Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 6 of 27
Found at i:624479 original size:32 final size:32
Alignment explanation
Indices: 624378--624481 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
624368 CCAAACCTAA
* * * *
624378 AAATAACATGAACCTGAAATGACCAGAAT-TCG
1 AAATAACCTTAACCCGAAATGACCCGAATAT-G
* *
624410 AAATGACCTTAACCCGAAATGACTCGAACTCA-G
1 AAATAACCTTAACCCGAAATGACCCGAA-T-ATG
* *
624443 -AATAACTTTAATCCGAAATGACCCGAATATG
1 AAATAACCTTAACCCGAAATGACCCGAATATG
624474 AAATAACC
1 AAATAACC
624482 CGAACTCGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
30 1 0.02
31 2 0.04
32 51 0.91
33 2 0.04
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (32 bp):
AAATAACCTTAACCCGAAATGACCCGAATATG
Found at i:628044 original size:30 final size:30
Alignment explanation
Indices: 628010--628102 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
628000 ATTTAAATTA
* *
628010 GATAGTGGTGCACTAGTTCTTAATCTAAAG
1 GATAGTGATGCACTAGTCCTTAATCTAAAG
* * *
628040 GATAGTGATGAACTAATCCTTAATCTAAGG
1 GATAGTGATGCACTAGTCCTTAATCTAAAG
* * * * * *
628070 GAAAGTGCTGCATTAGTCTTTATTCTAAGG
1 GATAGTGATGCACTAGTCCTTAATCTAAAG
628100 GAT
1 GAT
628103 TTAAATTGAT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (30 bp):
GATAGTGATGCACTAGTCCTTAATCTAAAG
Found at i:628313 original size:28 final size:30
Alignment explanation
Indices: 628262--628321 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
628252 CCTAGGAGTA
*
628262 TTTTTTTCTATTCAACCTTCATTGCTGATT
1 TTTTTTTCTAATCAACCTTCATTGCTGATT
* *
628292 TTTTTTTCTAAT-AGCCTT-ATTGCTGCTT
1 TTTTTTTCTAATCAACCTTCATTGCTGATT
628320 TT
1 TT
628322 CAAATTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 5 0.19
30 11 0.41
ACGTcount: A:0.15, C:0.18, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTTTCTAATCAACCTTCATTGCTGATT
Found at i:632820 original size:30 final size:30
Alignment explanation
Indices: 632781--632839 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
632771 ATTTAAATTA
*
632781 GATAATGGTGCACTAGTCCTTAATCTAAGG
1 GATAATGGTGCACTAGTACTTAATCTAAGG
* * *
632811 GATAGTGGTGTACTAGTATTTAATCTAAG
1 GATAATGGTGCACTAGTACTTAATCTAAG
632840 AGATTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (30 bp):
GATAATGGTGCACTAGTACTTAATCTAAGG
Found at i:634368 original size:22 final size:22
Alignment explanation
Indices: 634323--634368 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
634313 TATTTTTATA
* *
634323 ATTTATTTATTAAAAATTATTT
1 ATTTATTTATTAAAAATAAGTT
634345 ATTTATTTATATAAAAA-AAGTT
1 ATTTATTTAT-TAAAAATAAGTT
634367 AT
1 AT
634369 AAAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTATTTATTAAAAATAAGTT
Found at i:634387 original size:25 final size:25
Alignment explanation
Indices: 634359--634419 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
634349 ATTTATATAA
* *
634359 AAAAAGTTATAAAATAATTTTTTAT
1 AAAAAGTTATAAAATAAATATTTAT
634384 -AAAA-TTAATGAAAATAAATATTTAT
1 AAAAAGTT-AT-AAAATAAATATTTAT
*
634409 AAATAGTTATA
1 AAAAAGTTATA
634420 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 14 0.48
26 5 0.17
27 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (25 bp):
AAAAAGTTATAAAATAAATATTTAT
Found at i:634429 original size:17 final size:15
Alignment explanation
Indices: 634394--634443 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 15
634384 AAAATTAATG
634394 AAAATAA-ATATTTA
1 AAAATAATATATTTA
* *
634408 TAAATAGTTATATTTTA
1 AAAATA-ATATA-TTTA
634425 AAAATAATATATTTA
1 AAAATAATATATTTA
634440 AAAA
1 AAAA
634444 ACTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 7 0.24
17 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATAATATATTTA
Found at i:634452 original size:30 final size:31
Alignment explanation
Indices: 634394--634452 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
634384 AAAATTAATG
* *
634394 AAAATAAATATTTATAAATAGTTATATTTTA
1 AAAATAAATATTTATAAAAACTTATATTTTA
634425 AAAATAATATATTTA-AAAAACTT-TATTT
1 AAAATAA-ATATTTATAAAAACTTATATTT
634453 ATAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 13 0.52
32 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
AAAATAAATATTTATAAAAACTTATATTTTA
Found at i:634929 original size:21 final size:20
Alignment explanation
Indices: 634890--634930 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
634880 TTTATTTTTA
*
634890 TTAAAATAAAATTTAATTAT
1 TTAAAATAAAATATAATTAT
*
634910 TTAAAATAATATAATAATTAT
1 TTAAAATAAAAT-ATAATTAT
634931 ACACATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAATAAAATATAATTAT
Found at i:635429 original size:16 final size:16
Alignment explanation
Indices: 635410--635518 Score: 78
Period size: 16 Copynumber: 6.8 Consensus size: 16
635400 GAATCAACCC
*
635410 GAACTCGAAATGATTT
1 GAACTCGAAATGACTT
* * *
635426 GAACCCAAAATGACTC
1 GAACTCGAAATGACTT
*
635442 GAA-TCTGAAATGACTC
1 GAACTC-GAAATGACTT
* *
635458 GAATTCGAAATAACTT
1 GAACTCGAAATGACTT
* *
635474 AAATTC-AAAGTGACTT
1 GAACTCGAAA-TGACTT
* *
635490 GAACCCGAAATAACTT
1 GAACTCGAAATGACTT
*
635506 AAACTCGAAATGA
1 GAACTCGAAATGA
635519 TTCGAATTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
15 4 0.06
16 63 0.88
17 5 0.07
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (16 bp):
GAACTCGAAATGACTT
Found at i:636163 original size:16 final size:14
Alignment explanation
Indices: 636144--636177 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
636134 AGTATATATG
636144 ATAATATTAATATAAT
1 ATAATATTAA-A-AAT
636160 ATAATATTAAAAAT
1 ATAATATTAAAAAT
636174 ATAA
1 ATAA
636178 AAATTATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATTAAAAAT
Found at i:638586 original size:29 final size:29
Alignment explanation
Indices: 638528--638586 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
638518 TTTATATTAA
* *
638528 ATTTAATATTTTTCATAATATATGATAAG
1 ATTTAATATTTTTCATAATATATAAAAAG
*
638557 ATTTAATA-TTTTCTATGATATATAAAAAG
1 ATTTAATATTTTTC-ATAATATATAAAAAG
638586 A
1 A
638587 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
ATTTAATATTTTTCATAATATATAAAAAG
Found at i:639099 original size:14 final size:15
Alignment explanation
Indices: 639077--639109 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
639067 TTTATTTTTT
*
639077 ATATATTTATATAAG
1 ATATATTTATAAAAG
639092 ATAT-TTTATAAAAG
1 ATATATTTATAAAAG
639106 ATAT
1 ATAT
639110 GTGTCTGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATATATTTATAAAAG
Found at i:640746 original size:31 final size:31
Alignment explanation
Indices: 640711--640769 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
640701 GGTTTTAGTG
640711 AATCTATGTGTTTTCTAGCAATTTATGAGTT
1 AATCTATGTGTTTTCTAGCAATTTATGAGTT
640742 AATCTATGTGTTTTCTAGCAATTTATGA
1 AATCTATGTGTTTTCTAGCAATTTATGA
640770 AAATCTAATC
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:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (31 bp):
AATCTATGTGTTTTCTAGCAATTTATGAGTT
Found at i:641656 original size:39 final size:39
Alignment explanation
Indices: 641613--641712 Score: 191
Period size: 39 Copynumber: 2.6 Consensus size: 39
641603 GGGTGATCTT
*
641613 AATATTAGATACTTAGAGTTAGGAATAAAAGCAGACAAC
1 AATATTAGATACTTAGAGTTAGGAAGAAAAGCAGACAAC
641652 AATATTAGATACTTAGAGTTAGGAAGAAAAGCAGACAAC
