Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 18 of 82
Found at i:6152072 original size:2 final size:2
Alignment explanation
Indices: 6152065--6152102 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
6152055 CGTGTCTGAT
* *
6152065 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6152103 CGTACTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6152513 original size:14 final size:14
Alignment explanation
Indices: 6152494--6152520 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6152484 CAAAATTAAT
6152494 TAATTAACTAAAAC
1 TAATTAACTAAAAC
6152508 TAATTAACTAAAA
1 TAATTAACTAAAA
6152521 TTTAAACTAA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:6152543 original size:18 final size:18
Alignment explanation
Indices: 6152517--6152551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6152507 CTAATTAACT
* *
6152517 AAAATTTAAACTAATAAG
1 AAAAATTAAAATAATAAG
6152535 AAAAATTAAAATAATAA
1 AAAAATTAAAATAATAA
6152552 TAATTTGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATTAAAATAATAAG
Found at i:6153931 original size:58 final size:59
Alignment explanation
Indices: 6153804--6153932 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 59
6153794 GTAGTCAGAT
* * *
6153804 ACACATGCTTGTGATACCTATCTAGAAAGGTTTGGTGCTAGACATGTGTAGTCATGAAG
1 ACACATGCTTGTGATACCTATATAGAAAGGATTGGTGCTAGACATGTGCAGTCATGAAG
* * ** * *
6153863 ACACAAGCTTGTGATGCCTATATA-AAAGGATTGGTTTTAGACATTTGCAGTGA-GTAAG
1 ACACATGCTTGTGATACCTATATAGAAAGGATTGGTGCTAGACATGTGCAGTCATG-AAG
*
6153921 AGACATGCTTGT
1 ACACATGCTTGT
6153933 TGTTTATCTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 1 0.02
58 36 0.62
59 21 0.36
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (59 bp):
ACACATGCTTGTGATACCTATATAGAAAGGATTGGTGCTAGACATGTGCAGTCATGAAG
Found at i:6154107 original size:57 final size:58
Alignment explanation
Indices: 6153820--6154136 Score: 185
Period size: 57 Copynumber: 5.6 Consensus size: 58
6153810 GCTTGTGATA
* * *
6153820 CCTATCTAGAAAGGTTTGGTGCTAGACATGTGTAGTCATG-AAGACACAAGCTTGTGA-TG
1 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAGTTATGTAAGACACATG-TT-T-ATTG
* * * ** * * * * * *
6153879 CCTATATA-AAAGGATTGGTTTTAGACATTTGCAGTGA-GTAAGAGACATGCTTGTTG
1 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAGTTATGTAAGACACATGTTTATTG
** * * * *
6153935 TTTATCTAGCAAGGCTTT-GTGCTAGAC--GTGTACTTCATG--AG--ACATATTTGTCG
1 CCTATCTAGCAAGG-TTTGGTGCTAGACATGTGTAGTT-ATGTAAGACACATGTTTATTG
* * * * * * * *
6153988 CCTATCTAGTAACGCTTGGTGCTAGATATTTGTA-TTGTGTAAGACACATGCTTGA-TA
1 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAGTTATGTAAGACACATG-TTTATTG
6154045 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTA-TTATGTAAGACACATGTTTATTG
1 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAGTTATGTAAGACACATGTTTATTG
* * * * *
6154102 TCTATCTAACAAGGCTCGGTGCTAAACATGTGTAG
1 CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAG
6154137 GGAGTGAGAC
Statistics
Matches: 191, Mismatches: 51, Indels: 33
0.69 0.19 0.12
Matches are distributed among these distances:
52 2 0.01
53 29 0.15
54 2 0.01
55 12 0.06
56 12 0.06
57 92 0.48
58 35 0.18
59 7 0.04
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (58 bp):
CCTATCTAGCAAGGTTTGGTGCTAGACATGTGTAGTTATGTAAGACACATGTTTATTG
Found at i:6154632 original size:22 final size:22
Alignment explanation
Indices: 6154602--6154643 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6154592 TCTGTTAAAG
6154602 AAAGATCAAACCCCAAAAGAAA
1 AAAGATCAAACCCCAAAAGAAA
* * *
6154624 AAAGGTCAATCCCTAAAAGA
1 AAAGATCAAACCCCAAAAGA
6154644 CAGAACCTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAGATCAAACCCCAAAAGAAA
Found at i:6166751 original size:15 final size:15
Alignment explanation
Indices: 6166731--6166760 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6166721 AAACATCGTA
6166731 AACATAACGTGTAAC
1 AACATAACGTGTAAC
*
6166746 AACATAGCGTGTAAC
1 AACATAACGTGTAAC
6166761 TTGGTCTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (15 bp):
AACATAACGTGTAAC
Found at i:6166964 original size:26 final size:26
Alignment explanation
Indices: 6166914--6166964 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
6166904 GTTAAAAACC
*
6166914 TCAAGCATGGCGTGTAACAACTTTTT
1 TCAAGCATGGCATGTAACAACTTTTT
*
6166940 TCAA-CATGGCATGTAATAACTTTTT
1 TCAAGCATGGCATGTAACAACTTTTT
6166965 ATTTTCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (26 bp):
TCAAGCATGGCATGTAACAACTTTTT
Found at i:6167068 original size:98 final size:99
Alignment explanation
Indices: 6166942--6167164 Score: 279
Period size: 98 Copynumber: 2.3 Consensus size: 99
6166932 AACTTTTTTC
* * * * *
6166942 AACATGGCATGTAATAACTTTTTATTTTCAACATGGTGTGTAACTCGGTTTTTATGTTTGTATTT
1 AACATGGCGTGTAACAA-TTTTTTTTTTCAACATGGTGTGTAACTCGGTCTCTATGTTTGTATTT
* * *
6167007 CA-TTAGCACATAAACTATTGGAGTTAAGCA-CTTA
65 CACTT-GAAAATAAACTATTGGAGTTAAACACCTTA
** * *
6167041 AATGTGGCGTGTAACAATTTTTTTTTTCAACATGGTGTGTAACTTGGTCTCTATTTTTGTATTTC
1 AACATGGCGTGTAACAATTTTTTTTTTCAACATGGTGTGTAACTCGGTCTCTATGTTTGTATTTC
*
6167106 ACTTGAAAATAAACTCTTGGAGTTAAACACCTTA
66 ACTTGAAAATAAACTATTGGAGTTAAACACCTTA
* *
6167140 AACATGGTGTATAACAATTTTTTTT
1 AACATGGCGTGTAACAATTTTTTTT
6167165 CAACACGTGT
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
98 65 0.62
99 40 0.38
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (99 bp):
AACATGGCGTGTAACAATTTTTTTTTTCAACATGGTGTGTAACTCGGTCTCTATGTTTGTATTTC
ACTTGAAAATAAACTATTGGAGTTAAACACCTTA
Found at i:6171776 original size:9 final size:9
Alignment explanation
Indices: 6171762--6171791 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6171752 GTTATCTCCC
*
6171762 TATTTTTAG
1 TATTTTTAA
6171771 TATTTTTAA
1 TATTTTTAA
6171780 TATTTTTAA
1 TATTTTTAA
6171789 TAT
1 TAT
6171792 GTTGACAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:6177266 original size:63 final size:63
Alignment explanation
Indices: 6177150--6177273 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
6177140 GCTCAACTTT
* *
6177150 CTCTTTCAGCTCTCTAAACTATATCAACTCTGTCAACTTTCTGTTGAACACCATCGTCATCAG
1 CTCTTTCAGCTCTCTAAACTATATCAACTCTGCCAACTTTCTATTGAACACCATCGTCATCAG
* ** *
6177213 CTCTTTCAGCTCTCTAAACTATATCAGCTCTGCCAACTCTT-TATTGAGTACCATTGTCATC
1 CTCTTTCAGCTCTCTAAACTATATCAACTCTGCCAACT-TTCTATTGAACACCATCGTCATC
6177274 CTGCTGTGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 52 0.96
64 2 0.04
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36
Consensus pattern (63 bp):
CTCTTTCAGCTCTCTAAACTATATCAACTCTGCCAACTTTCTATTGAACACCATCGTCATCAG
Found at i:6177544 original size:11 final size:12
Alignment explanation
Indices: 6177516--6177554 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6177506 ATTTTTATTG
*
6177516 AACATGGCGTGT
1 AACATGGTGTGT
*
6177528 AACATGTTGTG-
1 AACATGGTGTGT
6177539 AACATGGTGTGT
1 AACATGGTGTGT
6177551 AACA
1 AACA
6177555 ATTTTTGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (12 bp):
AACATGGTGTGT
Found at i:6177544 original size:23 final size:22
Alignment explanation
Indices: 6177492--6177621 Score: 136
Period size: 23 Copynumber: 5.7 Consensus size: 22
6177482 ATGTGTTAGC
*
6177492 ACATGGCATGTAACATTTTTATTGA
1 ACATGGCGTGTAACA--TTT-TTGA
*
6177517 ACATGGCGTGTAACATGTTGTGA
1 ACATGGCGTGTAACAT-TTTTGA
*
6177540 ACATGGTGTGTAACAATTTTTGA
1 ACATGGCGTGTAAC-ATTTTTGA
* *
6177563 AC-TTGCGTGTAACATTTTTGG
1 ACATGGCGTGTAACATTTTTGA
*
6177584 ACATGACGTGTAACATTTTTTGA
1 ACATGGCGTGTAACA-TTTTTGA
*
6177607 ACATGGCGTGCAACA
1 ACATGGCGTGTAACA
6177622 ACATGACTGA
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.10
22 19 0.21
23 43 0.48
24 4 0.04
25 14 0.16
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (22 bp):
ACATGGCGTGTAACATTTTTGA
Found at i:6182527 original size:28 final size:25
Alignment explanation
Indices: 6182445--6182548 Score: 127
Period size: 25 Copynumber: 4.0 Consensus size: 25
6182435 TTTCAACTTG
6182445 TGGCCTTGCCACGTATAACAACCCA
1 TGGCCTTGCCACGTATAACAACCCA
6182470 TGGCCTTGCCACGTATAACAACCCA
1 TGGCCTTGCCACGTATAACAACCCA
* *
6182495 TGGCCTTGCCACATATAATCACAAACCA
1 TGGCCTTGCCACGTAT-A--ACAACCCA
* * * *
6182523 TGGCCTAGCCATGTCTAACAGCCCA
1 TGGCCTTGCCACGTATAACAACCCA
6182548 T
1 T
6182549 TGGTGACCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 47 0.69
26 1 0.01
27 1 0.01
28 19 0.28
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (25 bp):
TGGCCTTGCCACGTATAACAACCCA
Found at i:6182548 original size:53 final size:50
Alignment explanation
Indices: 6182445--6182548 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 50
6182435 TTTCAACTTG
* * *
6182445 TGGCCTTGCCACGTATAACAACCCATGGCCTTGCCACGTATAACAACCCA
1 TGGCCTTGCCACATATAACAAACCATGGCCTAGCCACGTATAACAACCCA
* * *
6182495 TGGCCTTGCCACATATAATCACAAACCATGGCCTAGCCATGTCTAACAGCCCA
1 TGGCCTTGCCACATAT-A--ACAAACCATGGCCTAGCCACGTATAACAACCCA
6182548 T
1 T
6182549 TGGTGACCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 15 0.33
