCA
* * *
1994710 TTTAGGTCATTCTCCATAATATAGGGAATTTGATGCAATTTTATGAATGTTGGAGTCA
1 TTTAGGTCATTTTCCATGATCTA-GGAATTTGATGCAATTTTATGAATGTTGG-GTCA
* * * * *
1994768 TTTAAGTCGTTTTCGATGATCTATGAACTTGTATGCAATTTTATGAATGTTGGGATCA
1 TTTAGGTCATTTTCCATGATCTAGGAATTTG-ATGCAATTTTATGAATGTTGGG-TCA
* * * **
1994826 TTTAGGTCATTTTCTATGATCTATGGATTTTTATATAATTTTATGAATGTTGGGGTCA
1 TTTAGGTCATTTTCCATGATCTA-GGAATTTGATGCAATTTTATGAATGTT-GGGTCA
* * *
1994884 TTTAAGTTATTTTCTATGAT
1 TTTAGGTCATTTTCCATGAT
1994904 TTAAAGATTT
Statistics
Matches: 159, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
57 9 0.06
58 137 0.86
59 11 0.07
60 2 0.01
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (56 bp):
TTTAGGTCATTTTCCATGATCTAGGAATTTGATGCAATTTTATGAATGTTGGGTCA
Found at i:1994844 original size:31 final size:30
Alignment explanation
Indices: 1994809--1994902 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
1994799 TATGCAATTT
*
1994809 TATGAATGTTGGGATCATTTAGGTCATTTTC
1 TATGAATGTTGGGATCATTTAAGT-ATTTTC
* * *
1994840 TATG-ATCTAT-GGAT-TTTTATA-TAATTT-
1 TATGAATGT-TGGGATCATTTA-AGTATTTTC
*
1994867 TATGAATGTTGGGGTCATTTAAGTTATTTTC
1 TATGAATGTTGGGATCATTTAAG-TATTTTC
1994898 TATGA
1 TATGA
1994903 TTTAAAGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 5 0.11
28 11 0.23
29 9 0.19
30 12 0.26
31 10 0.21
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (30 bp):
TATGAATGTTGGGATCATTTAAGTATTTTC
Found at i:1994913 original size:58 final size:58
Alignment explanation
Indices: 1994745--1994924 Score: 209
Period size: 58 Copynumber: 3.1 Consensus size: 58
1994735 GAATTTGATG
* * * * * * *
1994745 CAATTTTATGAATGTTGGAGTCATTTAAGTCGTTTTCGATGATCT-ATGAACTTGTATG
1 CAATTTTATGAATGTTGGGGTCATTTAAGTCATTTTCTATGATCTAAAG-ATTTTTATA
* * **
1994803 CAATTTTATGAATGTTGGGATCATTTAGGTCATTTTCTATGATCTATGGATTTTTATA
1 CAATTTTATGAATGTTGGGGTCATTTAAGTCATTTTCTATGATCTAAAGATTTTTATA
* * * *
1994861 TAATTTTATGAATGTTGGGGTCATTTAAGTTATTTTCTATGATTTAAAGATTTTTATG
1 CAATTTTATGAATGTTGGGGTCATTTAAGTCATTTTCTATGATCTAAAGATTTTTATA
1994919 CAATTT
1 CAATTT
1994925 CATACATTTT
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 101 0.99
59 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.48
Consensus pattern (58 bp):
CAATTTTATGAATGTTGGGGTCATTTAAGTCATTTTCTATGATCTAAAGATTTTTATA
Found at i:1994945 original size:116 final size:116
Alignment explanation
Indices: 1994652--1994954 Score: 258
Period size: 116 Copynumber: 2.6 Consensus size: 116
1994642 CTGGGTATCG
* * * * *
1994652 TTTAGGTCATTTTTC-ATGATCTAAGGACTTTTATTCAATTT--TGCACATGTTAAGGTCATTTA
1 TTTAAGTCA-TTTTCGATGATCTAAGAACTTGTATGCAATTTCATG-A-ATGTTAAGATCATTTA
* * * * * * * * **
1994714 GGTCATTCTCCATAATATAGGGAATTTGATGCAATTTTATGAATGTTGGAGTCA
63 AGTCATTTTCTATGATCTATGGATTTTTATATAATTTTATGAATGTTGGAGTCA
* * * ** *
1994768 TTTAAGTCGTTTTCGATGATCTATGAACTTGTATGCAATTTTATGAATGTTGGGATCATTTAGGT
1 TTTAAGTCATTTTCGATGATCTAAGAACTTGTATGCAATTTCATGAATGTTAAGATCATTTAAGT
*
1994833 CATTTTCTATGATCTATGGATTTTTATATAATTTTATGAATGTTGGGGTCA
66 CATTTTCTATGATCTATGGATTTTTATATAATTTTATGAATGTTGGAGTCA
* * * * * *
1994884 TTTAAGTTATTTTCTATGATTTAA-AGATTTTTATGCAATTTCAT-ACATTTTAAAGAT-ATTTA
1 TTTAAGTCATTTTCGATGATCTAAGA-ACTTGTATGCAATTTCATGA-ATGTT-AAGATCATTTA
1994946 AGTCATTTT
63 AGTCATTTT
1994955 TCATGACTTA
Statistics
Matches: 150, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
115 7 0.05
116 137 0.91
117 4 0.03
118 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.46
Consensus pattern (116 bp):
TTTAAGTCATTTTCGATGATCTAAGAACTTGTATGCAATTTCATGAATGTTAAGATCATTTAAGT
CATTTTCTATGATCTATGGATTTTTATATAATTTTATGAATGTTGGAGTCA
Found at i:1997443 original size:11 final size:11
Alignment explanation
Indices: 1997427--1997451 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1997417 ATAAAATCAA
1997427 AAACATCAACC
1 AAACATCAACC
1997438 AAACATCAACC
1 AAACATCAACC
1997449 AAA
1 AAA
1997452 TAGATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (11 bp):
AAACATCAACC
Found at i:2002430 original size:15 final size:17
Alignment explanation
Indices: 2002396--2002433 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2002386 AATATGAATG
2002396 TTTAATACGAATATATA
1 TTTAATACGAATATATA
2002413 TTTAATACGAA-A-ATA
1 TTTAATACGAATATATA
2002428 TTTAAT
1 TTTAAT
2002434 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.43
16 1 0.05
17 11 0.52
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAATACGAATATATA
Found at i:2002450 original size:19 final size:19
Alignment explanation
Indices: 2002426--2002462 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2002416 AATACGAAAA
2002426 TATTTAATTT-TTTAAAATT
1 TATTT-ATTTATTTAAAATT
2002445 TATTTATTTATTTAAAAT
1 TATTTATTTATTTAAAAT
2002463 GTCACGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATTTATTTAAAATT
Found at i:2005451 original size:15 final size:15
Alignment explanation
Indices: 2005415--2005464 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2005405 AATAATATAT
*
2005415 TAAAATTTATATAAATA
1 TAAAATATAT-TAAA-A
*
2005432 TAAAATATTTTAAAA
1 TAAAATATATTAAAA
*
2005447 TAAAATATATTAATA
1 TAAAATATATTAAAA
2005462 TAA
1 TAA
2005465 TACAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 17 0.59
16 4 0.14
17 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATATATTAAAA
Found at i:2007317 original size:2 final size:2
Alignment explanation
Indices: 2007310--2007348 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2007300 ATATACTAAG
*
2007310 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2007349 GACTTCTGAT
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2012029 original size:12 final size:12
Alignment explanation
Indices: 2012012--2012057 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
2012002 TAAATATGAT
2012012 ATAAATATATTA
1 ATAAATATATTA
2012024 ATAAATATATTA
1 ATAAATATATTA
* *
2012036 A-AATTATAAT-
1 ATAAATATATTA
2012046 ATAAAT-TATTA
1 ATAAATATATTA
2012057 A
1 A
2012058 AATATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
10 4 0.14
11 11 0.39
12 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAATATATTA
Found at i:2012043 original size:23 final size:22
Alignment explanation
Indices: 2011996--2012060 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
2011986 ATATGTAAAA
2011996 ATAATATAAATATGA-TATAAA-T
1 ATAATATAAATAT-ATTA-AAATT
*
2012018 ATATTAATAAATATATTAAAATT
1 ATAAT-ATAAATATATTAAAATT
2012041 ATAATATAAAT-TATTAAAAT
1 ATAATATAAATATATTAAAAT
2012061 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 9 0.24
22 14 0.37
23 15 0.39
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATATAAATATATTAAAATT
Found at i:2012043 original size:29 final size:29
Alignment explanation
Indices: 2012011--2012086 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
2012001 ATAAATATGA
2012011 TATAAATATATTAATAAATATATTAAAA-T
1 TATAAATATATTAATAAA-ATATTAAAATT
* *
2012040 TATAATATAAATTATTAAAATATTAAAATTTT
1 TATAA-ATATATTAATAAAATATTAAAA--TT
2012072 TATAAATATA-TAATA
1 TATAAATATATTAATA
2012087 TTTTACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 14 0.36
30 15 0.38
31 4 0.10
32 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TATAAATATATTAATAAAATATTAAAATT
Found at i:2012080 original size:18 final size:18
Alignment explanation
Indices: 2012033--2012090 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
2012023 AATAAATATA
*
2012033 TTAAAATTATAATATAAATTA
1 TTAAAA-TAT-ATA-AAATTT
2012054 TTAAAATAT-TAAAATTT
1 TTAAAATATATAAAATTT
*
2012071 TTATAAATATATAATATTT
1 TTA-AAATATATAAAATTT
2012090 T
1 T
2012091 ACAAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 8 0.24
20 3 0.09
21 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAATATATAAAATTT
Found at i:2012091 original size:18 final size:17
Alignment explanation
Indices: 2012044--2012117 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 17
2012034 TAAAATTATA
2012044 ATATAA-ATTATTAAAAT
1 ATATAATATT-TTAAAAT
*
2012061 AT-TAAAATTTTTATAAAT
1 ATATAATA-TTTTA-AAAT
2012079 ATATAATATTTTACAAAT
