Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 188 of 213
Found at i:56709055 original size:21 final size:21
Alignment explanation
Indices: 56709009--56709056 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
56708999 GTTCCCATAT
56709009 TTTTTCTTTTATGTTCTTCTA
1 TTTTTCTTTTATGTTCTTCTA
* * *
56709030 ATTTTCTTTTTTTTTTCTT-TA
1 TTTTTC-TTTTATGTTCTTCTA
56709051 TTTTTC
1 TTTTTC
56709057 ATTCTCTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTTATGTTCTTCTA
Found at i:56709660 original size:3 final size:3
Alignment explanation
Indices: 56709654--56709706 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
56709644 CTTCCTCCTC
56709654 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
56709702 TCT TC
1 TCT TC
56709707 ATTTCTTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:56713113 original size:21 final size:22
Alignment explanation
Indices: 56713076--56713119 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56713066 ATATTTTACC
56713076 ATTTTTAAATTTAGGTATCGAT
1 ATTTTTAAATTTAGGTATCGAT
*
56713098 ATTTTTACATTT-GGTATCGAT
1 ATTTTTAAATTTAGGTATCGAT
56713119 A
1 A
56713120 CCTAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (22 bp):
ATTTTTAAATTTAGGTATCGAT
Found at i:56713711 original size:6 final size:7
Alignment explanation
Indices: 56713694--56713723 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
56713684 ATTATTAAAA
56713694 AAAAATC
1 AAAAATC
56713701 AAAAATC
1 AAAAATC
*
56713708 AAAAATA
1 AAAAATC
56713715 AAAAATC
1 AAAAATC
56713722 AA
1 AA
56713724 CAAAAGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATC
Found at i:56715382 original size:17 final size:19
Alignment explanation
Indices: 56715355--56715397 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
56715345 TAATTTAATA
56715355 ATAATTTAATTA-ATTTTT
1 ATAATTTAATTAGATTTTT
56715373 ATAA-TTAATTAGATTTTT
1 ATAATTTAATTAGATTTTT
*
56715391 ATTATTT
1 ATAATTT
56715398 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATAATTTAATTAGATTTTT
Found at i:56716705 original size:34 final size:34
Alignment explanation
Indices: 56716634--56716705 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
56716624 AGCATATATT
* * * *
56716634 TATACTTATCAACTACATGTGCCGAATGCGCATA
1 TATACTTATCAACCACATATGCCGAATGCACACA
*
56716668 TATACTTAT-AATCCACATATGCCGAATGCATACA
1 TATACTTATCAA-CCACATATGCCGAATGCACACA
56716702 TATA
1 TATA
56716706 TATATCCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (34 bp):
TATACTTATCAACCACATATGCCGAATGCACACA
Found at i:56717083 original size:41 final size:41
Alignment explanation
Indices: 56716880--56717068 Score: 297
Period size: 41 Copynumber: 4.6 Consensus size: 41
56716870 TTAATTTAAA
* *
56716880 CAGATTCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
56716922 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * *
56716963 CAAATCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
56717004 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
56717045 CAGATCATCGGCACTTAGCCTGCT
1 CAGATCACCGGCACTTAGCCTGCT
56717069 GGGCGCTATG
Statistics
Matches: 134, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
41 130 0.97
42 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:56718065 original size:4 final size:4
Alignment explanation
Indices: 56718058--56718092 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
56718048 TAAAATAGAT
56718058 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
56718093 TATATATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:56722788 original size:33 final size:33
Alignment explanation
Indices: 56722751--56722821 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
56722741 TGAACCAATT
*
56722751 AAAAAA-TCAATAAAATTGGCGGTTGAATCGACC
1 AAAAAACT-AATAAAACTGGCGGTTGAATCGACC
** * *
56722784 AAAAAACTAATTGAACTGGTGGTTGAATCGACT
1 AAAAAACTAATAAAACTGGCGGTTGAATCGACC
56722817 AAAAA
1 AAAAA
56722822 TGATTGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (33 bp):
AAAAAACTAATAAAACTGGCGGTTGAATCGACC
Found at i:56725431 original size:11 final size:11
Alignment explanation
Indices: 56725415--56725452 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56725405 TAAATTTTAG
56725415 TAATTTTTAAA
1 TAATTTTTAAA
56725426 TAATTTTTAAA
1 TAATTTTTAAA
*
56725437 T-ATATCTTAAA
1 TAAT-TTTTAAA
56725448 TAATT
1 TAATT
56725453 ATTTTTAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTTTAAA
Found at i:56727763 original size:18 final size:18
Alignment explanation
Indices: 56727742--56727784 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
56727732 GTTATAGTGC
56727742 TTTTAATCTATTTTTCTA
1 TTTTAATCTATTTTTCTA
** * *
56727760 TTTTAAAGTGTTTTTCTT
1 TTTTAATCTATTTTTCTA
56727778 TTTTAAT
1 TTTTAAT
56727785 TTTTTAATCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTAATCTATTTTTCTA
Found at i:56735365 original size:7 final size:7
Alignment explanation
Indices: 56735355--56735382 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
56735345 TGATGGATAG
56735355 AAATAAA
1 AAATAAA
56735362 AAATAAA
1 AAATAAA
56735369 AAATAAA
1 AAATAAA
56735376 AAATAAA
1 AAATAAA
56735383 CCTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:56737114 original size:13 final size:13
Alignment explanation
Indices: 56737096--56737121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56737086 CAGAGGTAAA
56737096 ACTTGTAACTTCT
1 ACTTGTAACTTCT
56737109 ACTTGTAACTTCT
1 ACTTGTAACTTCT
56737122 GCAAGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTTGTAACTTCT
Found at i:56740568 original size:42 final size:42
Alignment explanation
Indices: 56740503--56740699 Score: 234
Period size: 42 Copynumber: 4.7 Consensus size: 42
56740493 TCATGTTTAC
* * *
56740503 TTTCCGTTCAGCTTTTTTAAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
*
56740545 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAA-CTTATATGAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCT-TATGAG
* * *
56740587 TTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
* * * *
56740629 TTTTCGTTAAGCTCTTATGAGCTTCTGTTCAACCCTTATGAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
* * ** *
56740671 TTTCTGTTTAGCTCTCATGAACTTCTGTT
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTT
56740700 CAGCTTTCGA
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
41 2 0.02
42 129 0.97
43 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
Found at i:56740607 original size:21 final size:21
Alignment explanation
Indices: 56740537--56740704 Score: 117
Period size: 21 Copynumber: 8.0 Consensus size: 21
56740527 CTGTTTAACC
* *
56740537 CTTATGGGTTTCCGTTCAGCT
1 CTTATGAGTTTCTGTTCAGCT
* * * *
56740558 CTTTTGAGCTTCTGTTTAACT
1 CTTATGAGTTTCTGTTCAGCT
56740579 -TATATGAGTTTCTGTTCAGCT
1 CT-TATGAGTTTCTGTTCAGCT
* * * *
