Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold646
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: 91490
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2058 original size:25 final size:27
Alignment explanation
Indices: 1999--2059 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
1989 AGTATTATAT
*
1999 AAATAATTAATAATATAATATATGTGAA
1 AAATAATTAATAATATAATAGATGT-AA
2027 AATATAATTATATAA-ATAA-AGATGT-A
1 AA-ATAATTA-ATAATATAATAGATGTAA
2053 AAATAAT
1 AAATAAT
2060 ATTTAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 5 0.17
26 3 0.10
28 7 0.23
29 11 0.37
30 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (27 bp):
AAATAATTAATAATATAATAGATGTAA
Found at i:6576 original size:42 final size:41
Alignment explanation
Indices: 6473--6618 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 41
6463 ATATGTGTTA
* *
6473 TCGTGTAAGACCACGTCTGGGACGTTGGCATC-AACTTATGATT
1 TCGTGTAAGACC-CGTCTGGGACGTTAGCATCGTA-TT-TGATT
* *
6516 TACGTGTAAGACCAGTCTGGGACGTTAGCTTCGTATTTGATT
1 T-CGTGTAAGACCCGTCTGGGACGTTAGCATCGTATTTGATT
* *
6558 TCGTGTAAGACCCTGTCTGGAATAG-TAGCATCGATATTTGATT
1 TCGTGTAAGACCC-GTCTGGGA-CGTTAGCATCG-TATTTGATT
* *
6601 ACATGTAAGACCACGTCT
1 TCGTGTAAGACC-CGTCT
6619 AGGATGTTGG
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
41 11 0.13
42 20 0.23
43 43 0.49
44 13 0.15
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
TCGTGTAAGACCCGTCTGGGACGTTAGCATCGTATTTGATT
Found at i:10095 original size:23 final size:25
Alignment explanation
Indices: 10052--10097 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10042 TATACCTAAT
10052 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
10077 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
10098 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:10683 original size:60 final size:58
Alignment explanation
Indices: 10573--10743 Score: 222
Period size: 60 Copynumber: 2.9 Consensus size: 58
10563 TAGGTACAAG
* * ** *
10573 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGTAGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGTTGGTGGTGGA-AAAGTGTGGCTAGTGGA-T
*
10633 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGTGGAT
1 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAA-GTGTGGCTAGTGGAT
*
10692 TGGTGGTGGAAAAGGTGTGGC-AGTGGAGTT-GTGGTGGAAAAGTGTGGCTAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGTGTGGCTAGT
10744 TGAGAAAAGT
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
56 10 0.10
57 11 0.11
58 9 0.09
59 25 0.25
60 46 0.46
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.27
Consensus pattern (58 bp):
TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGTGTGGCTAGTGGAT
Found at i:10702 original size:29 final size:30
Alignment explanation
Indices: 10573--10743 Score: 201
Period size: 30 Copynumber: 5.8 Consensus size: 30
10563 TAGGTACAAG
* *
10573 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
10603 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
10633 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
10663 TGGTGGTGGAAAAGGAGTGGCTAGTGGA-T
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
10692 TGGTGGTGGAAAAGGTGTGGC-AGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
10721 T-GTGGTGGAAAA-GTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
10744 TGAGAAAAGT
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
27 7 0.06
28 20 0.16
29 25 0.20
30 73 0.58
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:11519 original size:13 final size:13
Alignment explanation
Indices: 11503--11546 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
11493 TAAATTGAAA
11503 AAAACAGAAATTG
1 AAAACAGAAATTG
*
11516 AAAAGCAGAAATTA
1 AAAA-CAGAAATTG
*
11530 AAAACAGAATTTG
1 AAAACAGAAATTG
11543 AAAA
1 AAAA
11547 GACCTCAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAACAGAAATTG
Found at i:11519 original size:14 final size:14
Alignment explanation
Indices: 11483--11546 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
11473 GAGTTGATTT
* *
11483 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
11497 TTGAAAAAAACAGAAA
1 TTG--AAAAACAGAAA
*
11513 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
11527 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
11540 TTGAAAA
1 TTGAAAA
11547 GACCTCAGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
16 12 0.29
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:11688 original size:74 final size:73
Alignment explanation
Indices: 11529--11765 Score: 257
Period size: 75 Copynumber: 3.2 Consensus size: 73
11519 AGCAGAAATT
* * * * *
11529 AAAAACAGAATTTGAAAA-GACCTCAGTGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATG-CCTCAGCGTGT-GACCGAGGCTCAAC-CTCCTCTCGCAATATGA