1 ATATAATATTTTA-AAAT
* *
2012097 AATTATAATATATAAAAAT
1 -A-TATAATATTTTAAAAT
2012116 AT
1 AT
2012118 TCTATATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.06
17 7 0.15
18 18 0.38
19 9 0.19
20 10 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATATTTTAAAAT
Found at i:2016553 original size:5 final size:5
Alignment explanation
Indices: 2016543--2016579 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2016533 TTTAATTAAA
2016543 AATTT AATTT AATTT AATTT AA-TT AATTT AA-TT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATT
2016580 AGATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:2016570 original size:9 final size:9
Alignment explanation
Indices: 2016546--2016579 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
2016536 AATTAAAAAT
2016546 TTAATTTAA
1 TTAATTTAA
2016555 TTTAATTTAA
1 -TTAATTTAA
2016565 TTAATTTAA
1 TTAATTTAA
2016574 TTAATT
1 TTAATT
2016580 AGATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTAATTTAA
Found at i:2016716 original size:14 final size:14
Alignment explanation
Indices: 2016714--2016769 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
2016704 TATTTAATAA
*
2016714 AATATAAATATGTTT
1 AATA-AAATATATTT
*
2016729 AACAAAATATA-TT
1 AATAAAATATATTT
*
2016742 --TAAAATACATTT
1 AATAAAATATATTT
2016754 AATAAAATATATTT
1 AATAAAATATATTT
2016768 AA
1 AA
2016770 AATCAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
11 7 0.21
12 2 0.06
13 2 0.06
14 19 0.58
15 3 0.09
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (14 bp):
AATAAAATATATTT
Found at i:2016722 original size:20 final size:20
Alignment explanation
Indices: 2016699--2016739 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2016689 AAGATATTTA
*
2016699 AAATATATTTAATAAAATAT
1 AAATATATTTAACAAAATAT
*
2016719 AAATATGTTTAACAAAATAT
1 AAATATATTTAACAAAATAT
2016739 A
1 A
2016740 TTTAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATATTTAACAAAATAT
Found at i:2016747 original size:25 final size:24
Alignment explanation
Indices: 2016692--2016772 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 24
2016682 AATATTTAAG
*
2016692 ATATTTAAAATATATTTAATAAA-
1 ATATTTAAAATATATTTAAAAAAT
*
2016715 ATA--T-AAATATGTTTAACAAAAT
1 ATATTTAAAATATATTTAA-AAAAT
*
2016737 ATATTTAAAATACATTTAATAAAAT
1 ATATTTAAAATATATTTAA-AAAAT
2016762 ATATTTAAAAT
1 ATATTTAAAAT
2016773 CAAAAAAACC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.23
21 4 0.08
22 3 0.06
23 3 0.06
24 1 0.02
25 26 0.54
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (24 bp):
ATATTTAAAATATATTTAAAAAAT
Found at i:2016889 original size:16 final size:17
Alignment explanation
Indices: 2016868--2016900 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2016858 TAACATTAAA
*
2016868 TTTAA-TTAAATTAATT
1 TTTAATTTAAATAAATT
2016884 TTTAATTTAAATAAATT
1 TTTAATTTAAATAAATT
2016901 AAACCGATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATAAATT
Found at i:2017057 original size:68 final size:68
Alignment explanation
Indices: 2016968--2017102 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
2016958 AAACTTATTA
** * * *
2016968 TTTTATTTAGACACAATAACAATTAAATATTCAATGCACACAAAATGAGCAACCTAAATTTATTC
1 TTTTATTTAGACACAATAACAAAAAAATATTAAATACACACAAAATGAGCAAACTAAATTTATTC
2017033 AGT
66 AGT
* * * *
2017036 TTTTAATTTGGACAC-ATAACAAAAAAATATTAAATATACATAAAATGAGCAAAGTAAATTTATT
1 TTTT-ATTTAGACACAATAACAAAAAAATATTAAATACACACAAAATGAGCAAACTAAATTTATT
2017100 CAG
65 CAG
2017103 CTTGAAAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 48 0.84
69 9 0.16
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (68 bp):
TTTTATTTAGACACAATAACAAAAAAATATTAAATACACACAAAATGAGCAAACTAAATTTATTC
AGT
Found at i:2017113 original size:23 final size:23
Alignment explanation
Indices: 2017086--2017138 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
2017076 TAAAATGAGC
2017086 AAAGTAAATTTATTCAGCTTGAA
1 AAAGTAAATTTATTCAGCTTGAA
2017109 AAAGTAAATTTATTCAGCTTGAA
1 AAAGTAAATTTATTCAGCTTGAA
2017132 AAAGTAA
1 AAAGTAA
2017139 GACGTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (23 bp):
AAAGTAAATTTATTCAGCTTGAA
Found at i:2017166 original size:16 final size:16
Alignment explanation
Indices: 2017145--2017177 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2017135 GTAAGACGTA
2017145 TAATATATTTTTTAAG
1 TAATATATTTTTTAAG
2017161 TAATATATTTTTTAAG
1 TAATATATTTTTTAAG
2017177 T
1 T
2017178 GAGTTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATATATTTTTTAAG
Found at i:2017280 original size:23 final size:24
Alignment explanation
Indices: 2017240--2017286 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2017230 TTAAAAAATA
* **
2017240 AAAAATTAATAATCAAT-ATTAAT
1 AAAAATAAATAAAAAATAATTAAT
2017263 AAAAATAAATAAAAAATAATTAAT
1 AAAAATAAATAAAAAATAATTAAT
2017287 GTTATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAATAAATAAAAAATAATTAAT
Found at i:2017512 original size:19 final size:19
Alignment explanation
Indices: 2017473--2017514 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2017463 ATTTTTAATT
*
2017473 TTTAATTTTAAATCTATAA
1 TTTAATTTTAAAACTATAA
2017492 TTTAATTTTAAAAC-ATAAA
1 TTTAATTTTAAAACTAT-AA
2017511 TTTA
1 TTTA
2017515 TAAATTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATTTTAAAACTATAA
Found at i:2018246 original size:12 final size:13
Alignment explanation
Indices: 2018229--2018257 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2018219 GTGACAAGTT
2018229 TTTTAAATTTTA-
1 TTTTAAATTTTAG
2018241 TTTTAAATTTTAG
1 TTTTAAATTTTAG
2018254 TTTT
1 TTTT
2018258 TTTAATAAAT
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAG
Found at i:2018536 original size:12 final size:12
Alignment explanation
Indices: 2018514--2018545 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2018504 ATTTAGTTAA
2018514 TATTA-ATTTAT
1 TATTATATTTAT
2018525 TATTATATTTAT
1 TATTATATTTAT
2018537 TATT-TATTT
1 TATTATATTT
2018546 TAAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:2019661 original size:18 final size:19
Alignment explanation
Indices: 2019635--2019680 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
2019625 CATGATCCTC
*
2019635 AAATTTTAAATAA-ATTAA
1 AAATTTTAAATAATATAAA
*
2019653 AAATATTAAATAATATAAA
1 AAATTTTAAATAATATAAA
2019672 AAATTTTAA
1 AAATTTTAA
2019681 TTATTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTTAAATAATATAAA
Found at i:2019676 original size:26 final size:28
Alignment explanation
Indices: 2019641--2019701 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
2019631 CCTCAAATTT
2019641 TAAATAAATTAAAAATATTAAATA-AT-A
1 TAAA-AAATTAAAAATATTAAATATATAA
** *
2019668 TAAAAAATTTTAATTATTAAATATATAA
1 TAAAAAATTAAAAATATTAAATATATAA
2019696 TAAAAA
1 TAAAAA
2019702 TATCTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.55
27 6 0.21
28 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAAATTAAAAATATTAAATATATAA
Found at i:2020810 original size:38 final size:38
Alignment explanation
Indices: 2020768--2020846 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
2020758 CTAAACATCA
*
2020768 AAAACATAAGAAGAAATCAAAAAATTTTAAAAGGATTT
1 AAAACATAAGAAGAAATCAAAAAATTTTAAAAGAATTT
* * *
2020806 AAAACATAAGAAGAAATTAAATAATTTTATAAGAATTT
1 AAAACATAAGAAGAAATCAAAAAATTTTAAAAGAATTT
2020844 AAA
1 AAA
2020847 TTGAGATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.27
Consensus pattern (38 bp):
AAAACATAAGAAGAAATCAAAAAATTTTAAAAGAATTT
Found at i:2021140 original size:13 final size:13
Alignment explanation
Indices: 2021122--2021148 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2021112 ATATCGCTAA
2021122 ATTTTGGGAATTT
1 ATTTTGGGAATTT
2021135 ATTTTGGGAATTT
1 ATTTTGGGAATTT
2021148 A
1 A
2021149 AAAGTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (13 bp):
ATTTTGGGAATTT
Found at i:2021951 original size:11 final size:11
Alignment explanation
Indices: 2021921--2021963 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2021911 TTTTAGTTAG
*
2021921 TATTAATTTAT
1 TATTTATTTAT