56740600 CTTTTGAGCTTT-TGTTTAACC
1 CTTATGAG-TTTCTGTTCAGCT
* *
56740621 CTTATAAGTTT-TCGTTAAGCT
1 CTTATGAGTTTCT-GTTCAGCT
* * *
56740642 CTTATGAGCTTCTGTTCAACC
1 CTTATGAGTTTCTGTTCAGCT
*
56740663 CTTATGAGTTTCTGTTTAGCT
1 CTTATGAGTTTCTGTTCAGCT
* **
56740684 CTCATGAACTTCTGTTCAGCT
1 CTTATGAGTTTCTGTTCAGCT
56740705 TTCGAACTTC
Statistics
Matches: 110, Mismatches: 32, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
20 5 0.05
21 100 0.91
22 5 0.05
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (21 bp):
CTTATGAGTTTCTGTTCAGCT
Found at i:56744169 original size:23 final size:23
Alignment explanation
Indices: 56744143--56744212 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
56744133 TCTGATTTAG
56744143 AATAATTCTAAGCTTTGGATACA
1 AATAATTCTAAGCTTTGGATACA
* * * *
56744166 AATAATGCTTAG-ATT---TA-G
1 AATAATTCTAAGCTTTGGATACA
56744184 AATAATTCTAAGCTTTGGATACA
1 AATAATTCTAAGCTTTGGATACA
56744207 AATAAT
1 AATAAT
56744213 GCAAACCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 10 0.29
19 4 0.12
22 4 0.12
23 16 0.47
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (23 bp):
AATAATTCTAAGCTTTGGATACA
Found at i:56744181 original size:41 final size:41
Alignment explanation
Indices: 56744136--56744214 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
56744126 AAATCTATCT
56744136 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
1 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
56744177 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGC
1 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGC
56744215 AAACCTCACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (41 bp):
GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
Found at i:56748450 original size:19 final size:20
Alignment explanation
Indices: 56748426--56748464 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
56748416 ATTCAAATTT
56748426 TATA-TTTTAAAAAATTATA
1 TATATTTTTAAAAAATTATA
56748445 TATATTTTTAAAAAATTATA
1 TATATTTTTAAAAAATTATA
56748465 AAGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATTTTTAAAAAATTATA
Found at i:56749235 original size:18 final size:19
Alignment explanation
Indices: 56749214--56749251 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
56749204 ATTTTGGCAT
*
56749214 TTTTATAAA-TAGTTTGAA
1 TTTTAAAAATTAGTTTGAA
*
56749232 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTAGTTTGAA
56749251 T
1 T
56749252 CTTTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATTAGTTTGAA
Found at i:56762386 original size:63 final size:63
Alignment explanation
Indices: 56762301--56762463 Score: 218
Period size: 63 Copynumber: 2.6 Consensus size: 63
56762291 CACGCACTAG
** * * * * *
56762301 TTTATTTTACACTTGCACCACAACACGCGCAATCATTCATTGCACCAACATAGTCAGCACCAT
1 TTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCAGCACCAA
* * *
56762364 TTTATTTTACACAAGCATCACAACATGCACAATCATTCCCTGCACCAACACAGTCATCACCAA
1 TTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCAGCACCAA
* *
56762427 TTTATTTTACACAAGCACCACAGCATGCTCAATCATT
1 TTTATTTTACACAAGCACCACAACATGCACAATCATT
56762464 TCCTACACCG
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.27
Consensus pattern (63 bp):
TTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCAGCACCAA
Found at i:56763716 original size:29 final size:30
Alignment explanation
Indices: 56763673--56763753 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
56763663 TTAGCGAGTA
* * * *
56763673 AGTGATTAAATTGTAATTT-TTTATAATTG
1 AGTGATCAAAGTGTAATTTACTAATAATTG
56763702 AGTGATCAAAGTGTAAATTTACTAATAATTG
1 AGTGATCAAAGTGT-AATTTACTAATAATTG
* *
56763733 AGTGACCATAGGTGTAATTTA
1 AGTGATCA-AAGTGTAATTTA
56763754 ACAAAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 12 0.28
30 5 0.12
31 21 0.49
32 5 0.12
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (30 bp):
AGTGATCAAAGTGTAATTTACTAATAATTG
Found at i:56763752 original size:31 final size:31
Alignment explanation
Indices: 56763695--56763753 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
56763685 GTAATTTTTT
*
56763695 ATAATTGAGTGATCAAAGTGTAAATTTACTA
1 ATAATTGAGTGACCAAAGTGTAAATTTACTA
*
56763726 ATAATTGAGTGACCATAGGTGT-AATTTA
1 ATAATTGAGTGACCA-AAGTGTAAATTTA
56763754 ACAAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (31 bp):
ATAATTGAGTGACCAAAGTGTAAATTTACTA
Found at i:56765711 original size:20 final size:20
Alignment explanation
Indices: 56765681--56765726 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
56765671 TTAACATTAA
56765681 TAATAATTTTAAT-AGTATCTT
1 TAAT-ATTTTAATAAGTAT-TT
*
56765702 TAATATTTTATTAAGTATTT
1 TAATATTTTAATAAGTATTT
56765722 TAATA
1 TAATA
56765727 ATAAATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TAATATTTTAATAAGTATTT
Found at i:56767253 original size:31 final size:31
Alignment explanation
Indices: 56767217--56767285 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
56767207 TTACAATTTT
**
56767217 GTCACTAAACTATTTGAAAGTTTTCATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
*
56767248 GTCACTAAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
56767279 GTCACTA
1 GTCACTA
56767286 GATTGTCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTCATTTAA
Found at i:56768171 original size:30 final size:31
Alignment explanation
Indices: 56768137--56768196 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
56768127 AAACCTTTTA
*
56768137 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
** *
56768167 TTTTCCCTTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
56768197 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:56778826 original size:29 final size:30
Alignment explanation
Indices: 56778789--56778845 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56778779 TCCGAGCCTT
*
56778789 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
56778818 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
56778846 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:56779075 original size:13 final size:13
Alignment explanation
Indices: 56779057--56779083 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56779047 TTTCCAGCAA
56779057 TTATGAATTTATT
1 TTATGAATTTATT
56779070 TTATGAATTTATT
1 TTATGAATTTATT
56779083 T
1 T
56779084 GATAATGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:56779296 original size:50 final size:50
Alignment explanation
Indices: 56779183--56779424 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
56779173 ATTTGGGTAA
* * *
56779183 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
56779239 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
56779289 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
56779339 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
56779389 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
