Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 194 of 210
Found at i:57046422 original size:24 final size:26
Alignment explanation
Indices: 57046395--57046442 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
57046385 TTTGAGTAAT
*
57046395 TTAACTTTTTTC-T-TTTATTTTCTG
1 TTAACTTTATTCTTCTTTATTTTCTG
57046419 TTAACTTTATTCTTCTTTATTTTC
1 TTAACTTTATTCTTCTTTATTTTC
57046443 CATTCTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 1 0.05
26 9 0.43
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.69
Consensus pattern (26 bp):
TTAACTTTATTCTTCTTTATTTTCTG
Found at i:57046732 original size:23 final size:24
Alignment explanation
Indices: 57046706--57046750 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
57046696 AGAAAAGTTA
57046706 AAAAAACAT-AAAACAAA-AAAATT
1 AAAAAAC-TCAAAACAAATAAAATT
*
57046729 AAAATACTCAAAACAAATAAAA
1 AAAAAACTCAAAACAAATAAAA
57046751 ATATGAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAACTCAAAACAAATAAAATT
Found at i:57051323 original size:17 final size:17
Alignment explanation
Indices: 57051303--57051337 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57051293 GTTTATGAAA
* *
57051303 AAATAAAATACGAAAAT
1 AAATAAAAAACAAAAAT
57051320 AAATAAAAAACAAAAAT
1 AAATAAAAAACAAAAAT
57051337 A
1 A
57051338 GTATATTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (17 bp):
AAATAAAAAACAAAAAT
Found at i:57051533 original size:157 final size:158
Alignment explanation
Indices: 57051315--57051862 Score: 811
Period size: 157 Copynumber: 3.5 Consensus size: 158
57051305 ATAAAATACG
* ** *
57051315 AAAATAAATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTCAAAAAAAAGAAAAAT
1 AAAAT-AATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAATAAGAAAAAT
* * *
57051380 ATGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATAT-AAAAAA-ACACTAAAATAATA
64 ACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATA
57051443 CATTTCAAACATTATGTACTAAAATAATAT
129 CATTTCAAACATTATGTACTAAAATAATAT
* * *
57051473 AAAATAATAAAACACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATA
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAATAAGAAAAATA
* * *
57051538 CGAATAAATGGCCAAAATAAAGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
65 CGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATAC
*
57051603 ATTTCAAACTTTATGTACTAAAATAATAT
130 ATTTCAAACATTATGTACTAAAATAATAT
* * * *
57051632 AAAATAATAAAATACGAAAGTATTATATTTTTTGAAAGTAATAAAATC--AGA-AA-AAAAATAC
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAATAAGAAAAATAC
* * *
57051693 GAACAAATGGCCAAAATAAGGGTTTTTTACTAGATTTACATAAAAAAGACACACTAAAACAATAC
66 GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAA-ACACACTAAAATAATAC
*
57051758 ATTTCAAATATTATGTACTAAAATAATAT
130 ATTTCAAACATTATGTACTAAAATAATAT
57051787 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAAATAAGAAAAATA
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATC-AAAAATAAGAAAAATA
57051852 CGAACAAATGG
65 CGAACAAATGG
57051863 GGGTGTCGCC
Statistics
Matches: 353, Mismatches: 29, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
154 51 0.14
155 89 0.25
156 2 0.01
157 91 0.26
158 15 0.04
159 87 0.25
160 18 0.05
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28
Consensus pattern (158 bp):
AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAATAAGAAAAATAC
GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACA
TTTCAAACATTATGTACTAAAATAATAT
Found at i:57051800 original size:155 final size:157
Alignment explanation
Indices: 57051315--57051862 Score: 786
Period size: 155 Copynumber: 3.5 Consensus size: 157
57051305 ATAAAATACG
* **
57051315 AAAATAAATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTCAAAAAAAAGAAAAAT
1 AAAAT-AATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC--AAAAAAGAAAAAT
* * *
57051380 ATGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATAT-AAAAAA-ACACTAAAATAATA
63 ACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATA
*
57051443 CATTTCAAACATTATGTACTAAAATAATAT
128 CATTTCAAATATTATGTACTAAAATAATAT
* *
57051473 AAAATAATAAAACACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATA
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC-AAAA-AAGAAAAATA
* * *
57051538 CGAATAAATGGCCAAAATAAAGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
64 CGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATAC
57051603 ATTTCAAACT-TTATGTACTAAAATAATAT
129 ATTTCAAA-TATTATGTACTAAAATAATAT
* * * *
57051632 AAAATAATAAAATACGAAAGTATTATATTTTTTGAAAGTAATAAAA-TC-AGAAA-AAAAATACG
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAAAAAAGAAAAATACG
* * *
57051694 AACAAATGGCCAAAATAAGGGTTTTTTACTAGATTTACATAAAAAAGACACACTAAAACAATACA
66 AACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAA-ACACACTAAAATAATACA
57051759 TTTCAAATATTATGTACTAAAATAATAT
130 TTTCAAATATTATGTACTAAAATAATAT
57051787 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAAATAAGAAAAAT
1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC--AAAA-AAGAAAAAT
57051851 ACGAACAAATGG
63 ACGAACAAATGG
57051863 GGGTGTCGCC
Statistics
Matches: 353, Mismatches: 26, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
154 52 0.15
155 89 0.25
156 6 0.02
157 87 0.25
158 15 0.04
159 86 0.24
160 18 0.05
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28
Consensus pattern (157 bp):
AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAAAAAAGAAAAATACG
AACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACAT
TTCAAATATTATGTACTAAAATAATAT
Found at i:57058619 original size:31 final size:30
Alignment explanation
Indices: 57058554--57058621 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
57058544 TTTCCCAAGA
** ***
57058554 GTAAATACTCAAAATTTGAAGGGTTAAAGT
1 GTAAATACAAAAAATTTGAAGGACCAAAGT
57058584 GTAAATACAAAAAATTTGAAGGACCAATAGT
1 GTAAATACAAAAAATTTGAAGGACCAA-AGT
57058615 GTAAATA
1 GTAAATA
57058622 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (30 bp):
GTAAATACAAAAAATTTGAAGGACCAAAGT
Found at i:57068388 original size:22 final size:22
Alignment explanation
Indices: 57068363--57068404 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
57068353 AGTAAGTAAA
*
57068363 TTGTTCTTTGT-TTCGTTCTCCT
1 TTGTTCTCTGTCTT-GTTCTCCT
57068385 TTGTTCTCTGTCTTGTTCTC
1 TTGTTCTCTGTCTTGTTCTC
57068405 TTCTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.00, C:0.24, G:0.14, T:0.62
Consensus pattern (22 bp):
TTGTTCTCTGTCTTGTTCTCCT
Found at i:57072368 original size:22 final size:21
Alignment explanation
Indices: 57072327--57072369 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
57072317 TAATATGGGC
57072327 AATAATAAAAAAAAGGAAGTAA
1 AATAATAAAAAAAA-GAAGTAA
57072349 AATACATAAAATAAAA-AAGTA
1 AATA-ATAAAA-AAAAGAAGTA
57072370 TATATGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AATAATAAAAAAAAGAAGTAA
Found at i:57077291 original size:22 final size:22
Alignment explanation
Indices: 57077266--57077309 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
57077256 AACAATCAAA
57077266 GGTATTACTTGAGCAATGGTTG
1 GGTATTACTTGAGCAATGGTTG
57077288 GGTATTACTTGAGCAATGGTTG
1 GGTATTACTTGAGCAATGGTTG
57077310 CAGGTAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (22 bp):
GGTATTACTTGAGCAATGGTTG
Found at i:57087788 original size:20 final size:21
Alignment explanation
Indices: 57087763--57087807 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
57087753 TTTTCCATTC
*
57087763 TTTCCT-ACTTCTCCCTCTAT
1 TTTCCTCACTTCTCCATCTAT
* *
57087783 TTTCCTCCCTTCTCCATCTCT
1 TTTCCTCACTTCTCCATCTAT
57087804 TTTC
1 TTTC
57087808 ATGTAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.07, C:0.42, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTCCTCACTTCTCCATCTAT
Found at i:57093834 original size:6 final size:6
Alignment explanation
Indices: 57093823--57093858 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
57093813 TACCAATTCA
*
57093823 TATATG TATATG TATATG TATTTG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG
57093859 CATACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (6 bp):
TATATG
Found at i:57101352 original size:61 final size:58
Alignment explanation
Indices: 57101249--57101413 Score: 186
Period size: 61 Copynumber: 2.7 Consensus size: 58
57101239 ACCAACAGTA
* * * *
57101249 GTCACCCAACTATGGATTTTTTTCTTTTTTGGTCACCTAACTATGAAAAGTTATAAATTG
1 GTCACCCAACTAT-TA-GTTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTATAAAATG
57101309 GTCACCCAACTATTAGTATTTTCTTTCTCTTGGTCACCCAACTATGAAAAGTTATAAAATG
1 GTCACCCAACTATTAGT-TTTTCTTT-T-TTGGTCACCCAACTATGAAAAGTTATAAAATG
* ** * *
57101370 ATCACTTAATTATTCAGTTTTATCTTTTTTGGTCAACCAACTAT
1 GTCACCCAACTATT-AGTTTT-TCTTTTTTGGTCACCCAACTAT
57101414 CTAGGATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
58 1 0.01
59 9 0.10
60 29 0.32
61 44 0.48
62 8 0.09
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (58 bp):
GTCACCCAACTATTAGTTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTATAAAATG
Found at i:57107265 original size:29 final size:28
Alignment explanation
Indices: 57107201--57107265 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
57107191 TAATTTAGAC
*
57107201 TTATTTAATTTTTTAATAATATAAAGAC
1 TTATTTAATTTTTTAATAATATAAAGAA
* * *
57107229 TAAATTAATTTATTTAATAATA-ATGAGAA
1 TTATTTAATTT-TTTAATAATATA-AAGAA
57107258 TTATTTAA
1 TTATTTAA
57107266 CTTGGTCCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TTATTTAATTTTTTAATAATATAAAGAA
Found at i:57109619 original size:234 final size:235
Alignment explanation
Indices: 57109207--57109684 Score: 859
Period size: 234 Copynumber: 2.0 Consensus size: 235
57109197 GATATCTTGG
*
57109207 TCATTTGTTCCTATTTTCTTTTTGATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA
1 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA
*
57109272 TAAACATTTTTAGACATTTATTTCCATGCTTTGCTAGCATAGTTATTGACTAATTTTTAGAGGAT
66 TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT
*
57109337 TAGGCATTAGATGAAGTTTTGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT
131 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT
*
57109402 TCCCTG-AAAAAAAAAACTAAAATAAACAATCCGGATAGT
196 TCCCTGAAAAAAAAAAACTAAAATAAACAATCCGGATAGC
57109441 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA
1 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA
*
57109506 TAAACATTTTTTGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT
66 TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT
*
57109571 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTGTGGTCATTCTGGATCTAAATCTT
131 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT
*
57109636 TCCCTGAAAAAAAAAAAAAATTAAAATAAACAATCCGGATAGC
196 TCCCTG---AAAAAAAAAAACTAAAATAAACAATCCGGATAGC
57109679 TCATTT
1 TCATTT
57109685 AAATAAAGAA
Statistics
Matches: 233, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
234 196 0.84
238 37 0.16
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (235 bp):
TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA
TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT
TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT
TCCCTGAAAAAAAAAAACTAAAATAAACAATCCGGATAGC
Found at i:57112569 original size:38 final size:38
Alignment explanation
Indices: 57112526--57112605 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
57112516 ATTATGGATA
*
57112526 GCTAAGATTATAAGATA-CTGTTAGGGTTTAGATCTAGG
1 GCTAAGATTATAAGATATCT-TTAGGGTTTAAATCTAGG
* *
57112564 GCTAAGATTATTAGTTATCTTTAGGGTTTAAATCTAGG
1 GCTAAGATTATAAGATATCTTTAGGGTTTAAATCTAGG
57112602 GCTA
1 GCTA
57112606 TTAGAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 36 0.95
39 2 0.05
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.38
Consensus pattern (38 bp):
GCTAAGATTATAAGATATCTTTAGGGTTTAAATCTAGG
Found at i:57119775 original size:31 final size:31
Alignment explanation
Indices: 57119712--57119775 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
57119702 TTAGGATTTG
* *
57119712 AAAAGTAAAGGGACTAAAATTGATCAATTTA
1 AAAAGTAAAGGGACTAAAATTAATCAAATTA
* *
57119743 AAAAGTATAA-GGATTAAAATTAATTAAATTA
1 AAAAGTA-AAGGGACTAAAATTAATCAAATTA
57119774 AA
1 AA
57119776 TTATAATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAAGTAAAGGGACTAAAATTAATCAAATTA
Found at i:57124387 original size:20 final size:20
Alignment explanation
Indices: 57124362--57124404 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
57124352 AGTTCAAGGT
*
57124362 TTCGAGTTTTGGGTTTAGGG
1 TTCGAGTTTTGAGTTTAGGG
*
57124382 TTCGAGTTTTGAGTTTGGGG
1 TTCGAGTTTTGAGTTTAGGG
57124402 TTC
1 TTC
57124405 TGGGTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.37, T:0.47
Consensus pattern (20 bp):
TTCGAGTTTTGAGTTTAGGG
Found at i:57125929 original size:38 final size:39
Alignment explanation
Indices: 57125860--57125937 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 39
57125850 ATAAACACCA
57125860 AAAAATTATTTTAAAAATAAAAAAAATAAAAAGTAT-TTT
1 AAAAATTATTTTAAAAATAAAAAAAATAAAAA-TATATTT
*
57125899 AAAAA-TATTTTAAAATTAAAAAAACA-AAAAATATATTT
1 AAAAATTATTTTAAAAATAAAAAAA-ATAAAAATATATTT
57125937 A
1 A
57125938 TTATATTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 3 0.08
38 27 0.75
39 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (39 bp):
AAAAATTATTTTAAAAATAAAAAAAATAAAAATATATTT
Found at i:57130560 original size:88 final size:90
Alignment explanation
Indices: 57130404--57130573 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 90
57130394 AATCGACCAG
* * * *
57130404 TTTTTTATCGATTTAATTGATTTTTTTACTAATTTAATTCTTCTTCGATTTTTTTTACTAGTTAG
1 TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG
57130469 ACTATCAATTTCTAGTTAGGCTAAT
66 ACTATCAATTTCTAGTTAGGCTAAT
* * *
57130494 TTTTTTATGGATTTAATT-AATTTTTTACT-GTTTAATTCTTCTTCGATTTTATATACTAGTCGG
1 TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG
57130557 ACTATCAATTTCTAGTT
66 ACTATCAATTTCTAGTT
57130574 GGATGTAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 46 0.63
89 10 0.14
90 17 0.23
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55
Consensus pattern (90 bp):
TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG
ACTATCAATTTCTAGTTAGGCTAAT
Found at i:57135213 original size:96 final size:85
Alignment explanation
Indices: 57135143--57135307 Score: 240
Period size: 85 Copynumber: 1.9 Consensus size: 85
57135133 CTCTTTTTTT
* * *
57135143 TTTTTTTGCACTCAGTTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTCTTC
1 TTTTTTT--ACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTC
* *
57135208 AAAAAAGCAATTAATCCCCTGC
64 AAAAAAGTAATTAAGCCCCTGC
* * *
57135230 TTTTTTTACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTTTTCAA
1 TTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTCAA
57135295 AAAAGTAATTAAG
66 AAAAGTAATTAAG
57135308 TCCATGTTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
85 63 0.90
87 7 0.10
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (85 bp):
TTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTCAA
AAAAGTAATTAAGCCCCTGC
Found at i:57135388 original size:19 final size:19
Alignment explanation
Indices: 57135342--57135390 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
57135332 AAAAAATATA
*
57135342 AATAATAAATAATAAATTTT
1 AATAA-AAATATTAAATTTT
*
57135362 -AGAAAAATATTAAATTTT
1 AATAAAAATATTAAATTTT
57135380 AATAAAAATAT
1 AATAAAAATAT
57135391 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATAAAAATATTAAATTTT
Found at i:57135402 original size:27 final size:28
Alignment explanation
Indices: 57135364--57135441 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
57135354 TAAATTTTAG
*
57135364 AAAAATATTAAATTTTAATAAAAAT-ATA
1 AAAAATATTAAAATTT-ATAAAAATCATA
*
57135392 AAAAAT-TTAAAATTTATAAAAATCGTAA
1 AAAAATATTAAAATTTATAAAAATCAT-A
** *
57135420 AAAAATAAAAAAAATTATAAAA
1 AAAAATATTAAAATTTATAAAA
57135442 TTTTATAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 8 0.19
27 9 0.21
28 13 0.31
29 12 0.29
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAAATATTAAAATTTATAAAAATCATA
Found at i:57135410 original size:26 final size:29
Alignment explanation
Indices: 57135364--57135423 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
57135354 TAAATTTTAG
*
57135364 AAAAATATTAAATTTTAATAAAAAT-ATA
1 AAAAATATTAAAATTTAATAAAAATCATA
*
57135392 AAAAAT-TTAAAATTT-ATAAAAATCGTA
1 AAAAATATTAAAATTTAATAAAAATCATA
57135419 AAAAA
1 AAAAA
57135424 ATAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 15 0.52
28 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAATATTAAAATTTAATAAAAATCATA
Found at i:57135441 original size:9 final size:9
Alignment explanation
Indices: 57135381--57135461 Score: 58
Period size: 9 Copynumber: 8.8 Consensus size: 9
57135371 TTAAATTTTA
57135381 ATAAAAA-T
1 ATAAAAATT
57135389 ATAAAAAATT
1 AT-AAAAATT
*
57135399 -TAAAATTT
1 ATAAAAATT
57135407 ATAAAAATCGT
1 ATAAAAAT--T
* *
57135418 AAAAAAATA
1 ATAAAAATT
*
57135427 AAAAAAATT
1 ATAAAAATT
*
57135436 ATAAAATTTT
1 ATAAAA-ATT
*
57135446 ATAGAAATT
1 ATAAAAATT
57135455 ATAAAAA
1 ATAAAAA
57135462 AAATCGACAA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
8 8 0.14
9 33 0.58
10 8 0.14
11 8 0.14
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:57135616 original size:11 final size:10
Alignment explanation
Indices: 57135596--57135738 Score: 61
Period size: 10 Copynumber: 14.4 Consensus size: 10
57135586 TTTTGGTAAG
57135596 ATAATTTTTT
1 ATAATTTTTT
57135606 ATAATTTTTT
1 ATAATTTTTT
* **
57135616 TTACGA-AATTT
1 ATA--ATTTTTT
57135627 AT-ATTTTTT
1 ATAATTTTTT
*
57135636 -TACATTTTGT
1 ATA-ATTTTTT
57135646 ATAATTTTCTT
1 ATAATTTT-TT
* *
57135657 ATGA--CTTT
1 ATAATTTTTT
**
57135665 ATAAAATTTT
1 ATAATTTTTT
*
57135675 AAAATTTTTT
1 ATAATTTTTT
57135685 AT-ATATTTTT
1 ATAAT-TTTTT
57135695 ATATATTTTTT
1 ATA-ATTTTTT
57135706 ACT-A-TTTTT
1 A-TAATTTTTT
57135715 ATATATTTTTT
1 ATA-ATTTTTT
*
57135726 AT-ATTTTTA
1 ATAATTTTTT
57135735 ATAA
1 ATAA
57135739 ATTGTTAATA
Statistics
Matches: 99, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
8 8 0.08
9 20 0.20
10 44 0.44
11 23 0.23
12 4 0.04
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:57135697 original size:30 final size:30
Alignment explanation
Indices: 57135662--57135732 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
57135652 TTCTTATGAC
57135662 TTTATAAAATTTTAAAAT-TTTTTATATATT
1 TTTAT-AAATTTTAAAATATTTTTATATATT
* ** *
57135692 TTTATATATTTTTTACTATTTTTATATATT
1 TTTATAAATTTTAAAATATTTTTATATATT
*
57135722 TTT-TATATTTT
1 TTTATAAATTTT
57135733 TAATAAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTATAAATTTTAAAATATTTTTATATATT
Found at i:57135711 original size:20 final size:19
Alignment explanation
Indices: 57135680--57135734 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
57135670 ATTTTAAAAT
57135680 TTTTTATATATTTTTATATA
1 TTTTT-TATATTTTTATATA
57135700 TTTTTTACTATTTTTATATA
1 TTTTTTA-TATTTTTATATA
57135720 TTTTTTATATTTTTA
1 TTTTTTATATTTTTA
57135735 ATAAATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.29
20 24 0.71
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTATATTTTTATATA
Found at i:57135749 original size:20 final size:19
Alignment explanation
Indices: 57135687--57135751 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
57135677 AATTTTTTAT
* *
57135687 ATATTTTTATATATTTTTTA
1 ATATTTTTATA-AATTGTTA
* * * *
57135707 CTATTTTTATATATTTTTT
1 ATATTTTTATAAATTGTTA
57135726 ATATTTTTAATAAATTGTTA
1 ATATTTTT-ATAAATTGTTA
57135746 ATATTT
1 ATATTT