11593 GTTGATTTTTG
63 GTTGATTTTTG
*
11604 AAAAGA-AGAAATTGAAAATGCCTCAGCGTGTGACCGAGGTTCAACCTCCTCTCGCAATATGAGT
1 AAAA-ACAGAAATTGAAAATGCCTCAGCGTGTGACCGAGGCTCAACCTCCTCTCGCAATATGAGT
11668 TGATTCTTTG
65 TGATT-TTTG
* * ** **
11678 AAAAGCAGAAATTAAAAATTG-CTCAGCACGTGAGCAAAGGCTCAA-CTCACTTCTCGCAATATG
1 AAAAACAGAAATTGAAAA-TGCCTCAGCGTGTGA-CCGAGGCTCAACCTC-C-TCTCGCAATATG
11741 AGTTGATTTTTG
62 AGTTGATTTTTG
11753 AAAAACAGAAATT
1 AAAAACAGAAATT
11766 AAAGGCTCAA
Statistics
Matches: 140, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
73 23 0.16
74 43 0.31
75 52 0.37
76 22 0.16
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (73 bp):
AAAAACAGAAATTGAAAATGCCTCAGCGTGTGACCGAGGCTCAACCTCCTCTCGCAATATGAGTT
GATTTTTG
Found at i:11817 original size:52 final size:52
Alignment explanation
Indices: 11713--11820 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
11703 GCACGTGAGC
*
11713 AAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
1 AAAGGCTCAACTCACTTCTC-CAATATGAGTTGATTTTTGAAAAACAAAAATT
**
11766 AAAGGCTCAACTCACCTTCT-CAATATGAGTTGATTTTTGAAAAGTAAAAATT
1 AAAGGCTCAACTCA-CTTCTCCAATATGAGTTGATTTTTGAAAAACAAAAATT
11818 AAA
1 AAA
11821 AATAGAGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 32 0.63
53 14 0.27
54 5 0.10
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (52 bp):
AAAGGCTCAACTCACTTCTCCAATATGAGTTGATTTTTGAAAAACAAAAATT
Found at i:11956 original size:76 final size:75
Alignment explanation
Indices: 11838--12076 Score: 293
Period size: 77 Copynumber: 3.2 Consensus size: 75
11828 TTTGAAAGAT
* * * * *
11838 AGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATA
1 AGAAATTGAAAATAGCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-
11903 TTTTGAAAAGC
65 TTTTGAAAAGC
* * *
11914 AGAAATTGGAAA-CGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AGAAATTGAAAATAG-CTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
11978 TCTTTTGAAAAGC
64 T-TTTTGAAAAGC
* * ** * *
11991 AGAAATTGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCACAATATGAGTTGATT
1 AGAAATTGAAAATAGCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
12056 TTTGAAAAAC
66 TTTGAAAAGC
12066 AGAAATT-AAAA
1 AGAAATTGAAAA
12077 GGCTCAACTC
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
74 4 0.03
75 17 0.12
76 55 0.39
77 64 0.45
78 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (75 bp):
AGAAATTGAAAATAGCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTGAAAAGC
Found at i:12126 original size:54 final size:54
Alignment explanation
Indices: 12020--12130 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
12010 GCACGTGAGC
* *
12020 AAAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTA
1 AAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAAAAATTA
** **
12074 AAAGGCTCAACTCACCTCTTTCAATATGAGTTGATTTTTGAAAAGTAAAAATTA
1 AAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAAAAATTA
12128 AAA
1 AAA
12131 ATAGAGTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (54 bp):
AAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAAAAATTA
Found at i:12182 original size:309 final size:304
Alignment explanation
Indices: 11533--12234 Score: 1181
Period size: 309 Copynumber: 2.3 Consensus size: 304
11523 GAAATTAAAA
* * ** * * * *
11533 ACAGAATTTGAAAAGACCTCAGTGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAGTTGA
1 ACAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
* * * * *
11598 T-TTTTGAAAAGAAGAAATTGAAAATGCCTCAGCGTGTGACCGAGGTTCAACCTCCTCTCGCAAT
66 TATTTTGAAAAGCAGAAATTGGAAACGCCTCAGCGTGTGACCGAGGCTCAACCACCTCTCGCAAT
*
11662 ATGAGTTGATTCTTTGAAAAGCAGAAATTAAAAATTGCTCAGCACGTGAGCAAAGGCTCAACTCA
131 ATGAGTTGATTCTTTGAAAAGCAGAAATTAAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCA
*
11727 CTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAGGCTCAACTCACCTTCTCAATAT
196 CTTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTAAAGGCTCAACTCACCTTCTCAATAT
11792 GAGTTGATTTTTGAAAAGTAAAAATTAAAAATAGAGTTTGAAAG
261 GAGTTGATTTTTGAAAAGTAAAAATTAAAAATAGAGTTTGAAAG
*
11836 ATAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
1 ACAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
11901 TATTTTGAAAAGCAGAAATTGGAAACGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
66 TATTTTGAAAAGCAGAAATTGGAAACGCCTCAGCGTGTGA-CCGAGGCTCAAC-CACCTCTCGCA
*
11966 ATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTCAGCACGTGAGCAAAGGCTCAAC
129 ATATGAGTTGATTC-TTTGAAAAGCAGAAATTAAAAATAGCTCAGCACGTGAGCAAAGGCTCAAC
*
12031 TCACTTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTTTC
193 TCACTTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAGGCTCAACTCACCT-TCTC
12096 AATATGAGTTGATTTTTGAAAAGTAAAAATTAAAAATAGAGTTTGAAAG
256 AATATGAGTTGATTTTTGAAAAGTAAAAATTAAAAATAGAGTTTGAAAG
*