56779425 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:56779372 original size:100 final size:103
Alignment explanation
Indices: 56779183--56779432 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
56779173 ATTTGGGTAA
56779183 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
56779248 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
56779289 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
56779351 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
56779389 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
56779433 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:56784206 original size:22 final size:22
Alignment explanation
Indices: 56784174--56784242 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
56784164 TATGCACTAT
*
56784174 TAAACAAAGAGCACCAAAGTGC
1 TAAACAGAGAGCACCAAAGTGC
*
56784196 TATACAGAGAGCA-CAAATGTGC
1 TAAACAGAGAGCACCAAA-GTGC
* * * *
56784218 GAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACCAAAGTGC
56784240 TAA
1 TAA
56784243 TAATAGGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.11
22 31 0.84
23 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (22 bp):
TAAACAGAGAGCACCAAAGTGC
Found at i:56786221 original size:22 final size:23
Alignment explanation
Indices: 56786196--56786239 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
56786186 AATATAATAG
56786196 CAAAATGACAACAAA-ACAACAT
1 CAAAATGACAACAAACACAACAT
* * *
56786218 CAAAGTGGCAGCAAACACAACA
1 CAAAATGACAACAAACACAACA
56786240 GTAAACAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.25, G:0.11, T:0.07
Consensus pattern (23 bp):
CAAAATGACAACAAACACAACAT
Found at i:56788810 original size:45 final size:45
Alignment explanation
Indices: 56788760--56788848 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
56788750 GAGCACAATC
*
56788760 AAATTCATATTTTCCTATATTAACAATAATATTCATACCAAGCTG
1 AAATTCATATTATCCTATATTAACAATAATATTCATACCAAGCTG
*
56788805 AAATTCATATTATCCTATATTGACAATAATATTCATACCAAGCT
1 AAATTCATATTATCCTATATTAACAATAATATTCATACCAAGCT
56788849 AAAACTTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (45 bp):
AAATTCATATTATCCTATATTAACAATAATATTCATACCAAGCTG
Found at i:56797410 original size:142 final size:142
Alignment explanation
Indices: 56797154--56797447 Score: 588
Period size: 142 Copynumber: 2.1 Consensus size: 142
56797144 CAAGAGCTTC
56797154 CCTTGTGTTGCCAGTTGTGCAACATAAATTCTGCAAATAGTATAATTTAGTTTTCATTTTCTTTT
1 CCTTGTGTTGCCAGTTGTGCAACATAAATTCTGCAAATAGTATAATTTAGTTTTCATTTTCTTTT
56797219 TTCAAAAACAATTCAATGTTTTGTTCATCATGGAAAACTTACAAGACATGCATAGCTAAAAGGAT
66 TTCAAAAACAATTCAATGTTTTGTTCATCATGGAAAACTTACAAGACATGCATAGCTAAAAGGAT
56797284 GTTGGTCCATTT
131 GTTGGTCCATTT
56797296 CCTTGTGTTGCCAGTTGTGCAACATAAATTCTGCAAATAGTATAATTTAGTTTTCATTTTCTTTT
1 CCTTGTGTTGCCAGTTGTGCAACATAAATTCTGCAAATAGTATAATTTAGTTTTCATTTTCTTTT
56797361 TTCAAAAACAATTCAATGTTTTGTTCATCATGGAAAACTTACAAGACATGCATAGCTAAAAGGAT
66 TTCAAAAACAATTCAATGTTTTGTTCATCATGGAAAACTTACAAGACATGCATAGCTAAAAGGAT
56797426 GTTGGTCCATTT
131 GTTGGTCCATTT
56797438 CCTTGTGTTG
1 CCTTGTGTTG
56797448 AATGAATTTC
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 152 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (142 bp):
CCTTGTGTTGCCAGTTGTGCAACATAAATTCTGCAAATAGTATAATTTAGTTTTCATTTTCTTTT
TTCAAAAACAATTCAATGTTTTGTTCATCATGGAAAACTTACAAGACATGCATAGCTAAAAGGAT
GTTGGTCCATTT
Found at i:56799562 original size:14 final size:14
Alignment explanation
Indices: 56799543--56799572 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56799533 TTGCAACACT
56799543 AAAAAAGTAAAAAC
1 AAAAAAGTAAAAAC
56799557 AAAAAAGTAAAAAC
1 AAAAAAGTAAAAAC
56799571 AA
1 AA
56799573 GGTAAAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAAAAGTAAAAAC
Found at i:56800718 original size:26 final size:26
Alignment explanation
Indices: 56800679--56800730 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
56800669 CATACTCAGC
56800679 CAAAAAATGACTGAACCAAGGGTAAA
1 CAAAAAATGACTGAACCAAGGGTAAA
*
56800705 CAAAAAATGGCTGAACCAAGGGTAAA
1 CAAAAAATGACTGAACCAAGGGTAAA
56800731 TAGATACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.21, T:0.12
Consensus pattern (26 bp):
CAAAAAATGACTGAACCAAGGGTAAA
Found at i:56804019 original size:28 final size:27
Alignment explanation
Indices: 56803986--56804084 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
56803976 TAATGAGATT
*
56803986 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTATAATTGAA
*
56804013 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATTG-AA
* *
56804042 AGCACTAAGTGTGCGAGTGTGATT-ATTA
1 AGCACTAAGTGTGCGAGTATAATTGA--A
56804070 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
56804085 TACTTATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 58 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTATAATTGAA
Found at i:56808125 original size:41 final size:40
Alignment explanation
Indices: 56808080--56808195 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
56808070 TTGTATAAAA
*
56808080 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTGA-TACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAGTA-A-TT
* * *
56808121 CACCGGCACAAAGCTTGCT-GGACATAAAGTCTGAAGTAATT
1 CACCGGCATAAAGCCTGCTAGG-CATAAAGCCTG-AGTAATT
* *
56808162 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
56808196 AAATCTCAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
40 3 0.05
41 53 0.85
42 4 0.06
43 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAGTAATT
Found at i:56808346 original size:68 final size:64
Alignment explanation
Indices: 56808235--56808411 Score: 203
Period size: 64 Copynumber: 2.7 Consensus size: 64
56808225 ATAATTTACA
* * *
56808235 ACATTAAAATTCAGTTCAAAGAA-TTTGTAACCTATATTCGAACCACACACATATGTATGTAAAA
1 ACATT-AAATTCAGCTC-AAGAACTTTATAACCTATATTCG-A--AC-CACATATGTATATAAAA
56808299 TTCAT
60 TTCAT
* *
56808304 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTTGAACCACATATGTATATAAAATTCGT
1 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACATATGTATATAAAATTCAT
* * **
56808368 ACATTAATTTCAGCTCAAGAACTTTAAATATATATATTCGAACC
1 ACATTAAATTCAGCTCAAGAACTTTATA-ACCTATATTCGAACC
56808412 GTATGTGCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
64 46 0.48
65 14 0.15
67 6 0.06
68 25 0.26
69 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (64 bp):
ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACATATGTATATAAAATTCAT
Found at i:56808374 original size:64 final size:67
Alignment explanation
Indices: 56808235--56808393 Score: 209
Period size: 64 Copynumber: 2.4 Consensus size: 67
56808225 ATAATTTACA
* * *
56808235 ACATTAAAATTCAGTTCAAAGAA-TTTGTAACCTATATTCGAACCACACACATATGTATGTAAAA
1 ACATT-AAATTCAGCTC-AAGAACTTTATAACCTATATTCGAA-CACACACATATGTATATAAAA