57135752 GAATTTTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 12 0.33
20 24 0.67
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATATTTTTATAAATTGTTA
Found at i:57135976 original size:90 final size:90
Alignment explanation
Indices: 57135819--57136039 Score: 284
Period size: 90 Copynumber: 2.4 Consensus size: 90
57135809 AATTTTTAAT
* * * *
57135819 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTG-GGGTCTTTTTTATGCATTTTGAAAGTT
1 AAAACCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTT
* *
57135883 CAAATACTCAATTGAGTG-AAAAAA
66 CAAATACCCAAATGAGTGCAAAAAA
* * ** *
57135907 GAGAGTAGGGGATTAATTGCTTTTTTTGAAAATGTTTGAGAGCCTTTTTGATGCATTTTGAAAGT
1 AAAACCAGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAGCCTTTTTGATGCATTTTGAAAGT
57135972 TCAAATACCCAAATGAGTGCCAAAAAAA
65 TCAAATACCCAAATGAGTG-C-AAAAAA
*
57136000 AAAACCAGAGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG
1 AAAACCAGGGGCTTAATTGCTTTTTTTG-AAAAGTTTGAG
57136040 GAATTTTTGC
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 28 0.25
89 5 0.04
90 40 0.36
93 35 0.31
94 4 0.04
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (90 bp):
AAAACCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTT
CAAATACCCAAATGAGTGCAAAAAA
Found at i:57143738 original size:13 final size:13
Alignment explanation
Indices: 57143722--57143752 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57143712 AGTTTAATAT
57143722 TTATTATGATTTA
1 TTATTATGATTTA
*
57143735 TTATTATTATTTA
1 TTATTATGATTTA
57143748 TTATT
1 TTATT
57143753 GTACTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTATGATTTA
Found at i:57144833 original size:30 final size:29
Alignment explanation
Indices: 57144799--57144953 Score: 138
Period size: 30 Copynumber: 5.2 Consensus size: 29
57144789 ATTTTTTTTA
* *
57144799 AAAATTACATTTTGACACTTAATCTTTTCT
1 AAAATTACATTTTGACCCCTAA-CTTTTCT
* **
57144829 AAAATTACTTTTTGACCCC-AAAATTTCTT
1 AAAATTACATTTTGACCCCTAACTTTTC-T
**
57144858 AAAATTACATTTCAACCCCTGAACTTTTCT
1 AAAATTACATTTTGACCCCT-AACTTTTCT
*
57144888 -AAATTACCTTTTGACCCCTAAAC-TTTCT
1 AAAATTACATTTTGACCCCT-AACTTTTCT
*
57144916 AAAAATTACATTTTTACCCCTTAAC-TTTCT
1 -AAAATTACATTTTGACCCC-TAACTTTTCT
57144946 ATAAATTA
1 A-AAATTA
57144954 TGTTTTAGCC
Statistics
Matches: 102, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.09
29 39 0.38
30 47 0.46
31 7 0.07
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAACTTTTCT
Found at i:57144861 original size:29 final size:30
Alignment explanation
Indices: 57144799--57144950 Score: 125
Period size: 29 Copynumber: 5.1 Consensus size: 30
57144789 ATTTTTTTTA
* * * *
57144799 AAAATTACATTTTGACACTTAATCTTT-TCT
1 AAAATTACTTTTTGACCCCTAAACTTTCT-T
*
57144829 AAAATTACTTTTTGACCCC-AAAATTTCTT
1 AAAATTACTTTTTGACCCCTAAACTTTCTT
* ** *
57144858 AAAATTACATTTCAACCCCTGAACTTT-TCT
1 AAAATTACTTTTTGACCCCTAAACTTTCT-T
* *
57144888 -AAATTACCTTTTGACCCCTAAACTTTCTA
1 AAAATTACTTTTTGACCCCTAAACTTTCTT
*
57144917 AAAATTACATTTTT-ACCCCTTAACTTTCTAT
1 AAAATTAC-TTTTTGACCCCTAAACTTTCT-T
57144948 AAA
1 AAA
57144951 TTATGTTTTA
Statistics
Matches: 97, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
29 45 0.46
30 45 0.46
31 7 0.07
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTACTTTTTGACCCCTAAACTTTCTT
Found at i:57144862 original size:59 final size:59
Alignment explanation
Indices: 57144797--57144953 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 59
57144787 GAATTTTTTT
* * *
57144797 TAAAAATTACATTTTGA-CACTTAATCTTTTCTAAAATTACTTTTTGACCCC-AAAATTTC
1 TAAAAATTACATTTTAACCACTGAA-CTTTTCT-AAATTACCTTTTGACCCCTAAAATTTC
* * * *
57144856 TTAAAATTACATTTCAACCCCTGAACTTTTCTAAATTACCTTTTGACCCCTAAACTTTC
1 TAAAAATTACATTTTAACCACTGAACTTTTCTAAATTACCTTTTGACCCCTAAAATTTC
* * * *
57144915 TAAAAATTACATTTTTACCCCTTAACTTTCTATAAATTA
1 TAAAAATTACATTTTAACCACTGAACTTT-TCTAAATTA
57144954 TGTTTTAGCC
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 17 0.20
59 53 0.64
60 13 0.16
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (59 bp):
TAAAAATTACATTTTAACCACTGAACTTTTCTAAATTACCTTTTGACCCCTAAAATTTC
Found at i:57145288 original size:3 final size:3
Alignment explanation
Indices: 57145280--57145330 Score: 84
Period size: 3 Copynumber: 16.3 Consensus size: 3
57145270 GCTAAGTTTT
57145280 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GGAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA -GAA
57145327 GAA G
1 GAA G
57145331 GAAGGGGGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:57145569 original size:22 final size:19
Alignment explanation
Indices: 57145522--57145558 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
57145512 CAAAGTACAA
57145522 GGCCCAAAGCAAAAAAAGG
1 GGCCCAAAGCAAAAAAAGG
57145541 GGCCCAAAGCAAAAAAAG
1 GGCCCAAAGCAAAAAAAG
57145559 AAGCAGGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.22, G:0.24, T:0.00
Consensus pattern (19 bp):
GGCCCAAAGCAAAAAAAGG
Found at i:57145664 original size:13 final size:13
Alignment explanation
Indices: 57145643--57145691 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
57145633 GCAGCCCAGC
*
57145643 AGAGAAAAAAAAG
1 AGAGGAAAAAAAG
57145656 AGAGGAAAAAAAG
1 AGAGGAAAAAAAG
57145669 AGA-GAAGAAAAA-
1 AGAGGAA-AAAAAG
57145681 AGAGGAAAAAA
1 AGAGGAAAAAA
57145692 GAACAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGGAAAAAAAG
Found at i:57145667 original size:15 final size:15
Alignment explanation
Indices: 57145647--57145681 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57145637 CCCAGCAGAG
*
57145647 AAAAAAAAGAGAGGA
1 AAAAAAAAGAGAAGA
*
57145662 AAAAAAGAGAGAAGA
1 AAAAAAAAGAGAAGA
57145677 AAAAA
1 AAAAA
57145682 GAGGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGAAGA
Found at i:57146037 original size:12 final size:11
Alignment explanation
Indices: 57146016--57146040 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57146006 AATTGTAAAT
57146016 ATTCAAAAAAA
1 ATTCAAAAAAA
57146027 ATTCAAAAAAA
1 ATTCAAAAAAA
57146038 ATT
1 ATT
57146041 TTCCGTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
ATTCAAAAAAA
Found at i:57146095 original size:21 final size:22
Alignment explanation
Indices: 57146057--57146097 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57146047 GTTTCGAAAT
* *
57146057 TTTCGTGTCTTCAGAAAAAAAA
1 TTTCGTATCTTCAAAAAAAAAA
57146079 TTTCGTAT-TTCAAAAAAAA
1 TTTCGTATCTTCAAAAAAAA
57146098 TATTCGCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (22 bp):
TTTCGTATCTTCAAAAAAAAAA
Found at i:57146273 original size:18 final size:18
Alignment explanation
Indices: 57146252--57146730 Score: 301
Period size: 18 Copynumber: 26.9 Consensus size: 18
57146242 AATTCCGGTG
* *
57146252 TTTCAAAAATTTTCATGA
1 TTTCAAAAATTTTCGTGT
*
57146270 TTTCAAAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
*** *
57146288 TTTCAAAAAAACTCAT-T
1 TTTCAAAAATTTTCGTGT
*
57146305 TTT-AAAATTTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
57146322 TTTCTAAATATTTCCGTG-
1 TTTC-AAAAATTTTCGTGT
* * * *
57146340 TCTCAATAATTTTCATGA
1 TTTCAAAAATTTTCGTGT
*
57146358 TTTCAAAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
57146376 TTTCAAAAAAATTT-AT-T
1 TTTC-AAAAATTTTCGTGT
*
57146393 TTT-AAAATTTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
57146410 TTTCTAAAAATTTCCGTG-
1 TTTC-AAAAATTTTCGTGT
* * *
57146428 TCTCAAAAATTTTCATGA
1 TTTCAAAAATTTTCGTGT
*
57146446 TTTCAAAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
*** *
57146464 TTTCAAAAAAAATCAT-T
1 TTTCAAAAATTTTCGTGT
* *
57146481 TTT-AAAATTTTTCGTTT
1 TTTCAAAAATTTTCGTGT
*
57146498 TTTCTAAAAATTTCCGTG-
1 TTTC-AAAAATTTTCGTGT
* *
57146516 TCTCAAAAATTTTCATGT
1 TTTCAAAAATTTTCGTGT
*
57146534 TTTCAAAAATTTTCGTGC
1 TTTCAAAAATTTTCGTGT
*
57146552 TTTC-AAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
* * *
57146569 TTTTAACAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
*
57146587 TTT-ACTAAATTTTCGTG-
1 TTTCA-AAAATTTTCGTGT
* *
57146604 TTTCAAAAAATTGT-ATGT
1 TTTC-AAAAATTTTCGTGT
* *
57146622 TTTAAAAAAAAATTCTCGTG-
1 TTT---CAAAAATTTTCGTGT
57146642 TTTCAAAAATTGTT-GTGCT
1 TTTCAAAAATT-TTCGTG-T
57146661 TTT-AAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
57146678 TTT-TAAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
*
57146695 TTTAAAAAAATTTTCGTGT
1 TTT-CAAAAATTTTCGTGT
* *
57146714 TTTAAAAAAATTTCGTG
1 TTTCAAAAATTTTCGTG
57146731 CTTCAAAATT
Statistics
Matches: 353, Mismatches: 79, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
15 7 0.02
16 15 0.04
17 106 0.30
18 155 0.44
19 57 0.16
20 11 0.03
21 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:57146363 original size:88 final size:88
Alignment explanation
Indices: 57146238--57146559 Score: 536
Period size: 88 Copynumber: 3.6 Consensus size: 88
57146228 TGTGCTTTTA
* * *
57146238 AAAAAATTCCGGTGTTTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAACTCA
1 AAAAATTTCC-GTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCA
57146303 TTTTTAAAATTTTTCGTGTTTTCT
65 TTTTTAAAATTTTTCGTGTTTTCT
* * * *
57146327 AAATATTTCCGTGTCTCAATAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT
1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT
57146392 TTTTAAAATTTTTCGTGTTTTCT
66 TTTTAAAATTTTTCGTGTTTTCT
57146415 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT
1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT
*
57146480 TTTTAAAATTTTTCGTTTTTTCT
66 TTTTAAAATTTTTCGTGTTTTCT
* * *
57146503 AAAAATTTCCGTGTCTCAAAAATTTTCATGTTTTCAAAAATTTTCGTGCTTTCAAAA
1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAA
57146560 TTTTTGTGTT
Statistics
Matches: 219, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
88 211 0.96
89 8 0.04
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (88 bp):
AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT
TTTTAAAATTTTTCGTGTTTTCT
Found at i:57146597 original size:88 final size:87
Alignment explanation
Indices: 57146239--57146688 Score: 516
Period size: 88 Copynumber: 5.1 Consensus size: 87
57146229 GTGCTTTTAA
* * * *
57146239 AAAAATTCCGGTGTTTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAACTCAT
1 AAAATTTCC-GTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT
57146304 TTTTAAAATTTTTCGTGTTTTCT
65 TTTTAAAATTTTTCGTGTTTTCT
*
57146327 AAATATTTCCGTGTCTCAATAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT
1 AAA-ATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT
57146392 TTTTAAAATTTTTCGTGTTTTCT
65 TTTTAAAATTTTTCGTGTTTTCT
* *
57146415 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT
1 -AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT
*
57146480 TTTTAAAATTTTTCGTTTTTTCT
65 TTTTAAAATTTTTCGTGTTTTCT
* * * *** *
57146503 AAAAATTTCCGTGTCTCAAAAATTTTCATGTTTTCAAAAATTTTCGTGCTTTCAAAATTTTTGTG
1 -AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATT-TA
*
57146568 TTTTTAACAA-TTCTCGTGTTTTACT
64 TTTTTAA-AATTTTTCGTGTTTT-CT
* * * * * *
57146593 -AAATTTTCGTGTTTCAAAAAATTGT-ATGTTTTAAAAAAAAATTCTCGTG-TTTC-AAAAATTG
1 AAAATTTCCGTGTCTC-AAAAATTTTCATGATTT---CAAAAATTCTCGTGTTTTCAAAAAAAT-
* *
57146654 TTGTGCTTTTAAAAATTTTCGTGTTTT-T
61 TTAT--TTTTAAAATTTTTCGTGTTTTCT
57146682 AAAATTT
1 AAAATTT
57146689 TTGTGTTTTA
Statistics
Matches: 320, Mismatches: 28, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
88 232 0.73
89 42 0.13
90 17 0.05
91 29 0.09
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (87 bp):
AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTATT
TTTAAAATTTTTCGTGTTTTCT
Found at i:57146641 original size:38 final size:39
Alignment explanation
Indices: 57146593--57146668 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
57146583 GTGTTTTACT
*
57146593 AAATTTTCGTGTTTCAAAAAATTG-TATG-TTTTAAAAAA
1 AAATTCTCGTGTTTC-AAAAATTGTTATGCTTTTAAAAAA
*
57146631 AAATTCTCGTGTTTCAAAAATTGTTGTGCTTTTAAAAA
1 AAATTCTCGTGTTTCAAAAATTGTTATGCTTTTAAAAA
57146669 TTTTCGTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 8 0.24
38 17 0.50
39 9 0.26
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (39 bp):
AAATTCTCGTGTTTCAAAAATTGTTATGCTTTTAAAAAA
Found at i:57146738 original size:18 final size:19
Alignment explanation
Indices: 57146682--57146738 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
57146672 TCGTGTTTTT
* * *
57146682 AAAATTTTTGTGTTTTAAA
1 AAAATTTTCGTGCTTCAAA
* *
57146701 AAAATTTTCGTGTTTTAAA
1 AAAATTTTCGTGCTTCAAA
57146720 AAAA-TTTCGTGCTTCAAA
1 AAAATTTTCGTGCTTCAAA
57146738 A
1 A
57146739 TTCCCGTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 13 0.37
19 22 0.63
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (19 bp):
AAAATTTTCGTGCTTCAAA
Found at i:57154305 original size:19 final size:19
Alignment explanation
Indices: 57154265--57154320 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
57154255 ATTACAAAAC
57154265 AAAA-TCAAAATGATTT-TCA
1 AAAATTCAAAAT-ATTTAT-A
57154284 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
*
57154303 AAAATTCCAAA-ATTTATA
1 AAAATTCAAAATATTTATA
57154321 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.21
19 19 0.56
20 8 0.24
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:57161878 original size:19 final size:18
Alignment explanation
Indices: 57161854--57161930 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
57161844 TTTTTGTATA
57161854 TTTAAAATTTATTTTTAAT
1 TTTAAAATTTA-TTTTAAT
* *
57161873 TTTAAAAATTTA-ATTGAT
1 TTT-AAAATTTATTTTAAT
*
57161891 TTCAAAATTTATATTTAAT
1 TTTAAAATTTAT-TTTAAT
* *
57161910 TATTAACA-TTATTATAAT
1 T-TTAAAATTTATTTTAAT
57161928 TTT
1 TTT
57161931 TATGTTAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
17 10 0.22
18 12 0.26
19 12 0.26
20 12 0.26
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTAAAATTTATTTTAAT
Found at i:57164999 original size:24 final size:24
Alignment explanation
Indices: 57164967--57165013 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
57164957 GGTGCTTCCC
*
57164967 GTTAATTGCTCTTCGGAGCTACCT
1 GTTAATTGCTCTTCGAAGCTACCT
*
57164991 GTTAATTGCTCTTTGAAGCTACC
1 GTTAATTGCTCTTCGAAGCTACC
57165014 CATTATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (24 bp):
GTTAATTGCTCTTCGAAGCTACCT
Found at i:57166695 original size:44 final size:42
Alignment explanation
Indices: 57166627--57166767 Score: 131
Period size: 42 Copynumber: 3.3 Consensus size: 42
57166617 AATGTGACAT
** * *
57166627 CGTGTAAGACCACATCTGGAACATTGGCCTCG-ATTTGAGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATAT--GA-TTA
* *
57166671 CGTGTAAGATCATGTCTGGGACATTGGCGTCGTATATGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATATGATTA
* * * * *
57166713 CGTGTAAGACCCTGTCTGCGACAGTGGCATCGTTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCCTCG-TATATGATTA
*
57166756 CATGTAAGACCA
1 CGTGTAAGACCA
57166768 CGTTTGGGGC
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
42 30 0.37
43 21 0.26
44 27 0.33
45 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATATGATTA
Found at i:57170137 original size:52 final size:51
Alignment explanation
Indices: 57170059--57170212 Score: 194
Period size: 52 Copynumber: 3.1 Consensus size: 51
57170049 GATCAAGTGA
57170059 CAAGTGGA-AAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGT-GACAAGT-GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
*
57170111 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGACAAGTG-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
* * **
57170163 CAAGAGAC-----AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
57170209 CAAG
1 CAAG
57170213 AAACAAAGTG
Statistics
Matches: 94, Mismatches: 6, Indels: 10
0.85 0.05 0.09
Matches are distributed among these distances:
46 38 0.40
51 3 0.03
52 53 0.56
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (51 bp):
CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
Found at i:57170202 original size:46 final size:43
Alignment explanation
Indices: 57170125--57170298 Score: 185
Period size: 37 Copynumber: 4.2 Consensus size: 43
57170115 TGACAAGTGA
* *
57170125 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGT-ATAGCTT--GCTACACTTATCTGATCAAGAAAC
57170171 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGT-ATAGC-TT-GCTACACTTATCTGATCAAGAAAC
57170217 AAAGTGATAAG--T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC
57170254 AAAGTGATAAG--T-G---GCTACACTTATCTGATC-AGAAAC
1 AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC
57170290 AAAGTGATA
1 AAAGTGATA
57170299 GGTGGCTACA
Statistics
Matches: 123, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
36 15 0.12
37 54 0.44
42 1 0.01
43 1 0.01
46 50 0.41
47 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (43 bp):
AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC
Found at i:57170295 original size:36 final size:37
Alignment explanation
Indices: 57170193--57170337 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
57170183 AATAGCTTTA
57170193 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57170230 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
57170267 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
57170303 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57170338 ATCATACGTA
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
35 11 0.11
36 39 0.38
37 54 0.52
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:57170313 original size:73 final size:72
Alignment explanation
Indices: 57170193--57170337 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 72
57170183 AATAGCTTTA
57170193 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC-AGAAAC-AAG
57170258 TGATAAGTG
64 TGATAAGTG
* **
57170267 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTGGCTACACTTATCTGATCAGGGACAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG
57170331 ATAAGTG
66 ATAAGTG
57170338 ATCATACGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 12 0.18
72 4 0.06
73 35 0.51
74 17 0.25
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (72 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG
ATAAGTG
Found at i:57179119 original size:2 final size:2
Alignment explanation
Indices: 57179112--57179141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57179102 AATTCCTCTT
57179112 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
57179142 AGTTGTTTAC
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:57189787 original size:23 final size:23
Alignment explanation
Indices: 57189757--57189807 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
57189747 CGAAATGTAT
* *
57189757 AACTCTTACCAATTATAATATCA
1 AACTCTTACCAAATACAATATCA
57189780 AACTCTTACCAAATACAATATCA
1 AACTCTTACCAAATACAATATCA
57189803 AACTC
1 AACTC
57189808 AAGTATTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
AACTCTTACCAAATACAATATCA
Found at i:57201947 original size:26 final size:25
Alignment explanation
Indices: 57201916--57201971 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
57201906 AAAAAGTTAA
57201916 TTAATTATTTTAATGAC-TTTTAATT-T
1 TTAATTA-TTT-AT-ACTTTTTAATTAT
57201942 TTAATTATTTATACTTTTTAATTAT
1 TTAATTATTTATACTTTTTAATTAT
57201967 TTAAT
1 TTAAT
57201972 GACTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.07
24 10 0.36
25 9 0.32
26 7 0.25
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (25 bp):
TTAATTATTTATACTTTTTAATTAT
Found at i:57201959 original size:17 final size:19
Alignment explanation
Indices: 57201939--57201979 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
57201929 TGACTTTTAA
57201939 TTTTTAATTATTT-AT-AC
