Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 6 of 20
Found at i:824515 original size:2 final size:2
Alignment explanation
Indices: 824508--824536 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
824498 ATATGATGTG
824508 AT AT 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 AT AT A
824537 ATGAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:827482 original size:22 final size:23
Alignment explanation
Indices: 827448--827493 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
827438 AAATATTAAA
827448 ATATTATTTTTAT-ATTAATATTT
1 ATATTATTTTTATAATTAA-ATTT
827471 ATATT-TTTTTATAATTAAATTT
1 ATATTATTTTTATAATTAAATTT
827493 A
1 A
827494 ACAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTTTTATAATTAAATTT
Found at i:827649 original size:17 final size:19
Alignment explanation
Indices: 827605--827649 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
827595 TTATTTTGAT
827605 TTATTCTATCACTATTTTAG
1 TTATT-TATCACTATTTTAG
*
827625 TAATTTATC-CTATTTT-G
1 TTATTTATCACTATTTTAG
827642 TTATTTAT
1 TTATTTAT
827650 TTGTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 4 0.17
20 4 0.17
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATTTATCACTATTTTAG
Found at i:841180 original size:17 final size:17
Alignment explanation
Indices: 841160--841224 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
841150 TCTCTTTTTC
**
841160 TTATTTTTAAATTGATT
1 TTATTTTTAAATTGAAA
*
841177 TTATTTTTAATTTGAAA
1 TTATTTTTAAATTGAAA
* *
841194 TTATTTTAAAATTTAATA
1 TTATTTTTAAATTGAA-A
841212 TT-TTTATTAAATT
1 TTATTT-TTAAATT
841225 TTTTTAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 30 0.77
18 9 0.23
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTATTTTTAAATTGAAA
Found at i:841491 original size:18 final size:18
Alignment explanation
Indices: 841468--841503 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
841458 TCACACTTTA
*
841468 ACTTTGTTTTATAAAAAG
1 ACTTTGTCTTATAAAAAG
841486 ACTTTGTCTTATAAAAAG
1 ACTTTGTCTTATAAAAAG
841504 GATAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
ACTTTGTCTTATAAAAAG
Found at i:844490 original size:16 final size:16
Alignment explanation
Indices: 844466--844499 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
844456 CTTAAAAGGA
*
844466 TATTATTTATTTTATT
1 TATTATTTATTATATT
*
844482 TATTTTTTATTATATT
1 TATTATTTATTATATT
844498 TA
1 TA
844500 AAATATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTATTTATTATATT
Found at i:844738 original size:2 final size:2
Alignment explanation
Indices: 844731--844769 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
844721 TTTGGAATGA
844731 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
844770 GGACTGACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:846320 original size:2 final size:2
Alignment explanation
Indices: 846313--846343 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
846303 ATTGGTTAAT
*
846313 AC AC AC AC AC AC AC AC AC AC AC AA AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
846344 AGCAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:848793 original size:144 final size:144
Alignment explanation
Indices: 848533--848801 Score: 382
Period size: 144 Copynumber: 1.9 Consensus size: 144
848523 CTAGAATGTA
* *
848533 TTTTTAAGATGTCCAGACGAGACTACATATAATTGAACAGAAAACATAAGTACCTACGAAGGCAC
1 TTTTTAAGATGTCCAGACAAGACTACATAAAATTGAACAGAAAACATAAGTACCTACGAAGGCAC
* * *
848598 AGGATGCTATCTAAAAATAGAGAAATTCTGGTGAAAGTGTAGCCGCAAAACACTGCCATTTCATG
66 AGCATGCTATCTAAAAATAGAGAAATTCTGGTGAAACTGTAGCAGCAAAACACTGCCATTTCATG
848663 AATGCTCTATTCAC
131 AATGCTCTATTCAC
* *
848677 TTTTTAAGATGTCCAGACAAGACTGCATAAAATTGAACAGACAACATAAG-AGCCTAC-AATGGC
1 TTTTTAAGATGTCCAGACAAGACTACATAAAATTGAACAGAAAACATAAGTA-CCTACGAA-GGC
** * * *
848740 ACAGCATTTTCTCTTAAAATTGAGAAATTCTGGT-ACAACTGTAGCAGCAAAACACTGCCATT
64 ACAGCATGCTATCTAAAAATAGAGAAATTCTGGTGA-AACTGTAGCAGCAAAACACTGCCATT
848802 ATGTGACTGC
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
143 4 0.04
144 106 0.96
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (144 bp):
TTTTTAAGATGTCCAGACAAGACTACATAAAATTGAACAGAAAACATAAGTACCTACGAAGGCAC
AGCATGCTATCTAAAAATAGAGAAATTCTGGTGAAACTGTAGCAGCAAAACACTGCCATTTCATG
AATGCTCTATTCAC
Found at i:853353 original size:22 final size:21
Alignment explanation
Indices: 853302--853354 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
853292 TAATAAATTT
853302 TAATTTTAATTTATTTAAATA
1 TAATTTTAATTTATTTAAATA
**
853323 TAATATTTAATTTAATTTTGATA
1 TAAT-TTTAATTT-ATTTAAATA
*
853346 TGATTTTAA
1 TAATTTTAA
853355 AAAAATGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 13 0.48
23 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TAATTTTAATTTATTTAAATA
Found at i:853617 original size:46 final size:45
Alignment explanation
Indices: 853521--853626 Score: 112
Period size: 46 Copynumber: 2.4 Consensus size: 45
853511 AAATTATCAT
* * *
853521 ATATTTTATTTTTATTTTTAATTTATTTTTATTATATTTTAAAAAA
1 ATATTTTATTTTAATTTTTAATTAATTTATATTATATTTT-AAAAA
*
853567 ATATTTTATTTATAAATTATTTAATTAATTTATATTAT-TTTT-AAAG
1 ATATTTTATTT-T-AATT-TTTAATTAATTTATATTATATTTTAAAAA
853613 ATA--TTATTTTAATT
1 ATATTTTATTTTAATT
853627 AATTTATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
42 4 0.08
43 1 0.02
44 6 0.11
46 17 0.32
47 1 0.02
48 7 0.13
49 17 0.32
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (45 bp):
ATATTTTATTTTAATTTTTAATTAATTTATATTATATTTTAAAAA
Found at i:853623 original size:49 final size:46
Alignment explanation
Indices: 853521--853611 Score: 121
Period size: 49 Copynumber: 1.9 Consensus size: 46
853511 AAATTATCAT
* * *
853521 ATATTTTATTTTTATTTTTAATTTATTTTTATTATATTTTAAAAAA
1 ATATTTTATTTTAATTTTTAATTAATTTATATTATATTTTAAAAAA
853567 ATATTTTATTTATAAATTATTTAATTAATTTATATTAT-TTTTAAA
1 ATATTTTATTT-T-AATT-TTTAATTAATTTATATTATATTTTAAA
853612 GATATTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 11 0.28
47 1 0.03
48 10 0.26
49 17 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (46 bp):
ATATTTTATTTTAATTTTTAATTAATTTATATTATATTTTAAAAAA
Found at i:853644 original size:17 final size:17
Alignment explanation
Indices: 853614--853646 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
853604 TTTTTAAAGA
853614 TATTATTTTAATTAATT
1 TATTATTTTAATTAATT
853631 TATTAGTTTT-ATTAAT
1 TATTA-TTTTAATTAAT
853647 GATGTGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTATTTTAATTAATT
Found at i:853738 original size:15 final size:16
Alignment explanation
Indices: 853713--853742 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
853703 TTATTATTAA
853713 GAAAAAGAAAAAGGGG
1 GAAAAAGAAAAAGGGG
853729 GAAAAA-AAAAAGGG
1 GAAAAAGAAAAAGGG
853743 AAAAGAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAAAAGAAAAAGGGG
Found at i:859449 original size:4 final size:4
Alignment explanation
Indices: 859440--859484 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
859430 TGCTGCTGAA
*
859440 AAAG AAAG AAAG AAAG AAAG -AA- AAAG AAAG AAAG AAAG GAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
859485 AAAAAAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 4 0.11
4 33 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:859465 original size:22 final size:22
Alignment explanation
Indices: 859437--859486 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
859427 ACATGCTGCT
859437 GAAAAAGAAAGAAAGAAAGAAA
1 GAAAAAGAAAGAAAGAAAGAAA