56808299 TTCAT
63 TTCAT
*
56808304 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTTG-A-AC-CACATATGTATATAAAATTC
1 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACACACACATATGTATATAAAATTC
*
56808366 GT
66 AT
*
56808368 ACATTAATTTCAGCTCAAGAACTTTA
1 ACATTAAATTCAGCTCAAGAACTTTA
56808394 AATATATATA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
64 45 0.54
65 2 0.02
67 6 0.07
68 25 0.30
69 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (67 bp):
ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACACACACATATGTATATAAAATTC
AT
Found at i:56812897 original size:21 final size:22
Alignment explanation
Indices: 56812872--56812915 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
56812862 TAAAAAAGTC
*
56812872 AATAAATAAAAATTAT-TAAAT
1 AATAAATAAAAATCATATAAAT
*
56812893 AATAAATTAAAATCATATAAAT
1 AATAAATAAAAATCATATAAAT
56812915 A
1 A
56812916 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAATAAAAATCATATAAAT
Found at i:56814958 original size:48 final size:48
Alignment explanation
Indices: 56814905--56815000 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
56814895 AAAAAAACCA
* * *
56814905 AAAAAATAAAGGGGGACTCATGACTGATGCTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
*
56814953 AAAAAATAAAAGGGGACCCATGACCGATGTTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
56815001 TTGTATTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
Found at i:56816923 original size:73 final size:73
Alignment explanation
Indices: 56816846--56816999 Score: 175
Period size: 73 Copynumber: 2.1 Consensus size: 73
56816836 TGTATAACGA
* * *
56816846 GAAGCTCATAAGAGCCATA-GTCAGAAAGCTCATGCGAGCCAATAACAGGTAGCTCCGAACAGCC
1 GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCC-ATAACAGGTAGCTCCGAACAGCC
56816910 ATTAATCGG
65 ATTAATCGG
* * * * * * * * *
56816919 GAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGTGAGCCATATCAGGTAGCTCCGAAGAGCCA
1 GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAACAGCCA
56816984 TTAATCGG
66 TTAATCGG
*
56816992 GAAACTCA
1 GAAGCTCA
56817000 CAAAGAGCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
73 51 0.77
74 15 0.23
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (73 bp):
GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAACAGCCA
TTAATCGG
Found at i:56816925 original size:25 final size:25
Alignment explanation
Indices: 56816896--56817036 Score: 103
Period size: 25 Copynumber: 5.6 Consensus size: 25
56816886 AATAACAGGT
*
56816896 AGCTCCGAACAGCCATTAATCGGGA
1 AGCTCCGAAGAGCCATTAATCGGGA
* *
56816921 AGCTCCGGATAGCCA-TATATCGGGA
1 AGCTCCGAAGAGCCATTA-ATCGGGA
* * *
56816946 AG-TTC-AAGTGAGCCA-T-ATCAGGT
1 AGCTCCGAA--GAGCCATTAATCGGGA
56816969 AGCTCCGAAGAGCCATTAATCGGGA
1 AGCTCCGAAGAGCCATTAATCGGGA
* * **
56816994 AACTCACAAAGAGCTTTTAATCGGGA
1 AGCTC-CGAAGAGCCATTAATCGGGA
*
56817020 AGCTCATGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
56817037 ATAACAGGAC
Statistics
Matches: 89, Mismatches: 19, Indels: 15
0.72 0.15 0.12
Matches are distributed among these distances:
23 14 0.16
24 7 0.08
25 39 0.44
26 29 0.33
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCGGGA
Found at i:56817031 original size:26 final size:26
Alignment explanation
Indices: 56816974--56817036 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
56816964 CAGGTAGCTC
56816974 CGAAGAGCCATTAATCGGGAAACTCA
1 CGAAGAGCCATTAATCGGGAAACTCA
* ** *
56817000 CAAAGAGCTTTTAATCGGGAAGCTCA
1 CGAAGAGCCATTAATCGGGAAACTCA
*
56817026 TGAAGAGCCAT
1 CGAAGAGCCAT
56817037 ATAACAGGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CGAAGAGCCATTAATCGGGAAACTCA
Found at i:56821989 original size:19 final size:20
Alignment explanation
Indices: 56821947--56821989 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
56821937 TCATGCTTTC
* *
56821947 TATTCGCATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
56821967 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
56821985 TATTC
1 TATTC
56821990 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:56823506 original size:51 final size:54
Alignment explanation
Indices: 56823426--56823572 Score: 194
Period size: 56 Copynumber: 2.7 Consensus size: 54
56823416 TGATAATAAC
* **
56823426 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATG-TT-GG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATGATTAGG
* *
56823478 -TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATGATCTTAAGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATGA--TT-AGG
56823533 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
56823573 TCTTTACCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
50 7 0.09
51 34 0.42
53 2 0.02
55 2 0.02
56 35 0.43
57 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (54 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATGATTAGG
Found at i:56823692 original size:12 final size:12
Alignment explanation
Indices: 56823670--56823700 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
56823660 GCTTGGATCA
56823670 TCATCAAATAAAT
1 TCAT-AAATAAAT
56823683 TCATAAATAAAT
1 TCATAAATAAAT
56823695 TCATAA
1 TCATAA
56823701 TTTCTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (12 bp):
TCATAAATAAAT
Found at i:56824874 original size:21 final size:22
Alignment explanation
Indices: 56824844--56824907 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
56824834 CATAAGCAGT
* *
56824844 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
56824866 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
56824886 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
56824908 TCGGCAAGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:56825030 original size:18 final size:17
Alignment explanation
Indices: 56824993--56825052 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
56824983 TAATAGGGTA
*
56824993 TTCAAATCACTTTCTCAAT
1 TTCAATTCAC-TT-TCAAT
56825012 TTCAATTGCACTTTCAAT
1 TTCAATT-CACTTTCAAT
*
56825030 TTACAATTTACTTTCAAT
1 TT-CAATTCACTTTCAAT
*
56825048 ATCAA
1 TTCAA
56825053 AGTCTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 17 0.47
19 13 0.36
20 3 0.08
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (17 bp):
TTCAATTCACTTTCAAT
Found at i:56832579 original size:46 final size:44
Alignment explanation
Indices: 56832527--56832620 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
56832517 ATAGAATTGT
*
56832527 AATGGAATA-AAGCTGTAATCAGTAATTCAAT-TGTTTGATTGAATGG
1 AATGGAATAGAA-CTGTAAT-AGT-ATTC-ATGTGTTTGATTGAATGA
* *
56832573 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATGA
56832617 AATG
1 AATG
56832621 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 3 0.07
46 16 0.37
47 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATGA
Found at i:56834829 original size:16 final size:16