1 TTTTTAATTATTTAATGAC
57201956 TTTTTAATTATTTAATGAC
1 TTTTTAATTATTTAATGAC
57201975 TTTTT
1 TTTTT
57201980 TGCTTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
18 2 0.09
19 7 0.32
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTAATTATTTAATGAC
Found at i:57203829 original size:57 final size:58
Alignment explanation
Indices: 57203768--57203889 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 58
57203758 CCAGAGTTGG
* *
57203768 CAACATTGGGTCCTGTGGGAATGGGACCACTGGCTGCA-GCA-CCTACACCAGGGTTCC
1 CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCACGCAGCC-ACACCAGGGTTCC
* * *
57203825 CAACAGTGGTTCCTGTGGGAATAGGACCAGTGGCTGCACCTGCAGCCACACCAGGGTTGC
1 CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCA-C-GCAGCCACACCAGGGTTCC
57203885 CAACA
1 CAACA
57203890 ACGGCTCCAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
57 34 0.61
60 20 0.36
61 2 0.04
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18
Consensus pattern (58 bp):
CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCACGCAGCCACACCAGGGTTCC
Found at i:57208651 original size:20 final size:22
Alignment explanation
Indices: 57208613--57208658 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
57208603 AAAATAGTAG
*
57208613 AAAGAAGAACCCAAGAAAGAGA
1 AAAGAAGAACCCAAGAAAGAAA
57208635 AAAGAA-AACCC-AGAAAGAAA
1 AAAGAAGAACCCAAGAAAGAAA
57208655 AAAG
1 AAAG
57208659 GGGAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
21 5 0.22
22 6 0.26
ACGTcount: A:0.67, C:0.13, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAAGAACCCAAGAAAGAAA
Found at i:57211946 original size:67 final size:67
Alignment explanation
Indices: 57211866--57212000 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
57211856 TTTGGCATAT
*
57211866 TCCCTGAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT
1 TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT
57211931 TA
66 TA
* *
57211933 TCCCTAAAGCGAATATTGCATATAATTGTTTGGAAATTATATTTATTTTTTTGACTTAGTGACAT
1 TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT
57211998 TA
66 TA
57212000 T
1 T
57212001 AATATTCACA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (67 bp):
TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT
TA
Found at i:57217694 original size:28 final size:28
Alignment explanation
Indices: 57217654--57217711 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
57217644 TTAACATTAA
57217654 TATAATAATTTAAGATAAGATTGGATCG
1 TATAATAATTTAAGATAAGATTGGATCG
57217682 TATAATAATTTAAGATAAGATTGGATCG
1 TATAATAATTTAAGATAAGATTGGATCG
57217710 TA
1 TA
57217712 GTCTTAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.36
Consensus pattern (28 bp):
TATAATAATTTAAGATAAGATTGGATCG
Found at i:57219038 original size:17 final size:16
Alignment explanation
Indices: 57219005--57219060 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
57218995 GTAATTTTCT
57219005 TTCT-ATTTTTGATCC
1 TTCTAATTTTTGATCC
*
57219020 TTCTAATTTTTTATCCC
1 TTCTAATTTTTGAT-CC
* *
57219037 TTC-AAATTTTCATCC
1 TTCTAATTTTTGATCC
*
57219052 TTCCAATTT
1 TTCTAATTT
57219061 CCTTTCTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.26
16 20 0.59
17 5 0.15
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (16 bp):
TTCTAATTTTTGATCC
Found at i:57223744 original size:23 final size:23
Alignment explanation
Indices: 57223714--57224292 Score: 230
Period size: 23 Copynumber: 22.9 Consensus size: 23
57223704 TACAATTTAA
57223714 TTAGGGTTTTTAATTAAATAGGG
1 TTAGGGTTTTTAATTAAATAGGG
57223737 TTAGGGTTTTTAATTTAATTAAATTA-GG
1 TTAGGG---TT--TTTAATTAAA-TAGGG
*
57223765 TTAGGGTTTTTAATTAAGTAGGG
1 TTAGGGTTTTTAATTAAATAGGG
*
57223788 TTAGGGTTTTTAATTAAGTAGGG
1 TTAGGGTTTTTAATTAAATAGGG
*
57223811 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG---TT--TTTAATTAAATAGGG
57223839 TTAGGGTTTTTAATTAAATTA-GG
1 TTAGGGTTTTTAATTAAA-TAGGG
*
57223862 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG---TT--TTTAATTAAATAGGG
57223890 TTAGGGTTTTTAATT-AA-A---
1 TTAGGGTTTTTAATTAAATAGGG
*** **
57223908 TTA-GGTAACCTAATTAGGTTA-GG
1 TTAGGGT-TTTTAATTA-AATAGGG
*
57223931 TTAGTGTTTTTAATTTAATTAAATTA-GG
1 TTAG-G--GTT--TTTAATTAAA-TAGGG
57223959 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTAAA-TA-G---GG
*
57223987 TTAGGGTTAGGGTTTTTAATTAAGTAGGG
1 TTAGGG------TTTTTAATTAAATAGGG
*
57224016 TTTAGGGTTTTTAATTTAATTAAATAAGG
1 -TTAGGG---TT--TTTAATTAAATAGGG
* **
57224045 TTAGGGTTTTTAATTTAATTA-AA
1 TTAGGGTTTTTAA-TTAAATAGGG
*
57224068 TTAGGGTTTTTAATTAAGTAGGG
1 TTAGGGTTTTTAATTAAATAGGG
*
57224091 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG---TT--TTTAATTAAATAGGG
*
57224119 TTAGGGTTTTTAATTTAAGTAGGTTAGG
1 TTAGGGTTTTTAA-TTAAATA-G---GG
57224147 TTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTAAA-TA-G---GG
57224175 TTAGGGTTTTTAATTTAATTAAATTA-GG
1 TTAGGG---TT--TTTAATTAAA-TAGGG
*
57224203 TTAGGGTTTTTAATTAAGTAGGG
1 TTAGGGTTTTTAATTAAATAGGG
* * **
57224226 TTTAGGATTTTTAATTTAATTA-AA
1 -TTAGGGTTTTTAA-TTAAATAGGG
* *
57224250 TTATGGTTTTTAATTAAGTAGGG
1 TTAGGGTTTTTAATTAAATAGGG
* *
57224273 TTAGGGATTTTAATCAAATA
1 TTAGGGTTTTTAATTAAATA
57224293 ATGTCAAAAT
Statistics
Matches: 442, Mismatches: 46, Indels: 136
0.71 0.07 0.22
Matches are distributed among these distances:
17 3 0.01
18 8 0.02
21 2 0.00
22 18 0.04
23 154 0.35
24 26 0.06
25 21 0.05
26 8 0.02
27 10 0.02
28 140 0.32
29 17 0.04
30 6 0.01
31 2 0.00
32 1 0.00
33 15 0.03
34 11 0.02
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATAGGG
Found at i:57223766 original size:28 final size:28
Alignment explanation
Indices: 57223722--57224257 Score: 354
Period size: 28 Copynumber: 19.6 Consensus size: 28
57223712 AATTAGGGTT
57223722 TTTAATTAAA-TAGGGTTAGGGTTTTTAA
1 TTTAATTAAATTA-GGTTAGGGTTTTTAA
57223750 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
57223778 -TTAAGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
57223801 -TTAAGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
57223824 TTTAATTAAATAAGGTTAGGG---TT--
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
57223847 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
57223875 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
57223903 TTAAATTAGGTAACCTAATTAGGTTA-GGTTAGTGTT--
1 TTTAA-T---T-A---AATTAGGTTAGGGTT--T-TTAA
* *
57223939 TTTAATTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATT--A--GG-TTAGGGTTTTTAA
* ** *
57223972 TTAAATTAGGTTAGGTTAGGGTTAGGGTT--
1 TTTAATTAAATTAGGTTAGGGTT---TTTAA
*
57224001 TTTAATT-AAGTAGGGTTTAGGGTTTTTAA
1 TTTAATTAAATTA-GG-TTAGGGTTTTTAA
*
57224030 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
57224058 TTTAATT-AA--A--TTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
57224081 -TTAAGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
57224104 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
57224132 TTTAAGTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
57224160 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
57224188 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* * *
57224216 -TTAAGT--A--GGGTTTAGGATTTTTAA
1 TTTAATTAAATTAGG-TTAGGGTTTTTAA
57224240 TTTAATTAAATTATGGTT
1 TTTAATTAAATTA-GGTT
57224258 TTTAATTAAG
Statistics
Matches: 414, Mismatches: 42, Indels: 103
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.00
22 5 0.01
23 86 0.21
24 22 0.05
25 10 0.02
26 4 0.01
27 15 0.04
28 188 0.45
29 23 0.06
30 14 0.03
31 5 0.01
32 4 0.01
33 12 0.03
34 4 0.01
35 5 0.01
36 13 0.03
37 1 0.00
38 2 0.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (28 bp):
TTTAATTAAATTAGGTTAGGGTTTTTAA
Found at i:57223787 original size:51 final size:51
Alignment explanation
Indices: 57223714--57224286 Score: 353
Period size: 51 Copynumber: 10.7 Consensus size: 51
57223704 TACAATTTAA
57223714 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
* * *
57223765 TTAGGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAA-TTAAGT--A--GGG
1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
*
57223811 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGG---TT--TTTAATTAAATTAGG
1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
* *
57223862 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTAAATTAGGTAACCTAATTAGG
1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAA-T---T-A---AATTAGG
* *
57223926 TTAGGTTAGTGTTTTTAATTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTA
1 TTA-G---G-GTTTTT-A----ATTAAA-TAGGGTTAGGGTTTTTAATTTAATTA----A-ATTA
57223990 GGG
50 -GG
* *
57223993 TTAGGGTTTTTAATTAAGTAGGGTTTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGGTTTTTAATTAAATAGGG-TTAGGGTTTTTAATTTAATTAAATTAGG
* ** * *
57224045 TTAGGGTTTTTAATTTAATTA-AATTAGGGTTTTTAA-TTAAGT--A--GGG
1 TTAGGGTTTTTAA-TTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
* * **
57224091 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGG
1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
57224147 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAA-TA-G---GGTTAGGGTTTTTAATTTAATTAAATTAGG
* *
57224203 TTAGGGTTTTTAATTAAGTAGGGTTTAGGATTTTTAATTTAATTAAATTA--
1 TTAGGGTTTTTAATTAAATAGGG-TTAGGGTTTTTAATTTAATTAAATTAGG
* *
57224253 -T--GGTTTTTAATTAAGTAGGGTTAGGGATTTTAAT
1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAAT
57224287 CAAATAATGT
Statistics
Matches: 432, Mismatches: 33, Indels: 119
0.74 0.06 0.20
Matches are distributed among these distances:
46 28 0.06
47 24 0.06
48 4 0.01
49 6 0.01
50 16 0.04
51 133 0.31
52 48 0.11
53 10 0.02
54 4 0.01
55 2 0.00
56 58 0.13
57 8 0.02
58 20 0.05
60 1 0.00
61 2 0.00
62 6 0.01
63 1 0.00
64 14 0.03
65 5 0.01
66 6 0.01
67 5 0.01
68 2 0.00
69 27 0.06
70 2 0.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (51 bp):
TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
Found at i:57224091 original size:17 final size:18
Alignment explanation
Indices: 57224058--57224092 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57224048 GGGTTTTTAA
*
57224058 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
57224076 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
57224093 AGGGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:57224521 original size:21 final size:21
Alignment explanation
Indices: 57224480--57224524 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
57224470 GGCGGTTGTT
* *
57224480 GTTCTTCCGGTGGGGATTCTG
1 GTTCTTCCGGTCGGCATTCTG
57224501 GTTCTTCCGGTTCGGCA-TCTG
1 GTTCTTCCGG-TCGGCATTCTG
57224522 GTT
1 GTT
57224525 GTCGGACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.04, C:0.22, G:0.33, T:0.40
Consensus pattern (21 bp):
GTTCTTCCGGTCGGCATTCTG
Found at i:57226592 original size:28 final size:29
Alignment explanation
Indices: 57226560--57226615 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
57226550 TGAAAATATT
57226560 AAAAATTTTAAAATTAT-TTAAAAAAATA
1 AAAAATTTTAAAATTATCTTAAAAAAATA
*
57226588 AAAAATTTTAAAATTTTCTTAAAAAAAT
1 AAAAATTTTAAAATTATCTTAAAAAAAT
57226616 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAAAATTATCTTAAAAAAATA
Found at i:57226687 original size:22 final size:22
Alignment explanation
Indices: 57226657--57226698 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
57226647 ATTTGGAGAT
*
57226657 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
57226679 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
57226699 TTTGAGAGAA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:57226719 original size:52 final size:51
Alignment explanation
Indices: 57226648--57226750 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
57226638 TTAATATAGA
* * *
57226648 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
57226699 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
57226751 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:57226725 original size:22 final size:23
Alignment explanation
Indices: 57226700--57226791 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
57226690 ATTTGAGAGT
57226700 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
57226722 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
57226744 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
57226766 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
57226788 TTGA
1 TTGA
57226792 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:57226749 original size:44 final size:44
Alignment explanation
Indices: 57226700--57226791 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
57226690 ATTTGAGAGT
* * * *
57226700 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
57226744 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
57226788 TTGA
1 TTGA
57226792 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:57229662 original size:19 final size:19
Alignment explanation
Indices: 57229625--57229663 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
57229615 ATTGATTTTT
57229625 TAAATTTTGAATTAAAATGA
1 TAAATTTTGAA-TAAAATGA
57229645 TAAATTTTGTAA-AAAATGA
1 TAAATTTTG-AATAAAATGA
57229664 GGGCTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TAAATTTTGAATAAAATGA
Found at i:57230569 original size:42 final size:37
Alignment explanation
Indices: 57230474--57230549 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
57230464 ATTACTAATA
* *
57230474 AAATAAA-AAGAAAAATTATATAAAATTTATAATATGT
1 AAATAAAGAA-AAAAATAATATAAAATTTATAATATAT
* *
57230511 AAATTAAGTAAAAAATAATATAAAATTTATAATATAT
1 AAATAAAGAAAAAAATAATATAAAATTTATAATATAT
57230548 AA
1 AA
57230550 CCTTTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (37 bp):
AAATAAAGAAAAAAATAATATAAAATTTATAATATAT
Found at i:57234595 original size:18 final size:17
Alignment explanation
Indices: 57234551--57234602 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
57234541 ATCATTATTA
*
57234551 AAAATCATT-AAAAATAT
1 AAAAT-ATTCAAAAAAAT
*
57234568 ATAATATTCAAAAAAAT
1 AAAATATTCAAAAAAAT
57234585 AAAATATTTCAAAGAAAA
1 AAAATA-TTCAAA-AAAA
57234603 ATATAAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 6 0.21
19 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATTCAAAAAAAT
Found at i:57236528 original size:14 final size:14
Alignment explanation
Indices: 57236509--57236535 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57236499 TTATTTAGTT
57236509 GTAGAATCAAAATA
1 GTAGAATCAAAATA
57236523 GTAGAATCAAAAT
1 GTAGAATCAAAAT
57236536 TTAAGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
GTAGAATCAAAATA
Found at i:57245173 original size:39 final size:39
Alignment explanation
Indices: 57245119--57245196 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
57245109 ATAAGTCGCC
*
57245119 GGCACTCGGGGATGCGTAGGTTATATCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
*
57245158 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
57245197 ATCGGAGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
Found at i:57251745 original size:21 final size:21
Alignment explanation
Indices: 57251721--57251790 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 21
57251711 AATTTAATTT
57251721 TTTATTTTAATATTATATATA
1 TTTATTTTAATATTATATATA
*
57251742 TTTAATGTGTTATTATTA-ATA-A
1 TTT-AT-T-TTAATATTATATATA
*
57251764 TTAATTTTAA-ATTATATAT-
1 TTTATTTTAATATTATATATA
*
57251783 TTCATTTT
1 TTTATTTT
57251791 TTATTGTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 4 0.10
19 13 0.32
20 1 0.03
21 5 0.12
22 5 0.12
23 4 0.10
24 8 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTATTTTAATATTATATATA
Found at i:57254501 original size:14 final size:14
Alignment explanation
Indices: 57254482--57254513 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
57254472 TAAAATCTTC
*
57254482 GATTCCAACTACAG
1 GATTCCAACTAAAG
57254496 GATTCCAACTAAAG
1 GATTCCAACTAAAG
57254510 GATT
1 GATT
57254514 TCTCCACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (14 bp):
GATTCCAACTAAAG
Found at i:57256242 original size:26 final size:26
Alignment explanation
Indices: 57256213--57256264 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
57256203 ATAAGAAAGT
57256213 GACACGTTGATGAAAGAAACATTAGG
1 GACACGTTGATGAAAGAAACATTAGG
57256239 GACACGTTGATGAAAGAAACATTAGG
1 GACACGTTGATGAAAGAAACATTAGG
57256265 AGGTGCCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (26 bp):
GACACGTTGATGAAAGAAACATTAGG
Found at i:57258801 original size:2 final size:2
Alignment explanation
Indices: 57258796--57258825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57258786 AGTCTAACAC
57258796 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
57258826 CAATAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57259973 original size:14 final size:14
Alignment explanation
Indices: 57259954--57259984 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
57259944 TTCTAGTTTG
57259954 TTTTGTTCTAATAT
1 TTTTGTTCTAATAT
*
57259968 TTTTGTTGTAATAT
1 TTTTGTTCTAATAT
57259982 TTT
1 TTT
57259985 AGTTTATGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (14 bp):
TTTTGTTCTAATAT
Found at i:57262981 original size:15 final size:15
Alignment explanation
Indices: 57262936--57262981 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
57262926 AAGTTGTGGA
57262936 TTTAATC-TATATTT
1 TTTAATCTTATATTT
57262950 TTTAAT-TTGAT-TATT
1 TTTAATCTT-ATAT-TT
57262965 TTTAATCTTATATTT
1 TTTAATCTTATATTT
57262980 TT
1 TT
57262982 CAAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 8 0.30
15 16 0.59
16 3 0.11
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTAATCTTATATTT
Found at i:57279034 original size:39 final size:39
Alignment explanation
Indices: 57278991--57279072 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
57278981 TTGAGGAAGG
*
57278991 ATTATTGTAAATTCTAAACATTATATCAA-AAAAGTAAAA
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAA-TAAAA
* * *
57279030 ATTATGGTAAATTTTAAACATTATATTAAGAAAATAAAG
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
57279069 ATTA
1 ATTA
57279073 AGAGAGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.35
Consensus pattern (39 bp):
ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
Found at i:57281448 original size:25 final size:27
Alignment explanation
Indices: 57281398--57281448 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
57281388 ACAAATAATT
*
57281398 AAAAAATTATAATAAAATATTAAAAAC
1 AAAAAATTATAATAAAATATCAAAAAC
57281425 AAAAAA-TAT-ATAAAAT-TCATAAAA
1 AAAAAATTATAATAAAATATCA-AAAA
57281449 ATTTAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.09
25 11 0.50
26 3 0.14
27 6 0.27
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAATTATAATAAAATATCAAAAAC
Found at i:57282179 original size:19 final size:19
Alignment explanation
Indices: 57282157--57282195 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
57282147 ATCTTCATAA
57282157 AAGCTTCCACAAAAAAAAT
1 AAGCTTCCACAAAAAAAAT
57282176 AAGCTTCCACAAAAAAAAT
1 AAGCTTCCACAAAAAAAAT
57282195 A
1 A
57282196 TCCACACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (19 bp):
AAGCTTCCACAAAAAAAAT
Found at i:57287015 original size:11 final size:10
Alignment explanation
Indices: 57286993--57287023 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
57286983 CTTGATGTCG
57286993 AAAATTAAAA
1 AAAATTAAAA
*
57287003 AAACTTAAAA
1 AAAATTAAAA
57287013 AAAATTAAAA
1 AAAATTAAAA
57287023 A
1 A
57287024 TACGATCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:57288086 original size:29 final size:28
Alignment explanation
Indices: 57288024--57288088 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