*
859459 GAAAAAGAAAGAAAGAAAGGAA
1 GAAAAAGAAAGAAAGAAAGAAA
859481 GAAAAA
1 GAAAAA
859487 AAAAAGGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
GAAAAAGAAAGAAAGAAAGAAA
Found at i:859642 original size:13 final size:14
Alignment explanation
Indices: 859573--859656 Score: 71
Period size: 14 Copynumber: 5.6 Consensus size: 14
859563 ATTAATACTT
859573 TATTTTATTTTATA
1 TATTTTATTTTATA
859587 TATATTTATATATATATA
1 TAT-TTTAT-T-T-TATA
*
859605 TATGTATTCATATTATA
1 TAT-T-TT-ATTTTATA
*
859622 TATATTATTTT-TA
1 TATTTTATTTTATA
*
859635 TATTTTATTTTAAA
1 TATTTTATTTTATA
859649 TATTTTAT
1 TATTTTAT
859657 AGAAATATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
13 12 0.21
14 16 0.28
15 7 0.12
16 1 0.02
17 8 0.14
18 9 0.16
19 2 0.04
20 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (14 bp):
TATTTTATTTTATA
Found at i:859643 original size:25 final size:25
Alignment explanation
Indices: 859554--859652 Score: 60
Period size: 25 Copynumber: 4.0 Consensus size: 25
859544 TTTTGTATAT
* * * *
859554 TTTTTATATATTAATACTTTATTTTA
1 TTTTTATATTTTATTA-TATATATTA
859580 TTTTATATATATTTA-TATATATA-TA
1 TTTT-TATAT-TTTATTATATATATTA
* * **
859605 TATGTAT-TCATATTATATATATTA
1 TTTTTATATTTTATTATATATATTA
* *
859629 TTTTTATATTTTATTTTAAATATT
1 TTTTTATATTTTATTATATATATT
859653 TTATAGAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
22 2 0.04
23 9 0.16
24 10 0.18
25 16 0.29
26 8 0.15
27 7 0.13
28 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (25 bp):
TTTTTATATTTTATTATATATATTA
Found at i:860207 original size:25 final size:28
Alignment explanation
Indices: 860179--860243 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
860169 TTTGTACATA
*
860179 TTTTAATATATT-CG-TTT-ATTATTTT
1 TTTTATTATATTGCGTTTTAATTATTTT
* *
860204 TTTTTTTATATTGTGTTTTAATTATTTT
1 TTTTATTATATTGCGTTTTAATTATTTT
*
860232 TTATATTATATT
1 TTTTATTATATT
860244 TGAGTCGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 10 0.31
26 1 0.03
27 3 0.09
28 18 0.56
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (28 bp):
TTTTATTATATTGCGTTTTAATTATTTT
Found at i:860725 original size:21 final size:19
Alignment explanation
Indices: 860701--860752 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
860691 ATGTAATATA
860701 TTTAAATTTAAATTATATAAT
1 TTTAAATTTAAATTA-A-AAT
860722 TTTAAATTT-AATTAAAAT
1 TTTAAATTTAAATTAAAAT
860740 TTATAAATATTAA
1 TT-TAAAT-TTAA
860753 GAATCTCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.18
19 6 0.21
20 7 0.25
21 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATTTAAATTAAAAT
Found at i:860752 original size:26 final size:27
Alignment explanation
Indices: 860700--860752 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
860690 TATGTAATAT
* *
860700 ATTTAAATTTAAATTATATAATTTTAA
1 ATTTAAATTAAAATTATATAATATTAA
860727 ATTT-AATTAAAATT-TATAAATATTAA
1 ATTTAAATTAAAATTATAT-AATATTAA
860753 GAATCTCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 16 0.70
27 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAAATTAAAATTATATAATATTAA
Found at i:860879 original size:16 final size:16
Alignment explanation
Indices: 860858--860912 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
860848 ATGTGTTGGA
860858 AAAAAAAGAAAGAAAG
1 AAAAAAAGAAAGAAAG
860874 AAAAAAAGAAAG-AAG
1 AAAAAAAGAAAGAAAG
* *
860889 AAAAAACTGAAAAAAAG
1 AAAAAA-AGAAAGAAAG
860906 AAAAAAA
1 AAAAAAA
860913 AATTATATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.26
16 16 0.47
17 9 0.26
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAGAAAG
Found at i:860908 original size:8 final size:8
Alignment explanation
Indices: 860858--860912 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
860848 ATGTGTTGGA
860858 AAAAAAAG
1 AAAAAAAG
*
860866 AAAGAAAG
1 AAAAAAAG
860874 AAAAAAAG
1 AAAAAAAG
*
860882 -AAAGAAG
1 AAAAAAAG
*
860889 AAAAAACTG
1 AAAAAA-AG
860898 AAAAAAAG
1 AAAAAAAG
860906 AAAAAAA
1 AAAAAAA
860913 AATTATATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 6 0.15
8 26 0.67
9 7 0.18
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:861079 original size:12 final size:13
Alignment explanation
Indices: 861050--861077 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
861040 ATTTTAAGAG
861050 TTTATATTTTTTA
1 TTTATATTTTTTA
861063 TTTATATTTTTTA
1 TTTATATTTTTTA
861076 TT
1 TT
861078 ATTTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:861184 original size:24 final size:24
Alignment explanation
Indices: 861148--861207 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
861138 TCATATTTAT
* *
861148 TTTTTTATATTGTGTTT-TAATTAA
1 TTTTTAATATTGTATTTGT-ATTAA
* *
861172 TTTTTAATTTTGTATTTGTATTAT
1 TTTTTAATATTGTATTTGTATTAA
861196 TTTTTATATATT
1 TTTTTA-ATATT
861208 TAAAGTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (24 bp):
TTTTTAATATTGTATTTGTATTAA
Found at i:862714 original size:20 final size:21
Alignment explanation
Indices: 862681--862735 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
862671 CATATTTGTG
*
862681 TTATTTTTTATATATA-AAATT
1 TTATATTTTATATA-ACAAATT
*
862702 TTATATTTT-TATAACAATTT
1 TTATATTTTATATAACAAATT
*
862722 TTATATATTA-ATAA
1 TTATATTTTATATAA
862736 TTCATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 20 0.69
21 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATTTTATATAACAAATT
Found at i:863373 original size:27 final size:27
Alignment explanation
Indices: 863342--863393 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
863332 TAACAGTAAC
863342 AAATAAGTAAAATATAAGATATCTAGT
1 AAATAAGTAAAATATAAGATATCTAGT
863369 AAATAAGTAAAATATAAGATATCTA
1 AAATAAGTAAAATATAAGATATCTA
863394 TGTATACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.29
Consensus pattern (27 bp):
AAATAAGTAAAATATAAGATATCTAGT
Found at i:863567 original size:20 final size:20
Alignment explanation
Indices: 863538--863582 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
863528 TATGTTTGTG
863538 TTAT-TTTTTATATAAAA-TT
1 TTATATTTTTATA-AAAATTT
863557 TTATATTTTTATAAAAATTT
1 TTATATTTTTATAAAAATTT
863577 TTATAT
1 TTATAT
863583 ATTAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTTTATAAAAATTT
Found at i:863590 original size:20 final size:19
Alignment explanation
Indices: 863551--863590 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
863541 TTTTTTATAT
* *
863551 AAAATTTTATATTTTTATA
1 AAAATTTTATATATTAATA
863570 AAAATTTTTATATATTAATA
1 AAAA-TTTTATATATTAATA
863590 A
1 A
863591 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATTTTATATATTAATA
Found at i:863706 original size:22 final size:22
Alignment explanation
Indices: 863637--863707 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 22
863627 TATTCATGTC
* *
863637 ATGTGTATATTATTTTTATGTT
1 ATGTTTATATTATTTTTATATT
863659 ATGTTTTAAATATT-TTTTAAATATATT
1 ATG-TTT--ATATTATTTT---TATATT
863686 ATGTTTATATTATTTTTATATT
1 ATGTTTATATTATTTTTATATT
863708 GATAAAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
22 9 0.22
23 2 0.05
24 9 0.22
25 9 0.22
26 3 0.08
27 8 0.20
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
ATGTTTATATTATTTTTATATT
Found at i:864013 original size:18 final size:18
Alignment explanation
Indices: 863982--864020 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
863972 ACACGGACAT
*
863982 ATAAATATTTATGTA-AA
1 ATAAATATTAATGTATAA
863999 ATAAATTATTAATGTATAA
1 ATAAA-TATTAATGTATAA
864018 ATA
1 ATA