1 AATATTAGATACTTAGAGTTAGGAAGAAAAGCAGACAAC
641691 AATATTAGATACTTAGAGTTAG
1 AATATTAGATACTTAGAGTTAG
641713 TAACTCCACA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (39 bp):
AATATTAGATACTTAGAGTTAGGAAGAAAAGCAGACAAC
Found at i:649556 original size:2 final size:2
Alignment explanation
Indices: 649545--649578 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
649535 GTTTTTCAAT
649545 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
649579 TAGTGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:651624 original size:2 final size:2
Alignment explanation
Indices: 651617--651651 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
651607 GGAGGAAGGC
651617 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
651652 TTACCTGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:652720 original size:18 final size:18
Alignment explanation
Indices: 652694--652729 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
652684 CCCTATGATC
*
652694 TTTTGTTTTCCCAATTAG
1 TTTTATTTTCCCAATTAG
*
652712 TTTTATTTTCTCAATTAG
1 TTTTATTTTCCCAATTAG
652730 CAGCATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTTATTTTCCCAATTAG
Found at i:657002 original size:15 final size:15
Alignment explanation
Indices: 656982--657033 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
656972 ATTTTGTGAT
656982 AAAATATATATTTAA
1 AAAATATATATTTAA
656997 AAAATAT-TATATTAA
1 AAAATATATAT-TTAA
* *
657012 AAAAAATA-AGTTAA
1 AAAATATATATTTAA
*
657026 TAAATATA
1 AAAATATA
657034 CAAATGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATATATATTTAA
Found at i:657387 original size:26 final size:26
Alignment explanation
Indices: 657358--657407 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
657348 TTTTGATTAG
657358 TTTATTTTTATATATTATATAATTTT
1 TTTATTTTTATATATTATATAATTTT
*
657384 TTTATTTTTATGTATTATATAATT
1 TTTATTTTTATATATTATATAATT
657408 ATTTATTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTTTTATATATTATATAATTTT
Found at i:657897 original size:2 final size:2
Alignment explanation
Indices: 657890--657917 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
657880 GTAGCCTAAG
657890 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
657918 GCATATTTTA
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:662055 original size:35 final size:35
Alignment explanation
Indices: 661994--662103 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
661984 ACATGAGTGG
* * *
661994 AAAAA-AAATTATTTT-AAAATCATGATATTTTTA
1 AAAAATAAATAATTTTAAAAAACATGATAATTTTA
*
662027 ATTAAATAAATAATTTTAAAAAAC-TGATAATTTTA
1 A-AAAATAAATAATTTTAAAAAACATGATAATTTTA
*
662062 AAAAATAAATAAATATTTAAATAAATAT-ATAATTTTA
1 AAAAATAAAT-AAT-TTTAAA-AAACATGATAATTTTA
662099 AAAAA
1 AAAAA
662104 ATAATTATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 11 0.17
35 23 0.36
36 11 0.17
37 17 0.27
38 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (35 bp):
AAAAATAAATAATTTTAAAAAACATGATAATTTTA
Found at i:662083 original size:16 final size:18
Alignment explanation
Indices: 662022--662107 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
662012 ATCATGATAT
*
662022 TTTTAATTAAATAAATAA
1 TTTTAAATAAATAAATAA
*
662040 TTTTAAA-AAACT-GATAA
1 TTTTAAATAAA-TAAATAA
662057 TTTTAAA-AAATAAATAAA
1 TTTTAAATAAATAAAT-AA
*
662075 TATTTAAATAAATATATAA
1 T-TTTAAATAAATAAATAA
*
662094 TTTTAAAAAAATAA
1 TTTTAAATAAATAA
662108 TTATAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.02
17 19 0.33
18 21 0.37
19 9 0.16
20 7 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (18 bp):
TTTTAAATAAATAAATAA
Found at i:662100 original size:18 final size:17
Alignment explanation
Indices: 662030--662103 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
662020 ATTTTTAATT
662030 AAATAAATAATTTTAAA
1 AAATAAATAATTTTAAA
*
662047 AAACT-GATAATTTTAAA
1 AAA-TAAATAATTTTAAA
662064 AAATAAATAAATATTTAAA
1 AAATAAAT-AAT-TTTAAA
*
662083 TAAATATATAATTTTAAA
1 -AAATAAATAATTTTAAA
662101 AAA
1 AAA
662104 ATAATTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 1 0.02
17 22 0.45
18 10 0.20
19 9 0.18
20 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
AAATAAATAATTTTAAA
Found at i:662103 original size:38 final size:36
Alignment explanation
Indices: 662016--662118 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 36
662006 TTTAAAATCA
* *
662016 TGATATTTTTAATTAAATAAAT-AAT-TTTAAAAAAC
1 TGATAATTTTAA-AAAATAAATAAATATTTAAAAAAC
662051 TGATAATTTTAAAAAATAAATAAATATTTAAATAAA-
1 TGATAATTTTAAAAAATAAATAAATATTTAAA-AAAC
*
662087 TATATAATTTTAAAAAAATAATTATAAATATT
1 T-GATAATTTT-AAAAAATAA--ATAAATATT
662119 AAACGATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
34 8 0.14
35 14 0.24
36 7 0.12
37 11 0.19
38 9 0.16
40 9 0.16
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (36 bp):
TGATAATTTTAAAAAATAAATAAATATTTAAAAAAC
Found at i:662112 original size:22 final size:21
Alignment explanation
Indices: 662080--662121 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
662070 ATAAATATTT
*
662080 AAATAAATATATAATTTTAAAA
1 AAATAAATATA-AATATTAAAA
*
662102 AAATAATTATAAATATTAAA
1 AAATAAATATAAATATTAAA
662122 CGATATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATATAAATATTAAAA
Found at i:662234 original size:18 final size:18
Alignment explanation
Indices: 662213--662280 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
662203 TATTATTTTA
662213 TTATTTAATTTTATAAAT
1 TTATTTAATTTTATAAAT
*
662231 TTATTTATTTTTTATAAAT
1 TTATTTA-ATTTTATAAAT
** *
662250 TTA-TTAATTAAATTAAT
1 TTATTTAATTTTATAAAT
662267 ATTATTT-ATTTTAT
1 -TTATTTAATTTTAT
662281 GATATTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 18 0.45
19 15 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTTAATTTTATAAAT
Found at i:664485 original size:97 final size:97
Alignment explanation
Indices: 664382--664566 Score: 307
Period size: 97 Copynumber: 1.9 Consensus size: 97
664372 GAAAGATATT
** *
664382 AATATAATTCAAATATTGGATTTTTTTTTGAATTTAAAGCTGTAAAAAATTGAATCTTAATAATT
1 AATATAATTCAAATATTGGATTTTTTTGGGAATTTAAAGCTGTAAAAAATTGAATCCTAATAATT
664447 GAAATTAAAAACTCAATATTCTACAAGAAGTG
66 GAAATTAAAAACTCAATATTCTACAAGAAGTG
* * *
664479 AATATAATTCAAATATTGGATTTTTTTGGGGATTTAAAGTTGTAAAAAATTGAATCCTAATATTT
1 AATATAATTCAAATATTGGATTTTTTTGGGAATTTAAAGCTGTAAAAAATTGAATCCTAATAATT
*
664544 GAAATTAAAAATTCAATATTCTA
66 GAAATTAAAAACTCAATATTCTA
664567 TGAACGAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 81 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.39
Consensus pattern (97 bp):
AATATAATTCAAATATTGGATTTTTTTGGGAATTTAAAGCTGTAAAAAATTGAATCCTAATAATT
GAAATTAAAAACTCAATATTCTACAAGAAGTG
Found at i:664659 original size:16 final size:16
Alignment explanation
Indices: 664640--664674 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
664630 TTACTATAAT
664640 TAATTTTTAAAAAAAA
1 TAATTTTTAAAAAAAA
* *
664656 TAATTTTTCAAAAATA
1 TAATTTTTAAAAAAAA
664672 TAA
1 TAA
664675 AGATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTTTTAAAAAAAA
Found at i:664830 original size:14 final size:14
Alignment explanation
Indices: 664808--664867 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
664798 TTATTGTTAA
*
664808 AATATTAATATCTT