57288014 ATAAAATTGC
* *
57288024 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
57288052 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
57288082 TAAAATA
1 TAAAATA
57288089 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:57289621 original size:46 final size:45
Alignment explanation
Indices: 57289559--57289980 Score: 241
Period size: 46 Copynumber: 9.8 Consensus size: 45
57289549 CTGGCTTCAA
*
57289559 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG
* * * * *
57289605 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG-A--C-GCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG
* ** * * **
57289646 TCTACTCTGCTGTAA-CTTTAGAGAGATAAGATC---A-T-TT-AA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCGG
* * * * *
57289685 TCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATCTTTGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCGG
* * *
57289729 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTTTTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG
* * * *
57289775 TCTGCTCCACTGTAATTTCAGGGAGATAAGACCT-AA---TACGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG
** * * **
57289816 TCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCT---TTAATC--
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGAATTCTTCGG
* * *
57289857 -C-GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTATCTTTGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCGG
* *
57289899 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG
* *
57289945 TCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA
57289981 TATGATCCAC
Statistics
Matches: 290, Mismatches: 57, Indels: 59
0.71 0.14 0.15
Matches are distributed among these distances:
37 1 0.00
39 50 0.17
40 6 0.02
41 53 0.18
42 4 0.01
43 4 0.01
44 60 0.21
45 3 0.01
46 103 0.36
47 6 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG
Found at i:57289751 original size:44 final size:43
Alignment explanation
Indices: 57289688--57290070 Score: 296
Period size: 46 Copynumber: 9.0 Consensus size: 43
57289678 CATTTAATCC
*
57289688 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* *
57289732 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTT-TTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGA--T-TACTTCTTT-GATCT
* * * * *
57289778 GCTCCACTGTAATTTCAGGGAGATAAGACCTAATAC---GATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGA-TTACTTCTTTGATCT
* * * * *
57289819 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
57289858 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* * *
57289902 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTTGATCT
* * ** * *
57289948 GTTCCACTGTAATCTCAGGGAGATAAGA--CCTGATATGATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
* * * *
57289989 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
57290027 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
57290071 ACTTCACTTA
Statistics
Matches: 268, Mismatches: 44, Indels: 54
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.00
38 23 0.09
39 35 0.13
40 4 0.01
41 56 0.21
43 7 0.03
44 64 0.24
45 5 0.02
46 66 0.25
47 7 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
Found at i:57290103 original size:170 final size:170
Alignment explanation
Indices: 57289558--57290070 Score: 875
Period size: 170 Copynumber: 3.0 Consensus size: 170
57289548 ACTGGCTTCA
*
57289558 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT
* ** * * * *
57289623 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCATTTAATCC
66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
*
57289688 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTG
131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
* * * *
57289728 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTTTTTCGGTCTGCTCCACTGTAATTT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT
*
57289793 CAGGGAGATAAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
57289858 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
*
57289898 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTGTAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT
*
57289963 CAGGGAGATAAGACCTGATATGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAAT-C
66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
57290027 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
57290067 ATCT
1 ATCT
57290071 ACTTCACTTA
Statistics
Matches: 323, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
169 45 0.14
170 278 0.86
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (170 bp):
ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT
CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
Found at i:57301783 original size:9 final size:10
Alignment explanation
Indices: 57301764--57301795 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
57301754 CTTGATGTCG
57301764 AAAATTAAAA
1 AAAATTAAAA
57301774 AAAATTAAAAA
1 AAAATT-AAAA
57301785 AAAATTAAAA
1 AAAATTAAAA
57301795 A
1 A
57301796 TACGATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:57301786 original size:11 final size:11
Alignment explanation
Indices: 57301764--57301795 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
57301754 CTTGATGTCG
57301764 AAAATT-AAAA
1 AAAATTAAAAA
57301774 AAAATTAAAAA
1 AAAATTAAAAA
57301785 AAAATTAAAAA
1 AAAATTAAAAA
57301796 TACGATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:57302860 original size:29 final size:28
Alignment explanation
Indices: 57302798--57302862 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
57302788 ATAAAATTGC
* *
57302798 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
57302826 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
57302856 TAAAATA
1 TAAAATA
57302863 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:57304346 original size:12 final size:12
Alignment explanation
Indices: 57304329--57304355 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57304319 AATAAATCAT
57304329 ATATGTATATTA
1 ATATGTATATTA
57304341 ATATGTATATTA
1 ATATGTATATTA
57304353 ATA
1 ATA
57304356 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:57304467 original size:22 final size:21
Alignment explanation
Indices: 57304438--57304478 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
57304428 TCCAAAAAAT
*
57304438 ATTAATAAATAATTTAAATTA
1 ATTAATAAATAATTAAAATTA
*
57304459 ATTACATAATTAATTAAAAT
1 ATTA-ATAAATAATTAAAAT
57304479 ATTGGAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAAATAATTAAAATTA
Found at i:57304697 original size:21 final size:21
Alignment explanation
Indices: 57304673--57304728 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
57304663 CACTATTATT
* * *
57304673 TCTAATTTCACTGCTATAGTA
1 TCTAATCTCACCGCTACAGTA
57304694 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
57304715 ACTAATCTCACCGC
1 TCTAATCTCACCGC
57304729 CACCGCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:57305556 original size:23 final size:23
Alignment explanation
Indices: 57305499--57305543 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
57305489 CATATAATCA
57305499 AATCAAACTAAAAATGATAAATG
1 AATCAAACTAAAAATGATAAATG
57305522 AATCAAACTAAAAATGATAAAT
1 AATCAAACTAAAAATGATAAAT
57305544 TATAGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAAACTAAAAATGATAAATG
Found at i:57306989 original size:14 final size:14
Alignment explanation
Indices: 57306965--57306998 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
57306955 TTTATTTTCC
*
57306965 CCCTCTTTTTCTCT
1 CCCTCTCTTTCTCT
*
57306979 CTCTCTCTTTCTCT
1 CCCTCTCTTTCTCT
57306993 CCCTCT
1 CCCTCT
57306999 TCAGTTTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
CCCTCTCTTTCTCT
Found at i:57320845 original size:2 final size:2
Alignment explanation
Indices: 57320838--57320877 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
57320828 NNNNNNNNNN
57320838 TA TA TA TA 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 TA TA TA TA
57320878 GTGACTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57322923 original size:42 final size:42
Alignment explanation
Indices: 57322827--57322929 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
57322817 GTTTTCGAAC
* *
57322827 CTTGGTCAAAATGGCTATGGCACTAGTCAAAATAATTTTTCT
1 CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
* *
57322869 -TCTGGTCAAAATTGCTATGG-ATTTGGTCAAAATAATTTTGCT
1 CT-TGGTCAAAATTGCTATGGCA-CTAGTCAAAATAATTTTGCT
*
57322911 CTTGGTCAAAATTGTTATG
1 CTTGGTCAAAATTGCTATG
57322930 CTGATGGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (42 bp):
CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
Found at i:57322931 original size:21 final size:20
Alignment explanation
Indices: 57322871--57322931 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
57322861 ATTTTTCTTC
* *
57322871 TGGTCAAAATTGCTATGGATT
1 TGGTCAAAATTGTTAT-GCTT
** *
57322892 TGGTCAAAATAATTTTGCTCT
1 TGGTCAAAATTGTTATGCT-T
57322913 TGGTCAAAATTGTTATGCT
1 TGGTCAAAATTGTTATGCT
57322932 GATGGATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGTCAAAATTGTTATGCTT
Found at i:57333796 original size:3 final size:3
Alignment explanation
Indices: 57333778--57333827 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
57333768 CATTAAATTA
* *
57333778 ATT ATT -TT AAT ATT ATT ATT ACT ATT A-T ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
57333823 GTT AT
1 ATT AT
57333828 GATTTACTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:57334916 original size:21 final size:21
Alignment explanation
Indices: 57334892--57334932 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57334882 TAATGCATTG
57334892 GATATG-GCATTTTATTTTCTC