864021 TTTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATAAATATTAATGTATAA
Found at i:864443 original size:26 final size:26
Alignment explanation
Indices: 864384--864443 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
864374 TTGATATATA
* *
864384 AAAAATTATATAAATTTATATTTTTTT
1 AAAAA-TAAATAAATTTATATTTTTAT
*
864411 TAAAATAAATAAATTTAT-TTTTTAT
1 AAAAATAAATAAATTTATATTTTTAT
864436 AAATAATA
1 AAA-AATA
864444 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 8 0.29
26 16 0.57
27 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAAAATAAATAAATTTATATTTTTAT
Found at i:864542 original size:88 final size:87
Alignment explanation
Indices: 864386--864545 Score: 191
Period size: 88 Copynumber: 1.8 Consensus size: 87
864376 GATATATAAA
* ** *
864386 AAATTATATAAATTTATATTTTTTTTAAAATAAATAAATTTATTTTTTATAAATAATATATTAAA
1 AAATTATATAAATTTATATTTATTTTAAAATAAATAAATTTATAATATATAAATAATATATTAAA
864451 AAATTAATCGACACTAACTCTT
66 AAATTAATCGACACTAACTCTT
* * * *
864473 AAATTAATTTAAATTTTATATCTTATTTTTAAATAAA-AAATTTA-AATATATAATTATTAT-TT
1 AAATT-ATATAAA-TTTATAT-TTATTTTAAAATAAATAAATTTATAATATATAAATAATATATT
864535 AATAAAATTAA
63 AA-AAAATTAA
864546 ATTTTAGATT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
87 9 0.15
88 25 0.41
89 14 0.23
90 13 0.21
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (87 bp):
AAATTATATAAATTTATATTTATTTTAAAATAAATAAATTTATAATATATAAATAATATATTAAA
AAATTAATCGACACTAACTCTT
Found at i:865428 original size:2 final size:2
Alignment explanation
Indices: 865421--865456 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
865411 ATTTCATGAG
865421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
865457 CTTGCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:865526 original size:12 final size:12
Alignment explanation
Indices: 865509--865536 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
865499 TTATTATATA
865509 TATATATGTATG
1 TATATATGTATG
865521 TATATATGTATG
1 TATATATGTATG
865533 TATA
1 TATA
865537 AGTCTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:870722 original size:36 final size:36
Alignment explanation
Indices: 870651--870731 Score: 83
Period size: 37 Copynumber: 2.2 Consensus size: 36
870641 ATAAGCGTTT
* * *
870651 AAATTATCAAATTTAATTTAAAAATTTTAAAAATTTA
1 AAATTATTAAATTAAATTTAAAAA-TATAAAAATTTA
* *
870688 AAATTATTAAATTAAATTTAAATAA-ATAATAATTTT
1 AAATTATTAAATTAAATTTAAA-AATATAAAAATTTA
*
870724 TAATTATT
1 AAATTATT
870732 TTATAATAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 15 0.41
37 20 0.54
38 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (36 bp):
AAATTATTAAATTAAATTTAAAAATATAAAAATTTA
Found at i:870821 original size:28 final size:28
Alignment explanation
Indices: 870788--870844 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
870778 ATGTTAAATG
*
870788 TAAAAAAGTAGATT-AAGATAAATATAATA
1 TAAAAAA-TA-ATTAAAAATAAATATAATA
870817 TAAAAAATAATTAAAAATAAATATAATA
1 TAAAAAATAATTAAAAATAAATATAATA
870845 AATGATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (28 bp):
TAAAAAATAATTAAAAATAAATATAATA
Found at i:870908 original size:34 final size:35
Alignment explanation
Indices: 870865--870943 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 35
870855 ATTCGATCAC
* *
870865 TAATA-ATTAAGTTATATTAAAATTTATATAAA-ATA
1 TAATATATTAA-TT-TATCAAAAATTATATAAATATA
870900 -AAT-TATTAATTTATCAAAAATTATATAAATATA
1 TAATATATTAATTTATCAAAAATTATATAAATATA
870933 TAATATATTAA
1 TAATATATTAA
870944 AATATAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 16 0.42
33 5 0.13
34 11 0.29
35 6 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TAATATATTAATTTATCAAAAATTATATAAATATA
Found at i:871224 original size:24 final size:21
Alignment explanation
Indices: 871197--871300 Score: 67
Period size: 21 Copynumber: 5.0 Consensus size: 21
871187 TTAAATTTGA
871197 TTAATTAATATTAATTAAAAATAT
1 TTAATTAATATT--TTAAAAAT-T
*
871221 TTAATTATTATTTTAAAAATT
1 TTAATTAATATTTTAAAAATT
* *
871242 TT-ATATAATATATT---ATTT
1 TTAAT-TAATATTTTAAAAATT
*
871260 TTTATTAA-ATTTTAAAAAATT
1 TTAATTAATATTTT-AAAAATT
*
871281 ATTAATTTAT-TTTTAAAAAT
1 -TTAATTAATATTTTAAAAAT
871301 CATTTTAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.06
18 8 0.12
19 2 0.03
20 2 0.03
21 19 0.30
22 18 0.28
24 11 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATTAATATTTTAAAAATT
Found at i:871366 original size:21 final size:22
Alignment explanation
Indices: 871333--871373 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
871323 TTTTTTAAAT
871333 TTTATATAAATATATTTATTAC
1 TTTATATAAATATATTTATTAC
* *
871355 TTTA-ATATATATTTTTATT
1 TTTATATAAATATATTTATT
871374 TTGGTTGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATATAAATATATTTATTAC
Found at i:872699 original size:24 final size:24
Alignment explanation
Indices: 872648--872707 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
872638 CTAAACAAGG
*
872648 ACAGTAATCAACATACCATCACCG
1 ACAGTAATCAACATACCATCACCA
*
872672 ACAGTAATCAACATACCATCGCCA
1 ACAGTAATCAACATACCATCACCA
*
872696 ACAGGAA-CAACA
1 ACAGTAATCAACA
872708 ACAGGGAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.15
24 28 0.85
ACGTcount: A:0.45, C:0.32, G:0.10, T:0.13
Consensus pattern (24 bp):
ACAGTAATCAACATACCATCACCA
Found at i:873316 original size:16 final size:16
Alignment explanation
Indices: 873281--873315 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
873271 TAATAGAAAG
*
873281 AAAATTGAAAAGATGA
1 AAAATTGAAAAGAGGA
873297 AAAATTGAAAA-AGGA
1 AAAATTGAAAAGAGGA
873312 AAAA
1 AAAA
873316 AAGTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAATTGAAAAGAGGA
Found at i:873697 original size:22 final size:22
Alignment explanation
Indices: 873650--873691 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
873640 TTCAAATTCA
* *
873650 TTTTCTTTCTATTTTTTCACCC
1 TTTTCTATCTATTCTTTCACCC
873672 TTTTCTATCTATTCTTTCAC
1 TTTTCTATCTATTCTTTCAC
873692 TTTTTTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTCTATCTATTCTTTCACCC
Found at i:879469 original size:2 final size:2
Alignment explanation
Indices: 879462--879495 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
879452 TTGGAGTTAA
879462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
879496 CATGACTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:880544 original size:58 final size:58
Alignment explanation
Indices: 880448--880558 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
880438 TAATCAATTA
* *
880448 TTAATTGATGATATCTAAATGTGTTCATGGTTACGACTGTTCAATTAATGCTTAATAT
1 TTAATTGATGATATCTAAATATGTTCATGGGTACGACTGTTCAATTAATGCTTAATAT
*
880506 TTAATTGATGATATCTAAATATGTTCATGGGTAGGACTGTTCAATTAATGCTT
1 TTAATTGATGATATCTAAATATGTTCATGGGTACGACTGTTCAATTAATGCTT
880559 GATTTTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (58 bp):
TTAATTGATGATATCTAAATATGTTCATGGGTACGACTGTTCAATTAATGCTTAATAT
Found at i:880705 original size:21 final size:22
Alignment explanation
Indices: 880659--880710 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
880649 ATATTTATAA
*
880659 TTAAATTTAAATAAAAAATAAAT
1 TTAAA-TTACATAAAAAATAAAT
* *
880682 TTATATTACATAAATAAT-AAT
1 TTAAATTACATAAAAAATAAAT
880703 TTAAATTA
1 TTAAATTA
880711 AACTAATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
22 11 0.44
23 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATTACATAAAAAATAAAT
Found at i:880766 original size:32 final size:33
Alignment explanation