1 AATAGTAATATCTT
*
664822 AATAGTAATATTCCT
1 AATAGTAATA-TCTT
*
664837 AATAGTAATATTTT
1 AATAGTAATATCTT
664851 AATCA-TAATAT-TT
1 AAT-AGTAATATCTT
664864 AATA
1 AATA
664868 ATAAAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 5 0.12
14 20 0.50
15 14 0.35
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (14 bp):
AATAGTAATATCTT
Found at i:664841 original size:15 final size:15
Alignment explanation
Indices: 664808--664848 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
664798 TTATTGTTAA
* *
664808 AATATTAATA-TCTT
1 AATAGTAATATTCCT
664822 AATAGTAATATTCCT
1 AATAGTAATATTCCT
664837 AATAGTAATATT
1 AATAGTAATATT
664849 TTAATCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (15 bp):
AATAGTAATATTCCT
Found at i:665035 original size:73 final size:74
Alignment explanation
Indices: 664931--665117 Score: 188
Period size: 73 Copynumber: 2.5 Consensus size: 74
664921 ATTAATTATA
* * *
664931 TAAATATTTAAAATATTA-TAATTATCATTAAAATATTATTTTACAATGTTCAATA-T-TAATAT
1 TAAATATTT-AAATAATACTATTTATCATTAAAATATTATTTT-CAATATTCAATACTATAATAT
664993 TGACATAAATAT
64 T-ACATAAATAT
* * *
665005 TAAATAATATT-AA-AA-ACTATTTATCATTAAATTATTAATTTTTAATATTTAATACTATAATA
1 TAAAT-AT-TTAAATAATACTATTTATCATTAAAATATT-ATTTTCAATATTCAATACTATAATA
* *
665067 TTATATTAATAT
63 TTACATAAATAT
*
665079 TAAATATTTAAAATAATACTATTTATTATTAAAATATTA
1 TAAATATTT-AAATAATACTATTTATCATTAAAATATTA
665118 ATTATATAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
72 3 0.03
73 29 0.31
74 28 0.30
75 12 0.13
76 21 0.23
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (74 bp):
TAAATATTTAAATAATACTATTTATCATTAAAATATTATTTTCAATATTCAATACTATAATATTA
CATAAATAT
Found at i:665077 original size:19 final size:20
Alignment explanation
Indices: 665053--665100 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
665043 TTTTTAATAT
*
665053 TTAATACTATAATA-TTATA
1 TTAATACTATAATATTTAAA
*
665072 TTAATATTA-AATATTTAAA
1 TTAATACTATAATATTTAAA
*
665091 ATAATACTAT
1 TTAATACTAT
665101 TTATTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATACTATAATATTTAAA
Found at i:665190 original size:23 final size:22
Alignment explanation
Indices: 665145--665208 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
665135 AATTTATTTC
* *
665145 CATTAATATTTCTACTATTAAAA
1 CATTCATATTTTTA-TATTAAAA
*
665168 TATTCATATTTTTATATTAAAAA
1 CATTCATATTTTTATATT-AAAA
** *
665191 CATTTTTATTATTATATT
1 CATTCATATTTTTATATT
665209 TTTATAAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
CATTCATATTTTTATATTAAAA
Found at i:665428 original size:14 final size:15
Alignment explanation
Indices: 665411--665479 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 15
665401 ATTATATTAA
665411 AATAATTTT-ATATT
1 AATAATTTTAATATT
*
665425 AATATTTTTAATATT
1 AATAATTTTAATATT
* * *
665440 AAGAAAATTAAATATT
1 AA-TAATTTTAATATT
* *
665456 AAAAATTTGTTAATAAT
1 AATAA-TT-TTAATATT
665473 AATAATT
1 AATAATT
665480 GACTCGAGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
14 8 0.19
15 10 0.24
16 14 0.33
17 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
AATAATTTTAATATT
Found at i:665631 original size:19 final size:19
Alignment explanation
Indices: 665594--665631 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
665584 GATTAATATG
*
665594 TTATTTTTTAATAATTAAA
1 TTATTTTTTAATAAATAAA
665613 TTATTTTTT-ATGAAATAAA
1 TTATTTTTTAAT-AAATAAA
665632 CACTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATTTTTTAATAAATAAA
Found at i:666641 original size:15 final size:16
Alignment explanation
Indices: 666612--666648 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
666602 ATTATATATA
*
666612 ACATATAATATTTTAT
1 ACATATAATAATTTAT
666628 ACATA-AATAATTTAT
1 ACATATAATAATTTAT
666643 A-ATATA
1 ACATATA
666649 TATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 11 0.58
16 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
ACATATAATAATTTAT
Found at i:666707 original size:5 final size:5
Alignment explanation
Indices: 666697--666756 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
666687 ATATTACCTT
* * * *
666697 TTATA TTATA TCATA TTATA TTTTAA TTATTT TTATA TTATA ATATAA
1 TTATA TTATA TTATA TTATA TTAT-A TTA-TA TTATA TTATA TTAT-A
666745 TTATA TTATA TT
1 TTATA TTATA TT
666757 CAAAATTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 33 0.75
6 10 0.23
7 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:666734 original size:22 final size:21
Alignment explanation
Indices: 666701--666756 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
666691 TACCTTTTAT
* * *
666701 ATTATATCATATTATATTTTA
1 ATTATATTATATTATAATATA
*
666722 ATTATTTTTATATTATAATATA
1 ATTA-TATTATATTATAATATA
666744 ATTATATTATATT
1 ATTATATTATATT
666757 CAAAATTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATATTATATTATAATATA
Found at i:666752 original size:27 final size:27
Alignment explanation
Indices: 666669--666753 Score: 71
Period size: 32 Copynumber: 2.9 Consensus size: 27
666659 AATACGTTTA
* * *
666669 TATATTCAAAATATATTTATATTACCTTT
1 TATATT-ATAATATAATTATATTA-TTTT
*
666698 TATATTATATCATATTATATTTTAATTATTTT
1 TATATTATA--ATA-TA-ATTAT-ATTATTTT
666730 TATATTATAATATAATTATATTAT
1 TATATTATAATATAATTATATTAT
666754 ATTCAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
27 5 0.11
28 6 0.13
29 8 0.17
30 6 0.13
31 2 0.04
32 15 0.33
33 4 0.09
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (27 bp):
TATATTATAATATAATTATATTATTTT
Found at i:667401 original size:50 final size:51
Alignment explanation
Indices: 667314--667421 Score: 137
Period size: 50 Copynumber: 2.1 Consensus size: 51
667304 CAGCTTGTTT
* **
667314 TAATTCAAATTTAAATAATTAATATTTGAATAAATTTATTAATAAATTAAA
1 TAATTTAAATTTAAATAATTAATATTCAAATAAATTTATTAATAAATTAAA
* * * **
667365 TAATTTAAATTTTAA-AATTAATATTCAAATAGATTTATTAATAGATTGGA
1 TAATTTAAATTTAAATAATTAATATTCAAATAAATTTATTAATAAATTAAA
667415 TAATTTA
1 TAATTTA
667422 TTTAGTCTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 36 0.73
51 13 0.27
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (51 bp):
TAATTTAAATTTAAATAATTAATATTCAAATAAATTTATTAATAAATTAAA
Found at i:669452 original size:18 final size:18
Alignment explanation
Indices: 669429--669498 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 18
669419 GTGGTTATAA
669429 ATTTATAATATTATAATT
1 ATTTATAATATTATAATT
*
669447 ATTTATAAAATATT-T-TTT
1 ATTTAT--AATATTATAATT
* *
669465 ATTTATATAAATTTTAATAT
1 ATTTATA-ATATTATAAT-T
669485 ATTTATAAT-TTATA
1 ATTTATAATATTATA
669499 TTTTATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
16 1 0.02
17 4 0.10
18 19 0.46
19 3 0.07
20 14 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATAATATTATAATT
Found at i:669460 original size:20 final size:19
Alignment explanation
Indices: 669435--669492 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
669425 ATAAATTTAT
669435 AATATTATAATTATTTATAA
1 AATATT-TAATTATTTATAA
*
669455 AATATTT-TTTATTTATATA
1 AATATTTAATTATTTATA-A
669474 AAT-TTTAATATATTTATAA
1 AATATTTAAT-TATTTATAA
669493 TTTATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 12 0.36
19 7 0.21
20 14 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTTAATTATTTATAA
Found at i:669486 original size:27 final size:28
Alignment explanation
Indices: 669429--669499 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
669419 GTGGTTATAA
*
669429 ATTTATAATATTATA-ATTATTTATAAAAT
1 ATTTATAAT-TTATATA-AATTTATAAAAT
* * *
669458 ATTTTTTATTTATATAAATTT-TAATAT
1 ATTTATAATTTATATAAATTTATAAAAT
669485 ATTTATAATTTATAT
1 ATTTATAATTTATAT
669500 TTTATAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 18 0.51
28 9 0.26
29 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTATAATTTATATAAATTTATAAAAT
Found at i:669503 original size:38 final size:38
Alignment explanation
Indices: 669432--669504 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
669422 GTTATAAATT
*
669432 TATAATATTATAATTATTTATAAAATATTTTTTATTTA
1 TATAATATTATAATTATTTATAAAATATATTTTATTTA
* **
669470 TATAA-ATTTTAATATATTTATAATTTATATTTTAT
1 TATAATATTATAAT-TATTTATAAAATATATTTTAT
669505 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 7 0.23
38 23 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (38 bp):
TATAATATTATAATTATTTATAAAATATATTTTATTTA
Found at i:669521 original size:23 final size:25
Alignment explanation
Indices: 669468--669553 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 25
669458 ATTTTTTATT
*
669468 TATATAAATTTTAATATATTTATAA
1 TATATATATTTTAATATATTTATAA
*
669493 T-T-TATATTTT-ATA-ATTTTTAA
1 TATATATATTTTAATATATTTATAA
* **
669514 TATATATA-TAT-ATATATGTTATGT
1 TATATATATTTTAATATAT-TTATAA
669538 TATATTATATTTTAAT
1 TATA-TATATTTTAAT
669554 TAAAAAAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 8 0.17
22 9 0.19
23 13 0.28
24 8 0.17
25 5 0.11
26 2 0.04
27 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TATATATATTTTAATATATTTATAA
Found at i:669760 original size:35 final size:35
Alignment explanation
Indices: 669710--669787 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
669700 AACATGTTGG
* *
669710 TAGAATATTAGATTAATGATTTAATAATCTATTAA
1 TAGAATATTAAATTAATAATTTAATAATCTATTAA
* *
669745 TAGAATATTAAATTAATAATTTAATAATTTATTAG
1 TAGAATATTAAATTAATAATTTAATAATCTATTAA
*
669780 TTGAATAT
1 TAGAATAT
669788 CGACTAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (35 bp):
TAGAATATTAAATTAATAATTTAATAATCTATTAA
Found at i:670144 original size:2 final size:2
Alignment explanation
Indices: 670137--670168 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
670127 TTCAAATTTA
670137 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
670169 TGATTTCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673135 original size:23 final size:24
Alignment explanation
Indices: 673095--673144 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
673085 TTTTATATTT
673095 ATTTTTAATGAAAGTAATTATTA-A
1 ATTTTTAATGAAAGTAATT-TTATA
673119 ATTTTTAA-GTAAA-TAATTTTATA
1 ATTTTTAATG-AAAGTAATTTTATA
673142 ATT
1 ATT
673145 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.12
23 10 0.42
24 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
ATTTTTAATGAAAGTAATTTTATA
Found at i:674109 original size:18 final size:19
Alignment explanation
Indices: 674075--674121 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 19
674065 AATACGATAT
674075 AATATAAATTATTTATAAA
1 AATATAAATTATTTATAAA
*
674094 AATAT-AA-T-TTTAT-AT
1 AATATAAATTATTTATAAA
674109 AATATAAATTATT
1 AATATAAATTATT
674122 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 2 0.08
18 4 0.17
19 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATAAATTATTTATAAA
Found at i:674126 original size:18 final size:17
Alignment explanation
Indices: 674071--674147 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
674061 TTAAAATACG
674071 ATATAATATAAATTATT
1 ATATAATATAAATTATT
*
674088 -TATAAAAATATAATT-TT
1 ATAT-AATATA-AATTATT
674105 ATATAATATAAATTATT
1 ATATAATATAAATTATT
*
674122 A-AT-ATATTAAAAT-TT
1 ATATAATA-TAAATTATT
674137 ATATAAATATA
1 ATAT-AATATA
674148 CAATAATTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
15 6 0.12
16 16 0.33
17 17 0.35
18 10 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATAAATTATT
Found at i:675986 original size:2 final size:2
Alignment explanation
Indices: 675979--676010 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
675969 ATGTAAAGTG
675979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
676011 CACAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:676577 original size:3 final size:3
Alignment explanation
Indices: 676562--676594 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
676552 CATTATCAAG
*
676562 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
676595 TCTCATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:677102 original size:37 final size:37
Alignment explanation
Indices: 677052--677125 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
677042 AAAGAATGCT
* *
677052 TCATCGCACTGAACCAAATGAAGGCTGAGATTTGGTA
1 TCATCGCACTGAACCAAATCAAGGCTCAGATTTGGTA
677089 TCATCGCACTGAACCAAATCAAGGCTCAGATTTGGTA
1 TCATCGCACTGAACCAAATCAAGGCTCAGATTTGGTA
677126 AGATTAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (37 bp):
TCATCGCACTGAACCAAATCAAGGCTCAGATTTGGTA
Found at i:679886 original size:14 final size:15
Alignment explanation
Indices: 679863--679894 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
679853 TAATTTTATA
679863 AAAATAAAATATAAT
1 AAAATAAAATATAAT
679878 AAAAT-AAATATAAT
1 AAAATAAAATATAAT
679892 AAA
1 AAA
679895 GATATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAAAATATAAT
Found at i:679907 original size:25 final size:24
Alignment explanation
Indices: 679865--679916 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
679855 ATTTTATAAA
679865 AATAAAATATAATAAAATA-AATAT
1 AATAAAATATAATAAAATATAAT-T
* *
679889 AATAAAGATATATTTAAATATAATT
1 AATAAA-ATATAATAAAATATAATT
679914 AAT
1 AAT
679917 TTTAATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 15 0.62
26 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAAAATATAATAAAATATAATT
Found at i:680339 original size:20 final size:19
Alignment explanation
Indices: 680308--680353 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
680298 TTTATTTATT
680308 TTAATTTTTAAT-TATTTA
1 TTAATTTTTAATGTATTTA
680326 TTAACTTTTCTAATGTA-TTA
1 TTAA-TTTT-TAATGTATTTA
*
680346 TAAATTTT
1 TTAATTTT
680354 ATTATATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 8 0.33
20 10 0.42
21 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTAATTTTTAATGTATTTA
Found at i:680353 original size:19 final size:19
Alignment explanation
Indices: 680299--680353 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
680289 TAAATTTGTT
*
680299 TTATTTATTTTAATTTTTAA
1 TTATTTA-TTAAATTTTTAA
*
680319 TTATTTATTAACTTTTCTAA
1 TTATTTATTAAATTTT-TAA
680339 TGTA-TTA-TAAATTTT
1 T-TATTTATTAAATTTT
680354 ATTATATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 14 0.47
20 14 0.47
21 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTATTAAATTTTTAA
Found at i:680486 original size:19 final size:20
Alignment explanation
Indices: 680457--680506 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
680447 TCATAAATTT
*
680457 TAATCTTATTATCATAATAA
1 TAATTTTATTATCATAATAA
*
680477 -AATTTTATTATTATAATAA
1 TAATTTTATTATCATAATAA
680496 TTAATTTTATT
1 -TAATTTTATT