2021932 TATTATATTTAT
1 TATT-TATTTAT
2021944 TATTTATTT-T
1 TATTTATTTAT
2021954 ATATTTATTT
1 -TATTTATTT
2021964 TTAAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 1 0.03
11 18 0.62
12 10 0.34
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTATTTAT
Found at i:2021964 original size:11 final size:12
Alignment explanation
Indices: 2021927--2021964 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2021917 TTAGTATTAA
2021927 TTTATTA-TTAT
1 TTTATTATTTAT
2021938 ATTTATTATTTAT
1 -TTTATTATTTAT
2021951 TTTA-TATTTAT
1 TTTATTATTTAT
2021962 TTT
1 TTT
2021965 TAAATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
12 11 0.44
13 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:2022366 original size:29 final size:29
Alignment explanation
Indices: 2022333--2022388 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2022323 GTAACTTTAT
2022333 AATCATTTATATAATTATTATTTTAAATA
1 AATCATTTATATAATTATTATTTTAAATA
* *
2022362 AATCATTTATATATTTTTTATTTTAAA
1 AATCATTTATATAATTATTATTTTAAA
2022389 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
AATCATTTATATAATTATTATTTTAAATA
Found at i:2022388 original size:25 final size:26
Alignment explanation
Indices: 2022328--2022390 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
2022318 TTTAAGTAAC
2022328 TTTATAATCATTTATATAATTATTATT
1 TTTA-AATCATTTATATAATTATTATT
* *
2022355 TTAAATAAATCATTTATATATTTTTTATT
1 TT---TAAATCATTTATATAATTATTATT
*
2022384 TTAAAAT
1 TTTAAAT
2022391 ATGTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.13
27 2 0.07
29 22 0.73
30 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTAAATCATTTATATAATTATTATT
Found at i:2022947 original size:34 final size:32
Alignment explanation
Indices: 2022868--2022947 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 32
2022858 TTAATTATTG
* * *
2022868 AATTTAATATATATTTATTTAAATATTTTAATT
1 AATTAAATA-ATAATTATATAAATATTTTAATT
*
2022901 AATTAACTAATAATTATATAAATATATTT-ATT
1 AATTAAATAATAATTATATAAATAT-TTTAATT
2022933 ATATTAAATGAATAA
1 A-ATTAAAT-AATAA
2022948 ATAATTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 18 0.46
33 16 0.41
34 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (32 bp):
AATTAAATAATAATTATATAAATATTTTAATT
Found at i:2022976 original size:23 final size:21
Alignment explanation
Indices: 2022943--2023008 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
2022933 ATATTAAATG
* *
2022943 AATAAATAATTAAAAAATCTTAA
1 AATAAAAAATTAAAAAA--TAAA
2022966 AATAAAAAATTAATAAAATAAA
1 AATAAAAAATTAA-AAAATAAA
*
2022988 AATAAAGAAATTAAAAGATAA
1 AATAAA-AAATTAAAAAATAA
2023009 GTTAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 15 0.39
23 19 0.50
24 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (21 bp):
AATAAAAAATTAAAAAATAAA
Found at i:2024375 original size:22 final size:22
Alignment explanation
Indices: 2024347--2024393 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2024337 TTAACAATTA
2024347 ATAAAATA-AAATAACTATTATT
1 ATAAAATATAAATAACTA-TATT
*
2024369 ATAAAATATAAATAATTATATT
1 ATAAAATATAAATAACTATATT
2024391 ATA
1 ATA
2024394 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAATATAAATAACTATATT
Found at i:2024407 original size:22 final size:23
Alignment explanation
Indices: 2024349--2024407 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
2024339 AACAATTAAT
*
2024349 AAAATAAAATAACTATTATTATA
1 AAAATAAAATTACTATTATTATA
2024372 AAATATAAATAATTA-TATTA-TATA
1 AAA-AT-AA-AATTACTATTATTATA
2024396 AAAATATAAATT
1 AAAATA-AAATT
2024408 TTTAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 5 0.16
23 6 0.19
24 9 0.29
25 7 0.23
26 4 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATAAAATTACTATTATTATA
Found at i:2024415 original size:24 final size:25
Alignment explanation
Indices: 2024347--2024406 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
2024337 TTAACAATTA
*
2024347 ATAAAATA-AAATAA--CTATTATT
1 ATAAAATATAAATAATTATATTATT
2024369 ATAAAATATAAATAATTATATTA-T
1 ATAAAATATAAATAATTATATTATT
2024393 ATAAAAATATAAAT
1 AT-AAAATATAAAT
2024407 TTTTAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 8 0.24
23 6 0.18
24 3 0.09
25 16 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAAATATAAATAATTATATTATT
Found at i:2024616 original size:24 final size:24
Alignment explanation
Indices: 2024589--2024673 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
2024579 TGAATAACCC
*
2024589 TAAAAAATTTAGATTTTTTGTTTT
1 TAAAAAATTTAGATTTTTTATTTT
*
2024613 TAAAAAAATTATAAATATTATTTTATTTT
1 T-AAAAAATT-T--AGATT-TTTTATTTT
**
2024642 TAAAAAATAAATGA-TTTTTATTTT
1 TAAAAAATTTA-GATTTTTTATTTT
2024666 TAAAAAAT
1 TAAAAAAT
2024674 AAATTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 18 0.36
25 10 0.20
26 2 0.04
28 11 0.22
29 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TAAAAAATTTAGATTTTTTATTTT
Found at i:2025321 original size:24 final size:25
Alignment explanation
Indices: 2025294--2025346 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
2025284 ATATATTTTT
2025294 TAATATTAATTTT-TAATAATTTAA
1 TAATATTAATTTTATAATAATTTAA
* * *
2025318 TAAT-TTTATTTTATTATGATTTAA
1 TAATATTAATTTTATAATAATTTAA
2025342 -AATAT
1 TAATAT
2025347 AAATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATATTAATTTTATAATAATTTAA
Found at i:2025710 original size:21 final size:20
Alignment explanation
Indices: 2025657--2025711 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2025647 TTTTATTTTT
*
2025657 ATATTTAAAATTAAATAAATA
1 ATATTT-AAATCAAATAAATA
**
2025678 ATATTTTTATCAAATAAATA
1 ATATTTAAATCAAATAAATA
*
2025698 GTAATTTAAATCAA
1 AT-ATTTAAATCAA
2025712 TTCCAATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATTTAAATCAAATAAATA
Found at i:2033669 original size:19 final size:19
Alignment explanation
Indices: 2033645--2033702 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
2033635 TAATTCAATC
2033645 ATATAAATTACTTAAAAAT-
1 ATATAAATTA-TTAAAAATA
*
2033664 ATATAATATTATTAACAATA
1 ATATAA-ATTATTAAAAATA
2033684 ATATAAA-T-TTAAAAATA
1 ATATAAATTATTAAAAATA
2033701 AT
1 AT
2033703 CATGCCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 10 0.29
18 1 0.03
19 14 0.40
20 10 0.29
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAAATTATTAAAAATA
Found at i:2033965 original size:2 final size:2
Alignment explanation
Indices: 2033960--2033997 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2033950 GTGTGTGTAC
2033960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2033998 CGATTTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2041128 original size:28 final size:28
Alignment explanation
Indices: 2041057--2041362 Score: 296
Period size: 28 Copynumber: 10.9 Consensus size: 28
2041047 TACGACCTTT
* * * *
2041057 TTTCAAAGCCCACGAGTTAATGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
2041085 TTT-TAAGCTCATAAGTCAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
2041112 TTCCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
2041140 TTTCAAAGCCCACAAGTCAGTGGTAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
2041168 -TTCGAAAGCCCACAAGTCAGTGGCATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCC
* * * *
2041196 TTCCAAAGCTCACAAGTGTTAGTGGCACCC
1 TTTCAAAGCCCACAA--GTCAGTGGCATCC
* * *
2041226 TTTCAAAGCCCATAAGTTAGTGACA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
2041253 TTTTCAAAGCCTATAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
2041282 TTTCAAAGCCCACAAGTCAGTGGCA-CTT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* * *
2041310 TTTCAAAACCCACAAGTCAGCGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
2041338 TTTCAAAACCCACAAGTTAGTGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCA
2041363 ACTTTCTAGT
Statistics
Matches: 230, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
27 24 0.10
28 179 0.78
29 4 0.02
30 23 0.10
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:2041271 original size:86 final size:86
Alignment explanation
Indices: 2041089--2041329 Score: 298