51 1 0.02
53 29 0.64
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (50 bp):
TGGCCTTGCCACATATAACAAACCATGGCCTAGCCACGTATAACAACCCA
Found at i:6185582 original size:12 final size:12
Alignment explanation
Indices: 6185548--6185610 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
6185538 TGTTTATGAA
*
6185548 AAGAAAGAAAAGA
1 AAGAAAGAAAA-T
6185561 AAGAAA-AAAAT
1 AAGAAAGAAAAT
6185572 AAGAAAGAAAA-
1 AAGAAAGAAAAT
*
6185583 AGTGTAAAGAAAAGT
1 A-AG-AAAGAAAA-T
6185598 AA-AAAGAAAAT
1 AAGAAAGAAAAT
6185609 AA
1 AA
6185611 TTCAAGTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 10 0.24
12 17 0.40
13 14 0.33
15 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (12 bp):
AAGAAAGAAAAT
Found at i:6186117 original size:107 final size:106
Alignment explanation
Indices: 6185924--6186202 Score: 328
Period size: 107 Copynumber: 2.6 Consensus size: 106
6185914 GCCACATGCT
* * * *
6185924 CCAATTGTTAGATGTCAATGACATCTTCTGGTGATAC-ACTGAGTGGTAGCAGAATTATAGGGTG
1 CCAATTGTTAGATGTCGATGACATCTTGTGGTGACACTA-TGAGTGGTAGCAGAATTATGGGGTG
* *
6185988 ACGCGTTGAGTTGTTGCAGTATTATGGGGTGACACACCACACA
65 ACGCGCTGAGTTGTTGCAGTATTATAGGGTGACA-ACCACACA
* *
6186031 TCAATTGTTAGATGTCGATGACATATTGTGGTGACACTATGAGTGGTAGCAGAATTATGGGGTGA
1 CCAATTGTTAGATGTCGATGACATCTTGTGGTGACACTATGAGTGGTAGCAGAATTATGGGGTGA
* * ** ** * *
6186096 TGTGCTGAGTTGTTGTTGTATTATAGGGTGACATGCACGCC
66 CGCGCTGAGTTGTTGCAGTATTATAGGGTGACAACCACACA
* * * * *
6186137 CCAATTGTTAAATGTTGATGAGATCTTGTGGTGACACGT-TGAGTGGTAGCAAAATTATGCGGTG
1 CCAATTGTTAGATGTCGATGACATCTTGTGGTGACAC-TATGAGTGGTAGCAGAATTATGGGGTG
6186201 AC
65 AC
6186203 ACACCACGTG
Statistics
Matches: 146, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
106 60 0.41
107 85 0.58
108 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (106 bp):
CCAATTGTTAGATGTCGATGACATCTTGTGGTGACACTATGAGTGGTAGCAGAATTATGGGGTGA
CGCGCTGAGTTGTTGCAGTATTATAGGGTGACAACCACACA
Found at i:6186214 original size:31 final size:31
Alignment explanation
Indices: 6186179--6186239 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
6186169 GACACGTTGA
6186179 GTGGTAGCAAAATTATGCGGTGACACACCAC
1 GTGGTAGCAAAATTATGCGGTGACACACCAC
* * *
6186210 GTGGTTGCAGAATTATGGGGTGACACACCA
1 GTGGTAGCAAAATTATGCGGTGACACACCA
6186240 AGCCCCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.21
Consensus pattern (31 bp):
GTGGTAGCAAAATTATGCGGTGACACACCAC
Found at i:6187644 original size:38 final size:38
Alignment explanation
Indices: 6187584--6187663 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
6187574 GGTGGGAGTT
*
6187584 CATG-TGATGTTATTGAAATGTGCGAGTAGGGAGTGCA
1 CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
* * *
6187621 CATGATGATGATATTGCATTGTGCGTGTAGGGAGTGCA
1 CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
6187659 CATGA
1 CATGA
6187664 GCTGAGTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 4 0.11
38 34 0.89
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.30
Consensus pattern (38 bp):
CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
Found at i:6191851 original size:19 final size:21
Alignment explanation
Indices: 6191827--6191870 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
6191817 CCTATAAATA
*
6191827 TCTTGAAA-TTCTAGCAGCT-
1 TCTTGAAATTTCCAGCAGCTG
6191846 TCTTGAAATTTCCAGCAGCTG
1 TCTTGAAATTTCCAGCAGCTG
6191867 TCTT
1 TCTT
6191871 CTTCTTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 10 0.45
21 4 0.18
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (21 bp):
TCTTGAAATTTCCAGCAGCTG
Found at i:6197532 original size:196 final size:196
Alignment explanation
Indices: 6197198--6197581 Score: 501
Period size: 196 Copynumber: 2.0 Consensus size: 196
6197188 TGTAGACAAT
* *
6197198 GTATGTATATAATAAATGAGAAATGCCGATACGAGTTGGCAATGTCTATTACTATTTTGAATTTA
1 GTATGTATATAATAAATGAGAAATGCCAATACGAGTTGGAAATGTCTATTACTATTTTGAATTTA
* * * * * *
6197263 AGTTTTGAAAAATGACTTAGCAGTTTATGATGGAATGATAAACACGTCAGACTATTAGGCTTGCT
66 AGTTATGAAAAATGACTTAGCAATTTATGATGGAATGAGAAACACATAAGACGATTAGGCTTGCT
6197328 TGGGCTTAGTGGACTACGTCCATTGGGCCCATGCGCCGGTCATGGCCCGAAATTTGGGACATGAC
131 TGGGCTTAGTGGACTACGTCCATTGGGCCCATGCGCCGGTCATGGCCCGAAATTTGGGACATGAC
6197393 A
196 A
*
6197394 GTATGTATATTATAAATGAGTAAA-GCCAATACGAGTTGGAAATGTCTATTACTATTTTG-ATTT
1 GTATGTATATAATAAATGAG-AAATGCCAATACGAGTTGGAAATGTCTATTACTATTTTGAATTT
*** * * **
6197457 AAAGTTAT-AATTTGTGACTTAGCAATATT-TGATGGAATGAGGAGTAGA-ATAATTCGA-TAGG
65 -AAGTTATGAA-AAATGACTTAGCAAT-TTATGATGGAATGA-GA-AACACATAAGACGATTAGG
* * *
6197518 CTTGCTTGGGCTTAGTGGACTATGTCCATTGGGCCCATGCGTCGGTCATGGCTCGAAATTTGGG
125 CTTGCTTGGGCTTAGTGGACTACGTCCATTGGGCCCATGCGCCGGTCATGGCCCGAAATTTGGG
6197582 TCGTGACAAT
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
195 6 0.04
196 145 0.89
197 10 0.06
198 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (196 bp):
GTATGTATATAATAAATGAGAAATGCCAATACGAGTTGGAAATGTCTATTACTATTTTGAATTTA
AGTTATGAAAAATGACTTAGCAATTTATGATGGAATGAGAAACACATAAGACGATTAGGCTTGCT
TGGGCTTAGTGGACTACGTCCATTGGGCCCATGCGCCGGTCATGGCCCGAAATTTGGGACATGAC
A
Found at i:6199366 original size:20 final size:20
Alignment explanation
Indices: 6199341--6199379 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6199331 CTATAAATAT
6199341 CTCATTTCACCAGCAGCTTC
1 CTCATTTCACCAGCAGCTTC
**
6199361 CTCATTTTTCCAGCAGCTT
1 CTCATTTCACCAGCAGCTT
6199380 GTTTTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.36, G:0.10, T:0.36
Consensus pattern (20 bp):
CTCATTTCACCAGCAGCTTC
Found at i:6199858 original size:19 final size:20
Alignment explanation
Indices: 6199831--6199876 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6199821 AGGAGACAAG
*
6199831 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
6199850 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
6199869 ATAATATT
1 ATAATATT
6199877 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:6210990 original size:38 final size:38
Alignment explanation
Indices: 6210935--6211052 Score: 161
Period size: 38 Copynumber: 3.1 Consensus size: 38
6210925 GGCAGGAGTG
6210935 CATG-TGATGATATTGAAATGTGCGAGTAGGGAGTGCA
1 CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
**
6210972 CATGATGATGATATTGAAATGTAAGAGTAGGGAGTGCA
1 CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
*
6211010 CATGATGATGATATT-ACATTGTGC-ATGTAGGGAGTGCA
1 CATGATGATGATATTGA-AATGTGCGA-GTAGGGAGTGCA
*
6211048 TATGA
1 CATGA
6211053 GCTGAGAGTG
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
37 6 0.08
38 66 0.92
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (38 bp):
CATGATGATGATATTGAAATGTGCGAGTAGGGAGTGCA
Found at i:6218961 original size:14 final size:16
Alignment explanation
Indices: 6218937--6218969 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6218927 GCATGGAATT
6218937 AAGAATGAGGAAAG-G
1 AAGAATGAGGAAAGTG
6218952 AAGAAT-AGGAAAGTG
1 AAGAATGAGGAAAGTG
6218967 AAG
1 AAG
6218970 GTGGCAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (16 bp):
AAGAATGAGGAAAGTG
Found at i:6219125 original size:56 final size:56
Alignment explanation
Indices: 6219059--6219242 Score: 298
Period size: 56 Copynumber: 3.3 Consensus size: 56
6219049 AGATGGCAAA
* *
6219059 GTGGCCAAATGAAATAAAAACAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
1 GTGGCCAAATGAAATAAGAAGAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
6219115 GTGGCCAAATGAAATAAGAAGAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
1 GTGGCCAAATGAAATAAGAAGAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
* * * *
6219171 GTGACCAAATGAAGTAAGAAGAATAAGAATACATGTGTTTTGATTGGTTCATGAGA
1 GTGGCCAAATGAAATAAGAAGAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
*
6219227 GTGGCCAAGT-AAATAA
1 GTGGCCAAATGAAATAA
6219243 TTAAAAGAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 5 0.04
56 114 0.96
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (56 bp):
GTGGCCAAATGAAATAAGAAGAATAAGAATGCATGTGTTTTGATTGGTTCATGAGG
Found at i:6220376 original size:22 final size:22
Alignment explanation
Indices: 6220319--6220377 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
6220309 GAATTACACA
*
6220319 AGTAAAAGATATG-AATTCTTTT
1 AGTAAAA-ATATGTCATTCTTTT
6220341 AGTAAAAATATGTCATTCTTTT
1 AGTAAAAATATGTCATTCTTTT
6220363 AGTAAAAATATGTCA
1 AGTAAAAATATGTCA
6220378 AATGCATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
AGTAAAAATATGTCATTCTTTT
Found at i:6235986 original size:12 final size:12
Alignment explanation
Indices: 6235971--6236005 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
6235961 ATATGAAACA
*
6235971 ATATATATATAT
1 ATATATTTATAT
6235983 ATATATTTATAT
1 ATATATTTATAT
*
6235995 TTATATTTATA
1 ATATATTTATA
6236006 GACACACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:6241278 original size:55 final size:55
Alignment explanation
Indices: 6241196--6241407 Score: 298
Period size: 55 Copynumber: 3.8 Consensus size: 55