680507 TTTATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTTATTATCATAATAA
Found at i:680490 original size:22 final size:21
Alignment explanation
Indices: 680462--680511 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
680452 AATTTTAATC
*
680462 TTATTATCATAATAAAATTTTA
1 TTATTATAATAAT-AAATTTTA
*
680484 TTATTATAATAATTAATTTTA
1 TTATTATAATAATAAATTTTA
*
680505 TTTTTAT
1 TTATTAT
680512 TTATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTATAATAATAAATTTTA
Found at i:681842 original size:18 final size:18
Alignment explanation
Indices: 681789--681843 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
681779 TAATTAATAA
*
681789 AATATATTTTATATATTTT
1 AATATATTTAATA-ATTTT
681808 ATATATATTTTAA-AATTTT
1 A-ATATA-TTTAATAATTTT
681827 AATATATTTAATAATTT
1 AATATATTTAATAATTT
681844 ATTTTATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 7 0.22
20 6 0.19
21 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATATTTAATAATTTT
Found at i:681844 original size:8 final size:9
Alignment explanation
Indices: 681789--681844 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 9
681779 TAATTAATAA
681789 AATATATTT
1 AATATATTT
*
681798 TATATATTTT
1 AATATA-TTT
681808 ATATATATTTT
1 A-ATATA-TTT
*
681819 AAAAT-TTT
1 AATATATTT
681827 AATATATTT
1 AATATATTT
681836 AATA-ATTT
1 AATATATTT
681844 A
1 A
681845 TTTTATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 12 0.30
9 12 0.30
10 6 0.15
11 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
AATATATTT
Found at i:682649 original size:22 final size:22
Alignment explanation
Indices: 682622--682684 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 22
682612 TTATTTATTA
682622 TTAAATTAATAAAATTAAAATT
1 TTAAATTAATAAAATTAAAATT
*
682644 TTAAATATAAATTAAA-T-AAATT
1 TTAAAT-T-AATAAAATTAAAATT
682666 TTATTAA-TAATAAAATTAA
1 TTA--AATTAATAAAATTAA
682685 TATGATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
21 6 0.18
22 16 0.48
23 3 0.09
24 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATTAATAAAATTAAAATT
Found at i:683781 original size:27 final size:28
Alignment explanation
Indices: 683751--683803 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
683741 CTTTACTTAA
683751 AATTATATAATTA-AAT-TTTAATTTTTT
1 AATTATA-AATTATAATATTTAATTTTTT
*
683778 AATTATAAATTATAATATTTTATTTT
1 AATTATAAATTATAATATTTAATTTT
683804 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 10 0.43
28 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
AATTATAAATTATAATATTTAATTTTTT
Found at i:684253 original size:2 final size:2
Alignment explanation
Indices: 684242--684289 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
684232 AAACAAAAAC
684242 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
684282 TT CT CT CT
1 CT CT CT CT
684290 TCTTCAACCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:688106 original size:24 final size:27
Alignment explanation
Indices: 688078--688126 Score: 77
Period size: 24 Copynumber: 1.9 Consensus size: 27
688068 TTATTAAAAA
688078 TATATTAAAA-A-TTTTATT-TTATAT
1 TATATTAAAATACTTTTATTATTATAT
688102 TATATTAAAATACTTTTATTATTAT
1 TATATTAAAATACTTTTATTATTAT
688127 CAAATGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
26 7 0.32
27 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATATTAAAATACTTTTATTATTATAT
Found at i:688686 original size:5 final size:5
Alignment explanation
Indices: 688670--688730 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
688660 ATATTTAAAA
* * *
688670 ATATT ATA-T ATATT ATATT -TATAA ATTTT ATATT ATAATT ATTTT ATATT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT AT-ATT ATATT ATATT
688720 ATATTT ATATT
1 ATA-TT ATATT
688731 GTATAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 7 0.16
5 26 0.58
6 12 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:688686 original size:24 final size:26
Alignment explanation
Indices: 688640--688715 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 26
688630 TCATGTTAGT
688640 ATATTATATGTATAATAAATATATTTAAAA
1 ATATTATAT-TATAAT---TATATTTAAAA
*
688670 ATATTATA-TAT-ATTATATTTATAA
1 ATATTATATTATAATTATATTTAAAA
*
688694 ATTTTATATTATAATTAT-TTTA
1 ATATTATATTATAATTATATTTA
688716 TATTATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 17 0.40
25 7 0.17
26 5 0.12
27 2 0.05
28 3 0.07
30 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
ATATTATATTATAATTATATTTAAAA
Found at i:688726 original size:11 final size:11
Alignment explanation
Indices: 688670--688730 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
688660 ATATTTAAAA
688670 ATATTATA--T
1 ATATTATATTT
688679 ATATTATATTT
1 ATATTATATTT
*
688690 ATAAATTTTATATT
1 AT--ATTATAT-TT
688704 ATAATTAT-TTT
1 AT-ATTATATTT
688715 ATATTATATTT
1 ATATTATATTT
688726 ATATT
1 ATATT
688731 GTATAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 8 0.18
10 5 0.11
11 15 0.34
12 1 0.02
13 11 0.25
14 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTATATTT
Found at i:689506 original size:27 final size:30
Alignment explanation
Indices: 689476--689538 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 30
689466 ATTGTTGGGC
689476 ATTAAATAT-TATGTACAT-AAATAAAT-A
1 ATTAAATATGTATGTACATAAAATAAATAA
**
689503 ATT--ATATGTATGTATTTAAAATAAATAA
1 ATTAAATATGTATGTACATAAAATAAATAA
689531 ATTAAATA
1 ATTAAATA
689539 ATCAAGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 11 0.38
28 4 0.14
30 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
ATTAAATATGTATGTACATAAAATAAATAA
Found at i:689933 original size:27 final size:28
Alignment explanation
Indices: 689903--689961 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
689893 CAATTGAATC
* *
689903 AAATTTAAAAATC-AAATAAGATTTTTA
1 AAATTTAAAAATCTAAATAACATTTTAA
* *
689930 AAATTTTAAATTCTAAATAACATTTTAA
1 AAATTTAAAAATCTAAATAACATTTTAA
689958 AAAT
1 AAAT
689962 CAAAATTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (28 bp):
AAATTTAAAAATCTAAATAACATTTTAA
Found at i:690383 original size:20 final size:20
Alignment explanation
Indices: 690360--690413 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 20
690350 TAATTATATT
690360 TAAAATATTATATAT-TT-A
1 TAAAATATTATATATATTAA
*
690378 TATAAATTTTA-ATATATTAA
1 TA-AAATATTATATATATTAA
690398 TAAATTATATTATATA
1 TAAA--ATATTATATA
690414 AATTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
20 3 0.11
21 5 0.18
22 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATATTATATATATTAA
Found at i:690388 original size:27 final size:31
Alignment explanation
Indices: 690358--690419 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
690348 CATAATTATA
690358 TTTAAAATATT-AT-A-TAT-TTATATAAAT
1 TTTAAAATATTAATAATTATATTATATAAAT
*
690385 TTTAATATATTAATAAATTATATTATATAAAT
1 TTTAAAATATTAAT-AATTATATTATATAAAT
690417 TTT
1 TTT
690420 TATTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.34
28 2 0.07
30 1 0.03
31 3 0.10
32 13 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAAAATATTAATAATTATATTATATAAAT
Found at i:690411 original size:18 final size:18
Alignment explanation
Indices: 690352--690412 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
690342 ATATATCATA
690352 ATTATATTTAA-AATATTAT