Indices: 880691--880766 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 33
880681 TTTATATTAC
*
880691 ATAAATAATAATTTAAATTAAACTAATTCAAAAT
1 ATAAATAAT-ATTTAAATTAAACTAAATCAAAAT
* *
880725 ATAAA-AATATTT-ACTTAAACTAAATC-CAAT
1 ATAAATAATATTTAAATTAAACTAAATCAAAAT
880755 ATAAATTAATAT
1 ATAAA-TAATAT
880767 ATTGAGCCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 8 0.22
31 12 0.32
32 9 0.24
33 3 0.08
34 5 0.14
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (33 bp):
ATAAATAATATTTAAATTAAACTAAATCAAAAT
Found at i:892116 original size:16 final size:15
Alignment explanation
Indices: 892096--892137 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
892086 TCCATTTAAC
892096 AATTAATTTAT-TAA
1 AATTAATTTATATAA
892110 TATATTAATTATATATAA
1 -A-ATTAATT-TATATAA
892128 AATTAATTTA
1 AATTAATTTA
892138 ACCTCACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 4 0.17
18 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTTATATAA
Found at i:892596 original size:17 final size:17
Alignment explanation
Indices: 892574--892606 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
892564 ATTTATTAAT
892574 ATTAAACAT-AATATAAA
1 ATTAAA-ATAAATATAAA
892591 ATTAAAATAAATATAA
1 ATTAAAATAAATATAA
892607 TATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAAAATAAATATAAA
Found at i:892611 original size:11 final size:11
Alignment explanation
Indices: 892570--892616 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
892560 TTAAATTTAT
*
892570 TAATATTAAACA
1 TAATA-TAAATA
892582 TAATATAAA-A
1 TAATATAAATA
*
892592 TTAAAATAAATA
1 -TAATATAAATA
892604 TAATATAAATA
1 TAATATAAATA
892615 TA
1 TA
892617 TAAATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:892636 original size:18 final size:18
Alignment explanation
Indices: 892597--892676 Score: 69
Period size: 18 Copynumber: 4.5 Consensus size: 18
892587 TAAAATTAAA
* *
892597 ATAAATATAATATAAATAT
1 ATAAATATATTA-AAATTT
892616 ATAAATATATTAAAATTT
1 ATAAATATATTAAAATTT
*
892634 ATATAT-TA-T-AAA-TT
1 ATAAATATATTAAAATTT
*
892648 ATTAATATATTAAAATTT
1 ATAAATATATTAAAATTT
892666 ACATAAATATA
1 --ATAAATATA
892677 ACATTTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
16 2 0.04
17 5 0.10
18 12 0.24
19 11 0.22
20 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATATATTAAAATTT
Found at i:892637 original size:14 final size:14
Alignment explanation
Indices: 892620--892666 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
892610 AAATATATAA
892620 ATATATTAAAATTT
1 ATATATTAAAATTT
892634 ATATATTATAAATTATT
1 ATATATTA-AAA-T-TT
892651 AATATATTAAAATTT
1 -ATATATTAAAATTT
892666 A
1 A
892667 CATAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 9 0.31
15 5 0.17
16 2 0.07
17 5 0.17
18 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:892660 original size:32 final size:33
Alignment explanation
Indices: 892556--892677 Score: 119
Period size: 33 Copynumber: 3.7 Consensus size: 33
892546 TTATTGATTT
*
892556 TATATT-AAATTTAT-TAATATTAAACATAATATAA
1 TATATTAAAATTTATATAATA-TAAATAT-ATA-AA
**
892590 -A-ATTAAAATAAATATAATATAAATATATAAA
1 TATATTAAAATTTATATAATATAAATATATAAA
* *
892621 TATATTAAAATTTATATATTATAAAT-TATTAA
1 TATATTAAAATTTATATAATATAAATATATAAA
*
892653 TATATTAAAATTTACATAAATATAA
1 TATATTAAAATTTATAT-AATATAA
892678 CATTTTTTAC
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
31 2 0.03
32 28 0.38
33 39 0.53
34 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
TATATTAAAATTTATATAATATAAATATATAAA
Found at i:893378 original size:12 final size:12
Alignment explanation
Indices: 893335--893382 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
893325 TCATTATACG
*
893335 ATAT-AAATATT
1 ATATAAAATATA
893346 ATATAAAA-A-A
1 ATATAAAATATA
893356 A-ATAAAATATA
1 ATATAAAATATA
*
893367 ATATAAATTATA
1 ATATAAAATATA
893379 ATAT
1 ATAT
893383 CACATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 7 0.23
12 16 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:894685 original size:20 final size:20
Alignment explanation
Indices: 894657--894694 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
894647 TTAAATTTAA
894657 ATTAATTAAAAATATATTTT
1 ATTAATTAAAAATATATTTT
* *
894677 ATTATTTAAAATTATATT
1 ATTAATTAAAAATATATT
894695 AATATTTATA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATTAAAAATATATTTT
Found at i:894753 original size:20 final size:19
Alignment explanation
Indices: 894710--894753 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
894700 TTATAATTAA
* *
894710 ATTTAAATAAAATTTTATT
1 ATTTAAATAAAATTTAAAT
894729 ATTTAAATAATAATTTAAAT
1 ATTTAAATAA-AATTTAAAT
*
894749 CTTTA
1 ATTTA
894754 TAAATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAATAAAATTTAAAT
Found at i:894989 original size:4 final size:4
Alignment explanation
Indices: 894982--895008 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
894972 CTTTTATAAT
894982 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
895009 TGAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:895435 original size:27 final size:27
Alignment explanation
Indices: 895380--895432 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
895370 CAGTTTTTTT
895380 TTTTGGTTGATTTTGAATAATTTTGAA
1 TTTTGGTTGATTTTGAATAATTTTGAA
895407 TTTT-GTTGATTTCTGAA-AATTTTGAA
1 TTTTGGTTGATTT-TGAATAATTTTGAA
895433 ATTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (27 bp):
TTTTGGTTGATTTTGAATAATTTTGAA
Found at i:895943 original size:2 final size:2
Alignment explanation
Indices: 895936--895967 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
895926 AATAACATAC
*
895936 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
895968 CTGAACTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:896622 original size:14 final size:15
Alignment explanation
Indices: 896587--896628 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
896577 TATTAAAAAT
896587 AATTTTATTAAGTTAAA
1 AATTTTATT-A-TTAAA
*
896604 TATTTT-TTATTAAA
1 AATTTTATTATTAAA
896618 AATTTTATTAT
1 AATTTTATTAT
896629 ATTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 5 0.23
16 2 0.09
17 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
AATTTTATTATTAAA
Found at i:896648 original size:16 final size:16
Alignment explanation
Indices: 896627--896664 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
896617 AAATTTTATT
896627 ATATTTAATATTAAAA
1 ATATTTAATATTAAAA
* *
896643 ATATTTTATATTTAAA
1 ATATTTAATATTAAAA
896659 AT-TTTA
1 ATATTTA
896665 TTTATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTAATATTAAAA
Found at i:896651 original size:23 final size:24
Alignment explanation
Indices: 896611--896657 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
896601 AAATATTTTT
*
896611 TATTAAAAATTTTATTATATTTAA
1 TATTAAAAATATTATTATATTTAA
896635 TATTAAAAATATT-TTATATTTAA
1 TATTAAAAATATTATTATATTTAA
896658 AATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAAAAATATTATTATATTTAA
Found at i:896684 original size:40 final size:40
Alignment explanation
Indices: 896601--896682 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
896591 TTATTAAGTT
* *
896601 AAATATTTTTTATTAAAAATTTTATTATATTTAATATTAA
1 AAATATTTTATATTAAAAATTTTATTATATTAAATATTAA
*
896641 AAATATTTTATATTTAAAATTTTATT-TATATAAAT-TTAA
1 AAATATTTTATATTAAAAATTTTATTATAT-TAAATATTAA
896680 AAA
1 AAA
896683 ATTATCCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 10 0.26