12145 ACCGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
1 ACAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
12210 TATTTTGAAAAGCAGAAATTGGAAA
66 TATTTTGAAAAGCAGAAATTGGAAA
12235 AAAAAAATAG
Statistics
Matches: 373, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
303 57 0.15
304 35 0.09
305 11 0.03
306 24 0.06
307 89 0.24
308 17 0.05
309 140 0.38
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (304 bp):
ACAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA
TATTTTGAAAAGCAGAAATTGGAAACGCCTCAGCGTGTGACCGAGGCTCAACCACCTCTCGCAAT
ATGAGTTGATTCTTTGAAAAGCAGAAATTAAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCA
CTTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTAAAGGCTCAACTCACCTTCTCAATAT
GAGTTGATTTTTGAAAAGTAAAAATTAAAAATAGAGTTTGAAAG
Found at i:12492 original size:122 final size:122
Alignment explanation
Indices: 12272--12639 Score: 587
Period size: 122 Copynumber: 3.0 Consensus size: 122
12262 GCGTGTCCTG
* * ** * * *
12272 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATCAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
12337 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
63 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
12397 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
12462 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
* *
12519 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACAAAAAATACCTTAGCGTG-
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
* * *
12583 CCCGAGGCTCAACTCACTTCTATCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
12639 A
1 A
12640 ATACCTCAAC
Statistics
Matches: 231, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
120 15 0.06
121 39 0.17
122 143 0.62
123 6 0.03
124 1 0.00
125 27 0.12
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.24
Consensus pattern (122 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
Found at i:16647 original size:74 final size:76
Alignment explanation
Indices: 16501--16652 Score: 274
Period size: 75 Copynumber: 2.0 Consensus size: 76
16491 AAGAAATATT
16501 ATGCTTAAGATGAAAACCCGAAAAGGGCATCTTAAAAAAAAGGGGATCAAGGCGAAAACCCGAAA
1 ATGCTTAAGATGAAAACCCGAAAAGGGCATCTTAAAAAAAAGGGGATCAAGGCGAAAACCCGAAA
16566 AGGGCGTCTTG
66 AGGGCGTCTTG
16577 ATGCTTAAGATG-AAACCCG-AAAGGGCATCTTAAAAAAAAAGGGGATCAAGGCGAAAACCCGAA
1 ATGCTTAAGATGAAAACCCGAAAAGGGCATCTT-AAAAAAAAGGGGATCAAGGCGAAAACCCGAA
16640 AA-GGCGTCTTG
65 AAGGGCGTCTTG
16651 AT
1 AT
16653 TAGTACAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
74 23 0.31
75 40 0.53
76 12 0.16
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (76 bp):
ATGCTTAAGATGAAAACCCGAAAAGGGCATCTTAAAAAAAAGGGGATCAAGGCGAAAACCCGAAA
AGGGCGTCTTG
Found at i:17571 original size:53 final size:53
Alignment explanation
Indices: 17502--17702 Score: 163
Period size: 53 Copynumber: 3.5 Consensus size: 53
17492 GTTTAAATTG
17502 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCTTGTTTTTCAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCTTGTTTTTCAAAATCA
* * * * **
17555 ACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATT-TTAGTTTATGTTTAAAT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT--------TTTA---ATTCTT-GTTT-T-TCAAAAT
**
17619 TG
52 CA
17621 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCTTGTTTTTTCAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCTTG-TTTTTCAAAATCA
* *
17675 ACTCATA-TGCTAGAGGTGAGTTGAGCCT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT
17703 CGGGGCACGC
Statistics
Matches: 114, Mismatches: 18, Indels: 32
0.70 0.11 0.20
Matches are distributed among these distances:
53 46 0.40
54 12 0.11
55 5 0.04
56 5 0.04
58 2 0.02
61 2 0.02
63 2 0.02
64 7 0.06
65 1 0.01
66 32 0.28
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (53 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTCTTGTTTTTCAAAATCA
Found at i:17663 original size:119 final size:119
Alignment explanation
Indices: 17410--17774 Score: 527
Period size: 119 Copynumber: 3.0 Consensus size: 119
17400 GTTGAGGTAT
* * * *
17410 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGATAGAAGTGAGTTGAGCCTCGGGCACGCTA
1 TTTTAATTCTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTG
* *
17474 AGGTATTTTTTTGTTTTTGTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTA--TTTTAGTTTATGTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
17530 TTTTAATTCTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTG
1 TTTTAATTCTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTG
17595 AGGTATTTTAGTTTATGTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTAGTTTATGTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
17649 TTTTAATTCTTGTTTTTTCAAAATCAACTCATA-TGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTAATTCTTG-TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGC
* * * * * *
17713 TGAGGTATTTTCAATTTTTGTGTTTTGATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
64 TGAGGTATTTT--A-GTTTATG-TTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
17774 T
1 T
17775 CAGGACACGC
Statistics
Matches: 225, Mismatches: 12, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
119 81 0.36
120 50 0.22
121 54 0.24
122 1 0.00
123 5 0.02
124 6 0.03
125 28 0.12
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (119 bp):
TTTTAATTCTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTG
AGGTATTTTAGTTTATGTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:18160 original size:72 final size:73
Alignment explanation
Indices: 17975--18478 Score: 293
Period size: 74 Copynumber: 6.7 Consensus size: 73
17965 AGCCTTTTAA
* * * * * **
17975 TTCTGTTTTTCAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGC
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGTCACACGCTGAGC
*
18040 TATTTTCAAT
65 -AGTTTCAAT
18050 TTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCGGTCACACGCTGAG
1 TTCTGCTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACACGCTGA-
18114 GC-GTTTCAAT
63 GCAGTTTCAAT
* * *
18124 TTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGC-GAGG
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GTCACACGCTGA-G
* * *
18188 TATTTTCAAA
64 CAGTTTCAAT
* * * * ** *** **** * ** * * ** * * *
18198 TTCT-ATCTTTC-AAACTCTATTTTTAATTTTTACTTTTCAAAAATCA-ACTCATATTGAGAGAG
1 TTCTGCT-TTTCAAAAATCAACTCAT-ATTGCGAGAGGT--GAGTTGAGCCTC--GGTCACA-CG
* * *
18260 GTGAGTTGAGCCTTTTAAT
59 CTGAG--CAG--TTTCAAT
* * * * **
18279 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCTCACGTGCTGAGCA
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACACGCTGAGCA
* *
18344 ATTTTAAT
66 GTTTCAAT
*
18352 TTCTGC-TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGGTCACACGCTGA
1 TTCTGCTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACACGCTGA
*
18416 GGCATTTTCAAT
63 -GCAGTTTCAAT
* *
18428 TTCTTCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
18479 GCCACACACT
Statistics
Matches: 321, Mismatches: 82, Indels: 53
0.70 0.18 0.12
Matches are distributed among these distances:
72 33 0.10
73 35 0.11
74 79 0.25
75 68 0.21
76 29 0.09
77 40 0.12
78 4 0.01
79 4 0.01
80 2 0.01
81 18 0.06
82 9 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (73 bp):
TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACACGCTGAGCA
GTTTCAAT
Found at i:18164 original size:149 final size:148
Alignment explanation
Indices: 17966--18472 Score: 447
Period size: 149 Copynumber: 3.4 Consensus size: 148
17956 GGTGAGTTGA
* * *
17966 GCCTTTTAA-TTCTGTTTTTCAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTTGCTCA
1 GCCTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-TTGCTCA
18030 CGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
65 CGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
18095 AGCTCGGTCACACGCTGAG
130 AGCTCGGTCACACGCTGAG
* * * * * *
18114 GCGTTTCAATTTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
1 GCCTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTG-CTCA
* * * * *** * * ** * *
18179 CATGC-GAGGTATTTTCAAATTCT-ATCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAAT
65 CGTGCTGAGCTATTTTCAATTTCTGCT-TTTCAAA----AGAATCAACTCATA--TTGC---GA-
* ** * * *** * *
18242 CAACTCATATTGAGAGAGGT--GA-GTTGA-
119 GAGGTGA-GTTGAGCTCGGTCACACGCTGAG
* *
18269 GCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCTCAC
1 GCCTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCTCAC
*
18334 GTGCTGAGCAATTTT-AATTTCTGC-TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGA
66 GTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTG-
*
18397 ACCTCGGGTCACACGCTGAG
130 AGCTC-GGTCACACGCTGAG
* * *
18417 GCATTTTCAATTTCTTCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 GC-CTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAG
18473 TCTCGGGCCA
Statistics
Matches: 266, Mismatches: 70, Indels: 45
0.70 0.18 0.12
Matches are distributed among these distances:
142 3 0.01
143 4 0.02
144 4 0.02
146 1 0.00
147 8 0.03
148 34 0.13
149 104 0.39
152 7 0.03
153 7 0.03
154 16 0.06
155 61 0.23
156 4 0.02
157 2 0.01
158 3 0.01
159 8 0.03
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (148 bp):
GCCTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCTCAC
GTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGA
GCTCGGTCACACGCTGAG
Found at i:18195 original size:74 final size:74
Alignment explanation
Indices: 17975--18511 Score: 338
Period size: 75 Copynumber: 7.1 Consensus size: 74
17965 AGCCTTTTAA
* * * * * * *
17975 TTCTGTTTTTCAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGC
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGTCACATGCTGAGG
18040 TATTTTCAAT
65 TATTTTCAAT
*
18050 TTCTGCTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCGGTCACACGCTGAG
1 TTCTGCTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAG
**
18114 G-CGTTTCAAT
64 GTATTTTCAAT
* *
18124 TTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGC-GAGG
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GTCACATGCTGAGG
*
18188 TATTTTCAAA
65 TATTTTCAAT
* * * * ** *** **** * ** * * ** * * *
18198 TTCT-ATCTTTC-AAACTCTATTTTTAATTTTTACTTTTCAAAAATCA-ACTCATATTGAGAGAG
1 TTCTGCT-TTTCAAAAATCAACTCAT-ATTGCGAGAGGT--GAGTTGAGCCTC--GGTCACA-TG
* *
18260 GTGAGTTGAGCCTTTT-AAT
59 CTGAGGT-A---TTTTCAAT
* * * * * **
18279 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCTCACGTGCTGAGCA
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGT
18344 ATTTT-AAT
66 ATTTTCAAT
* *
18352 TTCTGC-TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGGTCACACGCTGA
1 TTCTGCTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGA
*
18416 GGCATTTTCAAT
63 GGTATTTTCAAT
* * * **
18428 TTCTTCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACACACTGAGG
1 TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGG
* *
18493 TCTTTTCAAA
65 TATTTTCAAT
18503 TTCTG-TTTT
1 TTCTGCTTTT
18512 AATTTCTGCT
Statistics
Matches: 349, Mismatches: 88, Indels: 51
0.72 0.18 0.10
Matches are distributed among these distances:
72 33 0.09
73 35 0.10
74 81 0.23
75 99 0.28
76 22 0.06
77 39 0.11
78 6 0.02
79 4 0.01
80 2 0.01
81 15 0.04
82 13 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (74 bp):
TTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGT
ATTTTCAAT
Found at i:18409 original size:303 final size:304
Alignment explanation
Indices: 17815--18506 Score: 1142
Period size: 304 Copynumber: 2.3 Consensus size: 304
17805 TTTTTTTTTC
17815 CAATTTCTGCTTTTCAAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGC
1 CAATTTCTGCTTTTC-AAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATG-
**
17880 CGAGGTA-TTTCAAATTCGGGTCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAATCAACT
64 CGAGGTATTTTCAAATTC-TATCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAATCAACT
*
17944 CATATTGAAAGAGGTGAGTTGAGCCTTTTAATTCTGTTTTTCAAAAATCAACTCATATTGTGAGA
128 CATATTGAAAGAGGTGAGTTGAGCCTTTTAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGA
*
18009 AGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAGAATCAACT
193 AGTGAGTTGAGCCTTTGCTCACGTGCTGAGCAATTTTCAATTTCTGCTTTTCAAAAGAATCAACT
*
18074 CATATTGCGAGAGGTGAGTTGAGCTCGGTCACACGCTGAGGC-GTTT
258 CATATTGCGAGAGGTGAGTTGACCTCGGTCACACGCTGAGGCAGTTT
18120 CAATTTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCG
1 CAATTTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCG
18185 AGGTATTTTCAAATTCTATCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAATCAACTCAT
66 AGGTATTTTCAAATTCTATCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAATCAACTCAT
*
18250 ATTGAGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAG
131 ATTGAAAGAGGTGAGTTGAGCCTTTTAA-TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAG
18315 TGAGTTGAGCC-TTGCTCACGTGCTGAGCAATTTT-AATTTCTGC-TTTCAAAAGAATCAACTCA
195 TGAGTTGAGCCTTTGCTCACGTGCTGAGCAATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCA
*
18377 TATTGCGAGAGGTGAGTTGAACCTCGGGTCACACGCTGAGGCATTTT
260 TATTGCGAGAGGTGAGTTG-ACCTC-GGTCACACGCTGAGGCAGTTT
* * * * * * **
18424 CAATTTCTTCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACACACT
1 CAATTTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGC-
*
18489 GAGGTCTTTTCAAATTCT
65 GAGGTATTTTCAAATTCT
18507 GTTTTAATTT
Statistics
Matches: 365, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
301 38 0.10
302 13 0.04
303 119 0.33
304 163 0.45
305 32 0.09
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (304 bp):
CAATTTCTGCTTTTCAAATATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCG
AGGTATTTTCAAATTCTATCTTTCAAACTCTATTTTTAATTTTTACTTTTCAAAAATCAACTCAT
ATTGAAAGAGGTGAGTTGAGCCTTTTAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGT
GAGTTGAGCCTTTGCTCACGTGCTGAGCAATTTTCAATTTCTGCTTTTCAAAAGAATCAACTCAT
ATTGCGAGAGGTGAGTTGACCTCGGTCACACGCTGAGGCAGTTT
Found at i:18538 original size:14 final size:13
Alignment explanation
Indices: 18495--18537 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
18485 CACTGAGGTC
*
18495 TTTTCAAATTCTG
1 TTTTCAATTTCTG
18508 TTTT-AATTTCTG
1 TTTTCAATTTCTG
18520 CTTTTCAATTTCTG
1 -TTTTCAATTTCTG
18534 TTTT
1 TTTT
18538 TTTCATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 12 0.44
14 8 0.30
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:19340 original size:30 final size:30
Alignment explanation