6241186 TATACAACCG
* * * *
6241196 CCGGCTCATCAACTCATGTGGACTCCCACACCGCACATAGCTGGGATCATCATCAA
1 CCGG-TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCA
* *
6241252 CCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATAATCCA
1 CCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCA
* ** *
6241307 CCGGTCATCAGCTTATGTGCACTCCCACACTACACATAGCTAGAATCATCATCCA
1 CCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCA
* * *
6241362 CCGATCATCAGCTCATGTGCACTTCCACACCGCACATAGCTAGAAT
1 CCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAAT
6241408 TACTCATCAT
Statistics
Matches: 141, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
55 137 0.97
56 4 0.03
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.22
Consensus pattern (55 bp):
CCGGTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCA
Found at i:6245632 original size:67 final size:67
Alignment explanation
Indices: 6245542--6245736 Score: 223
Period size: 67 Copynumber: 2.9 Consensus size: 67
6245532 TTACAATGGC
* * * * * *
6245542 TTTTACAAGGCTCAGCCAAAACCTTTTACACTAGTTTTTCACGGGCTAAACTAAAACCCAAAGTG
1 TTTTA-AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTAAACCAAAACCCAAAATG
6245607 ATT
65 ATT
* * *
6245610 TTTTAAAGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAATGG
1 TTTTAAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTAAACCAAAACCCAAAATGA
6245675 TT
66 TT
* * * * *
6245677 TTTCAAAGGCTCAACCACAACC-TACAACAATGGTTTTT-ATCGGGGTCAACCAAAACCCAA
1 TTTTAAAGGCTCAACCACAACCTTTC-ACAATAGTTTTTCA-CGGGCTAAACCAAAACCCAA
6245737 CAACCAACTT
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
66 3 0.03
67 105 0.93
68 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (67 bp):
TTTTAAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTAAACCAAAACCCAAAATGA
TT
Found at i:6245679 original size:32 final size:32
Alignment explanation
Indices: 6245575--6245736 Score: 137
Period size: 35 Copynumber: 4.9 Consensus size: 32
6245565 TTTTACACTA
* * *
6245575 GTTTTTCACGGGCTAAACTAAAACCCAAAGTG
1 GTTTTTCACGGGCTCAACCAAAACCCAAAATG
* * ** * *
6245607 ATTTTTTAAAGGCTCAACCACAACCTTTCACAATG
1 GTTTTTCACGGGCTCAACCAAAACC---CAAAATG
6245642 GTTTTTCACGGGCTCAACCAAAACCCAAAATG
1 GTTTTTCACGGGCTCAACCAAAACCCAAAATG
** *
6245674 GTTTTTCAAAGGCTCAACCACAACCTACAACAATG
1 GTTTTTCACGGGCTCAACCAAAACC--CAA-AATG
*
6245709 GTTTTT-ATCGGGGTCAACCAAAACCCAA
1 GTTTTTCA-CGGGCTCAACCAAAACCCAA
6245737 CAACCAACTT
Statistics
Matches: 101, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
32 46 0.46
33 3 0.03
34 4 0.04
35 48 0.48
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (32 bp):
GTTTTTCACGGGCTCAACCAAAACCCAAAATG
Found at i:6248770 original size:2 final size:2
Alignment explanation
Indices: 6248765--6248799 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6248755 CATATATGTG
6248765 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 T
6248800 CAATCATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6248892 original size:42 final size:42
Alignment explanation
Indices: 6248845--6248928 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
6248835 CATATGCATA
* * *
6248845 AGCTTATATGCACTCCCACTCGCGCATAGTCGGGTCAACATC
1 AGCTTATACGCACTCCCACTCGCACATAGCCGGGTCAACATC
* *
6248887 AGCTTATGCGTACTCCCACTCGCACATAGCCGGGTCAACATC
1 AGCTTATACGCACTCCCACTCGCACATAGCCGGGTCAACATC
6248929 GCCTTATGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.23
Consensus pattern (42 bp):
AGCTTATACGCACTCCCACTCGCACATAGCCGGGTCAACATC
Found at i:6248935 original size:42 final size:42
Alignment explanation
Indices: 6248856--6248937 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
6248846 GCTTATATGC
* *
6248856 ACTCCCACTCGCGCATAGTCGGGTCAACATCAGCTTATGCGT
1 ACTCCCACTCGCACATAGCCGGGTCAACATCAGCTTATGCGT
6248898 ACTCCCACTCGCACATAGCCGGGTCAACATC-GCCTTATGC
1 ACTCCCACTCGCACATAGCCGGGTCAACATCAG-CTTATGC
6248938 ACACTTTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (42 bp):
ACTCCCACTCGCACATAGCCGGGTCAACATCAGCTTATGCGT
Found at i:6250301 original size:20 final size:20
Alignment explanation
Indices: 6250273--6250310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6250263 CTTCAAGCAC
* *
6250273 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
6250293 TATTATCAATCATCATCA
1 TATTATCAATCATCATCA
6250311 TTCATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:6254197 original size:32 final size:32
Alignment explanation
Indices: 6254160--6254267 Score: 83
Period size: 32 Copynumber: 3.3 Consensus size: 32
6254150 TTTTACACTA
*
6254160 GTTTTTCATGGGCTAAACTAAAACCCAAAGTG
1 GTTTTTCAAGGGCTAAACTAAAACCCAAAGTG
* * * * *
6254192 GTTTTTCAAAGGCTTAACCACAAGCTTTCACAA-TG
1 GTTTTTCAAGGGCTAAACTA-AAAC--CCA-AAGTG
* * * *
6254227 GTTTTTCACGAGCTCAACTAGAACCCAAAGTG
1 GTTTTTCAAGGGCTAAACTAAAACCCAAAGTG
6254259 GTTTTTCAA
1 GTTTTTCAA
6254268 AAGCTCAACC
Statistics
Matches: 56, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
31 2 0.04
32 28 0.50
33 3 0.05
34 2 0.04
35 19 0.34
36 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (32 bp):
GTTTTTCAAGGGCTAAACTAAAACCCAAAGTG
Found at i:6254273 original size:32 final size:32
Alignment explanation
Indices: 6254175--6254276 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
6254165 TCATGGGCTA
* *
6254175 AACTAAAACCCAAAGTGGTTTTTCAAAGGCTT
1 AACTAAAACCCAAAGTGGTTTTTCAAAAGCTC
* * * **
6254207 AACCACAAGCTTTCACAA-TGGTTTTTCACGAGCTC
1 AACTA-AAAC--CCA-AAGTGGTTTTTCAAAAGCTC
*
6254242 AACTAGAACCCAAAGTGGTTTTTCAAAAGCTC
1 AACTAAAACCCAAAGTGGTTTTTCAAAAGCTC
6254274 AAC
1 AAC
6254277 CACAACGTAC
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
31 2 0.04
32 24 0.46
33 3 0.06
34 2 0.04
35 19 0.37
36 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (32 bp):
AACTAAAACCCAAAGTGGTTTTTCAAAAGCTC
Found at i:6254294 original size:67 final size:67
Alignment explanation
Indices: 6254160--6254299 Score: 183
Period size: 67 Copynumber: 2.1 Consensus size: 67
6254150 TTTTACACTA
* * * * * *
6254160 GTTTTTCATGGGCTAAACTAAAACCCAAAGTGGTTTTTCAAAGGCTTAACCACAAGCTTTCACAA
1 GTTTTTCACGAGCTAAACTAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTACACAA
6254225 TG
66 TG
* * *
6254227 GTTTTTCACGAGCTCAACTAGAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAA-CGTACAATA
1 GTTTTTCACGAGCTAAACTAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTAC-ACA
6254291 ATG
65 ATG
6254294 GTTTTT
1 GTTTTT
6254300 ACCGGGGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 3 0.05
67 60 0.95
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (67 bp):
GTTTTTCACGAGCTAAACTAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTACACAA
TG
Found at i:6254319 original size:67 final size:67
Alignment explanation
Indices: 6254160--6254321 Score: 166
Period size: 67 Copynumber: 2.4 Consensus size: 67
6254150 TTTTACACTA
* * * * * * * *
6254160 GTTTTTCATGGGCTAAACTAAAACCCAAAGTGGTTTTTCAAAGGCTTAACCACAAGCTTTCACAA
1 GTTTTTCACGAGCTCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTACACAA
6254225 TG
66 TG
* * *
6254227 GTTTTTCACGAGCTCAACTAGAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAA-CGTACAATA
1 GTTTTTCACGAGCTCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTAC-ACA
6254291 ATG
65 ATG
* * *
6254294 GTTTTT-ACCGGGGTTAACCAAAACCCAA
1 GTTTTTCA-CGAGCTCAACCAAAACCCAA
6254322 CAACCAACTT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
66 4 0.05
67 75 0.95
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (67 bp):
GTTTTTCACGAGCTCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAACCACAAGCGTACACAA
TG
Found at i:6258681 original size:20 final size:20
Alignment explanation
Indices: 6258658--6258698 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6258648 ATCAAATCTC
*
6258658 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
*
6258678 ATTTCATTTCGTAAAAATCA
1 ATTTCATTTCATAAAAATCA
6258698 A
1 A
6258699 CAAGGCTTAT
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:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:6262653 original size:20 final size:20
Alignment explanation
Indices: 6262624--6262663 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
6262614 TTCAGCTAGC
6262624 CATGAATTT-ACCATGAAAA
1 CATGAATTTAACCATGAAAA
6262643 CATGAAATTTAACCATGAAAA
1 CATG-AATTTAACCATGAAAA
6262664 ATAAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
CATGAATTTAACCATGAAAA
Found at i:6282949 original size:55 final size:55
Alignment explanation
Indices: 6282869--6283187 Score: 476
Period size: 55 Copynumber: 5.8 Consensus size: 55
6282859 AACCATCGGC
* * * *
6282869 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCATTATCCATCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* * * *
6282924 TCATTAGCTCATGTGCACTCTCACACCGCACATAGCTGGAATCATCATCCATCAG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* * *
6282979 TCATCAGCTCATGTGCACTTCTACACCGCACATAGCTAGAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