Period size: 86 Copynumber: 2.8 Consensus size: 86
2041079 GCATTCTTTT
* *
2041089 AAGCTCATAAGTCAGTAGCATCCTTCCAAAGCCCACAA--GTCAGTGGCACCCTTTCAAAGCCCA
1 AAGCCCATAAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGTCAGTGGCACCCTTTCAAAGCCCA
2041152 CAAGTCAGTGGTAACCTTCGA
66 CAAGTCAGTGGTAACCTTCGA
* * *
2041173 AAGCCCACAAGTCAGTGGCATCCTTCCAAAGCTCACAAGTGTTAGTGGCACCCTTTCAAAGCCCA
1 AAGCCCATAAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGTCAGTGGCACCCTTTCAAAGCCCA
* *
2041238 TAAGTTAGT-G-ACACCTTTTC-A
66 CAAGTCAGTGGTA-ACC--TTCGA
* * ** *
2041259 AAGCCTATAAGTCAGTGGCATCCTTTCAAAGCCCACAA--GTCAGTGGCACTTTTTCAAAACCCA
1 AAGCCCATAAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGTCAGTGGCACCCTTTCAAAGCCCA
2041322 CAAGTCAG
66 CAAGTCAG
2041330 CGGCATTCTT
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
84 62 0.46
85 4 0.03
86 66 0.49
87 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (86 bp):
AAGCCCATAAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGTCAGTGGCACCCTTTCAAAGCCCA
CAAGTCAGTGGTAACCTTCGA
Found at i:2041324 original size:114 final size:114
Alignment explanation
Indices: 2041110--2041326 Score: 285
Period size: 114 Copynumber: 1.9 Consensus size: 114
2041100 TCAGTAGCAT
* *
2041110 CCTTCCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTAACCTTCGAAA
1 CCTTCCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTCGAAA
* *
2041175 GCCCACAAGTCAGTGGCATCCTTCCAAAGCTCACAAGTGTTAGTGGCAC
66 GCCCACAAGTCAGTGGCATCCTTCCAAAACCCACAAGTGTTAGTGGCAC
* * * * * * *
2041224 CCTTTCAAAGCCCATAAGTTAGTGACACCTTTTCAAAGCCTATAAGTCAGTGGCATCCTTTC-AA
1 CCTTCCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAGTGGCAACC-TTCGAA
* *
2041288 AGCCCACAAGTCAGTGGCA-CTTTTTCAAAACCCACAAGT
65 AGCCCACAAGTCAGTGGCATC-CTTCCAAAACCCACAAGT
2041327 CAGCGGCATT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 1 0.01
114 84 0.95
115 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (114 bp):
CCTTCCAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTCGAAA
GCCCACAAGTCAGTGGCATCCTTCCAAAACCCACAAGTGTTAGTGGCAC
Found at i:2041417 original size:28 final size:28
Alignment explanation
Indices: 2041370--2041559 Score: 163
Period size: 28 Copynumber: 6.8 Consensus size: 28
2041360 GCAACTTTCT
*
2041370 AGTGGCATCCTTCCAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * *
2041398 AGTTGCATCCTTTCAGAGCCTACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * * *
2041426 AGTGGCATCCTTTTAGAGCTCACAAGTT
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * *
2041454 AGTGGTACCCTTTCAAAGCCCACAAAAT-
1 AGTGGCATCCTTTCAAAGCCCAC-AAGTC
* * *
2041482 AGTGGAACCCTTTCAAAGCCCACAAGTT
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * *
2041510 AATGGCA-CCTTTTCAAAACCCACAAATC
1 AGTGGCATCC-TTTCAAAGCCCACAAGTC
2041538 AGTGGAACAT--TTTCAAAGCCCA
1 AGTGG--CATCCTTTCAAAGCCCA
2041560 AACAAGTTGG
Statistics
Matches: 132, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
27 5 0.04
28 122 0.92
29 3 0.02
30 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (28 bp):
AGTGGCATCCTTTCAAAGCCCACAAGTC
Found at i:2041450 original size:98 final size:98
Alignment explanation
Indices: 2041272--2041458 Score: 250
Period size: 98 Copynumber: 1.9 Consensus size: 98
2041262 CCTATAAGTC
* * *
2041272 AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAACCCACAAGTCAGCGGCATT
1 AGTGGCATCCTTCCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTCAGCGGCATC
2041337 CTTTCAAAACCCACAAGTTAGTGGCAACTTTCT
66 CTTTCAAAACCCACAAGTTAGTGGCAACTTTCT
* * * * *
2041370 AGTGGCATCCTTCCAAAGCCCACAAGTCAGTTGCA-TCCTTTCAGAGCCTACAAGTCAGTGGCAT
1 AGTGGCATCCTTCCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAACCCACAAGTCAGCGGCAT
* * * *
2041434 CCTTTTAGAGCTCACAAGTTAGTGG
65 CCTTTCAAAACCCACAAGTTAGTGG
2041459 TACCCTTTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
97 1 0.01
98 75 0.99
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (98 bp):
AGTGGCATCCTTCCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTCAGCGGCATC
CTTTCAAAACCCACAAGTTAGTGGCAACTTTCT
Found at i:2041485 original size:126 final size:126
Alignment explanation
Indices: 2041257--2041486 Score: 291
Period size: 126 Copynumber: 1.8 Consensus size: 126
2041247 GACACCTTTT
* * *
2041257 CAAAGCCTATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAACCCA
1 CAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAACCCA
** **
2041322 CAAGTCAGCGGCATTCTTTCAAAACCCACAAGTTAGTGGCAACTTTCTAGTGGCATCCTTC
66 CAAGTCAGCGGCACCCTTTCAAAACCCACAAAATAGTGGCAACTTTCTAGTGGCATCCTTC
* * * * * *
2041383 CAAAGCCCACAAGTCAGTTGCATCCTTTCAGAGCCTACAAGTCAGTGGCATCCTTTT-AGAGCTC
1 CAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAACCC
* * * *
2041447 ACAAGTTAGTGGTACCCTTTCAAAGCCCACAAAATAGTGG
65 ACAAGTCAGCGGCACCCTTTCAAAACCCACAAAATAGTGG
2041487 AACCCTTTCA
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
126 81 0.94
127 5 0.06
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (126 bp):
CAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAACCCA
CAAGTCAGCGGCACCCTTTCAAAACCCACAAAATAGTGGCAACTTTCTAGTGGCATCCTTC
Found at i:2041495 original size:154 final size:154
Alignment explanation
Indices: 2041215--2041521 Score: 368
Period size: 154 Copynumber: 2.0 Consensus size: 154
2041205 TCACAAGTGT
* * * *
2041215 TAGTGGCACCCTTTCAAAGCCCATAAGTTAGTGACACCTTTTCAAAGCCTATAAGTCAGTGGCAT
1 TAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCTACAAGTCAGTGGCAT
** * * **
2041280 CCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAACCCACAAGTCAGCGGCATTCTTTCAAA
66 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAACCCACAAATCAGCGGAACCCTTTCAAA
*
2041345 ACCCACAAGTTAGTGGCAACTTTC
131 ACCCACAAGTTAATGGCAACTTTC
* *
2041369 TAGTGGCATCCTTCCAAAGCCCACAAGTCAGTTG-CATCC-TTTCAGAGCCTACAAGTCAGTGGC
1 TAGTGGCACCCTTCCAAAGCCCACAAGTCAG-TGACA-CCTTTTCAAAGCCTACAAGTCAGTGGC
* * * * * * *
2041432 ATCCTTTTAGAGCTCACAAGTTAGTGGTACCCTTTCAAAGCCCACAAAAT-AGTGGAACCCTTTC
64 ATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAACCCAC-AAATCAGCGGAACCCTTTC
* *
2041496 AAAGCCCACAAGTTAATGGCACCTTT
128 AAAACCCACAAGTTAATGGCAACTTT
2041522 TCAAAACCCA
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
154 121 0.95
155 7 0.05
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (154 bp):
TAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCTACAAGTCAGTGGCAT
CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAACCCACAAATCAGCGGAACCCTTTCAAA
ACCCACAAGTTAATGGCAACTTTC
Found at i:2041534 original size:84 final size:84
Alignment explanation
Indices: 2041406--2041559 Score: 184
Period size: 84 Copynumber: 1.8 Consensus size: 84
2041396 TCAGTTGCAT
* * * * * * * * * *
2041406 CCTTTCAGAGCCTACAAGTCAGTGGCATCCTTTTAGAGCTCACAAGTTAGTGGTACCCTTTCAAA
1 CCTTTCAAAGCCCACAAGTCAATGGCATCCTTTTAAAACCCACAAATCAGTGGAACACTTTCAAA
2041471 GCCCACAAAATAGTGGAAC
66 GCCCACAAAATAGTGGAAC
* *
2041490 CCTTTCAAAGCCCACAAGTTAATGGCA-CCTTTTCAAAACCCACAAATCAGTGGAACATTTTCAA
1 CCTTTCAAAGCCCACAAGTCAATGGCATCCTTTT-AAAACCCACAAATCAGTGGAACACTTTCAA
2041554 AGCCCA
65 AGCCCA
2041560 AACAAGTTGG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
83 6 0.11
84 51 0.89
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (84 bp):
CCTTTCAAAGCCCACAAGTCAATGGCATCCTTTTAAAACCCACAAATCAGTGGAACACTTTCAAA
GCCCACAAAATAGTGGAAC
Found at i:2041543 original size:56 final size:56
Alignment explanation
Indices: 2041378--2041577 Score: 188
Period size: 56 Copynumber: 3.5 Consensus size: 56
2041368 CTAGTGGCAT
* * * * * * * *
2041378 CCTTCCAAAGCCCACAAGTCAGTTGCATCC-TTTCAGAGCCTACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCCCACAAATCAGTGGAAC
* * * * *
2041434 CCTTTTAGAGCTCACAAGTTAGTGGTACCCTTTCAAAGCCCACAAAAT-AGTGGAAC
1 CCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCAC-AAATCAGTGGAAC
* *
2041490 CCTTTCAAAGCCCACAAGTTAATGGCACCTTTTCAAAACCCACAAATCAGTGGAAC
1 CCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGAAC
** *
2041546 ATTTTCAAAGCCCAAACAAGTTGGTGGCACCT
1 CCTTTCAAAGCCC--ACAAGTTAGTGGCACCT