Alignment explanation
Indices: 56834808--56834843 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
56834798 TGAATTACTG
* *
56834808 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCA
56834824 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
56834840 ATTA
1 ATTA
56834844 TAGTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:56835849 original size:22 final size:23
Alignment explanation
Indices: 56835822--56835866 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56835812 AGGTATCTAC
56835822 AAATCAAAT-ATCTAAGATTACA
1 AAATCAAATCATCTAAGATTACA
* *
56835844 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCATCTAAGATTACA
56835867 TATTATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCATCTAAGATTACA
Found at i:56845502 original size:18 final size:19
Alignment explanation
Indices: 56845466--56845503 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
56845456 ACGGTTTGCT
* *
56845466 AAGAAAAATAGATGGAGAA
1 AAGAAAAATAAATGAAGAA
56845485 AAGAAAAA-AAATGAAGAA
1 AAGAAAAATAAATGAAGAA
56845503 A
1 A
56845504 TGTAGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
AAGAAAAATAAATGAAGAA
Found at i:56849727 original size:5 final size:5
Alignment explanation
Indices: 56849717--56849768 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
56849707 TTTGACCTCC
56849717 TTAAA TTAAA TT--A TTAAA TTAAAA TT--A TTAAA -TAAA TTAAA TTAAAA
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TT-AAA
56849764 TTAAA
1 TTAAA
56849769 GAATTAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
3 6 0.15
4 4 0.10
5 20 0.50
6 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:56849743 original size:14 final size:13
Alignment explanation
Indices: 56849717--56849755 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
56849707 TTTGACCTCC
56849717 TTAAATTAAATTA
1 TTAAATTAAATTA
56849730 TTAAATTAAAATTA
1 TTAAATT-AAATTA
56849744 TTAAA-TAAATTA
1 TTAAATTAAATTA
56849756 AATTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 8 0.32
14 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATTAAATTA
Found at i:56849758 original size:23 final size:22
Alignment explanation
Indices: 56849721--56849766 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
56849711 ACCTCCTTAA
*
56849721 ATTAAATTATTAAATTAAAATT
1 ATTAAATAATTAAATTAAAATT
56849743 ATTAAATAAATTAAATTAAAATT
1 ATTAAAT-AATTAAATTAAAATT
56849766 A
1 A
56849767 AAGAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAATAATTAAATTAAAATT
Found at i:56849814 original size:22 final size:22
Alignment explanation
Indices: 56849789--56849831 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56849779 GGTCAGTAAA
56849789 AAAAAGG-TATGTTAATTAATCC
1 AAAAAGGCT-TGTTAATTAATCC
56849811 AAAAAGGCTTGTTAATTAATC
1 AAAAAGGCTTGTTAATTAATC
56849832 AAAGGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
AAAAAGGCTTGTTAATTAATCC
Found at i:56852509 original size:22 final size:22
Alignment explanation
Indices: 56852484--56852528 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
56852474 ATGTAAGTGA
56852484 TCAAATTGTTAAGTATGGATAC
1 TCAAATTGTTAAGTATGGATAC
56852506 TCAAATTGTTAAGTATGGATAC
1 TCAAATTGTTAAGTATGGATAC
56852528 T
1 T
56852529 TGATTATATA
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:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TCAAATTGTTAAGTATGGATAC
Found at i:56853570 original size:15 final size:15
Alignment explanation
Indices: 56853550--56853592 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
56853540 AATTATAGGA
56853550 AAACGGGCCAAAACT
1 AAACGGGCCAAAACT
56853565 AAACGGGCCAAAACT
1 AAACGGGCCAAAACT
*
56853580 AAACGGGCTAAAA
1 AAACGGGCCAAAA
56853593 AATCTCATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.07
Consensus pattern (15 bp):
AAACGGGCCAAAACT
Found at i:56855185 original size:47 final size:47
Alignment explanation
Indices: 56855111--56855204 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
56855101 CCATTCTTTC
*
56855111 CTCTTGATTACGTAGCGTTAAGTGGCACTTGTGCAAATTCAGTAAGT
1 CTCTTGATTACGTAGCGTTAAGCGGCACTTGTGCAAATTCAGTAAGT
56855158 CTCTTGATTACGTAGCGTTAAGCGGCACTTGTGCAAATTCAGTAAGT
1 CTCTTGATTACGTAGCGTTAAGCGGCACTTGTGCAAATTCAGTAAGT
56855205 TGTTGGGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (47 bp):
CTCTTGATTACGTAGCGTTAAGCGGCACTTGTGCAAATTCAGTAAGT
Found at i:56857398 original size:25 final size:25
Alignment explanation
Indices: 56857370--56857434 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
56857360 CTGTCTTTGA
* *
56857370 TAGTATATCCTGAAACTGCTATACG
1 TAGTATATACTGAAACTACTATACG
*
56857395 TAGTATATACTGAGACTACTATA-G
1 TAGTATATACTGAAACTACTATACG
56857419 ATAG-ACTATACTGAAA
1 -TAGTA-TATACTGAAA
56857435 ACACTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATACG
Found at i:56863424 original size:18 final size:17
Alignment explanation
Indices: 56863398--56863445 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
56863388 ACAATAAGAA
56863398 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
56863416 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
56863434 AATGTTTTGAAA
1 AACGTTTTGAAA
56863446 GCAAATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:56864590 original size:25 final size:25
Alignment explanation
Indices: 56864500--56864590 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
56864490 TTCATATTCA
56864500 GGAATGCTCATACGAGCATGTA-AAC-
1 GGAA-GCTCATACGAGC-TGTATAACG
* * **
56864525 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATACGAGCTGTATAACG
* * **
56864550 GGAAACCCATGTGAGCTGTATAACG
1 GGAAGCTCATACGAGCTGTATAACG
*
56864575 GGAAGCTCTTACGAGC
1 GGAAGCTCATACGAGC
56864591 CATTTATTGG
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
23 2 0.04
24 13 0.27
25 33 0.69
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATACGAGCTGTATAACG
Found at i:56866570 original size:10 final size:11
Alignment explanation
Indices: 56866549--56866577 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
56866539 TTTCTTATTT
56866549 CTATTCTTTAG
1 CTATTCTTTAG
56866560 CTATT-TTTAG
1 CTATTCTTTAG
56866570 CTATTCTT
1 CTATTCTT
56866578 CTCACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
CTATTCTTTAG
Found at i:56868075 original size:6 final size:6
Alignment explanation
Indices: 56868064--56868092 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56868054 GGCTCATCAG
56868064 GATAGA GATAGA GATAGA GATAGA GATAG
1 GATAGA GATAGA GATAGA GATAGA GATAG
56868093 GAAAGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
GATAGA
Found at i:56869017 original size:13 final size:13
Alignment explanation
Indices: 56868999--56869023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56868989 ATTATTTATC
56868999 ATTTAAATATATA
1 ATTTAAATATATA
56869012 ATTTAAATATAT