1 ATTATA-TTAATAA-ATTAT
*
690371 A-TAT-TTATATAAATTTT
1 ATTATATTA-ATAAATTAT
*
690388 AATATATTAATAAATTAT
1 ATTATATTAATAAATTAT
690406 ATTATAT
1 ATTATAT
690413 AAATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 3 0.09
17 6 0.17
18 22 0.63
19 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATTAATAAATTAT
Found at i:692083 original size:23 final size:22
Alignment explanation
Indices: 692047--692097 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
692037 TTTTATTTAA
* *
692047 TAATTTTAATTTAATCTTTTTGT
1 TAATTTTAATTTAA-ATTTATGT
692070 TAATTTTCAA-TTAAATTTATGT
1 TAATTTT-AATTTAAATTTATGT
692092 TAATTT
1 TAATTT
692098 ACTGAGCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 11 0.44
24 2 0.08
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (22 bp):
TAATTTTAATTTAAATTTATGT
Found at i:696369 original size:14 final size:14
Alignment explanation
Indices: 696336--696377 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
696326 AATACATATC
*
696336 ATATAAATAAT-AA
1 ATATAAATATTAAA
696349 ATATAAATATTAAA
1 ATATAAATATTAAA
*
696363 ATGTAAATATTAAA
1 ATATAAATATTAAA
696377 A
1 A
696378 AATATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATAAATATTAAA
Found at i:696921 original size:22 final size:22
Alignment explanation
Indices: 696893--696937 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
696883 TAATTTTAAA
696893 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
696915 ATATATTTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
696937 A
1 A
696938 AATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:696938 original size:29 final size:30
Alignment explanation
Indices: 696915--696973 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
696905 ATTAATATTT
696915 ATATATTTTTATAATTAAAT-TTAA-ATAAA
1 ATAT-TTTTTATAATTAAATATTAATATAAA
* *
696944 ATATTTTTTATAATTTAATATTAATTTAAA
1 ATATTTTTTATAATTAAATATTAATATAAA
696974 TCAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 14 0.54
29 8 0.31
30 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTTTTTATAATTAAATATTAATATAAA
Found at i:696947 original size:35 final size:34
Alignment explanation
Indices: 696908--696974 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
696898 TTTTTATATT
* *
696908 AATA-TTTATATATTTTTATAATTAAATTTAAATAA
1 AATATTTTATATAATTTAAT-ATT-AATTTAAATAA
*
696943 AATATTTTTTATAATTTAATATTAATTTAAAT
1 AATATTTTATATAATTTAATATTAATTTAAAT
696975 CAAACTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 9 0.32
35 7 0.25
36 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
AATATTTTATATAATTTAATATTAATTTAAATAA
Found at i:697252 original size:19 final size:18
Alignment explanation
Indices: 697228--697274 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
697218 AATAGTTAAA
*
697228 ATTAATAACTTAATATTTT
1 ATTAATAACTTAATA-ATT
*
697247 ATTAATAAATTTAATAATT
1 ATTAAT-AACTTAATAATT
697266 ATTAATAAC
1 ATTAATAAC
697275 ATATCAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.58
20 8 0.33
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATAACTTAATAATT
Found at i:698126 original size:23 final size:23
Alignment explanation
Indices: 698083--698127 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
698073 TAAAATTTTA
*
698083 TAAATATAATATATTTATATTAT
1 TAAATATAATATAATTATATTAT
698106 TAAATATAATGATAATT-TATTA
1 TAAATATAAT-ATAATTATATTA
698128 AATATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATATAATATAATTATATTAT
Found at i:698138 original size:15 final size:15
Alignment explanation
Indices: 698118--698150 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
698108 AATATAATGA
698118 TAATTTATTAAATAT
1 TAATTTATTAAATAT
698133 TAATTTATTAAATAT
1 TAATTTATTAAATAT
698148 TAA
1 TAA
698151 CGTAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTTATTAAATAT
Found at i:699009 original size:13 final size:12
Alignment explanation
Indices: 698991--699034 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
698981 TTTTATTTTT
698991 TATTTATTATTAA
1 TATTTATTA-TAA
699004 TATTTATTATAA
1 TATTTATTATAA
*
699016 TTAATTATTATAA
1 -TATTTATTATAA
699029 TATTTA
1 TATTTA
699035 ATACATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTATTATAA
Found at i:700197 original size:3 final size:3
Alignment explanation
Indices: 700191--700215 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
700181 ATAACAACTC
700191 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
700216 ATAAAAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:700552 original size:18 final size:18
Alignment explanation
Indices: 700529--700571 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
700519 AATAATAAAA
700529 ATATTAAAAAATAATTTT
1 ATATTAAAAAATAATTTT
* * *
700547 ATATT-AATATTTATTTT
1 ATATTAAAAAATAATTTT
700564 ATATTAAA
1 ATATTAAA
700572 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAAAAAATAATTTT
Found at i:700564 original size:17 final size:16
Alignment explanation
Indices: 700542--700575 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
700532 TTAAAAAATA
700542 ATTTTATATTAATATTT
1 ATTTTATATTAA-ATTT
700559 ATTTTATATTAAATTT
1 ATTTTATATTAAATTT
700575 A
1 A
700576 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTATATTAAATTT
Found at i:700593 original size:23 final size:24
Alignment explanation
Indices: 700567--700612 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
700557 TTATTTTATA
*
700567 TTAAATTTAAATT-AATTAAAAAT
1 TTAAAATTAAATTAAATTAAAAAT
*
700590 TTAAAATTAATTTAAATTAAAAA
1 TTAAAATTAAATTAAATTAAAAA
700613 AATTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAAATTAAATTAAATTAAAAAT
Found at i:700606 original size:17 final size:17
Alignment explanation
Indices: 700567--700611 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
700557 TTATTTTATA
700567 TTAAATTT-AAATTAAT
1 TTAAATTTAAAATTAAT
*
700583 TAAAAATTTAAAATTAAT
1 T-TAAATTTAAAATTAAT
700601 TTAAA-TTAAAA
1 TTAAATTTAAAA
700612 AAATTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 7 0.28
17 9 0.36
18 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATTAAT
Found at i:700608 original size:10 final size:10
Alignment explanation
Indices: 700570--700609 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
700560 TTTTATATTA
700570 AATTTAAATT
1 AATTTAAATT
700580 AA-TTAAA--
1 AATTTAAATT
700587 AATTTAAAATT
1 AATTT-AAATT
700598 AATTTAAATT
1 AATTTAAATT
700608 AA
1 AA
700610 AAAAATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.08
8 2 0.08
9 8 0.31
10 9 0.35
11 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTAAATT
Found at i:701961 original size:20 final size:18
Alignment explanation
Indices: 701928--701965 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
701918 ATTCGAATAT
701928 AATATAAAAAATATTTAA
1 AATATAAAAAATATTTAA
701946 AATATAATATAAATATTTAA
1 AATATAA-A-AAATATTTAA
701966 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATAAAAAATATTTAA
Found at i:701984 original size:16 final size:16
Alignment explanation
Indices: 701955--702005 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
701945 AAATATAATA
701955 TAAATATTTAATATTT
1 TAAATATTTAATATTT
*
701971 TAAA-ATTTATATATTA
1 TAAATATTTA-ATATTT