40 28 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
AAATATTTTATATTAAAAATTTTATTATATTAAATATTAA
Found at i:900737 original size:18 final size:17
Alignment explanation
Indices: 900714--900749 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
900704 TCCATATATT
900714 TTATATTTATATTTTAAA
1 TTATATTTAT-TTTTAAA
900732 TTATATTTATTTTTAAA
1 TTATATTTATTTTTAAA
900749 T
1 T
900750 ATTACATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTTATTTTTAAA
Found at i:900787 original size:25 final size:25
Alignment explanation
Indices: 900742--900789 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
900732 TTATATTTAT
* *
900742 TTTTAAATATTACATATTTTATAAA
1 TTTTAAAAATTACATAATTTATAAA
900767 TTTTAATAAATTA-ATAATTTATA
1 TTTTAA-AAATTACATAATTTATA
900790 TTATTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAAATTACATAATTTATAAA
Found at i:900796 original size:25 final size:25
Alignment explanation
Indices: 900768--900817 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
900758 TTTTATAAAT
900768 TTTAATAAATTAATA-ATTTATATTA
1 TTTAAT-AATTAATATATTTATATTA
**
900793 TTTAATTTTTAATATATTTATATTA
1 TTTAATAATTAATATATTTATATTA
900818 AAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAATAATTAATATATTTATATTA
Found at i:900840 original size:31 final size:31
Alignment explanation
Indices: 900797--900862 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
900787 ATATTATTTA
900797 ATTTTTAATATATTTATATTAAAATTTTATT
1 ATTTTTAATATATTTATATTAAAATTTTATT
* * *
900828 ATTTTTATTATATTTATATTATATTTTTATT
1 ATTTTTAATATATTTATATTAAAATTTTATT
900859 ATTT
1 ATTT
900863 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTAATATATTTATATTAAAATTTTATT
Found at i:900841 original size:11 final size:11
Alignment explanation
Indices: 900797--900860 Score: 69
Period size: 11 Copynumber: 6.0 Consensus size: 11
900787 ATATTATTTA
*
900797 ATTTTTAATAT
1 ATTTTTATTAT
* *
900808 ATTTATATTAA
1 ATTTTTATTAT
*
900819 AATTTTA-T-T
1 ATTTTTATTAT
900828 ATTTTTATTAT
1 ATTTTTATTAT
*
900839 ATTTATATTAT
1 ATTTTTATTAT
900850 ATTTTTATTAT
1 ATTTTTATTAT
900861 TTAAAATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 34 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTTTATTAT
Found at i:901852 original size:18 final size:18
Alignment explanation
Indices: 901807--901969 Score: 56
Period size: 18 Copynumber: 8.8 Consensus size: 18
901797 ATTTTAGAAA
901807 ATTTT-TTA-ATTTATAT
1 ATTTTATTATATTTATAT
* *
901823 ATTTAAATTATATTTCTAT
1 ATTT-TATTATATTTATAT
901842 ATTTTATTATA-TTATAATT
1 ATTTTATTATATTTAT-A-T
**
901861 ATATTTAAAATATTT-TAT
1 AT-TTTATTATATTTATAT
* *
901879 A-TTTATATAAATTTTTAT
1 ATTTTAT-TATATTTATAT
*
901897 ACGTTAATAATT-TATTTATAT
1 A--TT--TTATTATATTTATAT
**
901918 AAATTTTAAAATATTTATAT
1 --ATTTTATTATATTTATAT
901938 ATTTATATTAT-TTT-T-T
1 ATTT-TATTATATTTATAT
901954 ATTTTAATTATTATTT
1 ATTTT-ATTA-TATTT
901970 TTCTTATGTC
Statistics
Matches: 109, Mismatches: 17, Indels: 40
0.66 0.10 0.24
Matches are distributed among these distances:
15 1 0.01
16 17 0.16
17 10 0.09
18 26 0.24
19 21 0.19
20 17 0.16
21 12 0.11
22 1 0.01
23 4 0.04
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTTTATTATATTTATAT
Found at i:912851 original size:2 final size:2
Alignment explanation
Indices: 912844--912869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
912834 TGTAGATTTG
912844 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
912870 AATTAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:915249 original size:10 final size:10
Alignment explanation
Indices: 915215--915248 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
915205 ACCTTTTACG
915215 TATAAATATA
1 TATAAATATA
*
915225 TACAAATATA
1 TATAAATATA
*
915235 TATATATATA
1 TATAAATATA
915245 TATA
1 TATA
915249 TGTATAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATAAATATA
Found at i:916315 original size:3 final size:3
Alignment explanation
Indices: 916307--916342 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
916297 CACTCGTCTC
916307 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
916343 ATTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:916347 original size:3 final size:3
Alignment explanation
Indices: 916341--916374 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
916331 CTTCTTCTTC
916341 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
916375 ACCAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:916455 original size:18 final size:19
Alignment explanation
Indices: 916422--916458 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
916412 TACTTATTTT
*
916422 ATAAAATATAAGTAAAATA
1 ATAAAATATAAATAAAATA
916441 ATAAAA-ATAAATAAAATA
1 ATAAAATATAAATAAAATA
916459 CATATTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAAAATATAAATAAAATA
Found at i:916586 original size:96 final size:93
Alignment explanation
Indices: 916415--916587 Score: 215
Period size: 96 Copynumber: 1.8 Consensus size: 93
916405 AAAATGATAC
*
916415 TTATTTTATAAAATATAAGTAAAATAATAAAAATAAATAAAATACATATTACTTGATTAAATTTT
1 TTATTTTATAAAATATAAGTAAAATAATAAAAATAAATAAAATACATATTACTTGATTAAATTTA
*
916480 TTATATAATTTTGTATGATAAAAAATAA
66 TAATATAATTTTGTATGATAAAAAATAA
* * * * *
916508 TTATTTTGTAAAATAT-ATTTAAATAATAAAAATAAATAAATAAGATACATATTATTTTATT-AA
1 TTATTTTATAAAATATAAGTAAAATAATAAAAATAAAT--A-AA-ATACATATTACTTGATTAAA
*
916571 TTTATAATGTAAATTTT
62 TTTATAATAT-AATTTT
916588 TTTACCACTA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
92 19 0.28
93 15 0.22
94 1 0.01
95 11 0.16
96 21 0.31
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (93 bp):
TTATTTTATAAAATATAAGTAAAATAATAAAAATAAATAAAATACATATTACTTGATTAAATTTA
TAATATAATTTTGTATGATAAAAAATAA
Found at i:916761 original size:66 final size:66
Alignment explanation
Indices: 916665--916829 Score: 188
Period size: 69 Copynumber: 2.4 Consensus size: 66
916655 ATAATGATAT
* * *
916665 TTAACCAAAAAATTATAATAAATAATTTTTT-TTAAATCGAACAAAAACAATATATTATTTAGTT
1 TTAACCAAAAAA-TATCATTAATAATTTTTTCTTAAATCGAACAAAAACAATATATTACTTAGTT
916729 CA
65 CA
** * *
916731 TTAACCAAAAAGATATCATTAATGAATTTTTTTCTTGCATCGAACAAAAATAATATATTACTTAT
1 TTAACCAAAAA-ATATCATTAAT-AA-TTTTTTCTTAAATCGAACAAAAACAATATATTACTTAG
916796 TTCA
63 TTCA
* * *
916800 TTAACAAAAAAATACCATTAAATTATTTTT
1 TTAACCAAAAAATATCATT-AATAATTTTT
916830 AATCAATAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
66 19 0.23
67 8 0.10
68 14 0.17
69 43 0.51
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.39
Consensus pattern (66 bp):
TTAACCAAAAAATATCATTAATAATTTTTTCTTAAATCGAACAAAAACAATATATTACTTAGTTC
A
Found at i:917409 original size:24 final size:23
Alignment explanation
Indices: 917369--917415 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
917359 TAATAAATTT
*
917369 AAAAAATTAAAAGTAAATGTAAA
1 AAAAAATTAAAAGTAAATCTAAA
917392 AAAAAATATAAATA-TAAATCTAAA
1 AAAAAAT-TAAA-AGTAAATCTAAA
917416 CTTCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 13 0.62
25 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (23 bp):
AAAAAATTAAAAGTAAATCTAAA
Found at i:917926 original size:2 final size:2
Alignment explanation
Indices: 917919--917958 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
917909 TAGTCCTTTG
* *
917919 CT CT CT CT CC CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
917959 ATGCATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:918837 original size:51 final size:50