*
6283034 TCATCAGCTCATATGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* *
6283089 TCATCAGCTCATATGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCAG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* ** *
6283144 TCATTAGCTCATGTATACTCCCACATCGCACATAGCTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
6283188 CCCATCATCT
Statistics
Matches: 241, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 241 1.00
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
Found at i:6283031 original size:26 final size:26
Alignment explanation
Indices: 6283002--6283141 Score: 72
Period size: 26 Copynumber: 5.2 Consensus size: 26
6282992 TGCACTTCTA
6283002 CACCGCACATAGCTAGAATCATCATC
1 CACCGCACATAGCTAGAATCATCATC
** * *
6283028 CACCGGTCATCAGCTCA-TATGCACTC-CC
1 CACCGCACAT-AGCT-AGAAT-CA-TCATC
*
6283056 ACACCGCACATAGCTGGAATCATCATC
1 -CACCGCACATAGCTAGAATCATCATC
** * *
6283083 CACCGGTCATCAGCTCA-TATGCACTC-CC
1 CACCGCACAT-AGCT-AGAAT-CA-TCATC
*
6283111 ACACCGCACATAGCTGGAATCATCATC
1 -CACCGCACATAGCTAGAATCATCATC
6283138 CACC
1 CACC
6283142 AGTCATTAGC
Statistics
Matches: 81, Mismatches: 19, Indels: 28
0.63 0.15 0.22
Matches are distributed among these distances:
26 24 0.30
27 18 0.22
28 19 0.23
29 20 0.25
ACGTcount: A:0.29, C:0.39, G:0.14, T:0.19
Consensus pattern (26 bp):
CACCGCACATAGCTAGAATCATCATC
Found at i:6283057 original size:27 final size:27
Alignment explanation
Indices: 6283027--6283112 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
6283017 GAATCATCAT
6283027 CCACCGGTCATCAGCTCATATGCACTCC
1 CCACCGGTCATCAGCTCATATGCACT-C
** *
6283055 CACACCGCACAT-AGCTGGA-AT-CA-TC
1 C-CACCGGTCATCAGCT-CATATGCACTC
6283080 ATCCACCGGTCATCAGCTCATATGCACTC
1 --CCACCGGTCATCAGCTCATATGCACTC
6283109 CCAC
1 CCAC
6283113 ACCGCACATA
Statistics
Matches: 44, Mismatches: 6, Indels: 17
0.66 0.09 0.25
Matches are distributed among these distances:
25 1 0.02
26 10 0.23
27 13 0.30
28 9 0.20
29 11 0.25
ACGTcount: A:0.26, C:0.41, G:0.14, T:0.20
Consensus pattern (27 bp):
CCACCGGTCATCAGCTCATATGCACTC
Found at i:6283085 original size:28 final size:28
Alignment explanation
Indices: 6283054--6283140 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 28
6283044 ATATGCACTC
6283054 CCACACCGCACATAGCTGGAATCATCAT
1 CCACACCGCACATAGCTGGAATCATCAT
** *
6283082 -C-CACCGGTCATCAGCT--CAT-ATGCACT
1 CCACACCGCACAT-AGCTGGAATCAT-CA-T
6283108 CCCACACCGCACATAGCTGGAATCATCAT
1 -CCACACCGCACATAGCTGGAATCATCAT
6283137 CCAC
1 CCAC
6283141 CAGTCATTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 9 0.20
27 5 0.11
28 9 0.20
29 9 0.20
30 4 0.09
31 2 0.05
ACGTcount: A:0.29, C:0.39, G:0.14, T:0.18
Consensus pattern (28 bp):
CCACACCGCACATAGCTGGAATCATCAT
Found at i:6284286 original size:24 final size:23
Alignment explanation
Indices: 6284259--6284317 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
6284249 CTAACATCAT
6284259 TAAATTAAAATAAAC-AATTAAACA
1 TAAATTAAAATAAACTAA-TAAA-A
**
6284283 TAAATTAAGCTAAACTAATAAAA
1 TAAATTAAAATAAACTAATAAAA
*
6284306 TAAATAAAAATA
1 TAAATTAAAATA
6284318 CCTAAATTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 10 0.34
24 17 0.59
25 2 0.07
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (23 bp):
TAAATTAAAATAAACTAATAAAA
Found at i:6286452 original size:34 final size:34
Alignment explanation
Indices: 6286379--6286456 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
6286369 TTTGGCTACT
*
6286379 GAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAA
1 GAAAATTGGAGCTGTTTGCTGCCAATTTGTGCAA
* * ** * *
6286413 AAAAATTGGAGCTGTTTGTTGGTAGTTTGTGCAG
1 GAAAATTGGAGCTGTTTGCTGCCAATTTGTGCAA
6286447 GAAAATTGGA
1 GAAAATTGGA
6286457 CAACTTTGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (34 bp):
GAAAATTGGAGCTGTTTGCTGCCAATTTGTGCAA
Found at i:6303258 original size:43 final size:43
Alignment explanation
Indices: 6303182--6303270 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
6303172 TAATTATATG
* * * *
6303182 GACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGAT
1 GACTCGGCTATGTGCGAGTAAGGAATGCACATAAACCGATGAT
* * *
6303225 GACTCGGTTATGTGCGAGTAAGGAATGTACATAAACCGGTGAT
1 GACTCGGCTATGTGCGAGTAAGGAATGCACATAAACCGATGAT
6303268 GAC
1 GAC
6303271 CCAACCATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (43 bp):
GACTCGGCTATGTGCGAGTAAGGAATGCACATAAACCGATGAT
Found at i:6306660 original size:21 final size:21
Alignment explanation
Indices: 6306634--6306690 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
6306624 CCCTATTTCA
*
6306634 AATGTATCGATACATTGGGAC
1 AATGTATCAATACATTGGGAC
6306655 AATGTATCAATACATTGGGAC
1 AATGTATCAATACATTGGGAC
6306676 AATGTATCAATACAT
1 AATGTATCAATACAT
6306691 GTTCATTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (21 bp):
AATGTATCAATACATTGGGAC
Found at i:6307819 original size:19 final size:19
Alignment explanation
Indices: 6307797--6307864 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
6307787 ATTATTATTT
6307797 TTAATTTTAAATTTAAATA
1 TTAATTTTAAATTTAAATA
6307816 TTAATTGTTATAATTT--ATA
1 TTAATT-TTA-AATTTAAATA
*
6307835 TTAAAATTTAAAATTTAAAATA
1 TT--AATTTTAAATTT-AAATA
*
6307857 TTACTTTT
1 TTAATTTT
6307865 CATAATCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
19 16 0.41
20 9 0.23
21 9 0.23
22 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (19 bp):
TTAATTTTAAATTTAAATA
Found at i:6309352 original size:2 final size:2
Alignment explanation
Indices: 6309345--6309369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6309335 TGACAAACCA
6309345 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6309370 GATCTCATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6311846 original size:32 final size:32
Alignment explanation
Indices: 6311810--6311871 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
6311800 GTATGAAATA
6311810 TAAACAAAATCAAAAAGATTTTTGAAAATGAT
1 TAAACAAAATCAAAAAGATTTTTGAAAATGAT
6311842 TAAACAAAATCAAAAAGATTTTTGAAAATG
1 TAAACAAAATCAAAAAGATTTTTGAAAATG
6311872 TCTTCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.27
Consensus pattern (32 bp):
TAAACAAAATCAAAAAGATTTTTGAAAATGAT
Found at i:6312093 original size:13 final size:13
Alignment explanation
Indices: 6312075--6312099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6312065 ATGATGGTTG
6312075 GATTTTTCAAAAT
1 GATTTTTCAAAAT
6312088 GATTTTTCAAAA
1 GATTTTTCAAAA
6312100 GTGCTTTCCA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
GATTTTTCAAAAT
Found at i:6316568 original size:40 final size:40
Alignment explanation
Indices: 6316510--6316588 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
6316500 TGGGCTATTT
* **
6316510 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGAGTTTTCAACCTCACCAAGATTGGTGA
*
6316550 TTCACCTTAGTGGAGTTTTCAACCTCACCATGATTGGTG
1 TTCACCTTAGTGGAGTTTTCAACCTCACCAAGATTGGTG
6316589 TCTTTCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGAGTTTTCAACCTCACCAAGATTGGTGA
Found at i:6317389 original size:5 final size:5
Alignment explanation
Indices: 6317379--6317403 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6317369 AGCTTCTAAG
6317379 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
6317404 TTCTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:6317857 original size:40 final size:40
Alignment explanation
Indices: 6317790--6317870 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
6317780 TTTGGCTATT
* * * *
6317790 TTTCATCTTAGTGGGGTTTTCAGCCTTATCA-AGATTGGTG
1 TTTCACCTTAGTAGGGTTTTCAACCTTACCACA-ATTGGTG
6317830 TTTCACCTTAGTAGGG-TTTCTAACCTTACCACAATTGGTG
1 TTTCACCTTAGTAGGGTTTTC-AACCTTACCACAATTGGTG
6317870 T
1 T
6317871 CTTTCACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 4 0.11
40 30 0.86
41 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (40 bp):
TTTCACCTTAGTAGGGTTTTCAACCTTACCACAATTGGTG
Found at i:6318008 original size:56 final size:56
Alignment explanation
Indices: 6317943--6318076 Score: 155
Period size: 56 Copynumber: 2.4 Consensus size: 56
6317933 GGTGTTTTCA
* * * *
6317943 CCCCATTACTAAGGCGATGTTGAGGGTA-TCAATCCCATAAAATAGTGGTATTTCTG
1 CCCCATTACTAAGGCAATATTAAGGGCATTCAA-CCCATAAAATAGTGGTATTTCTG
* * *
6317999 CCCCATTACTTAGGTAATATTAAGGGCATTCAACCCATAAGATAGTGGTATTTCTG
1 CCCCATTACTAAGGCAATATTAAGGGCATTCAACCCATAAAATAGTGGTATTTCTG
** *
6318055 CCCCACCA-TAAGGCAAAATTAA
1 CCCCATTACTAAGGCAATATTAA
6318077 CATTCCCTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
55 11 0.17
56 50 0.77
57 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (56 bp):
CCCCATTACTAAGGCAATATTAAGGGCATTCAACCCATAAAATAGTGGTATTTCTG
Found at i:6321152 original size:43 final size:42
Alignment explanation
Indices: 6321045--6321174 Score: 174
Period size: 43 Copynumber: 3.0 Consensus size: 42
6321035 CCCTCCACAC
*
6321045 TCAGCTCATGTGCACTCCCTACTAC-CACATAGCCAGGTCATCA
1 TCAGCTCATGTGCACTCCC-AC-ACTCACATAGCTAGGTCATCA
* *