1 GATATGAGCATTTT-TTTTCTC
*
57334913 GATATGAGGATTTTTTTTCT
1 GATATGAGCATTTTTTTTCT
57334933 AAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (21 bp):
GATATGAGCATTTTTTTTCTC
Found at i:57337257 original size:22 final size:22
Alignment explanation
Indices: 57337206--57337250 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
57337196 TAGTTTAAAC
**
57337206 TTTAAATTCCTTTATCCTTTAT
1 TTTAAATTTATTTATCCTTTAT
57337228 TTTAAATTTATTTAT-CTTTAT
1 TTTAAATTTATTTATCCTTTAT
57337249 TT
1 TT
57337251 ATGAATTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAAATTTATTTATCCTTTAT
Found at i:57337924 original size:40 final size:41
Alignment explanation
Indices: 57337857--57337938 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
57337847 AAATGTGAAG
* * *
57337857 CTGCCGACTATTTGGCGGATTGAAGACATGT-GGATTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGG-TTGAATT
57337898 CTGCCGAATATTT-ACGGATTAAAGACATGTAGGTTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
57337938 C
1 C
57337939 GACAATTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (41 bp):
CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
Found at i:57340720 original size:236 final size:236
Alignment explanation
Indices: 57340156--57340862 Score: 1180
Period size: 236 Copynumber: 3.0 Consensus size: 236
57340146 AGAGTTGTGT
* * * *
57340156 GCTATATATAGAGAGGTTGACATGCAGCAACCAAGGGCCACAGAGAAGTGGAATGGTCAATTGTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAA-TG-C
* * * *
57340221 TAGTAAATAAGTCTTGGTGATTTACGAGTGTGATACTTCCCAATGATCTATATATCGACCACTGG
64 TAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGG
*
57340286 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGGGAATTCAATAAT
129 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAAT
*
57340351 CGATAATTATCTCTTATTTTACTTATGAGGTTACATATATCAGT
194 CGATAATTATCTCTTA-TTTACTTATGAGGTTACATATATCAGC
* *
57340395 GCTATATATAGAGAGGTTAATATGCAGTAAACAAGGGCCACAGAGAAGTGGAATGGTAAATGCTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
*
57340460 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATGTATCTACAACTGGCC
66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
* * **
57340525 TCCAACATTTGACTAGGAACTGATAACTAATGCTAATAATTTGTGTCTTGAGAATTCAATAATCG
131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
* *
57340590 ATAATTATCTCTTATTTACCTATGAGGTTAAATATATCAGC
196 ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC
*
57340631 GGTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
57340696 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
* * *
57340761 TCCAACATTTGTCCAGGAACTGATAACTAATGCTGATAATTACTATCTTGAGACTTCAATAATCG
131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
57340826 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT
196 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT
57340863 ACGTGATATG
Statistics
Matches: 436, Mismatches: 32, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
236 243 0.56
237 136 0.31
238 2 0.00
239 55 0.13
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (236 bp):
GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC
Found at i:57344996 original size:31 final size:31
Alignment explanation
Indices: 57344954--57345030 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
57344944 ACTATAAAAA
57344954 TAGTCA-TTTTGTTTGCCTCAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
* *
57344984 TAGTCACTTTTGTTTGTCTTAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
*
57345015 TAGTCACTTATGTTTG
1 TAGTCACTTTTGTTTG
57345031 AAATGTTACG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 6 0.14
31 37 0.86
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGCCTCAGGTTACATTT
Found at i:57347460 original size:18 final size:18
Alignment explanation
Indices: 57347437--57347475 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
57347427 TTTACCAACT
57347437 CCATTCTCCAAATTACCA
1 CCATTCTCCAAATTACCA
57347455 CCATTCTCCAAATTACCA
1 CCATTCTCCAAATTACCA
57347473 CCA
1 CCA
57347476 AGTCCGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (18 bp):
CCATTCTCCAAATTACCA
Found at i:57359472 original size:51 final size:51
Alignment explanation
Indices: 57359396--57359496 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
57359386 GGCTTCAAAA
57359396 GGGTGTCTTTGTTTACTGTTGGCTGAAT-TTAGGTATCATTCATATTCTCAT
1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTT-GGTATCATTCATATTCTCAT
*
57359447 GGGTGTCTTTGTTTGCTGTTGGCTGAATGTTGGTATCATTCATATTCTCA
1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCA
57359497 AGGCTGTCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 46 0.96
52 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.47
Consensus pattern (51 bp):
GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCAT
Found at i:57359788 original size:1 final size:1
Alignment explanation
Indices: 57359782--57359809 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
57359772 CTTTGGCAGC
57359782 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
57359810 CTGAAGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:57370273 original size:24 final size:23
Alignment explanation
Indices: 57370236--57370281 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
57370226 TGAAGTTAAA
57370236 TAAATGAATGATTAAATTAAAATT
1 TAAATGAATGATTAAA-TAAAATT
*
57370260 TAAAT-AATGAATTATATAAAAT
1 TAAATGAATG-ATTAAATAAAAT
57370282 AAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAATGAATGATTAAATAAAATT
Found at i:57370285 original size:27 final size:28
Alignment explanation
Indices: 57370231--57370284 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
57370221 AGGTGTGAAG
*
57370231 TTAAATAAATGAATGATTAAATTAAAAT
1 TTAAATAAATGAATGATTAAAATAAAAT
*
57370259 TTAAAT-AATGAATTATATAAAATAAA
1 TTAAATAAATGAATGAT-TAAAATAAA
57370285 TAAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
TTAAATAAATGAATGATTAAAATAAAAT
Found at i:57370287 original size:4 final size:4
Alignment explanation
Indices: 57370278--57370311 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
57370268 GAATTATATA
57370278 AAAT AAAT AAAT AAAT AAAT AAAT CAAAGT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT
57370312 GACTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.75
5 6 0.21
6 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:57370666 original size:3 final size:3
Alignment explanation
Indices: 57370658--57370716 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
57370648 GTCAAAAAAG
57370658 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
57370706 AAT AAT AAT AA
1 AAT AAT AAT AA
57370717 AACATTTCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57373868 original size:119 final size:119
Alignment explanation
Indices: 57373657--57373897 Score: 473
Period size: 119 Copynumber: 2.0 Consensus size: 119
57373647 ACTTTTTCTT
57373657 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
57373722 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
57373776 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
*
57373841 GGAGTAATTGTTAGATGATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
57373895 CCA
1 CCA
57373898 CCCTCATTTG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (119 bp):
CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
Found at i:57387399 original size:4 final size:4
Alignment explanation
Indices: 57387392--57387425 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
57387382 AGCTGTTTTT
* *
57387392 TTTA TTTA TTTA TCTA TTCA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
57387426 ACCTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:57387528 original size:17 final size:16
Alignment explanation
Indices: 57387476--57387535 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 16
57387466 TTTATGCATT
*
57387476 TTTTTATTATTGTCATTA
1 TTTTT-TTATT-TTATTA
57387494 TTATTTTTA-TTTATTTA
1 TT-TTTTTATTTTA-TTA
57387511 TTTTTGTTATTTTATTA
1 TTTTT-TTATTTTATTA
57387528 TTTCTTTT
1 TTT-TTTT
57387536 TGATATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.14
17 17 0.47
18 11 0.31
19 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTTTATTTTATTA
Found at i:57387530 original size:21 final size:22
Alignment explanation
Indices: 57387498--57387544 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
57387488 TCATTATTAT
*
57387498 TTTTATTTATTTATTTTTGTTA
1 TTTTATTTATTTATTTTTGATA
*
57387520 TTTTA-TTATTTCTTTTTGATA
1 TTTTATTTATTTATTTTTGATA
57387541 TTTT
1 TTTT
57387545 CATGTTACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTATTTATTTATTTTTGATA
Found at i:57389576 original size:13 final size:13
Alignment explanation
Indices: 57389549--57389595 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
57389539 TTTTTAAGTT
57389549 TTTATTTATTTTTC
1 TTTATTTA-TTTTC
57389563 TTTATTTATTTTC
1 TTTATTTATTTTC
*
57389576 TTTATTTGTTTTC
1 TTTATTTATTTTC
57389589 TTTATTT
1 TTTATTT
57389596 GTTTATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 24 0.75
14 8 0.25
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTTC
Found at i:57389587 original size:37 final size:36
Alignment explanation
Indices: 57389520--57389611 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 36
57389510 TGATTTGTCC
*
57389520 TTTTTCATTTCTTT-TTTTCTTTTTAAGTTTTTATTTA
1 TTTTTC-TTTATTTATTTTCTTTTTAAG-TTTTATTTA
* *
57389557 TTTTTCTTTATTTATTTTCTTTATT-TGTTTTCTTTA
1 TTTTTCTTTATTTATTTTCTTT-TTAAGTTTTATTTA
57389593 TTTGTT-TATTATTTATTTT
1 TTT-TTCT-TTATTTATTTT
57389612 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 18 0.38
37 28 0.58
38 2 0.04
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (36 bp):
TTTTTCTTTATTTATTTTCTTTTTAAGTTTTATTTA
Done.