Alignment explanation
Indices: 918709--918918 Score: 359
Period size: 50 Copynumber: 4.2 Consensus size: 50
918699 TATACTTAGA
918709 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
918759 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAA-TT
* *
918810 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* *
918860 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATT
918910 GTCAACAAT
1 GTCAACAAT
918919 GACAACAACT
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
50 103 0.67
51 50 0.33
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
Found at i:918886 original size:101 final size:101
Alignment explanation
Indices: 918709--918904 Score: 365
Period size: 101 Copynumber: 1.9 Consensus size: 101
918699 TATACTTAGA
*
918709 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
918774 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
*
918810 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
*
918875 CACCTCTCTCTATTGTCAAAGGTTGGTGAA
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAA
918905 TGATAGTCAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
Found at i:923441 original size:51 final size:50
Alignment explanation
Indices: 923313--923522 Score: 359
Period size: 50 Copynumber: 4.2 Consensus size: 50
923303 TATACTTAGA
923313 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
923363 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAA-TT
* *
923414 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* *
923464 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATT
923514 GTCAACAAT
1 GTCAACAAT
923523 GACAACAACT
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
50 103 0.67
51 50 0.33
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
Found at i:923490 original size:101 final size:101
Alignment explanation
Indices: 923313--923508 Score: 365
Period size: 101 Copynumber: 1.9 Consensus size: 101
923303 TATACTTAGA
*
923313 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
923378 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
*
923414 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
*
923479 CACCTCTCTCTATTGTCAAAGGTTGGTGAA
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAA
923509 TGATAGTCAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTT
Found at i:925855 original size:3 final size:3
Alignment explanation
Indices: 925840--925884 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
925830 TTACACGTTG
*
925840 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
925885 AAGTTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:926086 original size:3 final size:3
Alignment explanation
Indices: 926078--926114 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
926068 CGTATTTTTG
926078 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
926115 GTAATTGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:926605 original size:12 final size:11
Alignment explanation
Indices: 926564--926648 Score: 53
Period size: 12 Copynumber: 7.0 Consensus size: 11
926554 TATATTGTAT
*
926564 AATTAAATTTA
1 AATTAATTTTA
*
926575 AATAAAATTTTA
1 AAT-TAATTTTA
926587 ATTATTAATTATTA
1 A--ATTAATT-TTA
*
926601 AATTAAATTTA
1 AATTAATTTTA
*
926612 AATAAAATTTTA
1 AAT-TAATTTTA
926624 ATTATTAATTATTA
1 A--ATTAATT-TTA
*
926638 AATTAAATTTA
1 AATTAATTTTA
926649 TAAAAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
11 12 0.21
12 26 0.45
13 8 0.14
14 12 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTAATTTTA
Found at i:926605 original size:37 final size:37
Alignment explanation
Indices: 926564--926659 Score: 176
Period size: 37 Copynumber: 2.6 Consensus size: 37
926554 TATATTGTAT
926564 AATTAAATTTAAATAAAATTTTAATTATTAATTATTA
1 AATTAAATTTAAATAAAATTTTAATTATTAATTATTA
926601 AATTAAATTTAAATAAAATTTTAATTATTAATTATTA
1 AATTAAATTTAAATAAAATTTTAATTATTAATTATTA
*
926638 AATTAAATTTATA-AAAATTTTA
1 AATTAAATTTAAATAAAATTTTA
926660 TTTAAAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
36 9 0.16
37 49 0.84
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
AATTAAATTTAAATAAAATTTTAATTATTAATTATTA
Found at i:930168 original size:27 final size:26
Alignment explanation
Indices: 930130--930181 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
930120 TTATTCTTTT
930130 TAAATATGTAAA-ATTTTGTATATTAAA
1 TAAATATGTAAATATTTT-TA-ATTAAA
930157 TAAATAAT-TAAATATTTTTAATTAA
1 TAAAT-ATGTAAATATTTTTAATTAA
930182 TTTGAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 5 0.22
27 11 0.48
28 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAATATGTAAATATTTTTAATTAAA
Found at i:930488 original size:2 final size:2
Alignment explanation
Indices: 930481--930505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
930471 TCGGTTCAAC
930481 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
930506 GTCAGGTAAG
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:932378 original size:2 final size:2
Alignment explanation
Indices: 932315--932358 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
932305 TCTCTCTCTT
* *
932315 TA TA TA TA TG TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
932357 TA
1 TA
932359 CACACACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:932383 original size:14 final size:14
Alignment explanation
Indices: 932366--932404 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
932356 ATACACACAC
* *
932366 ACATATATATATAG
1 ACATACATATACAG
*
932380 ACATACATATACAT
1 ACATACATATACAG
932394 ACATACATATA
1 ACATACATATA
932405 AAAGAAGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (14 bp):
ACATACATATACAG
Found at i:932401 original size:18 final size:18
Alignment explanation
Indices: 932350--932402 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
932340 ATATATATAT
*
932350 ATATATATACACACACAC
1 ATATATATACACACATAC
* *
932368 ATATATATATAGACATAC
1 ATATATATACACACATAC
* *
932386 ATATACATACATACATA
1 ATATATATACACACATA
932403 TAAAAGAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (18 bp):
ATATATATACACACATAC
Found at i:935850 original size:19 final size:18
Alignment explanation
Indices: 935826--935881 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
935816 TAAAAAAATA
935826 ATTTTAAAATATATTATAT
1 ATTTTAAAATATATT-TAT
*
935845 ATTTTAAAA-ATAATTAT
1 ATTTTAAAATATATTTAT
* *
935862 ATTTAAAAAT-TATTTTT
1 ATTTTAAAATATATTTAT
935879 ATT
1 ATT
935882 ATTTACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 19 0.59
18 4 0.12
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAAAATATATTTAT
Found at i:935856 original size:20 final size:18
Alignment explanation
Indices: 935826--935863 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 18
935816 TAAAAAAATA
935826 ATTTTAAAATATATTATAT
1 ATTTTAAAATA-ATTATAT
935845 ATTTTAAAAATAATTATAT
1 ATTTT-AAAATAATTATAT
935864 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAAAATAATTATAT
Found at i:935864 original size:17 final size:18
Alignment explanation
Indices: 935826--935871 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
935816 TAAAAAAATA
*
935826 ATTTTAAAATATATTATAT
1 ATTTTAAAA-ATAATATAT
935845 ATTTTAAAAATAAT-TAT
1 ATTTTAAAAATAATATAT
935862 A-TTTAAAAAT
1 ATTTTAAAAAT
935872 TATTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.35
17 4 0.15
18 4 0.15
19 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTTAAAAATAATATAT
Found at i:935881 original size:17 final size:16
Alignment explanation
Indices: 935816--935871 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
935806 TCACAATTCA
*
935816 TAAAAA-AATAAT-TT
1 TAAAAATAATTATATT
*
935830 TAAAATATATTATATATTT
1 TAAAA-ATAAT-TATA-TT
935849 TAAAAATAATTATATT
1 TAAAAATAATTATATT
935865 TAAAAAT
1 TAAAAAT
935872 TATTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
16 11 0.32
17 6 0.18
18 4 0.12
19 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAAATAATTATATT
Found at i:937336 original size:21 final size:21
Alignment explanation
Indices: 937298--937337 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
937288 TTTGGTGAGA
* **
937298 ATGTTAGGTGTGTTAGATAAT
1 ATGTTAGGTGAGCAAGATAAT
937319 ATGTTAGGTGAGCAAGATA
1 ATGTTAGGTGAGCAAGATA
937338 TTTTATATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (21 bp):
ATGTTAGGTGAGCAAGATAAT
Found at i:937740 original size:34 final size:34
Alignment explanation
Indices: 937664--937741 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
937654 GTTAAGTGTG
* * ** *
937664 TTAGGTGAAGCATATTAGGTGTGTTAGGTGTTGTA
1 TTAGGTG-AGAATATTAGGTGTGTTAAGTAATATA
* *
937699 TTTGGTGAGAATGTTAGGTGTGTTAAGTAATATA
1 TTAGGTGAGAATATTAGGTGTGTTAAGTAATATA
937733 TTAGGTGAG
1 TTAGGTGAG
937742 TAAGATATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.26, C:0.01, G:0.33, T:0.40
Consensus pattern (34 bp):
TTAGGTGAGAATATTAGGTGTGTTAAGTAATATA
Found at i:937962 original size:410 final size:412
Alignment explanation
Indices: 937180--938000 Score: 1290
Period size: 410 Copynumber: 2.0 Consensus size: 412
937170 AACGGAGAGT
* *
937180 TGTTATTGTTAAAAATTATCATTAATTTGAGTGCTAGACCTACATATCTTTATTAATTTTTTTGT
1 TGTTATTGTTAAAAATAATCATTAATTTGAGTGCTAAACCTACATATCTTTATTAATTTTTTTGT
* *
937245 TAAGTGTGTTAGGTGAAGTATATTGGGTATGTTAAGTGATGTATTTGGTGAGAATGTTAGGTGTG
66 TAAGTGTGTTAGGTGAAGCATATTAGGTATGTTAAGTGATGTATTTGGTGAGAATGTTAGGTGTG
* *
937310 TTAGATAATATGTTAGGTGAGCAAGATATTTTATATTCATTATGGACAAGACTTGAACATATATA
131 TTAGATAATATATTAGGTGAGCAAGATATTTTATATTCATTATAGACAAGACTTGAACATATATA
* *
937375 TAAAAAGTTAATTGTCTAGCAATTCTTACAACAACAAGAAGCATTGACTTTAGTAGTTAAAAGCT
196 TAAAAAGCTAATTGTCTAGCAATTCTTACAACAACAAGAAGCATTGACTCTAGTAGTTAAAAGCT
*
937440 TTGTGTGAGGTATGAATGAAATATTTTCTTTGGTGAGTATGAGTGGTGATGAGTAAAAATATTTG
261 TTGTGTGAGGTATGAATGAAATATTTTCTTTGGTGAGTATGAGCGGTGATGAGTAAAAATATTTG
*
937505 TGAGTGTTTATTTGAGTTGTAATATTAGTCAATTTAATAAAAATATTTTAAGTTCACTTATATTT
326 TAAGTGTTTATTTGAGTTGTAATATTAGTCAATTTAATAAAAATATTTTAAGTTCACTTATATTT
937570 TTTCGTTCTATGCTCTACAATC
391 TTTCGTTCTATGCTCTACAATC
* *
937592 TGTTA-TGTTAAAAATAATCATTAATTTGTGTGCTAAACCTACATATTTTTATTAATTTTTTTGT
1 TGTTATTGTTAAAAATAATCATTAATTTGAGTGCTAAACCTACATATCTTTATTAATTTTTTTGT
* * *
937656 TAAGTGTGTTAGGTGAAGCATATTAGGTGTGTTAGGTGTTGTATTTGGTGAGAATGTTAGGTGTG
66 TAAGTGTGTTAGGTGAAGCATATTAGGTATGTTAAGTGATGTATTTGGTGAGAATGTTAGGTGTG
* * * * *
937721 TTA-AGTAATATATTAGGTGAGTAAGATATTTTATATTCATTATAGCCAAGATTTGAATATGTAT
131 TTAGA-TAATATATTAGGTGAGCAAGATATTTTATATTCATTATAGACAAGACTTGAACATATAT
** * * * *
937785 AT-AAGGGCTAATTGTCTAGCAATTTTTGCAACAACAAGAAGTATT-AGCTCTAGTAGTTGAAAG
195 ATAAAAAGCTAATTGTCTAGCAATTCTTACAACAACAAGAAGCATTGA-CTCTAGTAGTTAAAAG
* * * * * *
937848 CTTTGTGTGAGGTGTGAGTGAGATATTTTTTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATT
259 CTTTGTGTGAGGTATGAATGAAATATTTTCTTTGGTGAGTATGAGCGGTGATGAGTAAAAATATT
*
937913 TGTAAGTGTTTATTTGAGTTGTAATATTAGTGAATTTAATAAAAATATTTTAAGTTCACTTATAT
324 TGTAAGTGTTTATTTGAGTTGTAATATTAGTCAATTTAATAAAAATATTTTAAGTTCACTTATAT
*
937978 TTTTTCGTTTTATGCTCTACAAT
389 TTTTTCGTTCTATGCTCTACAAT
938001 TTGGTATCAG
Statistics
Matches: 373, Mismatches: 34, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
409 1 0.00
410 195 0.52
411 172 0.46
412 5 0.01
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (412 bp):
TGTTATTGTTAAAAATAATCATTAATTTGAGTGCTAAACCTACATATCTTTATTAATTTTTTTGT
TAAGTGTGTTAGGTGAAGCATATTAGGTATGTTAAGTGATGTATTTGGTGAGAATGTTAGGTGTG
TTAGATAATATATTAGGTGAGCAAGATATTTTATATTCATTATAGACAAGACTTGAACATATATA
TAAAAAGCTAATTGTCTAGCAATTCTTACAACAACAAGAAGCATTGACTCTAGTAGTTAAAAGCT
TTGTGTGAGGTATGAATGAAATATTTTCTTTGGTGAGTATGAGCGGTGATGAGTAAAAATATTTG
TAAGTGTTTATTTGAGTTGTAATATTAGTCAATTTAATAAAAATATTTTAAGTTCACTTATATTT
TTTCGTTCTATGCTCTACAATC
Found at i:943170 original size:34 final size:34
Alignment explanation
Indices: 943092--943171 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
943082 TTGTTAAGTG
* *
943092 TGTTAGGTGAAGCATATTAGGTGTGTTAGGTGATG
1 TGTTAGGTG-AGAATATTAGGTGTGTTAGGTGATA
* * * *
943127 TATTTGGTGAGAATGTTCGGTGTGTTAGGTGATA
1 TGTTAGGTGAGAATATTAGGTGTGTTAGGTGATA
943161 TGTTAGGTGAG
1 TGTTAGGTGAG
943172 CAAGATATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
34 30 0.81
35 7 0.19
ACGTcount: A:0.21, C:0.03, G:0.38, T:0.39
Consensus pattern (34 bp):
TGTTAGGTGAGAATATTAGGTGTGTTAGGTGATA
Found at i:943266 original size:31 final size:31
Alignment explanation
Indices: 943228--943286 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
943218 AAGGGCTAAT
943228 TGTCTAGCAATTCTTGCAACAACAAGAAGCA
1 TGTCTAGCAATTCTTGCAACAACAAGAAGCA
943259 TGTCTAGCAATTCTTGCAACAACAAGAA
1 TGTCTAGCAATTCTTGCAACAACAAGAA
943287 ACATTGGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (31 bp):
TGTCTAGCAATTCTTGCAACAACAAGAAGCA
Found at i:949091 original size:15 final size:15
Alignment explanation
Indices: 949073--949103 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
949063 CTGCTTTCAG
949073 TTAATTGGCTTGTGA
1 TTAATTGGCTTGTGA
949088 TTAATTGGCTTGTGA
1 TTAATTGGCTTGTGA
949103 T
1 T
949104 AGTATTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (15 bp):
TTAATTGGCTTGTGA
Found at i:951487 original size:2 final size:2
Alignment explanation
Indices: 951480--951506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
951470 TGATTTGATA
951480 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
951507 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:957126 original size:11 final size:11
Alignment explanation
Indices: 957086--957128 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
957076 TCATTTATTA
*
957086 TTTATTAATTT
1 TTTAATAATTT
*
957097 TTTAAAAATTT
1 TTTAATAATTT
957108 TTGCTAATAATTT
1 TT--TAATAATTT
957121 TTTAATAA
1 TTTAATAA
957129 GCCTAGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTAATAATTT
Found at i:958146 original size:21 final size:21
Alignment explanation
Indices: 958111--958151 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
958101 AAATAATTTA
*
958111 ATTTTTATTAATAATTTATAG
1 ATTTTTATTAATAATATATAG
958132 ATTTTTA-TAATTAATATATA
1 ATTTTTATTAA-TAATATATA
958152 AAAAATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTATTAATAATATATAG
Found at i:963240 original size:2 final size:2
Alignment explanation
Indices: 963233--963269 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
963223 CAAAGAAACT
963233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
963270 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:963692 original size:2 final size:2
Alignment explanation
Indices: 963687--963716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
963677 GCTAAAAATC
963687 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
963717 GGAATCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:965127 original size:2 final size:2
Alignment explanation