Indices: 19304--19478 Score: 237
Period size: 30 Copynumber: 5.8 Consensus size: 30
19294 ACTTTTCTCA
*
19304 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
*
19334 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
* *
19364 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
*
19394 ACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
** *
19424 ACTAGCCACA-CTTGCTCCATTACCTACTCC
1 ACTAGCCACACCTT-CTCCACCACCAACTCC
*
19454 ACTAACCACA-CTTGCTCCACCACCA
1 ACTAGCCACACCTT-CTCCACCACCA
19479 CTTGTACCTA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
29 3 0.02
30 129 0.98
ACGTcount: A:0.27, C:0.49, G:0.04, T:0.21
Consensus pattern (30 bp):
ACTAGCCACACCTTCTCCACCACCAACTCC
Found at i:23535 original size:43 final size:42
Alignment explanation
Indices: 23460--23576 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 42
23450 GTACAATGCC
* * * *
23460 AACATCCTAGAC-GTGGTCTTACATGTAATCAAATATCGATGCT
1 AACATCCCAGACAG-GGTCTTACACGAAATCAAATA-CGAAGCT
*
23503 -ACTATTCCAGACAGGGTCTTACACGAAATCAAATACGAAGCT
1 AAC-ATCCCAGACAGGGTCTTACACGAAATCAAATACGAAGCT
* *
23545 AACGTCCCAGACATGGTCTTACACGTAAATCA
1 AACATCCCAGACAGGGTCTTACACG-AAATCA
23577 TAAGTTGATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
42 27 0.44
43 34 0.55
44 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (42 bp):
AACATCCCAGACAGGGTCTTACACGAAATCAAATACGAAGCT
Found at i:23599 original size:44 final size:42
Alignment explanation
Indices: 23509--23614 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 42
23499 TGCTACTATT
* *
23509 CCAGACAGGGTCTTACACGAAATCAAATACGAAGCTAACGTC
1 CCAGACATGGTCTTACACGAAATCAAATACGAAGCCAACGTC
* *
23551 CCAGACATGGTCTTACACGTAAATCATAAGT-TGATGCCAACGTC
1 CCAGACATGGTCTTACACG-AAATCA-AA-TACGAAGCCAACGTC
*
23595 CCAGACGTGGTCTTACACGA
1 CCAGACATGGTCTTACACGA
23615 TAACACATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
42 18 0.32
43 7 0.12
44 30 0.54
45 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (42 bp):
CCAGACATGGTCTTACACGAAATCAAATACGAAGCCAACGTC
Found at i:27942 original size:19 final size:23
Alignment explanation
Indices: 27912--27958 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
27902 AACTTTAAAT
27912 TTATTCCTATAT-T-TATTA-TA
1 TTATTCCTATATATATATTATTA
27932 TTATT-CTATATATATATTATTA
1 TTATTCCTATATATATATTATTA
27954 TTATT
1 TTATT
27959 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 5 0.21
22 7 0.29
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTCCTATATATATATTATTA
Found at i:28046 original size:39 final size:38
Alignment explanation
Indices: 27934--28051 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 38
27924 TTATTATATT
* *
27934 ATTCTATATATATATTATTATTATTTTATTTTAATTTTA
1 ATTCTATATATATATTATTATTA-TTTATATTATTTTTA
* * * *
27973 CTTTTATATTATATATTATAAGATTATTTTTATTATTTTTA
1 ATTCTATA-TATATATTAT--TATTATTTATATTATTTTTA
*
28014 ATTCTATATAT-TATTATTACTTATTATGTATTATTTTT
1 ATTCTATATATATATTATTA-TTATT-TATATTATTTTT
28052 CTTAAATATT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
37 1 0.02
38 5 0.08
39 23 0.36
40 13 0.20
41 18 0.28
42 4 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (38 bp):
ATTCTATATATATATTATTATTATTTATATTATTTTTA
Found at i:28064 original size:3 final size:3
Alignment explanation
Indices: 27924--28048 Score: 52
Period size: 3 Copynumber: 41.7 Consensus size: 3
27914 ATTCCTATAT
*
27924 TTA TTA -TA TTA TT- CTA TATA TATA TTA TTA TTA TT- TTA TT- TTAA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TT-A
** * *
27968 TT- TTA CTT- TTA -TA TTA TATA TTA -TA AGA TTA TTT TTA TTA TTT
1 TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
28011 TTAA TT- CTA TATA TTA TTA TTA CTTA TTA TGTA TTA TT
1 TT-A TTA TTA T-TA TTA TTA TTA -TTA TTA T-TA TTA TT
28049 TTTCTTAAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
2 16 0.17
3 53 0.56
4 25 0.27
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:31276 original size:20 final size:20
Alignment explanation
Indices: 31251--31296 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
31241 AGTTTTTAGA
*
31251 TTTATTATGACAAATTAAAT
1 TTTATTATGACAAATTAAAC
31271 TTTATTATGACAAATTAAAC
1 TTTATTATGACAAATTAAAC
31291 TTTATT
1 TTTATT
31297 TTATAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTATTATGACAAATTAAAC
Found at i:32084 original size:2 final size:2
Alignment explanation
Indices: 32077--32111 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32067 ATGCAAATAC
*
32077 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32112 TGGAACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32728 original size:21 final size:21
Alignment explanation
Indices: 32704--32744 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32694 TTTAGGGATA
32704 AAAAATAAATAATA-AATTTTT
1 AAAAATAAA-AATATAATTTTT