6321088 TCAGCTTATGTGCACTCCCACACTGCACATAACTAGGTCATCA
1 TCAGCTCATGTGCACTCCCACACT-CACATAGCTAGGTCATCA
6321131 TCAGCTCATGTGCACTCCCACACTACACATAGCT-GGATCATCA
1 TCAGCTCATGTGCACTCCCACACT-CACATAGCTAGG-TCATCA
6321174 T
1 T
6321175 TATCACACAA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.03
42 4 0.05
43 72 0.92
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.25
Consensus pattern (42 bp):
TCAGCTCATGTGCACTCCCACACTCACATAGCTAGGTCATCA
Found at i:6322255 original size:23 final size:24
Alignment explanation
Indices: 6322229--6322277 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6322219 TCGTTATTTC
*
6322229 TATTTTCTTCA-TCATTT-TATCCT
1 TATTTTCATCATTCATTTGTA-CCT
6322252 TATTTTCATCATTCATTTGTACCT
1 TATTTTCATCATTCATTTGTACCT
6322276 TA
1 TA
6322278 GGCCTACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 11 0.48
25 2 0.09
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTCATCATTCATTTGTACCT
Found at i:6327856 original size:2 final size:2
Alignment explanation
Indices: 6327849--6327873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6327839 NNNNNNNNNN
6327849 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 T
6327874 GTTTTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6328032 original size:38 final size:40
Alignment explanation
Indices: 6327990--6328092 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 40
6327980 ATATTACCCG
*
6327990 TGTGCACGATGTGGGGGGATGTACACGATGGCAT-T-AAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGAC-TCTGAATA
* * * *
6328028 TGTGCATGATGTGGGGGGATGCACGCGATGACTCTGACTA
1 TGTGCACGATGTGGGGGGATGTACACGATGACTCTGAATA
*
6328068 TGTGCACAATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
6328093 TGAGCTGGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 1 0.02
38 29 0.55
39 2 0.04
40 21 0.40
ACGTcount: A:0.22, C:0.15, G:0.38, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGACTCTGAATA
Found at i:6328144 original size:2 final size:2
Alignment explanation
Indices: 6328139--6328163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6328129 TATGTTTAGG
6328139 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 T
6328164 GCAATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6328437 original size:39 final size:40
Alignment explanation
Indices: 6328386--6328466 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
6328376 CTGCAGCGAA
*
6328386 AAACGTTTTGTTTT-GCCTCTTG-AATTTCGCTGCAACAAG
1 AAACGTTTTGTTTTGGCCT-TTGAAATCTCGCTGCAACAAG
*
6328425 AAAC-TTTCTGTTTTGGCCTTTGAAATCTCGCTGCAACTAG
1 AAACGTTT-TGTTTTGGCCTTTGAAATCTCGCTGCAACAAG
6328465 AA
1 AA
6328467 TGAATTTCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
38 3 0.08
39 13 0.35
40 21 0.57
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (40 bp):
AAACGTTTTGTTTTGGCCTTTGAAATCTCGCTGCAACAAG
Found at i:6338828 original size:20 final size:20
Alignment explanation
Indices: 6338803--6338849 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
6338793 GAAATCAATT
6338803 CAAACCCTTGCCATTTAGAC
1 CAAACCCTTGCCATTTAGAC
6338823 CAAACCCTTGCCATTTAGAC
1 CAAACCCTTGCCATTTAGAC
*
6338843 AAAACCC
1 CAAACCC
6338850 CAGTAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (20 bp):
CAAACCCTTGCCATTTAGAC
Found at i:6341293 original size:35 final size:35
Alignment explanation
Indices: 6341253--6341329 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
6341243 CTGTTGATAG
*
6341253 CTGCTGAAACTTTGATGAAAATCTATCAACACTTA
1 CTGCTGAAACTTTAATGAAAATCTATCAACACTTA
* * * * *
6341288 CTGCTGAAAGTTTAATGACAATCTGTTAATACTTA
1 CTGCTGAAACTTTAATGAAAATCTATCAACACTTA
6341323 CTTGCTG
1 C-TGCTG
6341330 CAAATCACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (35 bp):
CTGCTGAAACTTTAATGAAAATCTATCAACACTTA
Found at i:6343648 original size:43 final size:43
Alignment explanation
Indices: 6343558--6343658 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
6343548 TGACTCGGTT
* * **
6343558 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAAGATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAACCCGAAGATGACCCAGCC
* *
6343601 ATGTGCGAGTAGGGAGTGCGCATAACCCTG-TGATGACCTAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAACCC-GAAGATGACCCAGCC
6343644 ATGTGCGAGTAGGGA
1 ATGTGCGAGTAGGGA
6343659 TTACGCATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.37, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAACCCGAAGATGACCCAGCC
Found at i:6344105 original size:21 final size:21
Alignment explanation
Indices: 6344067--6344106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6344057 GTTTCTGGGT
*
6344067 TTCAATTTCGCTGCAGCGAGA
1 TTCAATTTCGCTACAGCGAGA
*
6344088 TTCAATTTCGCTATAGCGA
1 TTCAATTTCGCTACAGCGA
6344107 AAAACCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCAATTTCGCTACAGCGAGA
Found at i:6346183 original size:43 final size:43
Alignment explanation
Indices: 6346133--6346257 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
6346123 TATTGACTCG
*
6346133 ACTATGTGCGAGTAGGGAGTGCGCATAAGCTGAG-GATGACCCG
1 ACTATGTGCGAGTAGGGAGTGCGCATAAGCTG-GTGATGACCCA
** * *
6346176 GTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
1 ACTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCA
* * *
6346219 ACCATGTACGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ACTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
6346258 TGATGATGGG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (43 bp):
ACTATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCA
Found at i:6346297 original size:22 final size:22
Alignment explanation
Indices: 6346252--6346297 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6346242 CATGAGCTGG
*
6346252 TGATGATGATGATGGGATGGTA
1 TGATGATGATGATGGGATGATA
6346274 TGATGATGATGATGGGTAT-ATA
1 TGATGATGATGATGGG-ATGATA
6346296 TG
1 TG
6346298 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (22 bp):
TGATGATGATGATGGGATGATA
Found at i:6351317 original size:46 final size:41
Alignment explanation
Indices: 6351242--6351328 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 41
6351232 TCTGTGGATG
6351242 CATAAATGTTTGAAAATGCTTTGATTATGTGTGTGTGTATA
1 CATAAATGTTTGAAAATGCTTTGATTATGTGTGTGTGTATA
6351283 NCATAAATAGTTTGTAAAATAGCTTTGTATTATGTGTGTGTGTATA
1 -CATAAAT-GTTTG-AAAAT-GCTTTG-ATTATGTGTGTGTGTATA
6351329 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 7 0.17
43 5 0.12
44 5 0.12
45 6 0.15
46 18 0.44
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (41 bp):
CATAAATGTTTGAAAATGCTTTGATTATGTGTGTGTGTATA
Found at i:6351330 original size:2 final size:2
Alignment explanation
Indices: 6351325--6351352 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6351315 TGTGTGTGTG
6351325 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
6351353 AGCTACATAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6352990 original size:18 final size:16
Alignment explanation
Indices: 6352955--6352998 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
6352945 TGATTCTTCT
6352955 TTAATTATTTAGTTAA
1 TTAATTATTTAGTTAA
6352971 TTAATTAATTTAGTTTAA
1 TTAATT-ATTTAG-TTAA
*
6352989 TTAATCATTT
1 TTAATTATTT
6352999 GAAAGCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (16 bp):
TTAATTATTTAGTTAA
Found at i:6360584 original size:36 final size:35
Alignment explanation
Indices: 6360537--6360668 Score: 133
Period size: 36 Copynumber: 3.7 Consensus size: 35
6360527 TCAACTCAGC
* *
6360537 TCATGTGCACTCCCACACCGCACATAGCTAGTATCT
1 TCATGTGCACTCCCACACCGCACATGGCTA-TATCA
* * *
6360573 TCATGTGCACTCTCACACTGCACATGGC-AAAT-A
1 TCATGTGCACTCCCACACCGCACATGGCTATATCA
* * *
6360606 TCATGTGCACTCTCATACTGCACATGGCATATATCA
1 TCATGTGCACTCCCACACCGCACATGGC-TATATCA
6360642 TCAGTGTGTGCACTCCCACACCGCACA
1 TCA---TGTGCACTCCCACACCGCACA
6360669 CGCACGATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
33 27 0.34
34 2 0.03
35 4 0.05
36 29 0.36
39 18 0.22
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACATGGCTATATCA
Found at i:6360615 original size:33 final size:33
Alignment explanation
Indices: 6360537--6360642 Score: 131
Period size: 33 Copynumber: 3.1 Consensus size: 33
6360527 TCAACTCAGC
* * * *
6360537 TCATGTGCACTCCCACACCGCACATAGCTAGTATCT
1 TCATGTGCACTCTCACACTGCACATGGC-A-TAT-A
*
6360573 TCATGTGCACTCTCACACTGCACATGGCAAATA
1 TCATGTGCACTCTCACACTGCACATGGCATATA
*
6360606 TCATGTGCACTCTCATACTGCACATGGCATATA
1 TCATGTGCACTCTCACACTGCACATGGCATATA
6360639 TCAT
1 TCAT
6360643 CAGTGTGTGC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 35 0.56
34 2 0.03
35 1 0.02
36 25 0.40
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (33 bp):
TCATGTGCACTCTCACACTGCACATGGCATATA
Found at i:6363463 original size:28 final size:28
Alignment explanation
Indices: 6363343--6363500 Score: 156
Period size: 29 Copynumber: 5.4 Consensus size: 28
6363333 TTTTAACTTG
* *
6363343 TTTGCCTTAATTTAGACAAGAAAATATG
1 TTTGTCTTAATTTAGACAAGAAAATATA
* * *