1 ATTTAAATATAT
56869024 TAATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:56869031 original size:24 final size:22
Alignment explanation
Indices: 56869002--56869058 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
56868992 ATTTATCATT
*
56869002 TAAATATATAATTTAAATATATTAA
1 TAAATATATAA--T-AATATATAAA
*
56869027 T-AATATAGAATAATATATAAA
1 TAAATATATAATAATATATAAA
56869048 TAAATATATAA
1 TAAATATATAA
56869059 AGAAAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 10 0.36
22 9 0.32
24 8 0.29
25 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAATATATAATAATATATAAA
Found at i:56869054 original size:10 final size:11
Alignment explanation
Indices: 56869002--56869058 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
56868992 ATTTATCATT
56869002 TAAATATATAA
1 TAAATATATAA
56869013 TTTAAATATATTAA
1 --TAAATATA-TAA
*
56869027 T-AATATAGAA
1 TAAATATATAA
56869037 T-AATATATAAA
1 TAAATATAT-AA
56869048 TAAATATATAA
1 TAAATATATAA
56869059 AGAAAATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.23
11 11 0.28
12 8 0.21
13 8 0.21
14 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATATATAA
Found at i:56878099 original size:62 final size:62
Alignment explanation
Indices: 56878017--56878142 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
56878007 GGGTGTTACA
*
56878017 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGGTTGCCTCTTTCAGTTACCTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
* * *
56878079 TCTATTTTACTCTTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTTAGTTACCTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
56878141 TC
1 TC
56878143 CTTACCATCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (62 bp):
TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
Found at i:56879392 original size:22 final size:22
Alignment explanation
Indices: 56879367--56879416 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
56879357 CTGCTTCTTT
56879367 TGCTTTACTGCTTGTGCCTTAC
1 TGCTTTACTGCTTGTGCCTTAC
* * *
56879389 TGCTTTACTTCTTTTGCTTTAC
1 TGCTTTACTGCTTGTGCCTTAC
56879411 TGCTTT
1 TGCTTT
56879417 CGATTAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (22 bp):
TGCTTTACTGCTTGTGCCTTAC
Found at i:56879447 original size:36 final size:37
Alignment explanation
Indices: 56879407--56879491 Score: 127
Period size: 39 Copynumber: 2.3 Consensus size: 37
56879397 TTCTTTTGCT
*
56879407 TTACTGCTTTCGATTAGAA-TCAGGGAAAATTCTGGC
1 TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
56879443 TTACTGCTTTCGATTAGAATTTTCAGGGAAAATTCTGGA
1 TTACTGCTTTCGATTAGAA--TTCAGGGAAAATTCTGGA
*
56879482 TTACCGCTTT
1 TTACTGCTTT
56879492 GCTTTACTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 19 0.43
39 25 0.57
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (37 bp):
TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
Found at i:56880760 original size:32 final size:32
Alignment explanation
Indices: 56880719--56880780 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
56880709 CATCTATTTT
56880719 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
56880751 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
56880781 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:56883549 original size:13 final size:13
Alignment explanation
Indices: 56883528--56883582 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
56883518 ACACTTAAAT
56883528 TTTTCAAAAACAC
1 TTTTCAAAAACAC
* **
56883541 TTCTCAAAAGTAC
1 TTTTCAAAAACAC
* * *
56883554 TTTTCCACAGCAC
1 TTTTCAAAAACAC
56883567 TTTTCAAAAACAC
1 TTTTCAAAAACAC
56883580 TTT
1 TTT
56883583 ACTAGCCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:56883998 original size:9 final size:9
Alignment explanation
Indices: 56883984--56884036 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
56883974 GATTCAACTT
56883984 GGTTAATTC
1 GGTTAATTC
56883993 GGTTAATTC
1 GGTTAATTC
* *
56884002 GGGTAATCC
1 GGTTAATTC
56884011 GGTTAATTC
1 GGTTAATTC
*
56884020 GGGTAATTC
1 GGTTAATTC
56884029 GGTTAATT
1 GGTTAATT
56884037 TTTAACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (9 bp):
GGTTAATTC
Found at i:56884013 original size:18 final size:18
Alignment explanation
Indices: 56883987--56884036 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
56883977 TCAACTTGGT
56883987 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
56884005 TAATCCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
56884023 TAATTCGGTTAATT
1 TAATTCGGTTAATT
56884037 TTTAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:56893539 original size:18 final size:20
Alignment explanation
Indices: 56893518--56893564 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
56893508 ACTTTGGATT
*
56893518 TTTTATAAAT-ATTTTG-AA
1 TTTTAAAAATCATTTTGAAA
56893536 TTTTAAAAATCATTTTGAAA
1 TTTTAAAAATCATTTTGAAA
56893556 TTTTGAAAA
1 TTTT-AAAA
56893565 GAAAATTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 6 0.24
21 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (20 bp):
TTTTAAAAATCATTTTGAAA
Found at i:56896199 original size:126 final size:127
Alignment explanation
Indices: 56895953--56896204 Score: 355
Period size: 126 Copynumber: 2.0 Consensus size: 127
56895943 CCCTTACTTT
*
56895953 AAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTTCCAAGACCAACTG
1 AAGCGTTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTTTTCCAAGACCAACTG
* * * *
56896018 TAGCAAAAACGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
66 TAGCAAAAACGCATACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGCATCCTGCTTG
* * * *
56896080 AAGCGTTTTTTTAAACTATTTACTCAGAAACGTCAAGTCGAAATTATTTTTT--TAGAACCTACT
1 AAGCGTTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTTTTCCAAG-ACCAACT
* * * * *
56896143 GTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGCTT
65 GTAGCAAAAACGCATACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGCATCCTGCTT
56896205 TGATTTTATC
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
125 2 0.02
126 59 0.54
127 49 0.45
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (127 bp):
AAGCGTTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTTTTCCAAGACCAACTG
TAGCAAAAACGCATACACGAGGGCGCGACTTCAAAAATCCTTCTCATAAAGCATCCTGCTTG
Found at i:56897245 original size:37 final size:37
Alignment explanation
Indices: 56897181--56897337 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
56897171 TACGTATGAT
*
56897181 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
56897217 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
56897254 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
56897297 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
56897337 C
1 C
56897338 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:56897307 original size:46 final size:46