2041578 ATATCCGAGT
Statistics
Matches: 116, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
55 6 0.05
56 92 0.79
57 3 0.03
58 15 0.13
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (56 bp):
CCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGAAC
Found at i:2042535 original size:165 final size:167
Alignment explanation
Indices: 2042171--2042591 Score: 600
Period size: 165 Copynumber: 2.5 Consensus size: 167
2042161 TTCAAACATC
* * * *
2042171 AAAATTCATCAAATATTATCATTTATTTCATATTAATTCATTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAACATCATAATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCA
* *
2042236 TGAGTTTTTGATTTTTTCCTTGAAATTCTCTTTTTTTCTAAAATAGAGTGTTTTCTACTCCGTAA
66 TGAGTTTTTGATTTTTTCCTTGAAATTCTCTTTTTTTCGAAAATAGAGTGTTTTCTACACCGTAA
2042301 ATTTTTTTGAGACGATTTTTCTTAGTTTTCAATATTT
131 ATTTTTTTGAGACGATTTTTCTTAGTTTTCAATATTT
* *
2042338 AAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAACATCATAATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCA
* * *
2042403 TGAGTTTTTTATTTTTTTCTTGAAA-TCTTTTTTTTTCG-AAATA-AGGTGTTTTCTACACCGTA
66 TGAGTTTTTGATTTTTTCCTTGAAATTCTCTTTTTTTCGAAAATAGA-GTGTTTTCTACACCGTA
* * * *
2042465 AATTTTTTTGAGAGGATTTTTCTTGGTTTTTAATTTTT
130 AATTTTTTTGAGACGATTTTTCTTAGTTTTCAATATTT
* * * *
2042503 AAAATTCATTAAACATCATAATTTGA-TTCATATTAATTCAATTTTAAAAAATTAATTTATTTTC
1 AAAATTCATCAAACATCATAATTT-ATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTC
* *
2042567 ATGAG-TTTTGAATTTTTCTTTGAAA
65 ATGAGTTTTTGATTTTTTCCTTGAAA
2042592 ATATTTTTCC
Statistics
Matches: 229, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
164 17 0.07
165 116 0.51
166 12 0.05
167 84 0.37
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (167 bp):
AAAATTCATCAAACATCATAATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTTCA
TGAGTTTTTGATTTTTTCCTTGAAATTCTCTTTTTTTCGAAAATAGAGTGTTTTCTACACCGTAA
ATTTTTTTGAGACGATTTTTCTTAGTTTTCAATATTT
Found at i:2042727 original size:19 final size:20
Alignment explanation
Indices: 2042703--2042741 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2042693 CATTAATTCA
2042703 ATTTTAAAAATTTT-AATTT
1 ATTTTAAAAATTTTGAATTT
**
2042722 ATTTTATTAATTTTGAATTT
1 ATTTTAAAAATTTTGAATTT
2042742 TTTGTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTAAAAATTTTGAATTT
Found at i:2046392 original size:52 final size:52
Alignment explanation
Indices: 2046336--2046815 Score: 412
Period size: 52 Copynumber: 9.2 Consensus size: 52
2046326 TATGACATCG
* * * * *
2046336 GACTTAATGATGATAAAAGTGCTAATGTGCTGATTCAAAGCTAGCAACATTA
1 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTA
* * * * *
2046388 GACTTAAAGATGATAAGAGATGCCAATATGTTGATTTAAGGCCAACAGCATTA
1 GACTTAAAGATGATAAAAG-TGCCAATATGCTGATTCAAGGCCAGCAACATTA
* * * * * * *
2046441 GACTTAAAGATGACAAGAGTGTCAATGTGCTGATTTAAGGCCAGCGACATTG
1 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTA
* * ** * * * *
2046493 GACTTAAAAATGGTAAAAGGTGCCAATATATTGA-TCAAGGCTAACGATATTA
1 GACTTAAAGATGATAAAA-GTGCCAATATGCTGATTCAAGGCCAGCAACATTA
* * * * * *
2046545 GACTTAAAGATGCTAAATGTGCCAATATACTGGTTCAATGCCAGCAATATT-
1 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTA
* * * * * * *
2046596 GACTTAAAGATGACAAAAGTGCCAATGTGCTGAATCAATGCCAACAATATTTG
1 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACA-TTA
* * * *
2046649 GATTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTA
1 GACTTAAAGATGATAAAA-GTGCCAATATGCTGATTCAAGGCCAGCAACATTA
2046702 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAA-G-CA-CAACGATATCA
1 GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAAC-AT-T-A
* * * * * *
2046754 GATTTAAAGATGATAAAAGTTACTAATGTGCTGATTTAAGGCCAGCGACATTA
1 GACTTAAAGATGATAAAAG-TGCCAATATGCTGATTCAAGGCCAGCAACATTA
*
2046807 GGCTTAAAG
1 GACTTAAAG
2046816 GAAATGCCAC
Statistics
Matches: 346, Mismatches: 69, Indels: 25
0.79 0.16 0.06
Matches are distributed among these distances:
49 2 0.01
50 4 0.01
51 56 0.16
52 138 0.40
53 112 0.32
54 27 0.08
55 4 0.01
56 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (52 bp):
GACTTAAAGATGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCAACATTA
Found at i:2046517 original size:105 final size:104
Alignment explanation
Indices: 2046336--2046815 Score: 463
Period size: 105 Copynumber: 4.6 Consensus size: 104
2046326 TATGACATCG
* * * *
2046336 GACTTAATGATGATAAAAGTG-CTAATGTGCTGATTCAAAGCTAGCAACATTAGACTTAAAGATG
1 GACTTAAAGATGATAAAAGTGTCTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
* * * *
2046400 ATAAGAGATGCCAATATGTTGATTTAAGGCCAACAGCATTA
66 ATAAAAG-TGCCAATATGCTGATTCAAGGCCAAC-GTATTA
* * * * *
2046441 GACTTAAAGATGACAAGAGTGTC-AATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAAATG
1 GACTTAAAGATGATAAAAGTGTCTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
* ** *
2046505 GTAAAAGGTGCCAATATATTGA-TCAAGGCTAACGATATTA
66 ATAAAA-GTGCCAATATGCTGATTCAAGGCCAACG-TATTA
* * * * * * * * *
2046545 GACTTAAAGATGCTAAATGTG-CCAATATACTGGTTCAATGCCAGCAATATT-GACTTAAAGATG
1 GACTTAAAGATGATAAAAGTGTCTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
* * * * * *
2046608 ACAAAAGTGCCAATGTGCTGAATCAATGCCAACAATATTTG
66 ATAAAAGTGCCAATATGCTGATTCAAGGCCAAC-GTA-TTA
* * *
2046649 GATTTAAAGATGATAAAAG-GTGCTAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGAT
1 GACTTAAAGATGATAAAAGTGT-CTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGAT
*
2046713 GATAAAAGTGCCAATATGCTGATTCAA-GCACAACGATATCA
65 GATAAAAGTGCCAATATGCTGATTCAAGGC-CAACG-TATTA
* * *
2046754 GATTTAAAGATGATAAAAGT-TACTAATGTGCTGATTTAAGGCCAGCGACATTAGGCTTAAAG
1 GACTTAAAGATGATAAAAGTGT-CTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAG
2046816 GAAATGCCAC
Statistics
Matches: 307, Mismatches: 55, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
102 12 0.04
103 29 0.09
104 69 0.22
105 154 0.50
106 43 0.14
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (104 bp):
GACTTAAAGATGATAAAAGTGTCTAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
ATAAAAGTGCCAATATGCTGATTCAAGGCCAACGTATTA
Found at i:2046684 original size:209 final size:209
Alignment explanation
Indices: 2046336--2046815 Score: 493
Period size: 209 Copynumber: 2.3 Consensus size: 209
2046326 TATGACATCG
* * * * *
2046336 GACTTAATGATGATAAAAGTGCTAATGTGCTGATTCAAAGCTAGCAACATTAGACTTAAAGATGA
1 GACTTAAAGATGATAAAAGTGCCAATATACTGATTCAAAGCCAGCAACATTAGACTTAAAGATGA
* * * * * * *
2046401 TAAGAGATGCCAATATGTTGATTTAAGGCCAACAGCATTAGACTTAAAGATGACAAGAGTGTCAA
66 CAAAAGATGCCAATATGCTGAATCAAGGCCAACAACATTAGACTTAAAGATGACAAAAGTGTCAA
* * * * *
2046466 TGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAAATGGTAAAAGGTGCCAATATATTGA-TCA
131 TATGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGATAAAA-GTGCCAATATACTGATTCA
* *
2046530 AGGC-TAACGATATTA
195 A-GCACAACGATATCA
* * * * *
2046545 GACTTAAAGATGCTAAATGTGCCAATATACTGGTTCAATGCCAGCAATATT-GACTTAAAGATGA
1 GACTTAAAGATGATAAAAGTGCCAATATACTGATTCAAAGCCAGCAACATTAGACTTAAAGATGA
* * * * * *
2046609 CAAAAG-TGCCAATGTGCTGAATCAATGCCAACAATATTTGGATTTAAAGATGATAAAAG-GTGC
66 CAAAAGATGCCAATATGCTGAATCAAGGCCAACAACA-TTAGACTTAAAGATGACAAAAGTGT-C
* * *
2046672 TAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGATGATAAAAGTGCCAATATGCTGATT
129 -AATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGATAAAAGTGCCAATATACTGATT
2046737 CAAGCACAACGATATCA
193 CAAGCACAACGATATCA
* * * * * * * * *
2046754 GATTTAAAGATGATAAAAGTTACTAATGTGCTGATTTAAGGCCAGCGACATTAGGCTTAAAG
1 GACTTAAAGATGATAAAAG-TGCCAATATACTGATTCAAAGCCAGCAACATTAGACTTAAAG
2046816 GAAATGCCAC
Statistics
Matches: 218, Mismatches: 46, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
207 25 0.11
208 51 0.23
209 111 0.51
210 23 0.11
211 8 0.04
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (209 bp):
GACTTAAAGATGATAAAAGTGCCAATATACTGATTCAAAGCCAGCAACATTAGACTTAAAGATGA
CAAAAGATGCCAATATGCTGAATCAAGGCCAACAACATTAGACTTAAAGATGACAAAAGTGTCAA
TATGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGATAAAAGTGCCAATATACTGATTCAA
GCACAACGATATCA