6363371 TTTAGTCTTAATTTCGATAAGAAAATATG
1 TTT-GTCTTAATTTAGACAAGAAAATATA
* *
6363400 TTTGTCTTAATTTAAGACAAGAAAAAAAAA
1 TTTGTCTTAATTT-AGACAAG-AAAATATA
*
6363430 TTTTGTCTTAATCTT-GACAAGAAAACATA
1 -TTTGTCTTAAT-TTAGACAAGAAAATATA
* *
6363459 TTTGTCTCAATTTAGACAAGATAAAATATT
1 TTTGTCTTAATTTAGACAAG--AAAATATA
6363489 TTTGTCTTAATT
1 TTTGTCTTAATT
6363501 AAACACAAGA
Statistics
Matches: 108, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.02
28 29 0.27
29 36 0.33
30 28 0.26
31 11 0.10
32 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAATATA
Found at i:6363478 original size:58 final size:58
Alignment explanation
Indices: 6363351--6363500 Score: 169
Period size: 59 Copynumber: 2.6 Consensus size: 58
6363341 TGTTTGCCTT
* ** * * * * *
6363351 AATTTAGACAAG-AAAATATGTTTAGTCTTAATTTCGATAAGAAAATATGTTTGTCTT
1 AATTTAGACAAGAAAAAAAAATTTTGTCTTAATTTCGACAAGAAAACATATTTGTCTC
6363408 AATTTAAGACAAGAAAAAAAAATTTTGTCTTAATCTT-GACAAGAAAACATATTTGTCTC
1 AATTT-AGACAAGAAAAAAAAATTTTGTCTTAAT-TTCGACAAGAAAACATATTTGTCTC
* * *
6363467 AATTTAGACAAGATAAAATATTTTTGTCTTAATT
1 AATTTAGACAAGAAAAAAAAATTTTGTCTTAATT
6363501 AAACACAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
57 6 0.08
58 32 0.41
59 39 0.49
60 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (58 bp):
AATTTAGACAAGAAAAAAAAATTTTGTCTTAATTTCGACAAGAAAACATATTTGTCTC
Found at i:6363533 original size:18 final size:18
Alignment explanation
Indices: 6363512--6363546 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6363502 AACACAAGAG
6363512 TTGTCTTAAATTAAGATC
1 TTGTCTTAAATTAAGATC
6363530 TTGTCTTAAATTAAGAT
1 TTGTCTTAAATTAAGAT
6363547 AATGATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTGTCTTAAATTAAGATC
Found at i:6363692 original size:17 final size:17
Alignment explanation
Indices: 6363670--6363702 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6363660 ATAATAATAA
6363670 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
6363687 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
6363703 TTATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:6364999 original size:21 final size:19
Alignment explanation
Indices: 6364975--6365020 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
6364965 TTAAAGTAAT
6364975 TTAAAATAAAATAACATAAAA
1 TTAAAA-AAAATAACAT-AAA
*
6364996 TTAAGCAAAAATAACATAAA
1 TTAA-AAAAAATAACATAAA
6365016 TTAAA
1 TTAAA
6365021 CTAATCATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (19 bp):
TTAAAAAAAATAACATAAA
Found at i:6365471 original size:55 final size:55
Alignment explanation
Indices: 6365389--6365597 Score: 283
Period size: 55 Copynumber: 3.8 Consensus size: 55
6365379 TGATGACGGG
* * *
6365389 TGATTCCAGCTATGTACGGTGTAGGAGTGCACATGAGCTGATGACTGGTGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAATGCACATGAGCTGATGACTGGTGGATGA
* * * *
6365444 TGATTCCAGCTATGTGCGATGGGGGAGTGCACATGAGCTGATGACTAGTGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAATGCACATGAGCTGATGACTGGTGGATGA
* * * *
6365499 TAATTTCAGCTATGTGCGGTGTGGGAATCCACATGAGCTGATGACTGATGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAATGCACATGAGCTGATGACTGGTGGATGA
* * * *
6365554 TGATTCTAGATATGTGTGGTCTGGGAATGCACATGAGCTGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAATGCACATGAGCTGATGA
6365598 GCCAGTGGTT
Statistics
Matches: 134, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 134 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.28
Consensus pattern (55 bp):
TGATTCCAGCTATGTGCGGTGTGGGAATGCACATGAGCTGATGACTGGTGGATGA
Found at i:6365676 original size:7 final size:7
Alignment explanation
Indices: 6365664--6365688 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6365654 ATGATTGCAC
6365664 TGAATGT
1 TGAATGT
6365671 TGAATGT
1 TGAATGT
6365678 TGAATGT
1 TGAATGT
6365685 TGAA
1 TGAA
6365689 ATTGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (7 bp):
TGAATGT
Found at i:6375166 original size:21 final size:21
Alignment explanation
Indices: 6375142--6375181 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6375132 ATAAAAACTA
*
6375142 ATAAATAATAACTAAATTACG
1 ATAAATAAAAACTAAATTACG
*
6375163 ATAAATAAAAATTAAATTA
1 ATAAATAAAAACTAAATTA
6375182 ACTTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
ATAAATAAAAACTAAATTACG
Found at i:6380129 original size:50 final size:52
Alignment explanation
Indices: 6380011--6380129 Score: 199
Period size: 51 Copynumber: 2.3 Consensus size: 52
6380001 CACTAAAAAT
*
6380011 GATTCTTGCTTTTTAAC-ACGAAATAATAACCCTTACACAATCCAGCAAAGG
1 GATTCTTGCTTTTTAACGACGAAACAATAACCCTTACACAATCCAGCAAAGG
*
6380062 GATTCTTGCTTTTTAACGA-GAAACGATAACCCTTACACAATCCA-CAAAGG
1 GATTCTTGCTTTTTAACGACGAAACAATAACCCTTACACAATCCAGCAAAGG
6380112 GATTCTTGCTTTTTAACG
1 GATTCTTGCTTTTTAACG
6380130 GGATCAAGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
50 24 0.37
51 40 0.62
52 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (52 bp):
GATTCTTGCTTTTTAACGACGAAACAATAACCCTTACACAATCCAGCAAAGG
Found at i:6383438 original size:47 final size:47
Alignment explanation
Indices: 6383327--6383423 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
6383317 CACACTTAAC
** *
6383327 GATACTTGCATGATTTATGGCCATAGGATCGACTCACCTTGCTCTAA
1 GATACTTGCATGATTTATGGCCATAGGATCGACTCACCTCACGCTAA
*
6383374 GATACTTGCATGATTTATGGCCATAGGATCGACTCGCCTCACGCTAA
1 GATACTTGCATGATTTATGGCCATAGGATCGACTCACCTCACGCTAA
6383421 GAT
1 GAT
6383424 TGATTGGAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (47 bp):
GATACTTGCATGATTTATGGCCATAGGATCGACTCACCTCACGCTAA
Found at i:6387482 original size:20 final size:20
Alignment explanation
Indices: 6387437--6387485 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
6387427 AAGTTTGCGA
* **
6387437 TGGTGAATTTATTTTTTTTT
1 TGGTGAATTTATTTTTCTGG
6387457 TGGGTGAATTTATTTTTCTGG
1 T-GGTGAATTTATTTTTCTGG
6387478 TGGTGAAT
1 TGGTGAAT
6387486 ATTCTGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.57
Consensus pattern (20 bp):
TGGTGAATTTATTTTTCTGG
Found at i:6391681 original size:34 final size:34
Alignment explanation
Indices: 6391615--6391682 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
6391605 AACCACTTTG
* *
6391615 GGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAAA
1 GGTTTTAGTTGAGCCCGCGAAAAACCAGTGTAAA
* * * *
6391649 GGTTTTGGTTGAGCCTGCGAAAAGCCATTGTAAA
1 GGTTTTAGTTGAGCCCGCGAAAAACCAGTGTAAA
6391683 AGCTTGGTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (34 bp):
GGTTTTAGTTGAGCCCGCGAAAAACCAGTGTAAA
Found at i:6398555 original size:34 final size:34
Alignment explanation
Indices: 6398488--6398555 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
6398478 AAACCACTTT
* *
6398488 GGGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAA
1 GGGTTTTAGCTGAGCCCGTGAAAAACCAGTGTAA
* * * *
6398522 GGGTTTTGGCTGAGCCTGTGAAAAGCCATTGTAA
1 GGGTTTTAGCTGAGCCCGTGAAAAACCAGTGTAA
6398556 AAGCTTGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.29
Consensus pattern (34 bp):
GGGTTTTAGCTGAGCCCGTGAAAAACCAGTGTAA
Found at i:6400420 original size:31 final size:33
Alignment explanation
Indices: 6400357--6400421 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 33
6400347 CATCAGTTCA
6400357 TGTGCACTCCCACACCACACATGGCTGGAATCATCT
1 TGTGCACTCCCACACCACACA-GGC--GAATCATCT
*
6400393 TGTGCACTCCCACACCGCACA-GC-AATCAT
1 TGTGCACTCCCACACCACACAGGCGAATCAT
6400422 ATATACAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 6 0.21
34 2 0.07
36 20 0.71
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.20
Consensus pattern (33 bp):
TGTGCACTCCCACACCACACAGGCGAATCATCT
Found at i:6400578 original size:2 final size:2
Alignment explanation
Indices: 6400561--6400599 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
6400551 TTATCAATAC
*
6400561 AT AT CAT AT AT CT 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
6400600 CAACATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6406593 original size:70 final size:72
Alignment explanation
Indices: 6406414--6406599 Score: 211
Period size: 72 Copynumber: 2.6 Consensus size: 72
6406404 GCAAAACTTG
* * * *
6406414 AAGATTACATAACCATAGTTGACTATAGAGGAGGCATAGTTGACCTTGACAAGTCAAAAGGCAAG
1 AAGATTACACAATCATAGTTGACTATAGAGGAGGCATAATTGACCTTAACAAGTCAAAAGGCAAG
6406479 AAAAGTC
66 AAAAGTC
* * *
6406486 AAGATTACACAATCATAGTTGACTATAAAAGAGGCATAATCT-ACC-TAACAAGTCAAAAGTC-A
1 AAGATTACACAATCATAGTTGACTATAGAGGAGGCATAAT-TGACCTTAACAAGTCAAAAGGCAA
6406548 GTAAAA-TC
65 G-AAAAGTC
* * * *
6406556 AAGATTACAC-AGCTATGGTTGACTATAGAGGAAGCATAGTTGAC
1 AAGATTACACAATC-ATAGTTGACTATAGAGGAGGCATAATTGAC
6406600 TATAGCAAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
69 3 0.03
70 37 0.38
71 18 0.19
72 38 0.39
73 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (72 bp):
AAGATTACACAATCATAGTTGACTATAGAGGAGGCATAATTGACCTTAACAAGTCAAAAGGCAAG
AAAAGTC
Found at i:6406799 original size:18 final size:20
Alignment explanation