Alignment explanation
Indices: 56897254--56897620 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
56897244 TAAGTGTAGC
* **
56897254 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
56897300 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
56897346 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
56897398 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
56897450 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
56897496 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
56897542 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
56897594 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
56897621 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:56897373 original size:52 final size:52
Alignment explanation
Indices: 56897297--56897614 Score: 417
Period size: 52 Copynumber: 6.3 Consensus size: 52
56897287 TAGCTAAAGC
* *
56897297 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
56897350 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
56897402 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
56897454 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
56897500 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
56897546 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
56897598 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
56897615 ATCAGAAGTA
Statistics
Matches: 238, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 83 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:56897562 original size:196 final size:196
Alignment explanation
Indices: 56897254--56897606 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
56897244 TAAGTGTAGC
* * * * * *
56897254 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
56897319 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
56897384 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
56897449 T
196 T
*
56897450 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
56897515 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
56897580 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
56897607 ATCACTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:56897610 original size:98 final size:97
Alignment explanation
Indices: 56897254--56897620 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
56897244 TAAGTGTAGC
* * * *
56897254 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACT
56897319 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
56897353 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----
* *
56897418 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
56897457 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
*
56897517 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
56897549 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTT
56897614 GATCAGA
65 GATCAGA
56897621 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 148 0.62
99 7 0.03
100 2 0.01
101 1 0.00
104 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:56902935 original size:14 final size:15
Alignment explanation
Indices: 56902911--56902939 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56902901 TGACATAAAT
56902911 ATTTTTAAATATTTA
1 ATTTTTAAATATTTA
56902926 ATTTTT-AATATTTA
1 ATTTTTAAATATTTA
56902940 TGTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTAAATATTTA
Found at i:56903513 original size:13 final size:14
Alignment explanation
Indices: 56903491--56903519 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56903481 AATAAATTTT
56903491 AAAAGCAAAAAAAA
1 AAAAGCAAAAAAAA
56903505 AAAAG-AAAAAAAA
1 AAAAGCAAAAAAAA
56903518 AA
1 AA
56903520 GCGAAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAGCAAAAAAAA
Found at i:56906742 original size:36 final size:36
Alignment explanation
Indices: 56906653--56906742 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 36
56906643 AAATATTTGC
* * *
56906653 ATTTATATTAAAAACATTTATTATTAAATATTTATA
1 ATTTATAATCAAAATATTTATTATTAAATATTTATA
* *
56906689 ATTTATAATCTATATATTTATTATTAAAATATTT-TA
1 ATTTATAATCAAAATATTTATTATT-AAATATTTATA
56906725 ATATT-TCAAT-AAAATATT
1 AT-TTAT-AATCAAAATATT
56906743 AAGAACGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (36 bp):
ATTTATAATCAAAATATTTATTATTAAATATTTATA
Found at i:56908919 original size:23 final size:23
Alignment explanation
Indices: 56908888--56908969 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
56908878 TCATAATTTT
*
56908888 TAGGGATTTGTTTGGCTAAATTG
1 TAGGTATTTGTTTGGCTAAATTG
* *
56908911 TAGGTATTTTTGTCTT--CCACAATTT
1 TAGGTA--TTTGT-TTGGCTA-AATTG
56908936 TAAGG-ATTTGTTTGGCTAAATTG
1 T-AGGTATTTGTTTGGCTAAATTG
56908959 TAGGTATTTGT
1 TAGGTATTTGT
56908970 CTTCCACAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
22 5 0.11
23 21 0.46
24 4 0.09
25 11 0.24
26 5 0.11
ACGTcount: A:0.22, C:0.07, G:0.23, T:0.48
Consensus pattern (23 bp):
TAGGTATTTGTTTGGCTAAATTG
Found at i:56908980 original size:23 final size:23
Alignment explanation
Indices: 56908906--56908992 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
56908896 TGTTTGGCTA
56908906 AATTGTAGGTATTTTTGTCTTCCAC
1 AATTGTAGGTA--TTTGTCTTCCAC
* *
56908931 AATTTTAAGG-ATTTGT-TTGGCTA-
1 AATTGT-AGGTATTTGTCTT--CCAC
56908954 AATTGTAGGTATTTGTCTTCCAC
1 AATTGTAGGTATTTGTCTTCCAC
* *
56908977 AATTTTAGGGATTTGT
1 AATTGTAGGTATTTGT
56908993 TTCTCTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 7 0.14
23 30 0.60
24 4 0.08
25 6 0.12
26 3 0.06
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (23 bp):
AATTGTAGGTATTTGTCTTCCAC
Found at i:56908989 original size:46 final size:47
Alignment explanation
Indices: 56908871--56908994 Score: 196
Period size: 48 Copynumber: 2.6 Consensus size: 47
56908861 TCAAGTCAAG
* *
56908871 TTGTCTTTCATAATTTTTAGGGATTTGTTTGGCTAAATTGTAGGTATTT
1 TTGTCTTCCACAA-TTTTAGGGATTTGTTTGGCTAAATTGTAGGTA-TT
*
56908920 TTGTCTTCCACAATTTTAAGGATTTGTTTGGCTAAATTGTAGGTA-T
1 TTGTCTTCCACAATTTTAGGGATTTGTTTGGCTAAATTGTAGGTATT
56908966 TTGTCTTCCACAATTTTAGGGATTTGTTT
1 TTGTCTTCCACAATTTTAGGGATTTGTTT
56908995 CTCTTTTATT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
46 29 0.41
48 31 0.44
49 11 0.15
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (47 bp):
TTGTCTTCCACAATTTTAGGGATTTGTTTGGCTAAATTGTAGGTATT
Found at i:56909740 original size:38 final size:38
Alignment explanation
Indices: 56909698--56909808 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 38
56909688 AGGGAAACTT
56909698 GCACATGAAGTGCATACTGGCACACGAAGTGCATACTG
1 GCACATGAAGTGCATACTGGCACACGAAGTGCATACTG
* *
56909736 GCACACGAAGTGCATACTGGCACACGAAGTGCATCCTG
1 GCACATGAAGTGCATACTGGCACACGAAGTGCATACTG
* * ** * * *
56909774 ACACATAAAGCACATTCTGGTACACAAAGTGCATA
1 GCACATGAAGTGCATACTGGCACACGAAGTGCATA