* *
701987 TAATTA-TTAATATAT
1 TAAATATTTAATATTT
702002 TAAA
1 TAAA
702006 ATTAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 12 0.43
16 15 0.54
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATATTTAATATTT
Found at i:702005 original size:31 final size:32
Alignment explanation
Indices: 701947--702027 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
701937 AATATTTAAA
*
701947 ATATAATATAAATATTTAATATTTTAAAATTT
1 ATATAATATAAATATTTAATATATTAAAATTT
* * *
701979 ATATATTATAATTA-TTAATATATTAAAATTA
1 ATATAATATAAATATTTAATATATTAAAATTT
*
702010 ATAAAAATATAAAATATT
1 AT-ATAATAT-AAATATT
702028 ATTTAATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 17 0.44
32 17 0.44
33 4 0.10
34 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAATATAAATATTTAATATATTAAAATTT
Found at i:702067 original size:22 final size:22
Alignment explanation
Indices: 702042--702086 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
702032 AATTATAAAT
702042 ATGATATGATAAAATATAAAAC
1 ATGATATGATAAAATATAAAAC
702064 ATGATATGATAAAATATAAAAC
1 ATGATATGATAAAATATAAAAC
702086 A
1 A
702087 GATCAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (22 bp):
ATGATATGATAAAATATAAAAC
Found at i:704085 original size:2 final size:2
Alignment explanation
Indices: 704078--704105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
704068 ATCAAGGCTA
704078 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
704106 TATGTTAACA
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:704967 original size:3 final size:3
Alignment explanation
Indices: 704959--705002 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
704949 CTGTTCCTCA
* *
704959 TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCC TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
705003 CATTACTCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:705003 original size:12 final size:12
Alignment explanation
Indices: 704952--705003 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
704942 TCTCTTTCTG
*
704952 TTCCTCATCTTC
1 TTCCTCTTCTTC
*
704964 TTCTTCTTCTTC
1 TTCCTCTTCTTC
* *
704976 TTCTTCTTCCTC
1 TTCCTCTTCTTC
704988 TTCCTCTTCTTC
1 TTCCTCTTCTTC
705000 TTCC
1 TTCC
705004 ATTACTCTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (12 bp):
TTCCTCTTCTTC
Found at i:705834 original size:28 final size:29
Alignment explanation
Indices: 705780--705835 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
705770 AAAAGTTAAT
*
705780 ATTAAAATGATAAATTTAATAAATATAAA
1 ATTAAAATAATAAATTTAATAAATATAAA
*
705809 ATTAATATAATAAA-TTAATAAATATAA
1 ATTAAAATAATAAATTTAATAAATATAA
705836 TATATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
ATTAAAATAATAAATTTAATAAATATAAA
Found at i:705846 original size:18 final size:18
Alignment explanation
Indices: 705812--705861 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
705802 ATATAAAATT
*
705812 AATATAATA-AATTAATA
1 AATATAATATATTTAATA
705829 AATATAATATATTTAATA
1 AATATAATATATTTAATA
*
705847 CATAT-ATCATATTTA
1 AATATAAT-ATATTTA
705862 TATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATAATATATTTAATA
Found at i:706057 original size:22 final size:23
Alignment explanation
Indices: 706024--706077 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
706014 ATAAATAAAA
*
706024 TTAAAATATTATTATA-TATTTT
1 TTAATATATTATTATATTATTTT
* *
706046 TTATTATATTATTGTATTATTTT
1 TTAATATATTATTATATTATTTT
706069 TTAATATAT
1 TTAATATAT
706078 AGGCTATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAATATATTATTATATTATTTT
Found at i:706131 original size:2 final size:2
Alignment explanation
Indices: 706124--706153 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
706114 ATGATAACTT
706124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
706154 AATGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:706637 original size:19 final size:21
Alignment explanation
Indices: 706595--706639 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
706585 ATAAAAAATC
*
706595 TTTTATATATATACTTTTAAT
1 TTTTAAATATATACTTTTAAT
*
706616 TTTTAAATA-ATA-TTTTATT
1 TTTTAAATATATACTTTTAAT
706635 TTTTA
1 TTTTA
706640 TTATATTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 3 0.14
21 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAAATATATACTTTTAAT
Found at i:707428 original size:19 final size:20
Alignment explanation
Indices: 707386--707436 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
707376 AAAAATTATT
*
707386 TTAATTAATATTTTTTAGTCA
1 TTAATTAATATTTTTTAG-AA
707407 TTAATTAATATTTTTTA-AA
1 TTAATTAATATTTTTTAGAA
707426 TTAATTAATAT
1 TTAATTAATAT
707437 GTCTAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTAATTAATATTTTTTAGAA
Found at i:710548 original size:3 final size:3
Alignment explanation
Indices: 710540--710565 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
710530 CACATTTGTG
710540 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
710566 CTTAGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:711455 original size:20 final size:20
Alignment explanation
Indices: 711390--711455 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
711380 TTTACTAATA
*
711390 ATTTAATATATTTAATAT-TT
1 ATTTAA-ATATTTAAAATCTT
*
711410 ATTT-ACTA-TTAAAATTCTT
1 ATTTAAATATTTAAAA-TCTT
*
711429 -TTAAAATATTTAAAATCTT
1 ATTTAAATATTTAAAATCTT
711448 ATTTAAAT
1 ATTTAAAT
711456 TTATCAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 5 0.14
18 5 0.14
19 10 0.28
20 16 0.44
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATATTTAAAATCTT
Found at i:713394 original size:35 final size:35
Alignment explanation
Indices: 713324--713435 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 35
713314 ATTATATTAA
*
713324 AAAATATATGTTTATAATAAA-AATTAAAAAT-TATT
1 AAAAT-TATGTTTATATTAAATAA-TAAAAATATATT
713359 AAAATTATGTTTATATTAAATAATAAAAATATATT
1 AAAATTATGTTTATATTAAATAATAAAAATATATT
* ** *
713394 -AAATTATATTTAGGTTAAATAATAATAATAT-TT
1 AAAATTATGTTTATATTAAATAATAAAAATATATT
713427 AAAAATTAT
1 -AAAATTAT
713436 TAAAATTACA
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.03
34 48 0.71
35 18 0.26
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (35 bp):
AAAATTATGTTTATATTAAATAATAAAAATATATT
Found at i:713437 original size:43 final size:44
Alignment explanation
Indices: 713382--713472 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
713372 TATTAAATAA
* *
713382 TAAAAATATATT-AAATTATATTTAGGTTAAATAATAATAAT-ATT
1 TAAAAATATATTAAAATTACATTTAGATTAAA-AATAA-AATAATT
*
713426 TAAAAAT-TATTAAAATTACATTTATATTAAAAATAAAATAATT
1 TAAAAATATATTAAAATTACATTTAGATTAAAAATAAAATAATT
713469 TAAA
1 TAAA
713473 GTTTTAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 3 0.07
43 16 0.38
44 23 0.55
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (44 bp):
TAAAAATATATTAAAATTACATTTAGATTAAAAATAAAATAATT
Found at i:715439 original size:14 final size:13
Alignment explanation
Indices: 715420--715469 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
715410 TAATGTAATG
715420 TTATAATTATTATT
1 TTATAATTATTA-T
715434 TTATAAATT-TTAT
1 TTAT-AATTATTAT
*
715447 TTAT-TTTATTAT
1 TTATAATTATTAT
*
715459 TTATATTTATT
1 TTATAATTATT