Indices: 6406762--6406799 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6406752 CATATTTGAT
6406762 CAAACTTGTGTCTAACAGCTC
1 CAAACTTGTGTC-AACAGCTC
6406783 CAAACTT-TGTC-ACAGCT
1 CAAACTTGTGTCAACAGCT
6406800 ATAAATAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (20 bp):
CAAACTTGTGTCAACAGCTC
Found at i:6409372 original size:24 final size:24
Alignment explanation
Indices: 6409323--6409387 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
6409313 AGAACCCCTT
6409323 TTATCAGATAATTATATATCAAAA
1 TTATCAGATAATTATATATCAAAA
* * *
6409347 TTATTAGATAATTTTGATAT-ATAA
1 TTATCAGATAATTAT-ATATCAAAA
* *
6409371 TTATCATATATTTATAT
1 TTATCAGATAATTATAT
6409388 TATTAACTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.06
24 27 0.82
25 4 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (24 bp):
TTATCAGATAATTATATATCAAAA
Found at i:6410001 original size:10 final size:10
Alignment explanation
Indices: 6409988--6410012 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6409978 ACAAAAAGTC
6409988 AAAAAAGGTA
1 AAAAAAGGTA
6409998 AAAAAAGGTA
1 AAAAAAGGTA
6410008 AAAAA
1 AAAAA
6410013 GCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (10 bp):
AAAAAAGGTA
Found at i:6422861 original size:38 final size:38
Alignment explanation
Indices: 6422809--6422892 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
6422799 GGTATCCTTG
*
6422809 CCCCCACATTTGGCTATAATAGCATGTGGTATTCTTAC
1 CCCCCACATCTGGCTATAATAGCATGTGGTATTCTTAC
* * ***
6422847 TCCCCACATCTGGCTATATTATTGTGTGGTATTCTTAC
1 CCCCCACATCTGGCTATAATAGCATGTGGTATTCTTAC
6422885 CCCCCACA
1 CCCCCACA
6422893 CTTAGCTGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (38 bp):
CCCCCACATCTGGCTATAATAGCATGTGGTATTCTTAC
Found at i:6422911 original size:38 final size:38
Alignment explanation
Indices: 6422833--6422931 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
6422823 TATAATAGCA
* *
6422833 TGTGGTATTCTTACTCCCCACATCTGGCTATATTATTG
1 TGTGGTATTCTTACCCCCCACATCTAGCTATATTATTG
6422871 TGTGGTATTCTTACCCCCCACA-CTTAGCTGCAT-TTA-TG
1 TGTGGTATTCTTACCCCCCACATC-TAGCT--ATATTATTG
* *
6422909 TGTGGTATGCTTACCCCTCACAT
1 TGTGGTATTCTTACCCCCCACAT
6422932 TTGGTTATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
37 1 0.02
38 47 0.89
39 3 0.06
40 2 0.04
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.38
Consensus pattern (38 bp):
TGTGGTATTCTTACCCCCCACATCTAGCTATATTATTG
Found at i:6430186 original size:26 final size:26
Alignment explanation
Indices: 6430157--6430215 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
6430147 ACCATATACC
6430157 CATCATCAACATGCACACCATCCCAT
1 CATCATCAACATGCACACCATCCCAT
*
6430183 CATCATCATCATGCACACCATCCCAT
1 CATCATCAACATGCACACCATCCCAT
6430209 CATCATC
1 CATCATC
6430216 TCATATGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.22
Consensus pattern (26 bp):
CATCATCAACATGCACACCATCCCAT
Found at i:6430838 original size:42 final size:42
Alignment explanation
Indices: 6430246--6430831 Score: 929
Period size: 42 Copynumber: 14.0 Consensus size: 42
6430236 GCATATAGTA
*
6430246 GGGTCAGCAACGGCTTATGTGCACTCCCACTCACACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* * *
6430288 GGGTTAGCAACAGCTTATGTGCACTCCTACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430330 TGGTCAGCAACGGCTTATGTGCATTCCCACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430372 GGGTCAGCAACGACTTATGTGCACTCCTACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430414 GAGTCAGCAACGGCTTATGTGCACTCCCACTCCCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
*
6430456 GGGTCAGCAACGGCTTATGTGCACTCCCATTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
** *
6430498 GGGTCAGCAACGGCTTATGTGCACTCATACTCGCACATAGCT
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
6430540 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
6430582 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* * *
6430624 GAGTCAGCAACGGCTTATGTGCACTCCTACTTGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* * * *
6430666 GGGTCAGTAACGACTTATGTGCACTCCCACTTGCACATAACC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430708 TGGTCAACAACGGCTTATGTGCACTCCCACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430750 GGGTCAGCAACGGCTTATGTACACTCCTACTCGCACATAGCC
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
* *
6430792 GGGTCAACAACGGCTTATGTGCACTCCTACTCGCACATAG
1 GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAG
6430832 TTGGGTCCAA
Statistics
Matches: 497, Mismatches: 47, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 497 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (42 bp):
GGGTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
Found at i:6433920 original size:21 final size:21
Alignment explanation
Indices: 6433896--6433944 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6433886 GCTATAGGAA
6433896 GTTTGGAAAGTGAAAGAGAGT
1 GTTTGGAAAGTGAAAGAGAGT
* * *
6433917 GTTTAGAGAGTGAAATAGAGT
1 GTTTGGAAAGTGAAAGAGAGT
6433938 GTTTGGA
1 GTTTGGA
6433945 GGCTAAGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
GTTTGGAAAGTGAAAGAGAGT
Found at i:6436134 original size:16 final size:16
Alignment explanation
Indices: 6436113--6436144 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6436103 CCAAAATTTA
6436113 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
*
6436129 GATTTTGATTTTTTTG
1 GATTTTGATTCTTTTG
6436145 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.19, T:0.66
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:6437761 original size:80 final size:80
Alignment explanation
Indices: 6437435--6437732 Score: 449
Period size: 80 Copynumber: 3.7 Consensus size: 80
6437425 GATAAGTTCC
*
6437435 ATTTATGAGA-T-TGTAACATGTATGCCATGAGATGTATGTGTTAAGCATA-TCATATACACTAT
1 ATTTATGAGACTATG-AA-ATGTATGCCATGAGATGTATGTGTTGAG-ATAGTCATATACACTAT
6437497 GGGCTAAGCATGTAAGTG
63 GGGCTAAGCATGTAAGTG
* ** * * *
6437515 ATTTATAAGTTTATGAAATGTATGCCATGATATGTATATGTTGAGATAGTCATATACATTATGGG
1 ATTTATGAGACTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
* *
6437580 CTAAGTACGTAAGTG
66 CTAAGCATGTAAGTG
*
6437595 ATTTATGAGACTATGAAATGTATGCCATGAGATGTATGAGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAGACTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
6437660 CTAAGCATGTAAGTG
66 CTAAGCATGTAAGTG
*
6437675 ATTTATGAGACTATGAACTGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACA
1 ATTTATGAGACTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACA
6437733 GTATATGCTA
Statistics
Matches: 196, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
79 3 0.02
80 188 0.96
81 3 0.02
82 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (80 bp):
ATTTATGAGACTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
CTAAGCATGTAAGTG
Found at i:6438450 original size:41 final size:41
Alignment explanation
Indices: 6438368--6438451 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
6438358 TTTGTGTGAA
* **
6438368 ATGTATCAATACATTACCAATGGTATCGATAGATTTTTTGC
1 ATGTATCAATACATTACCAATGGTATCGATAGAATGGTTGC
*
6438409 ATGTATCGATACATT-CCAAAAT-GTATCGATAGAATGGTTGC
1 ATGTATCAATACATTACC--AATGGTATCGATAGAATGGTTGC
6438450 AT
1 AT
6438452 AATTGATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.05
41 32 0.86
42 3 0.08
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (41 bp):
ATGTATCAATACATTACCAATGGTATCGATAGAATGGTTGC
Found at i:6441944 original size:36 final size:36
Alignment explanation
Indices: 6441904--6442023 Score: 131
Period size: 36 Copynumber: 3.3 Consensus size: 36
6441894 ATGTATAGGG
* *
6441904 GCCAAATGTGGGGCGTTGTACCATACAAATACCTAT
1 GCCAAATGTGGGGCGTTATACCATACAAATAACTAT
* * *
6441940 GCCAAATGTGGGAC-TTCATACC--ACAAATGATA-AAGG
1 GCCAAATGTGGGGCGTT-ATACCATACAAAT-A-ACTA-T
6441976 GCCAAATGTGGGGCGTTATACCATACAAATAACTAT
1 GCCAAATGTGGGGCGTTATACCATACAAATAACTAT
6442012 GCCAAATGTGGG
1 GCCAAATGTGGG
6442024 ACTTCATACC
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
34 6 0.09
35 4 0.06
36 48 0.71
37 4 0.06
38 6 0.09
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (36 bp):
GCCAAATGTGGGGCGTTATACCATACAAATAACTAT
Found at i:6442003 original size:72 final size:73
Alignment explanation
Indices: 6441902--6442071 Score: 297
Period size: 72 Copynumber: 2.3 Consensus size: 73
6441892 ACATGTATAG
* *
6441902 GGGCCAAATGTGGGGCGTTGTACCATACAAATACCTATGCCAAATGTGGGACTTCATACCACAAA
1 GGGCCAAATGTGGGGCGTTATACCATACAAATAACTATGCCAAATGTGGGACTTCATACCACAAA
6441967 TGAT-AAA
66 TGATAAAA
6441974 GGGCCAAATGTGGGGCGTTATACCATACAAATAACTATGCCAAATGTGGGACTTCATACCACAAA
1 GGGCCAAATGTGGGGCGTTATACCATACAAATAACTATGCCAAATGTGGGACTTCATACCACAAA
6442039 TGATAAAA
66 TGATAAAA
* *
6442047 GGACCAAATGTGGGGTGTTATACCA
1 GGGCCAAATGTGGGGCGTTATACCA
6442072 CACACTTTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 67 0.72
73 26 0.28
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (73 bp):
GGGCCAAATGTGGGGCGTTATACCATACAAATAACTATGCCAAATGTGGGACTTCATACCACAAA