*
32725 AAAAATTAAAATATAATTTT
1 AAAAATAAAAATATAATTTT
32745 ATTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATAAAAATATAATTTTT
Found at i:32740 original size:22 final size:21
Alignment explanation
Indices: 32702--32744 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
32692 ATTTTAGGGA
32702 TAAAAAATAAATAATAAATTTT
1 TAAAAAATAAATAAT-AATTTT
*
32724 TAAAAATTAAA-ATATAATTTT
1 TAAAAAATAAATA-ATAATTTT
32745 ATTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATAAATAATAATTTT
Found at i:35301 original size:29 final size:29
Alignment explanation
Indices: 35259--35317 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
35249 CCAAATTGTG
*
35259 TGACTTATCAAACCAAGTTTTCACATTAA
1 TGACTTATCAAACCAAGCTTTCACATTAA
35288 TGACTTATCAAACCAAGCTTTCACATTAA
1 TGACTTATCAAACCAAGCTTTCACATTAA
35317 T
1 T
35318 ATGAGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (29 bp):
TGACTTATCAAACCAAGCTTTCACATTAA
Found at i:37764 original size:92 final size:92
Alignment explanation
Indices: 37567--37749 Score: 307
Period size: 92 Copynumber: 2.0 Consensus size: 92
37557 TTTTAAACAT
* * * *
37567 AAAATTAG-AAAATGAGTAAAAACTCTTGTAAAAAATTTGATCTCTCCAAAATAAGTGAAAATTA
1 AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATTTGACCTCTCCAAAATAAGCGAAAAATA
37631 TTCCTTCTCTATTCCAAAAATAAGTCA
66 TTCCTTCTCTATTCCAAAAATAAGTCA
37658 AAAATTAGAAAAATAAGTAAAAACTCTTGT-AAAAATTATGACCTCTCCAAAATAAGCGAAAAAT
1 AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATT-TGACCTCTCCAAAATAAGCGAAAAAT
37722 ATTCCTTCTCTATTCCAAAAATAAGTCA
65 ATTCCTTCTCTATTCCAAAAATAAGTCA
37750 TGAGAATGGT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
91 15 0.17
92 71 0.83
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (92 bp):
AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATTTGACCTCTCCAAAATAAGCGAAAAATA
TTCCTTCTCTATTCCAAAAATAAGTCA
Found at i:40582 original size:20 final size:20
Alignment explanation
Indices: 40558--40601 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
40548 AAAAAACAAT
40558 ATTTTT-AT-ATAAAAATTTA
1 ATTTTTAATAATAAAAA-TTA
40577 ATTTTTAATAATAAAAATTA
1 ATTTTTAATAATAAAAATTA
40597 ATTTT
1 ATTTT
40602 AGAGTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTTAATAATAAAAATTA
Found at i:41328 original size:33 final size:33
Alignment explanation
Indices: 41286--41349 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
41276 ATGTTATAAA
*
41286 CATGCATGCATTGATAGAGTGAATTTAAGAGAT
1 CATGCATGCATTGATAGACTGAATTTAAGAGAT
41319 CATGCATGCATTGATAGACTGAATTTAAGAG
1 CATGCATGCATTGATAGACTGAATTTAAGAG
41350 GGCGTAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (33 bp):
CATGCATGCATTGATAGACTGAATTTAAGAGAT
Found at i:53287 original size:30 final size:30
Alignment explanation
Indices: 53252--53312 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
53242 GTGGCTAGGG
*
53252 TTTTTTGGTTTTTTTT-GGTTAAGTTTTTT
1 TTTTTTTGTTTTTTTTGGGTTAAGTTTTTT
*
53281 TTTTTTTTTTTTTTTTGGGTTAAGTTTTTT
1 TTTTTTTGTTTTTTTTGGGTTAAGTTTTTT
53311 TT
1 TT
53313 AGGGGGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.79
Consensus pattern (30 bp):
TTTTTTTGTTTTTTTTGGGTTAAGTTTTTT
Found at i:59818 original size:6 final size:6
Alignment explanation
Indices: 59807--59840 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
59797 TAGGTTTCCA
59807 AAAATG AAAATG AAAATG AAAATG AAAATAG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAAT-G AAA
59841 CTTGCAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:60025 original size:23 final size:24
Alignment explanation
Indices: 59985--60029 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59975 AATTTCTCGA
59985 AATTTTATCGAGGGTAAAATTGTC
1 AATTTTATCGAGGGTAAAATTGTC
*
60009 AATTTTAT-TAGGGTAAAATTG
1 AATTTTATCGAGGGTAAAATTG
60030 AGGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (24 bp):
AATTTTATCGAGGGTAAAATTGTC
Found at i:61435 original size:46 final size:46
Alignment explanation
Indices: 61382--61473 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
61372 TAACAAGTTT
61382 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC
1 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC
61428 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC
1 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC
61474 TAACAATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (46 bp):
AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC
Found at i:62183 original size:103 final size:104
Alignment explanation
Indices: 61999--62198 Score: 296
Period size: 103 Copynumber: 1.9 Consensus size: 104
61989 ACAATTTAGC
* ** *
61999 CCCTGAGCTTTAATTAATGATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTACA
1 CCCTGAGCTTAAATTAACAATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTAAA
*
62064 CTAACTCTATTCATCTTCCTATTTAATTCTTATGAGAGT
66 CTAACTCTATTAATCTTCCTATTTAATTCTTATGAGAGT
* *
62103 CCCTGAGCTTAAATTAACAATTTT-TCCTGTTAAATTACTT-ATCAATCTTTAATATATTTTTAA
1 CCCTGAGCTTAAATTAACAATTTTCT-CGGTTAAATTACTTAACCAATCTTTAATATATTTTTAA
* *
62166 ATTAACTCTATTAATCTTCCTATTTTATTCTTA
65 ACTAACTCTATTAATCTTCCTATTTAATTCTTA
62199 CAAGCTCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
103 52 0.60
104 34 0.40
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (104 bp):
CCCTGAGCTTAAATTAACAATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTAAA
CTAACTCTATTAATCTTCCTATTTAATTCTTATGAGAGT
Found at i:64295 original size:44 final size:43
Alignment explanation
Indices: 64184--64287 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 43
64174 TCATTTTGAC
64184 TTTTCATATAATTATTCTATACACTGTT-ATGAATTTAAAAAG
1 TTTTCATATAATTATTCTATACACTGTTAATGAATTTAAAAAG
64226 -TTT--TATAATTATTCTATACACTGTTAATGAATCTTAAAAAG
1 TTTTCATATAATTATTCTATACACTGTTAATGAAT-TTAAAAAG
*
64267 TTTTCATATAATTATTATATA
1 TTTTCATATAATTATTCTATA
64288 TATTGTTAGC
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
39 22 0.39
40 6 0.11
41 11 0.20
42 3 0.05
44 14 0.25
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (43 bp):
TTTTCATATAATTATTCTATACACTGTTAATGAATTTAAAAAG
Found at i:65676 original size:23 final size:25
Alignment explanation
Indices: 65639--65696 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
65629 AATAAATTCG
65639 TATAAAAAATCTAGTTATATT-ATT
1 TATAAAAAATCTAGTTATATTAATT
* *
65663 TATAAAATAT-TAGTTATTTTAAATT
1 TATAAAAAATCTAGTTATATT-AATT
65688 TATAAAAAA
1 TATAAAAAA
65697 AACCACATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.31
24 9 0.31
25 11 0.38
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (25 bp):
TATAAAAAATCTAGTTATATTAATT
Found at i:66802 original size:29 final size:30
Alignment explanation
Indices: 66715--66825 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
66705 GATTAAATTA
* * *
66715 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* * *
66745 ATAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
* *
66776 AAATTAAAG-TTCATGTATACAACTGCACATT
1 AAATTAAAGTTTCATGTATACAATTGCAC--C
*
66807 AAATCAAAGTTT-ATGTATA
1 AAATTAAAGTTTCATGTATA
66826 ATTTTTGGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 16 0.25
30 8 0.12
31 39 0.60
32 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:67454 original size:18 final size:18
Alignment explanation
Indices: 67420--67454 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
67410 TGTGTGATAC
*
67420 TTATAATTATAATTTAAT
1 TTATAATTATAAGTTAAT
*
67438 TTATAATTATTAGTTAA
1 TTATAATTATAAGTTAA
67455 AAATTTGAGG
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATAATTATAAGTTAAT
Found at i:68432 original size:11 final size:10
Alignment explanation
Indices: 68397--68432 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
68387 ATAATAAAAA
68397 TAATATTAAT
1 TAATATTAAT
68407 TAAATATTAAT
1 T-AATATTAAT
68418 TAATATTATAT
1 TAATATTA-AT
68429 TAAT
1 TAAT
68433 GTGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATATTAAT
Found at i:71831 original size:84 final size:84
Alignment explanation
Indices: 71690--71854 Score: 251
Period size: 84 Copynumber: 2.0 Consensus size: 84
71680 TTACTATAAA
* * *
71690 TATCACAACGGGTTGGTTTCAAAGAAAATTTTAAATTTTCATTATGCTTATTTTCACTCTTTTCA
1 TATCACAACGAGTTGGTTTCAAAGAAAAATTTAAATTTTCATTATGATTATTTTCACTCTTTTCA
71755 AACCGATTTTCCAACAAAT
66 AACCGATTTTCCAACAAAT
* * * *
71774 TATCACAACTAGTTGGTTTCAATGAAAAATTT-AATATTTCTTTCTGATTATTTTCACTCTTTTC
1 TATCACAACGAGTTGGTTTCAAAGAAAAATTTAAAT-TTTCATTATGATTATTTTCACTCTTTTC
71838 AAACCGATTTTCCAACA
65 AAACCGATTTTCCAACA
71855 TAGGCAACTT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
83 3 0.04
84 70 0.96
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (84 bp):
TATCACAACGAGTTGGTTTCAAAGAAAAATTTAAATTTTCATTATGATTATTTTCACTCTTTTCA
AACCGATTTTCCAACAAAT
Found at i:73708 original size:18 final size:19
Alignment explanation
Indices: 73681--73718 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
73671 AAAATGCTAA
*
73681 TTTTATTAAT-TTTAATAT
1 TTTTAGTAATATTTAATAT
*
73699 TTTTAGTAATATTTATTAT
1 TTTTAGTAATATTTAATAT
73718 T
1 T
73719 AATAAAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTAGTAATATTTAATAT
Found at i:83898 original size:21 final size:21
Alignment explanation
Indices: 83856--83898 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
83846 TTAGACCTTG
*
83856 TCCTGTGATTTTTGTTTTCTC
1 TCCTGTGATTTTTGTTTCCTC
*
83877 TCCTGTTGGTTTTTG-TTCCTC
1 TCCTG-TGATTTTTGTTTCCTC
83898 T
1 T
83899 TGCTACATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.02, C:0.21, G:0.16, T:0.60
Consensus pattern (21 bp):
TCCTGTGATTTTTGTTTCCTC
Done.