715470 TCAATTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.06
12 8 0.25
13 11 0.34
14 7 0.22
15 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATAATTATTAT
Found at i:715452 original size:9 final size:9
Alignment explanation
Indices: 715429--715470 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
715419 GTTATAATTA
715429 TTATTTTAT
1 TTATTTTAT
**
715438 AAATTTTAT
1 TTATTTTAT
715447 TTATTTTA-
1 TTATTTTAT
715455 TTATTTATAT
1 TTATTT-TAT
715465 TTATTT
1 TTATTT
715471 CAATTGATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 6 0.22
9 15 0.56
10 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTATTTTAT
Found at i:715452 original size:18 final size:18
Alignment explanation
Indices: 715429--715470 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
715419 GTTATAATTA
715429 TTATTTTATAAATTT-TAT
1 TTATTTTAT-AATTTATAT
*
715447 TTATTTTATTATTTATAT
1 TTATTTTATAATTTATAT
715465 TTATTT
1 TTATTT
715471 CAATTGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTATAATTTATAT
Found at i:716542 original size:14 final size:14
Alignment explanation
Indices: 716505--716547 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
716495 ATGTATCGTA
* *
716505 ATTATATTAATAAT
1 ATTATATTTATTAT
*
716519 ATT-TAATTATTAT
1 ATTATATTTATTAT
716532 ATTATATTTATTAT
1 ATTATATTTATTAT
716546 AT
1 AT
716548 AATTTTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATATTTATTAT
Found at i:718197 original size:27 final size:26
Alignment explanation
Indices: 718152--718203 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
718142 TAATTATAGG
* **
718152 TATATATTTAATATTTTATAATTTTTT
1 TATATATTTAAAAAATTAT-ATTTTTT
718179 TATATATTTAAAAAATTATATTTTT
1 TATATATTTAAAAAATTATATTTTT
718204 ATACTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATATTTAAAAAATTATATTTTTT
Found at i:718845 original size:15 final size:14
Alignment explanation
Indices: 718837--718912 Score: 59
Period size: 16 Copynumber: 5.3 Consensus size: 14
718827 TAAAAAATTA
718837 AATATTAAATAAAT
1 AATATTAAATAAAT
*
718851 AATATTAATCTTAAAT
1 AATATTAA--ATAAAT
718867 AAGTATTAAATATAAT
1 AA-TATTAAATA-AAT
718883 AAATATT-AATAAA-
1 -AATATTAAATAAAT
* *
718896 AAT-TTGATTAAAT
1 AATATTAAATAAAT
718909 AATA
1 AATA
718913 AAATTTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
11 2 0.04
12 8 0.16
13 3 0.06
14 10 0.20
15 6 0.12
16 14 0.27
17 8 0.16
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (14 bp):
AATATTAAATAAAT
Found at i:718859 original size:33 final size:34
Alignment explanation
Indices: 718822--718897 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 34
718812 ATTCAATGAT
718822 TTAATTAAAAAATTAAATATTAAATA-AAT-AATA
1 TTAATTAAAAAA-TAAATATTAAATATAATAAATA
* *
718855 TTAATCT--TAAATAAGTATTAAATATAATAAATA
1 TTAAT-TAAAAAATAAATATTAAATATAATAAATA
718888 TTAA-TAAAAA
1 TTAATTAAAAA
718898 TTTGATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
31 13 0.37
32 6 0.17
33 15 0.43
34 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (34 bp):
TTAATTAAAAAATAAATATTAAATATAATAAATA
Found at i:718885 original size:20 final size:19
Alignment explanation
Indices: 718833--718887 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
718823 TAATTAAAAA
718833 ATTAAATATTAAATAAATAAT
1 ATTAAATA-T-AATAAATAAT
*
718854 ATT-AATCT--TAAATAAGT
1 ATTAAATATAATAAATAA-T
718871 ATTAAATATAATAAATA
1 ATTAAATATAATAAATA
718888 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 7 0.25
17 4 0.14
18 4 0.14
19 1 0.04
20 9 0.32
21 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTAAATATAATAAATAAT
Found at i:718906 original size:31 final size:30
Alignment explanation
Indices: 718871--718930 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
718861 TTAAATAAGT
718871 ATTAAAT-ATAATAAATATTAATAAAAATTTG
1 ATTAAATAATAA-AAATATTAA-AAAAATTTG
* *
718902 ATTAAATAATAAAATTTTTAAAAAAATTT
1 ATTAAATAATAAAAATATTAAAAAAATTT
718931 AAAAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
ATTAAATAATAAAAATATTAAAAAAATTTG
Found at i:722566 original size:11 final size:11
Alignment explanation
Indices: 722550--722586 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
722540 TAGTAATTTA
*
722550 TATATTTATTT
1 TATATTTATAT
722561 TATATTTATAT
1 TATATTTATAT
*
722572 TATTTTTATAT
1 TATATTTATAT
722583 TATA
1 TATA
722587 ATCGATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:723791 original size:20 final size:19
Alignment explanation
Indices: 723766--723809 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
723756 TCATATTTTT
723766 ATATATTATAATTATATTTA
1 ATATATT-TAATTATATTTA
*
723786 ATATA-TTAATTATTTTTA
1 ATATATTTAATTATATTTA
723804 ATATAT
1 ATATAT
723810 CACGTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 16 0.73
19 1 0.05
20 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTTAATTATATTTA
Found at i:723847 original size:15 final size:15
Alignment explanation
Indices: 723827--723979 Score: 100
Period size: 16 Copynumber: 9.8 Consensus size: 15
723817 TTATATAATT
*
723827 TTTATATATTA-ATAA
1 TTTATATTTTATAT-A
723842 TTTATATTTTTATATA
1 TTTATA-TTTTATATA
* *
723858 TTTTTATTTGATATA
1 TTTATATTTTATATA
*
723873 TTCATATTTTATATA
1 TTTATATTTTATATA
*
723888 TTTATATATTT-TAACA
1 TTTATAT-TTTAT-ATA
*
723904 ATTATAATTTTAATATA
1 TTTAT-ATTTT-ATATA
*
723921 TTTATATTTT-CATA
1 TTTATATTTTATATA
723935 -TTATA-TTTATTATA
1 TTTATATTTTA-TATA
*
723949 TTTTAATTATTTTTTATA
1 -TTT-A-TATTTTATATA
723967 TTTATAATTTTAT
1 TTTAT-ATTTTAT
723980 CTAAAATTAT
Statistics
Matches: 108, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
12 3 0.03
13 5 0.05
14 6 0.06
15 34 0.31
16 36 0.33
17 14 0.13
18 7 0.06
19 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (15 bp):
TTTATATTTTATATA
Found at i:723948 original size:63 final size:64
Alignment explanation
Indices: 723750--723961 Score: 160
Period size: 63 Copynumber: 3.3 Consensus size: 64
723740 TAAAGCATTC
* * * * *
723750 TTATTATCATATTTTTATATATT-ATAA-TTATA-TTTAATATATTAATTATTTTTAATATATCA
1 TTATTAT-ATATTTATATATTTTAACAATTTATATTTTAATATATTTA-TATTTAT-ATAT-TCA
723812 CGTAT
62 --TAT
* * * * *
723817 TTA-TATA-ATTTTTATATATTAATAATTTATATTTTTATATATTTTTATTTGATATATTCATA-
1 TTATTATATATTTATATATTTTAACAATTTATATTTTAATATATTTATATTT-ATATATTCATAT
723879 TT-TTATATATTTATATATTTTAACAA-TTATAATTTTAATATATTTATATTT-TCATATT-ATA
1 TTATTATATATTTATATATTTTAACAATTTAT-ATTTTAATATATTTATATTTAT-ATATTCATA
723940 T
64 T
723941 TTATTATAT-TTTA-ATTATTTT
1 TTATTATATATTTATA-TATTTT
723962 TTATATTTAT
Statistics
Matches: 125, Mismatches: 9, Indels: 27
0.78 0.06 0.17
Matches are distributed among these distances:
61 5 0.04
62 27 0.22
63 41 0.33
64 13 0.10
65 8 0.06
66 17 0.14
67 14 0.11
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (64 bp):
TTATTATATATTTATATATTTTAACAATTTATATTTTAATATATTTATATTTATATATTCATAT
Found at i:724008 original size:19 final size:18
Alignment explanation
Indices: 723968--724013 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
723958 TTTTTTATAT
*
723968 TTATAATTTTATCTAAAA
1 TTATAAATTTATCTAAAA
* *
723986 TTATTAAATTTATCTATAG
1 TTA-TAAATTTATCTAAAA
724005 TTATAAATT
1 TTATAAATT
724014 ATATTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATAAATTTATCTAAAA
Done.