TGATAAAA
Found at i:6442059 original size:37 final size:36
Alignment explanation
Indices: 6441940--6442060 Score: 140
Period size: 36 Copynumber: 3.3 Consensus size: 36
6441930 AAATACCTAT
*
6441940 GCCAAATGTGGGACTTCATACCACAAATGATAAAGG
1 GCCAAATGTGGGACTTCATACCACAAATGATAAAAG
* ** *
6441976 GCCAAATGTGGGGCGTT-ATACCATACAAAT-A-ACTAT
1 GCCAAATGTGGGAC-TTCATACC--ACAAATGATAAAAG
6442012 GCCAAATGTGGGACTTCATACCACAAATGATAAAAG
1 GCCAAATGTGGGACTTCATACCACAAATGATAAAAG
6442048 GACCAAATGTGGG
1 G-CCAAATGTGGG
6442061 GTGTTATACC
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
34 6 0.09
35 3 0.04
36 40 0.58
37 14 0.20
38 6 0.09
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (36 bp):
GCCAAATGTGGGACTTCATACCACAAATGATAAAAG
Found at i:6445192 original size:2 final size:2
Alignment explanation
Indices: 6445185--6445209 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6445175 CCATAGATAC
6445185 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6445210 CTTAAACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6445619 original size:58 final size:59
Alignment explanation
Indices: 6445496--6445631 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
6445486 AGTAAGTCTG
* * * * * * **
6445496 AAGTGAAGGGCACATGACTATTGTATTGATTGGTGATGGTTATTTGGACTGCATCTGTA
1 AAGTGAAAGGCACATGTCTATGGTATTGATTGGTGATGATGATATGGACAACATCTGTA
* *
6445555 AAGTGAAAGGCACATGTCTATGGTATT-ATTGGTGATGATGATATGGGCAACATGTGTA
1 AAGTGAAAGGCACATGTCTATGGTATTGATTGGTGATGATGATATGGACAACATCTGTA
*
6445613 AGGTGAAAGGCACATGTCT
1 AAGTGAAAGGCACATGTCT
6445632 GTCGTGTTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
58 42 0.64
59 24 0.36
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (59 bp):
AAGTGAAAGGCACATGTCTATGGTATTGATTGGTGATGATGATATGGACAACATCTGTA
Found at i:6448996 original size:30 final size:31
Alignment explanation
Indices: 6448921--6449003 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
6448911 AACAAAGGAA
*
6448921 AGAAAAAAAAAAAGAGAAATAGCCGAGAGAG
1 AGAAAAAAAAAAAGAGAAATAGCCGACAGAG
* *
6448952 AGAAAAAGAAAAAAGAGAAA-AGTCGAACAGTG
1 AGAAAAA-AAAAAAGAGAAATAGCCG-ACAGAG
6448984 AGGAAAAAAAAAGAA-AGAAA
1 A-GAAAAAAAAA-AAGAGAAA
6449004 AGGAAGGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
31 11 0.24
32 26 0.58
33 8 0.18
ACGTcount: A:0.67, C:0.05, G:0.24, T:0.04
Consensus pattern (31 bp):
AGAAAAAAAAAAAGAGAAATAGCCGACAGAG
Found at i:6449126 original size:34 final size:34
Alignment explanation
Indices: 6449088--6449153 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
6449078 TTATTTTTGG
6449088 AGGAAGAAGAGAGCAACTTAGCTGTTGATTTTTT
1 AGGAAGAAGAGAGCAACTTAGCTGTTGATTTTTT
* * *
6449122 AGGAAGAATAGAGCAGCTTGGCTGTTGATTTT
1 AGGAAGAAGAGAGCAACTTAGCTGTTGATTTT
6449154 GAGGTGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (34 bp):
AGGAAGAAGAGAGCAACTTAGCTGTTGATTTTTT
Found at i:6454215 original size:30 final size:30
Alignment explanation
Indices: 6454181--6454240 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
6454171 ATACCTTTAG
* *
6454181 AGAAAAGGTAGTTAA-AGATTATATCTCCAT
1 AGAAAAGATAGTTAACAG-TTATACCTCCAT
6454211 AGAAAAGATAGTTAACAGTTATACCTCCAT
1 AGAAAAGATAGTTAACAGTTATACCTCCAT
6454241 TAAAGAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (30 bp):
AGAAAAGATAGTTAACAGTTATACCTCCAT
Found at i:6456137 original size:93 final size:92
Alignment explanation
Indices: 6455971--6456158 Score: 306
Period size: 93 Copynumber: 2.0 Consensus size: 92
6455961 TGCACTTTGG
* *
6455971 CCCACCTTGTTTTAAAATGCACTGTTACCCTCTTTGATTGCTCATTATCATTAGTCGACAATTAT
1 CCCACCTTGTTTCAAAATGCACTGTTACCCTCTTTGATTACTCATTATCATTAGTCGACAATTAT
6456036 TTACAAATATAAAAAAAAGAGTAAATTA
66 TTACAAATATAAAAAAAA-AGTAAATTA
* *
6456064 CCCATCTTGTTTCAAAATGCATTGTTACCCTCTTTGATTACTCATTATCATTAGTCAGA-AATTA
1 CCCACCTTGTTTCAAAATGCACTGTTACCCTCTTTGATTACTCATTATCATTAGTC-GACAATTA
*
6456128 TTTATAAATATAAAAAAAAAGTAAATTA
65 TTTACAAATATAAAAAAAAAGTAAATTA
6456156 CCC
1 CCC
6456159 CCATTCTTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
92 12 0.13
93 75 0.84
94 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (92 bp):
CCCACCTTGTTTCAAAATGCACTGTTACCCTCTTTGATTACTCATTATCATTAGTCGACAATTAT
TTACAAATATAAAAAAAAAGTAAATTA
Found at i:6462314 original size:6 final size:6
Alignment explanation
Indices: 6462226--6462377 Score: 70
Period size: 6 Copynumber: 25.3 Consensus size: 6
6462216 TGAGAAGGAC
* * * * * * * *
6462226 AGGGAT TGGGAT CGAGAT AGGGAA AGAGAA AGGGAA AGGGAC AGGGAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
* * * * * * * * * *
6462274 CGTGAT CGGGAT AGGAAC AGAGAT CGGGGT AGGGAT AGGGAT AGGAAC
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
* * * * * * *
6462322 AGGGAT CGGCAT AGGGAT AGGAAT AAGGAT AGGAAC AGGGAC AGGGAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
*
6462370 TGGGAT AG
1 AGGGAT AG
6462378 AGAAAGAGCC
Statistics
Matches: 104, Mismatches: 42, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
6 104 1.00
ACGTcount: A:0.36, C:0.07, G:0.44, T:0.13
Consensus pattern (6 bp):
AGGGAT
Found at i:6462315 original size:30 final size:30
Alignment explanation
Indices: 6462281--6462342 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
6462271 GATCGTGATC
**
6462281 GGGATAGGAACAGAGATCGGGGTAGGGATA
1 GGGATAGGAACAGAGATCGGCATAGGGATA
*
6462311 GGGATAGGAACAGGGATCGGCATAGGGATA
1 GGGATAGGAACAGAGATCGGCATAGGGATA
6462341 GG
1 GG
6462343 AATAAGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.47, T:0.13
Consensus pattern (30 bp):
GGGATAGGAACAGAGATCGGCATAGGGATA
Found at i:6466088 original size:19 final size:18
Alignment explanation
Indices: 6466058--6466097 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
6466048 CTAGTGGAAA
6466058 ATTTTATAATAAAATAAT
1 ATTTTATAATAAAATAAT
6466076 ATTTTATTAATAAAATAAT
1 ATTTTA-TAATAAAATAAT
6466095 ATT
1 ATT
6466098 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTATAATAAAATAAT
Found at i:6468726 original size:17 final size:17
Alignment explanation
Indices: 6468701--6468739 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6468691 ATTGGAGGAT
*
6468701 TGCTCCCCCTAAGTGTG
1 TGCTTCCCCTAAGTGTG
*
6468718 TGCTTCCCCTTAGTGTG
1 TGCTTCCCCTAAGTGTG
6468735 TGCTT
1 TGCTT
6468740 ATTTTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.31, G:0.23, T:0.38
Consensus pattern (17 bp):
TGCTTCCCCTAAGTGTG
Found at i:6469442 original size:18 final size:18
Alignment explanation
Indices: 6469416--6469454 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6469406 CACATTCAAG
* *
6469416 GGTTTAGGAGAGGGTTCA
1 GGTTGAGGAAAGGGTTCA
*
6469434 GGTTGAGGAAAGGGTTGA
1 GGTTGAGGAAAGGGTTCA
6469452 GGT
1 GGT
6469455 GGTGATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.26
Consensus pattern (18 bp):
GGTTGAGGAAAGGGTTCA
Found at i:6483684 original size:20 final size:20
Alignment explanation
Indices: 6483652--6483689 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6483642 ATGATTAATG
6483652 AAAATAAATAATAAATAAGT
1 AAAATAAATAATAAATAAGT
*
6483672 AAAATGAAA-AATATATAA
1 AAAAT-AAATAATAAATAA
6483690 AAATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATAAATAATAAATAAGT
Found at i:6486900 original size:36 final size:36
Alignment explanation
Indices: 6486848--6486949 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
6486838 TGGAGCCAAC
* *
6486848 ATTAGCTGTGCTCGATGTGGGGGAGCACACAATGGT
1 ATTAGTTGTGCACGATGTGGGGGAGCACACAATGGT
* *
6486884 ATTAGTTGTGCGCGATGTGGGGGAGCACACGATGGT
1 ATTAGTTGTGCACGATGTGGGGGAGCACACAATGGT
* *
6486920 ATTAGTTGTGCATGATGTGGGGGTGCACAC
1 ATTAGTTGTGCACGATGTGGGGGAGCACAC
6486950 GATGACTCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (36 bp):
ATTAGTTGTGCACGATGTGGGGGAGCACACAATGGT
Found at i:6491875 original size:15 final size:15
Alignment explanation
Indices: 6491851--6491880 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6491841 GAGATAGGGG
*
6491851 TTGTGGGAAGTTATT
1 TTGTGAGAAGTTATT
6491866 TTGTGAGAAGTTATT
1 TTGTGAGAAGTTATT
6491881 AATTCTCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (15 bp):
TTGTGAGAAGTTATT
Found at i:6505850 original size:16 final size:16
Alignment explanation
Indices: 6505829--6505863 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6505819 GCAAAATTTA
6505829 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
*
6505845 GATTTTGATTTTTTTG
1 GATTTTGATTCTTTTG
6505861 GAT
1 GAT
6505864 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.03, G:0.20, T:0.63
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:6505951 original size:17 final size:17
Alignment explanation
Indices: 6505929--6505963 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6505919 GTAAATGGAA
6505929 AGTAAAAAGTAAAAAGG
1 AGTAAAAAGTAAAAAGG
*
6505946 AGTAAAAAGTGAAAAGG
1 AGTAAAAAGTAAAAAGG
6505963 A
1 A
6505964 CATTTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
AGTAAAAAGTAAAAAGG
Done.