Indices: 965120--965147 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
965110 AAGCTGGTGA
965120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
965148 GAGGGCCAAT
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):
AT
Found at i:966189 original size:20 final size:20
Alignment explanation
Indices: 966127--966182 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
966117 CATGAAAGAA
* * *
966127 AAAGAAAAGCAAAGAAAAGG
1 AAAGCAAAGCAAAGCAACGG
* *
966147 -AAGGAAAGGAAAGCAACGG
1 AAAGCAAAGCAAAGCAACGG
966166 AAAGCAAAGCAAAGCAA
1 AAAGCAAAGCAAAGCAA
966183 GTGAAAGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.62, C:0.11, G:0.27, T:0.00
Consensus pattern (20 bp):
AAAGCAAAGCAAAGCAACGG
Found at i:966194 original size:20 final size:20
Alignment explanation
Indices: 966127--966194 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
966117 CATGAAAGAA
* * *
966127 AAAGAAAAGCAAAGAAAAGG
1 AAAGGAAAGCAAAGCAACGG
*
966147 -AAGGAAAGGAAAGCAACGG
1 AAAGGAAAGCAAAGCAACGG
*
966166 AAAGCAAAGCAAAGCAA-GTG
1 AAAGGAAAGCAAAGCAACG-G
966186 AAAGGAAAG
1 AAAGGAAAG
966195 GAGATTCTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.41
20 23 0.59
ACGTcount: A:0.60, C:0.09, G:0.29, T:0.01
Consensus pattern (20 bp):
AAAGGAAAGCAAAGCAACGG
Found at i:977496 original size:13 final size:13
Alignment explanation
Indices: 977478--977502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
977468 TTGGAGTGTT
977478 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
977491 TTTTTCTTTTTT
1 TTTTTCTTTTTT
977503 TATGAGAAAG
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:979503 original size:22 final size:23
Alignment explanation
Indices: 979462--979512 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
979452 TTTGTAGGAA
979462 AAAATAAA--TAAATAATATAAT
1 AAAATAAATTTAAATAATATAAT
*
979483 AATATAAATTTAAA-AATATAAT
1 AAAATAAATTTAAATAATATAAT
979505 AAAATAAA
1 AAAATAAA
979513 AAATTTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATAAATTTAAATAATATAAT
Found at i:979514 original size:17 final size:16
Alignment explanation
Indices: 979460--979516 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
979450 TCTTTGTAGG
979460 AAAAAATAAAT-AAAT
1 AAAAAATAAATAAAAT
* *
979475 AATATAATAATATAAATT
1 AA-AAAATAA-ATAAAAT
*
979493 TAAAAATATAATAAAAT
1 AAAAAATA-AATAAAAT
979510 AAAAAAT
1 AAAAAAT
979517 TTCACACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 19 0.59
18 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATAAATAAAAT
Found at i:979834 original size:21 final size:20
Alignment explanation
Indices: 979810--979870 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 20
979800 ATTCTGTATA
*
979810 AAATTAATTTAATTTTATATT
1 AAATTAATTTAATTATAT-TT
*
979831 AAATTTATTTAATTATATTT
1 AAATTAATTTAATTATATTT
*
979851 TAATTAA-TTAATTA-ATTT
1 AAATTAATTTAATTATATTT
979869 AA
1 AA
979871 TTATTAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 7 0.20
21 16 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTAATTTAATTATATTT
Found at i:985951 original size:81 final size:80
Alignment explanation
Indices: 985864--986138 Score: 309
Period size: 81 Copynumber: 3.4 Consensus size: 80
985854 TCGGCATCAT
* ** *
985864 TGATAATATTGATGCCAATGTGACAATCGGGATTGGGGTGAAGCCATGGTGGCGAGCAGGATCAG
1 TGATAATATTGATGCCAATGTGACAATCAGGATTAAGGCGAAGCCATGGTGGCGAGCAGGATCAG
*
985929 AATGACTTGATGTCAC
66 AGTGACTTG-TGTCAC
* * * * ** *
985945 TGATAATATTGATGCTAATGTGACGATCAGGATCAAGGCAAAGCCATGGTGGTAAGCAGGATGAG
1 TGATAATATTGATGCCAATGTGACAATCAGGATTAAGGCGAAGCCATGGTGGCGAGCAGGATCAG
*
986010 AGTGACTTGGTGCCAC
66 AGTGACTT-GTGTCAC
* * * * *
986026 TGATAATATTGATGCCAATGTAACAATCAGGATTACGGCGAAGCCAAGGTAGCGAG-AGGATTAG
1 TGATAATATTGATGCCAATGTGACAATCAGGATTAAGGCGAAGCCATGGTGGCGAGCAGGATCAG
*
986090 AGTGACTTTGTGTCAT
66 AGTGAC-TTGTGTCAC
* * * *
986106 TGATAATATTGATGTCAAGGTGGCGATCAGGAT
1 TGATAATATTGATGCCAATGTGACAATCAGGAT
986139 CAGGATCAGA
Statistics
Matches: 161, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
80 46 0.29
81 114 0.71
82 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (80 bp):
TGATAATATTGATGCCAATGTGACAATCAGGATTAAGGCGAAGCCATGGTGGCGAGCAGGATCAG
AGTGACTTGTGTCAC
Found at i:986643 original size:27 final size:26
Alignment explanation
Indices: 986613--986722 Score: 71
Period size: 24 Copynumber: 4.4 Consensus size: 26
986603 TTTTATCATA
986613 ATTATTTTAAATATAGTATACT-TTTAT
1 ATTATTTTAAATATA-TATA-TATTTAT
*
986640 ATTAATTTT-AATATATTTATATTTAT
1 ATT-ATTTTAAATATATATATATTTAT
986666 ATTATATTT--ATAT-TATAT-TTTAATT
1 ATTAT-TTTAAATATATATATATTT-A-T
986691 ATTATTTT--ATAT-TATAT-TTTA-
1 ATTATTTTAAATATATATATATTTAT
986712 ATTATATTTAA
1 ATTAT-TTTAA
986723 TATTATTAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 19
0.78 0.02 0.20
Matches are distributed among these distances:
21 5 0.07
22 3 0.04
23 4 0.05
24 20 0.27
25 13 0.18
26 14 0.19
27 9 0.12
28 5 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (26 bp):
ATTATTTTAAATATATATATATTTAT
Found at i:986672 original size:5 final size:5
Alignment explanation
Indices: 986636--986719 Score: 64
Period size: 5 Copynumber: 16.4 Consensus size: 5
986626 TAGTATACTT
* *
986636 TTATA TTA-A TTTTA ATATA TTTATA TTTATA TTATA TTTATA TTATA
1 TTATA TTATA TTATA TTATA -TTATA -TTATA TTATA -TTATA TTATA
* * * *
986683 TTTTA AT-TA TTATT TTATA TTATA TTTTAA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TT
986720 TAATATTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
4 6 0.10
5 38 0.60
6 19 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:986672 original size:11 final size:11
Alignment explanation
Indices: 986651--986728 Score: 88
Period size: 11 Copynumber: 6.7 Consensus size: 11
986641 TTAATTTTAA
986651 TATATTTATATT
1 TATA-TTATATT
986663 TATATTATATT
1 TATATTATATT
986674 TATATTATATT
1 TATATTATATT
986685 T-TAATTATTATTT
1 TAT-ATTA-TA-TT
986698 TATATTATATT
1 TATATTATATT
986709 T-TAATTATATT
1 TAT-ATTATATT
986720 TAATATTAT
1 T-ATATTAT
986729 TAAAATTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.03
11 35 0.59
12 13 0.22
13 8 0.14
14 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATATT
Found at i:986704 original size:24 final size:24
Alignment explanation
Indices: 986665--986728 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
986655 TTTATATTTA
986665 TATTATATTTATATTATATTTTAAT
1 TATTAT-TTTATATTATATTTTAAT
986690 TATTATTTTATATTATATTTTAAT
1 TATTATTTTATATTATATTTTAAT
*
986714 TA-TATTTAATATTAT
1 TATTATTTTATATTAT
986729 TAAAATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 12 0.32
24 20 0.53
25 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATTTTATATTATATTTTAAT
Found at i:987358 original size:25 final size:25
Alignment explanation
Indices: 987326--987374 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
987316 TGTAAGTATA
*
987326 TTTTTTAAGAGAATTAATTATAAAT
1 TTTTTTAAAAGAATTAATTATAAAT
*
987351 TTTTTTAAAAGAATTAATTTTAAA
1 TTTTTTAAAAGAATTAATTATAAA
987375 AAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (25 bp):
TTTTTTAAAAGAATTAATTATAAAT
Found at i:988192 original size:16 final size:15
Alignment explanation
Indices: 988171--988204 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
988161 TTACTGTTTT
988171 AATTTAAAATTTAATA
1 AATTTAAAATTTAA-A
988187 AATTTAAAATTTAAA
1 AATTTAAAATTTAAA
988202 AAT
1 AAT
988205 AATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTAAAATTTAAA
Done.