Found at i:2046704 original size:157 final size:156
Alignment explanation
Indices: 2046330--2046815 Score: 487
Period size: 157 Copynumber: 3.1 Consensus size: 156
2046320 AAGGCTTATG
* * * * * *
2046330 ACATCGGACTTAATGATGATAAAA-GTGCTAATGTGCTGATTCAAAGCTAGCAACATTAGACTTA
1 ACATTGGACTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCTAGCGATATTAGACTTA
* * * *
2046394 AAGATGATAAGAGATGCCAATATGTTGATTTAAGGCCAACAGCATTAGACTTAAAGATGACAAGA
66 AAGATGATAA-AG-TGCCAATATGCTGATTCAAGGCCAACAACATTAGACTTAAAGATGACAAAA
* * * * *
2046459 GTGTCAATGTGCTGATTTAAGGCCAGCG
129 GTGCCAATGTGCTGAATCAAGGCCAACA
* * * ** *
2046487 ACATTGGACTTAAAAATGGTAAAAGGTGCCAATATATTGA-TCAAGGCTAACGATATTAGACTTA
1 ACATTGGACTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCTAGCGATATTAGACTTA
* * * * * *
2046551 AAGATGCTAAATGTGCCAATATACTGGTTCAATGCCAGCAATATT-GACTTAAAGATGACAAAAG
66 AAGATGATAAA-GTGCCAATATGCTGATTCAAGGCCAACAACATTAGACTTAAAGATGACAAAAG
*
2046615 TGCCAATGTGCTGAATCAATGCCAACA
130 TGCCAATGTGCTGAATCAAGGCCAACA
* * *
2046642 ATATTTGGATTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTAGACTT
1 ACA-TTGGACTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCTAGCGATATTAGACTT
* * * * *
2046707 AAAGATGATAAAAGTGCCAATATGCTGATTCAA-GCACAACGATATCAGATTTAAAGATGATAAA
65 AAAGATGAT-AAAGTGCCAATATGCTGATTCAAGGC-CAACAACATTAGACTTAAAGATGACAAA
* * * * * *
2046771 AGTTACTAATGTGCTGATTTAAGGCCAGCG
128 AG-TGCCAATGTGCTGAATCAAGGCCAACA
2046801 ACATTAGG-CTTAAAG
1 ACATT-GGACTTAAAG
2046816 GAAATGCCAC
Statistics
Matches: 266, Mismatches: 54, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
155 41 0.15
156 58 0.22
157 104 0.39
158 39 0.15
159 24 0.09
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (156 bp):
ACATTGGACTTAAAGATGATAAAAGGTGCTAATATGCTGATTCAAGGCTAGCGATATTAGACTTA
AAGATGATAAAGTGCCAATATGCTGATTCAAGGCCAACAACATTAGACTTAAAGATGACAAAAGT
GCCAATGTGCTGAATCAAGGCCAACA
Found at i:2046914 original size:33 final size:33
Alignment explanation
Indices: 2046876--2046956 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
2046866 CTTTTGGAAA
* **
2046876 GGTTGCAACCAACTTGTATAGGTTTTTTAAAAG
1 GGTTGCAACCAACTTGTATAGGCTTTGAAAAAG
* *
2046909 GGTTGCTACCAACTTGTGTAGGCTTTGAAAAAG
1 GGTTGCAACCAACTTGTATAGGCTTTGAAAAAG
* *
2046942 GGTTACCACCAACTT
1 GGTTGCAACCAACTT
2046957 ATGTGGGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (33 bp):
GGTTGCAACCAACTTGTATAGGCTTTGAAAAAG
Found at i:2046966 original size:33 final size:33
Alignment explanation
Indices: 2046904--2046967 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2046894 TAGGTTTTTT
* * *
2046904 AAAAGGGTTGCTACCAACTTGTGTAGGCTTTGA
1 AAAAGGGTTACCACCAACTTATGTAGGCTTTGA
*
2046937 AAAAGGGTTACCACCAACTTATGTGGGCTTT
1 AAAAGGGTTACCACCAACTTATGTAGGCTTT
2046968 AAAGGGAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (33 bp):
AAAAGGGTTACCACCAACTTATGTAGGCTTTGA
Found at i:2047166 original size:29 final size:28
Alignment explanation
Indices: 2047011--2047493 Score: 296
Period size: 29 Copynumber: 16.8 Consensus size: 28
2047001 AGGTATCATA
* * *
2047011 GAGTTGTAAACTTTAAAAAGGTGCCACA
1 GAGTTGTAGACTTTAAAAGGGTGCCACG
* * * *
2047039 GAGTTATGGA-TTTGAAAAGGGTGTCACA
1 GAGTTGTAGACTTT-AAAAGGGTGCCACG
* * * *
2047067 AAATTGT-GAACTTTGAAATGGTGCCACG
1 GAGTTGTAG-ACTTTAAAAGGGTGCCACG
* * * * * *
2047095 AAGCTGTGGACTTTAGAATAGGGGTACTATG
1 GAGTTGTAGACTTTA-AA-A-GGGTGCCACG
* * *
2047126 GAGTTGTGGACTTTAGAAGGAGTACCACG
1 GAGTTGTAGACTTTAAAAGG-GTGCCACG
* *
2047155 GAGTTATAGACTTTACAAA-GGTGCCACA
1 GAGTTGTAGACTTTA-AAAGGGTGCCACG
*
2047183 GAGTTGT-GTACTTTAAAAGGGATGCCACA
1 GAGTTGTAG-ACTTTAAAAGGG-TGCCACG
*
2047212 TAGTTGTAGACTTTAAAAAGGGTGCCACG
1 GAGTTGTAGACTTT-AAAAGGGTGCCACG
* * **
2047241 GAGTTGTGGATTTTGGAAGAGGTGCCACG
1 GAGTTGTAGACTTTAAAAG-GGTGCCACG
* *
2047270 GAGTTATAGACTTTAAAAGTGGTGTCACG
1 GAGTTGTAGACTTTAAAAG-GGTGCCACG
* * *
2047299 GAGTTGTGGACTTTAAAAAGGATGCCATG
1 GAGTTGTAGACTTT-AAAAGGGTGCCACG
*
2047328 GAGTTAT-GAACTTTAAAAGGGTGCCACG
1 GAGTTGTAG-ACTTTAAAAGGGTGCCACG
* *
2047356 GAGTTGT-GAATTTTAAAAGGGGTGCCACA
1 GAGTTGTAG-ACTTTAAAA-GGGTGCCACG
* * * * *
2047385 GAGTTCTGGGCTTTAAAAAGTGATGCCACT
1 GAGTTGTAGACTTT-AAAAG-GGTGCCACG
* * *
2047415 GAGTTGTGGACTTGGAAGAAGGGTGCCACA
1 GAGTTGTAGACTT-TAA-AAGGGTGCCACG
* ** *
2047445 GAGTTGTAAACTTTAAAAATGTGCCATG
1 GAGTTGTAGACTTTAAAAGGGTGCCACG
2047473 GAGTTGT-GAACTTTAAAAGGG
1 GAGTTGTAG-ACTTTAAAAGGG
2047494 GTGTCACAGA
Statistics
Matches: 356, Mismatches: 75, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
27 8 0.02
28 123 0.35
29 143 0.40
30 60 0.17
31 22 0.06
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (28 bp):
GAGTTGTAGACTTTAAAAGGGTGCCACG
Found at i:2047244 original size:115 final size:114
Alignment explanation
Indices: 2046958--2047574 Score: 407
Period size: 116 Copynumber: 5.3 Consensus size: 114
2046948 CACCAACTTA
* * * * * ** ** *
2046958 TGTGGGCTTT-AAAGGGA-GCCTCAGAGTTATGGACTTTAAAAAAAGGTATCATAGAGTTGTAAA
1 TGTGGACTTTAAAAGGGATGCCACAGAGTTGTAGACTTT-AAAAAGGGTGCCACGGAGTTGTGAA
* * * * * *
2047021 CTTTAAAAAG-GTGCCACAGAGTTATGGA-TTTGAAAAGGGTGTCACAAAAT
65 CTTTAAAAGGAGTGCCACGGAGTTATAGACTTT-AAAA-GGTGCCACAGAGT
* * * * * * * * *
2047071 TGTGAACTTTGAAATGG-TGCCAC-GAAGCTGTGGACTTTAGAATAGGGGTACTATGGAGTTGTG
1 TGTGGACTTTAAAAGGGATGCCACAG-AGTTGTAGACTTTA-AA-AAGGGTGCCACGGAGTTGTG
* * *
2047134 GACTTTAGAAGGAGTACCACGGAGTTATAGACTTTACAAAGGTGCCACAGAGT
63 AACTTTAAAAGGAGTGCCACGGAGTTATAGACTTTA-AAAGGTGCCACAGAGT
* * * *
2047187 TGTGTACTTTAAAAGGGATGCCACATAGTTGTAGACTTTAAAAAGGGTGCCACGGAGTTGTGGAT
1 TGTGGACTTTAAAAGGGATGCCACAGAGTTGTAGACTTTAAAAAGGGTGCCACGGAGTTGTGAAC
** * *
2047252 TTTGGAA-GAGGTGCCACGGAGTTATAGACTTTAAAAGTGGTGTCACGGAGT
66 TTTAAAAGGA-GTGCCACGGAGTTATAGACTTTAAAA--GGTGCCACAGAGT
* ** *
2047303 TGTGGACTTTAAAAAGGATGCCATGGAGTTAT-GAACTTT-AAAAGGGTGCCACGGAGTTGTGAA
1 TGTGGACTTTAAAAGGGATGCCACAGAGTTGTAG-ACTTTAAAAAGGGTGCCACGGAGTTGTGAA
* * * * * * *
2047366 TTTTAAAAGGGGTGCCACAGAGTTCTGGGCTTTAAAAAGTGATGCCACTGAGT
65 CTTTAAAAGGAGTGCCACGGAGTTATAGACTTT-AAAAG-G-TGCCACAGAGT
* * * *
2047419 TGTGGACTTGGAAGAAGGG-TGCCACAGAGTTGTAAACTTTAAAAA-TGTGCCATGGAGTTGTGA
1 TGTGGACTT-TAA-AAGGGATGCCACAGAGTTGTAGACTTTAAAAAGGGTGCCACGGAGTTGTGA
* * * **
2047482 ACTTTAAAAGGGGTGTCACAGAGTTAT-GGGTTTAAAAAGTGATGCCACTA-AGT
64 ACTTTAAAAGGAGTGCCACGGAGTTATAGACTTT-AAAAG-G-TGCCAC-AGAGT
* * *
2047535 CGTGGACTTTGATAAA-GGATGCCACTGAGTTGTGGACTTT
1 TGTGGACTTT-A-AAAGGGATGCCACAGAGTTGTAGACTTT
2047575 TATAAGTTAG
Statistics
Matches: 408, Mismatches: 70, Indels: 49
0.77 0.13 0.09
Matches are distributed among these distances:
113 10 0.02
114 28 0.07
115 120 0.29
116 159 0.39
117 83 0.20
118 8 0.02
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (114 bp):
TGTGGACTTTAAAAGGGATGCCACAGAGTTGTAGACTTTAAAAAGGGTGCCACGGAGTTGTGAAC
TTTAAAAGGAGTGCCACGGAGTTATAGACTTTAAAAGGTGCCACAGAGT
Found at i:2047267 original size:58 final size:58
Alignment explanation
Indices: 2046958--2047544 Score: 369
Period size: 58 Copynumber: 10.2 Consensus size: 58
2046948 CACCAACTTA
* * * * * ** **
2046958 TGTGGGCTTT-AAAG-GGAGCCTCAGAGTTATGGACTTTAAAAAAAGGTATCATAGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTT-AAAAAGGGTGCCACGGAGT
** * * * ** *
2047015 TGTAAACTTTAAAA-AGGTGCCACAGAGTTATGGA-TTTGAAAAGGGTGTCACAAAAT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTTAAAAAGGGTGCCACGGAGT
* * * * * * * * * *
2047071 TGTGAACTTTGAAA-TGGTGCCAC-GAAGCTGTGGACTTTAGAATAGGGGTACTATGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAG-AGTTATAGACTTTA-AA-AAGGGTGCCACGGAGT
* * * * *
2047130 TGTGGACTTTAGAAG-GAGTACCACGGAGTTATAGACTTTACAAA-GGTGCCACAGAGT
1 TGTGGACTTTAAAAGAG-GTGCCACAGAGTTATAGACTTTAAAAAGGGTGCCACGGAGT
* * *
2047187 TGTGTACTTTAAAAG-GGATGCCACATAGTTGTAGACTTTAAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGAGG-TGCCACAGAGTTATAGACTTTAAAAAGGGTGCCACGGAGT
* ** * *
2047245 TGTGGATTTTGGAAGAGGTGCCACGGAGTTATAGACTTT-AAAAGTGGTGTCACGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTTAAAAAG-GGTGCCACGGAGT
**
2047303 TGTGGACTTTAAAA-AGGATGCCATGGAGTTAT-GAACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGAGG-TGCCACAGAGTTATAG-ACTTTAAAAAGGGTGCCACGGAGT
* * * * * * * *
2047360 TGTGAATTTTAAAAGGGGTGCCACAGAGTTCTGGGCTTTAAAAAGTGATGCCACTGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTTAAAAAG-GGTGCCACGGAGT
* * * * *
2047419 TGTGGACTTGGAAGAAG-GGTGCCACAGAGTTGTAAACTTTAAAAA-TGTGCCATGGAGT
1 TGTGGACTT-TAA-AAGAGGTGCCACAGAGTTATAGACTTTAAAAAGGGTGCCACGGAGT
* * * ** * **
2047477 TGTGAACTTTAAAAGGGGTGTCACAGAGTTAT-GGGTTTAAAAAGTGATGCCACTAAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTTAAAAAG-GGTGCCACGGAGT
*
2047535 CGTGGACTTT
1 TGTGGACTTT
2047545 GATAAAGGAT
Statistics
Matches: 413, Mismatches: 93, Indels: 47
0.75 0.17 0.08
Matches are distributed among these distances:
55 1 0.00
56 52 0.13
57 121 0.29
58 151 0.37
59 41 0.10
60 43 0.10
61 4 0.01
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (58 bp):
TGTGGACTTTAAAAGAGGTGCCACAGAGTTATAGACTTTAAAAAGGGTGCCACGGAGT
Found at i:2047287 original size:87 final size:85
Alignment explanation
Indices: 2047010--2047574 Score: 331
Period size: 87 Copynumber: 6.5 Consensus size: 85
2047000 AAGGTATCAT
* * * * * * ** *
2047010 AGAGTTGTAAACTTTAAAAAGGTGCCACAGAGTTATGGA-TTTGAAAAGGGTGTCACAAAATTGT
1 AGAGTTGTGAACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGATGCCACGGAGTTGT
*
2047074 GAACTTT-GAA-ATGGTGCCAC
66 GGA-TTTGGAAGA-GGTGCCAC
* * * * ** * *
2047094 -GAAGCTGTGGACTTTAGAATAGGGGTACTATGGAGTTGTGGACTTT-AGAAGGAGTACCACGGA
1 AG-AGTTGTGAACTTTA-AA-A-GGGTGCCACAGAGTTGTGGACTTTAAAAAGGA-TGCCACGGA
* * **
2047157 GTTATAGACTTTACAA-AGGTGCCAC
61 GTTGTGGA-TTTGGAAGAGGTGCCAC
* * * *
2047182 AGAGTTGTGTACTTTAAAAGGGATGCCACATAGTTGTAGACTTTAAAAAGGGTGCCACGGAGTTG
1 AGAGTTGTGAACTTTAAAAGGG-TGCCACAGAGTTGTGGACTTTAAAAAGGATGCCACGGAGTTG
2047247 TGGATTTTGGAAGAGGTGCCAC
65 TGGA-TTTGGAAGAGGTGCCAC
* * * * *
2047269 GGAGTTAT-AGACTTTAAAAGTGGTGTCACGGAGTTGTGGACTTTAAAAAGGATGCCATGGAGTT
1 AGAGTTGTGA-ACTTTAAAAG-GGTGCCACAGAGTTGTGGACTTTAAAAAGGATGCCACGGAGTT
* * **
2047333 ATGAACTTTAAAAG-GGTGCCAC
64 GTGGA-TTTGGAAGAGGTGCCAC
* * * * *
2047355 GGAGTTGTGAATTTTAAAAGGGGTGCCACAGAGTTCTGGGCTTTAAAAAGTGATGCCACTGAGTT
1 AGAGTTGTGAACTTTAAAA-GGGTGCCACAGAGTTGTGGACTTTAAAAAG-GATGCCACGGAGTT
*
2047420 GTGGACTTGGAAGAAGGGTGCCAC
64 GTGGATTTGGAAG-A-GGTGCCAC
* ** ** * * * * * *
2047444 AGAGTTGTAAACTTTAAAAATGTGCCATGGAGTTGTGAACTTTAAAAGGGGTGTCACAGAGTTAT
1 AGAGTTGTGAACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGATGCCACGGAGTTGT
* * *
2047509 GGGTTT-AAAAAGTGATGCCAC
66 GGATTTGGAAGAG-G-TGCCAC
* * * *
2047530 TA-AGTCGTGGACTTTGATAAAGGATGCCACTGAGTTGTGGACTTT
1 -AGAGTTGTGAACTTT-A-AAAGGGTGCCACAGAGTTGTGGACTTT
2047575 TATAAGTTAG
Statistics
Matches: 366, Mismatches: 91, Indels: 44
0.73 0.18 0.09
Matches are distributed among these distances:
83 1 0.00
84 12 0.03
85 7 0.02
86 107 0.29
87 130 0.36
88 81 0.22
89 28 0.08
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (85 bp):
AGAGTTGTGAACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGATGCCACGGAGTTGT
GGATTTGGAAGAGGTGCCAC
Found at i:2047558 original size:30 final size:31
Alignment explanation
Indices: 2047517--2047579 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
2047507 ATGGGTTTAA
2047517 AAAGTGATGCCACTAAGTCGTGGACTTTGAT
1 AAAGTGATGCCACTAAGTCGTGGACTTTGAT
* * *
2047548 AAAG-GATGCCACTGAGTTGTGGACTTTTAT
1 AAAGTGATGCCACTAAGTCGTGGACTTTGAT
2047578 AA
1 AA
2047580 GTTAGTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (31 bp):
AAAGTGATGCCACTAAGTCGTGGACTTTGAT
Found at i:2052848 original size:149 final size:151
Alignment explanation
Indices: 2052608--2052901 Score: 324
Period size: 149 Copynumber: 2.0 Consensus size: 151
2052598 CCGATATCCC
* * *
2052608 TAAAGGACTTAAAAAGGATTACAAAATAGGATAAACCTATCCTAAATACCCAACTTCGATATTAA
1 TAAAGGACTTAAAAAGGATCACAAAATAGGATAAACCTATCCTAAATACCCAACTTCGACATAAA
* * * * * * *
2052673 AGCAGACCCGGTGACAACCTAGGACTT-AGTTCTAGAAAATTATAAAAATACCCTGAGGGGATAC
66 AGCAGACCCAGAGAAAACCTAAGACTTCA-TTCAAAAAAATTACAAAAATACCCTGAGGGGATAC
*
2052737 CTTTGACATAAAAGTACACCCT
130 CTTCGACATAAAAGTACACCCT
* * * * * * *
2052759 TAAAGGA-TTTAAAAGGATCATAGAA-AGGATGAACCTATCCTAAATCCCCACCTTCGACGTAAA
1 TAAAGGACTTAAAAAGGATCACAAAATAGGATAAACCTATCCTAAATACCCAACTTCGACATAAA
* * * * * * *
2052822 AGTAGACTCAGAGAAAACCTAAGACTTCATTCAAAAAAATTACGAAAATGCCCTTATGGTATACC
66 AGCAGACCCAGAGAAAACCTAAGACTTCATTCAAAAAAATTACAAAAATACCCTGAGGGGATACC
*
2052887 TTCGACATGAAAGTA
131 TTCGACATAAAAGTA
2052902 TCCTGGTAAC
Statistics
Matches: 116, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
149 94 0.81
150 15 0.13
151 7 0.06
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (151 bp):
TAAAGGACTTAAAAAGGATCACAAAATAGGATAAACCTATCCTAAATACCCAACTTCGACATAAA
AGCAGACCCAGAGAAAACCTAAGACTTCATTCAAAAAAATTACAAAAATACCCTGAGGGGATACC
TTCGACATAAAAGTACACCCT
Found at i:2053687 original size:34 final size:34
Alignment explanation
Indices: 2053644--2053711 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
2053634 AGTATTTACA
*
2053644 CTTAAATCCCTAAACTTTTTTGAATTTGCAAATT
1 CTTAAATCCCTAAACTTTCTTGAATTTGCAAATT
2053678 CTTAAATCCCTAAACTTTCTTGAATTTGCAAATT
1 CTTAAATCCCTAAACTTTCTTGAATTTGCAAATT
2053712 AGTCTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (34 bp):
CTTAAATCCCTAAACTTTCTTGAATTTGCAAATT
Found at i:2055165 original size:163 final size:161
Alignment explanation
Indices: 2054811--2055278 Score: 473
Period size: 163 Copynumber: 2.9 Consensus size: 161
2054801 AAATAACAAA
* * *
2054811 ATTAGATGA-ATTTT-AAAATTTTAAATC-AAGAAAAAT-CCCTCTAAAAATATTTA-CGAAGTA
1 ATTAGAT-ACATTTTAAAAATTTTAGACCAAAG-AAAATCCCCTC-AAAAATATTTATAGAA-TA
* * * *
2054871 AAAAACTCGATTTTTTGAGAAAATAAGCATTTCAAAGAAAAAATCAAAAACTTATGAAAATCAAT
62 GAAAACTCGA-TTTTTGAAAAAAAAAGCATTTCAAAGAAAAAATCAAAAACTCATGAAAATCAAT
*
2054936 TAAATTTTCAAAACTAATTTAATGGGAATTCCATGACATC
126 TAAATTTTCAAAAC----TTAATGGGAATTCCATGAAATC
*
2054976 GTTAGATACATTTTAAAAATTTTAGACCAAAGAAAATCCCCTCAAAAATATTTATAGAATAGAAA
1 ATTAGATACATTTTAAAAATTTTAGACCAAAGAAAATCCCCTCAAAAATATTTATAGAATAGAAA
* * * *
2055041 ACTCAGATTTTTGAAAAAAAAAGTGGATTTCAAAGAAAAAATCCAAAACTCATGAATATGAATTA
66 ACTC-GATTTTTGAAAAAAAAA--GCATTTCAAAGAAAAAATCAAAAACTCATGAAAATCAATTA
* *** *
2055106 AATTTTCAAAAC-TGATGGGAATTTTGTGAAATT
128 AATTTTCAAAACTTAATGGGAATTCCATGAAATC
** **
2055139 ATTAGATACATTTTAAAAATTTTAGACCAAAGAAAATCTTCTCTGAAATATTTATAGAATAGAAA
1 ATTAGATACATTTTAAAAATTTTAGACCAAAGAAAATCCCCTCAAAAATATTTATAGAATAGAAA
* *** * * * *
2055204 ACTCGATTTTTTTGGAAAATGGAG-ATTCCAAAGAAAAAAATCTAAAACTCATGGAAATAAATTA
66 ACTCGA--TTTTTGAAAAAAAAAGCATTTCAAAG-AAAAAATCAAAAACTCATGAAAATCAATTA
*
2055268 AATTTTTAAAA
128 AATTTTCAAAA
2055279 ATAATTTAAT
Statistics
Matches: 259, Mismatches: 33, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
161 8 0.03
162 39 0.15
163 79 0.31
164 12 0.05
165 11 0.04
166 49 0.19
167 13 0.05
168 48 0.19
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (161 bp):
ATTAGATACATTTTAAAAATTTTAGACCAAAGAAAATCCCCTCAAAAATATTTATAGAATAGAAA
ACTCGATTTTTGAAAAAAAAAGCATTTCAAAGAAAAAATCAAAAACTCATGAAAATCAATTAAAT
TTTCAAAACTTAATGGGAATTCCATGAAATC
Found at i:2058517 original size:97 final size:97
Alignment explanation
Indices: 2058406--2058660 Score: 320
Period size: 97 Copynumber: 2.6 Consensus size: 97
2058396 GTTGGATTGG
* * * * * * *
2058406 AGTATCCCTAATAATGATAATTTGAGCAAAAGTAAGATTTAAAACTTGAAAAGTTTAAAAGTAGG
1 AGTATCCCTGATAATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAAT-GG
*
2058471 G-TTGGAGTATTCC-CTCAAAAAAAT-GAGGTTGA
65 GATTAGAGTA-TCCTCTCAAAAAAATAG-GGTTGA
2058503 AGTATCCCTGATAATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGG
1 AGTATCCCTGATAATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGG
* * *
2058568 ATTAGAGTATCCTCTCAGAAGAATAGGGTTGG
66 ATTAGAGTATCCTCTCAAAAAAATAGGGTTGA
* * *
2058600 AGTAT-CTTCGATGATGACAATCTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAA
1 AGTATCCCT-GATAATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAA
2058661 CGAAGTTGGA
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
96 8 0.06
97 131 0.94
98 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (97 bp):
AGTATCCCTGATAATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGG
ATTAGAGTATCCTCTCAAAAAAATAGGGTTGA
Found at i:2058692 original size:97 final size:97
Alignment explanation
Indices: 2058516--2058702 Score: 263
Period size: 97 Copynumber: 1.9 Consensus size: 97
2058506 ATCCCTGATA
* * * *
2058516 ATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGGATTAGAGTATCCT
1 ATGACAATCTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACGAGATTAGAGCATCCT
2058581 CTCAGAAGAATAGGGTTGGAGTATCTTCGATG
66 CTCAGAAGAATAGGGTTGGAGTATCTTCGATG
* **
2058613 ATGACAATCTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACGA-AGTTGGAGCATTT
1 ATGACAATCTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACGAGA-TTAGAGCATCC
2058677 TCTC-GAA-ATATTAGGGTTGGAGTATC
65 TCTCAGAAGA-A-TAGGGTTGGAGTATC
2058703 CCCATGAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 1 0.01
96 5 0.06
97 74 0.93
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (97 bp):
ATGACAATCTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAACGAGATTAGAGCATCCT
CTCAGAAGAATAGGGTTGGAGTATCTTCGATG
Found at i:2060919 original size:20 final size:16
Alignment explanation
Indices: 2060873--2060907 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2060863 GGTCAAAAAC
2060873 CCAAAATGTATTGATA
1 CCAAAATGTATTGATA
2060889 CCAAAATGTATTGATA
1 CCAAAATGTATTGATA
2060905 CCA
1 CCA
2060908 TGAATAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (16 bp):
CCAAAATGTATTGATA
Found at i:2064480 original size:21 final size:22
Alignment explanation
Indices: 2064454--2064495 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2064444 TGCATCTTTA
*
2064454 CATCCAATAAATATAT-ATTTT
1 CATCCAACAAATATATCATTTT
*
2064475 CATCCAACCAATATATCATTT
1 CATCCAACAAATATATCATTT
2064496 CATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (22 bp):
CATCCAACAAATATATCATTTT
Found at i:2067758 original size:24 final size:24
Alignment explanation
Indices: 2067731--2067778 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2067721 GGTGTAAAAG
2067731 ATGGCATAAAGTCTAACAGTCATA
1 ATGGCATAAAGTCTAACAGTCATA
2067755 ATGGCATAAAGTCTAACAGTCATA
1 ATGGCATAAAGTCTAACAGTCATA
2067779 GCGCAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (24 bp):
ATGGCATAAAGTCTAACAGTCATA
Found at i:2068858 original size:4 final size:5
Alignment explanation
Indices: 2068823--2068866 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
2068813 AGATTAAAAA
*
2068823 AATTA AATTT AATTT AATTT AATTT AATTT -ATTT -ATTT -ATTT AA
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AA
2068867 ATAAAATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
4 12 0.32
5 25 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:2069293 original size:25 final size:24
Alignment explanation
Indices: 2069265--2069328 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
2069255 TATATATATC
*
2069265 AAATTAATATTTTTTAATTTTCTTT
1 AAATTAATATTTTTTAAATTT-TTT
***
2069290 AAA-TAATAAAATTTAAATTTTTT
1 AAATTAATATTTTTTAAATTTTTT
*
2069313 AAATATAACATTTTTT
1 AAAT-TAATATTTTTT
2069329 TTTTACGTAG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
23 6 0.21
24 13 0.45
25 10 0.34
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATTAATATTTTTTAAATTTTTT
Found at i:2069317 original size:23 final size:23
Alignment explanation
Indices: 2069277--2069325 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2069267 ATTAATATTT
*
2069277 TTTAATTTTCTTTAAATAATAAAA
1 TTTAAATTTCTTTAAAT-ATAAAA
*
2069301 TTTAAATTT-TTTAAATATAACA
1 TTTAAATTTCTTTAAATATAAAA
2069323 TTT
1 TTT
2069326 TTTTTTTACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 7 0.30
24 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATTTCTTTAAATATAAAA
Found at i:2069776 original size:18 final size:20
Alignment explanation
Indices: 2069749--2069787 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2069739 TTATTATATG
2069749 TTTTATTTTTTAAT-TATTT
1 TTTTATTTTTTAATATATTT
2069768 TTTTA-TTTTTAATATATTT
1 TTTTATTTTTTAATATATTT
2069787 T
1 T
2069788 AAAGATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTTAATATATTT
Found at i:2071249 original size:19 final size:20
Alignment explanation
Indices: 2071217--2071254 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2071207 AACTTAATTA
*
2071217 TTAAAATTACTTAAAAATAT
1 TTAAAAATACTTAAAAATAT
*
2071237 TTAAAAATA-TTAACAATA
1 TTAAAAATACTTAAAAATA
2071255 ATATAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAATACTTAAAAATAT
Found at i:2071400 original size:21 final size:22
Alignment explanation
Indices: 2071375--2071423 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2071365 CTTAAATTTA
**
2071375 AATTATTTTA-TTTTTAAAAAT
1 AATTATTTTACTTTAAAAAAAT
*
2071396 AATTA-CTTACTTTAAAAAAAT
1 AATTATTTTACTTTAAAAAAAT
2071417 AATTATT
1 AATTATT
2071424 ATAAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTATTTTACTTTAAAAAAAT
Found at i:2072133 original size:27 final size:28
Alignment explanation
Indices: 2072083--2072147 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
2072073 TATTTATTTA
2072083 ATAATATATAAAAATAATTAAAATATAAT
1 ATAA-ATATAAAAATAATTAAAATATAAT
* *
2072112 AT-AATATAAAAATGA-TATAAATTTAAT
1 ATAAATATAAAAATAATTA-AAATATAAT
*
2072139 TTAAATATA
1 ATAAATATA
2072148 TTAATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 20 0.65
28 7 0.23
29 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
ATAAATATAAAAATAATTAAAATATAAT
Found at i:2072373 original size:13 final size:12
Alignment explanation
Indices: 2072357--2072391 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2072347 GTTAAAAAAG
2072357 ATATTTAATTCTC
1 ATATTTAATTC-C
*
2072370 ATATTTAACTCC
1 ATATTTAATTCC
2072382 ATATTTAATT
1 ATATTTAATT
2072392 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATTTAATTCC
Found at i:2072386 original size:12 final size:13
Alignment explanation
Indices: 2072357--2072389 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2072347 GTTAAAAAAG
*
2072357 ATATTTAATTCTC
1 ATATTTAACTCTC
2072370 ATATTTAACTC-C
1 ATATTTAACTCTC
2072382 ATATTTAA
1 ATATTTAA
2072390 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTAACTCTC
Found at i:2072782 original size:29 final size:29
Alignment explanation
Indices: 2072707--2072784 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
2072697 TATATCAAAG
*** *
2072707 AAAA-ATTTTAAAAAAAAATTAAATAACC
1 AAAATATTTTAAAAAATTTTTAAATAACA
* *
2072735 AAAATATTTTACACAATTTTTAAATAACA
1 AAAATATTTTAAAAAATTTTTAAATAACA
2072764 AAAAT-TTTTAAAAATATTTTT
1 AAAATATTTTAAAAA-ATTTTT
2072785 GAAAAGTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 11 0.28
29 29 0.73
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATATTTTAAAAAATTTTTAAATAACA
Found at i:2073791 original size:14 final size:14
Alignment explanation
Indices: 2073764--2073798 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2073754 AATTAAATTA
2073764 TAAAAATAT-TTTT
1 TAAAAATATATTTT
2073777 TAAAATATATATTTT
1 TAAAA-ATATATTTT
2073792 TAAAAAT
1 TAAAAAT
2073799 TTTAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 6 0.30
15 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAAAATATATTTT
Found at i:2073950 original size:8 final size:8
Alignment explanation
Indices: 2073912--2074009 Score: 64
Period size: 8 Copynumber: 12.1 Consensus size: 8
2073902 ATAAATTTTG
2073912 TATTTATA
1 TATTTATA
*
2073920 TTTTTATA
1 TATTTATA
2073928 TA-TTATA
1 TATTTATA
*
2073935 -ATCATATA
1 TAT-TTATA
2073943 TATTTATA
1 TATTTATA
2073951 TCAATTTATA
1 T--ATTTATA
2073961 TATGTTGATA
1 TAT-TT-ATA
2073971 -A-TT-TA
1 TATTTATA
2073976 TA-TTATA
1 TATTTATA
2073983 TATTTAAATA
1 TATTT--ATA
*
2073993 AATTTATA
1 TATTTATA
2074001 TATTTATA
1 TATTTATA
2074009 T
1 T
2074010 CGTATTTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
5 2 0.03
6 4 0.06
7 11 0.15
8 32 0.44
9 5 0.07
10 18 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (8 bp):
TATTTATA
Done.