56909809 AAGCCGTACA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (38 bp):
GCACATGAAGTGCATACTGGCACACGAAGTGCATACTG
Found at i:56909778 original size:19 final size:19
Alignment explanation
Indices: 56909698--56909769 Score: 135
Period size: 19 Copynumber: 3.8 Consensus size: 19
56909688 AGGGAAACTT
*
56909698 GCACATGAAGTGCATACTG
1 GCACACGAAGTGCATACTG
56909717 GCACACGAAGTGCATACTG
1 GCACACGAAGTGCATACTG
56909736 GCACACGAAGTGCATACTG
1 GCACACGAAGTGCATACTG
56909755 GCACACGAAGTGCAT
1 GCACACGAAGTGCAT
56909770 CCTGACACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (19 bp):
GCACACGAAGTGCATACTG
Found at i:56916688 original size:68 final size:71
Alignment explanation
Indices: 56916547--56916691 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
56916537 ATATTAAATC
* *
56916547 TATTAAATTAATAAAATATTTATCTACAAGTTAAATATTAAATTAAATTTAATATTAAGATAACC
1 TATTAAATTAATAAAATATCTATCTACAAG-TAAATATTAAATTAAATTTAATATTAAAATAACC
***
56916612 ACTTTAA
65 AAAATAA
* * **
56916619 TATTAAATTAATAAAATA-CTAT-TA-ATA-TAAGTATTAAATTAAATTTAATATTAAAATTATT
1 TATTAAATTAATAAAATATCTATCTACA-AGTAAATATTAAATTAAATTTAATATTAAAATAACC
56916680 AAAATAA
65 AAAATAA
56916687 TATTA
1 TATTA
56916692 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 38 0.60
69 1 0.02
70 3 0.05
71 3 0.05
72 18 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATCTATCTACAAGTAAATATTAAATTAAATTTAATATTAAAATAACCA
AAATAA
Found at i:56916771 original size:11 final size:11
Alignment explanation
Indices: 56916755--56916779 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56916745 CGTAATTTTT
56916755 CCACTACTCAA
1 CCACTACTCAA
56916766 CCACTACTCAA
1 CCACTACTCAA
56916777 CCA
1 CCA
56916780 TTAGTCGGCC
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:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (11 bp):
CCACTACTCAA
Found at i:56917016 original size:13 final size:13
Alignment explanation
Indices: 56916994--56917033 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
56916984 TAATTTTCGA
56916994 TTTCAAGTCCAAT
1 TTTCAAGTCCAAT
*
56917007 TTTTAAGTCCAAT
1 TTTCAAGTCCAAT
*
56917020 TTTCAAGTTCAAT
1 TTTCAAGTCCAAT
56917033 T
1 T
56917034 ACCCATTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (13 bp):
TTTCAAGTCCAAT
Found at i:56920871 original size:29 final size:29
Alignment explanation
Indices: 56920813--56920874 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
56920803 AAAAATATTG
**
56920813 AAAATAATTTTTTATAATTTATAATTTTA
1 AAAATAATTTTTTATAATTTATAAAATTA
* *
56920842 AAAAT-ATTTTTTCTGAATTTTTAAAATTA
1 AAAATAATTTTTTAT-AATTTATAAAATTA
56920871 AAAA
1 AAAA
56920875 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
AAAATAATTTTTTATAATTTATAAAATTA
Found at i:56934105 original size:21 final size:22
Alignment explanation
Indices: 56934081--56934125 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
56934071 GCCCTATGGG
56934081 AAAAGCACAGCAAAG-GAAAAA
1 AAAAGCACAGCAAAGTGAAAAA
*
56934102 AAAAGTACAGCAAAGTGAAAAA
1 AAAAGCACAGCAAAGTGAAAAA
56934124 AA
1 AA
56934126 GGAAAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.67, C:0.11, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAGCACAGCAAAGTGAAAAA
Found at i:56934122 original size:20 final size:20
Alignment explanation
Indices: 56934081--56934149 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
56934071 GCCCTATGGG
56934081 AAAAGCACAGCAAAG-GAAAAA
1 AAAAGCACAGCAAAGTG--AAA
*
56934102 AAAAGTACAGCAAAGTGAAA
1 AAAAGCACAGCAAAGTGAAA
* * * *
56934122 AAAAGGAAAGCAAAATTAAA
1 AAAAGCACAGCAAAGTGAAA
56934142 AAAAGCAC
1 AAAAGCAC
56934150 TGCCAATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 25 0.62
21 14 0.35
22 1 0.03
ACGTcount: A:0.65, C:0.12, G:0.17, T:0.06
Consensus pattern (20 bp):
AAAAGCACAGCAAAGTGAAA
Found at i:56934262 original size:25 final size:26
Alignment explanation
Indices: 56934234--56934334 Score: 98
Period size: 25 Copynumber: 3.8 Consensus size: 26
56934224 TTAAAATTTA
56934234 AAATTAAAAA-AGTGAAAAAAAGGGG
1 AAATTAAAAATAGTGAAAAAAAGGGG
* *
56934259 AAATTAAAAATAATG-GAAAAAGGGG
1 AAATTAAAAATAGTGAAAAAAAGGGG
**
56934284 AAAATTAAAAATAGTGAAAGAAGGGGGG
1 -AAATTAAAAATAGTGAAA-AAAAGGGG
* * *
56934312 AAATTTTAAAATGGTTAAAAAAA
1 AAA-TTAAAAATAGTGAAAAAAA
56934335 ATGAAAAAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
25 19 0.32
26 17 0.28
27 6 0.10
28 18 0.30
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (26 bp):
AAATTAAAAATAGTGAAAAAAAGGGG
Found at i:56934278 original size:26 final size:27
Alignment explanation
Indices: 56934233--56934309 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 27
56934223 TTTAAAATTT
*
56934233 AAAATTAAAAA-AGTGAAAAAAAGGGG
1 AAAATTAAAAATAGTGGAAAAAAGGGG
*
56934259 -AAATTAAAAATAATGG-AAAAAGGGG
1 AAAATTAAAAATAGTGGAAAAAAGGGG
*
56934284 AAAATTAAAAATAGT-GAAAGAAGGGG
1 AAAATTAAAAATAGTGGAAAAAAGGGG
56934310 GGAAATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
25 20 0.45
26 24 0.55
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (27 bp):
AAAATTAAAAATAGTGGAAAAAAGGGG
Found at i:56934462 original size:23 final size:23
Alignment explanation
Indices: 56934422--56934476 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
56934412 AACCGTTAAA
56934422 AAAATAAAAAGAGAGAAAAAAAAG
1 AAAA-AAAAAGAGAGAAAAAAAAG
* *
56934446 TAAAAAAAAA-AGTGAAAAAGAAG
1 -AAAAAAAAAGAGAGAAAAAAAAG
56934469 AAAAAAAA
1 AAAAAAAA
56934477 TTGAAACTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 11 0.39
24 5 0.18
25 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAGAGAGAAAAAAAAG
Found at i:56934463 original size:20 final size:20
Alignment explanation
Indices: 56934440--56934482 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
56934430 AAGAGAGAAA
56934440 AAAAAGTAA-AAAAAAAAGTG
1 AAAAAG-AAGAAAAAAAAGTG
*
56934460 AAAAAGAAGAAAAAAAATTG
1 AAAAAGAAGAAAAAAAAGTG
56934480 AAA
1 AAA
56934483 CTAGTGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAGTG
Found at i:56936196 original size:34 final size:34
Alignment explanation
Indices: 56936153--56936219 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
56936143 TTTATTCACT
56936153 TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
1 TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
56936187 TGTGTCTTGATCCGTAGAAATCTCTAAATTATG
1 TGTGTCTTGATCCGTAGAAATCTCTAAATTATG
56936220 TTAATATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (34 bp):
TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
Found at i:56936929 original size:30 final size:30
Alignment explanation
Indices: 56936883--56936939 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
56936873 CACGAGCTGG
*
56936883 CACATGGGCGTGTGGCCAGCCCGTGTGTCT
1 CACACGGGCGTGTGGCCAGCCCGTGTGTCT
* *
56936913 CACACGGGCTTGTGGCCAGCTCGTGTG
1 CACACGGGCGTGTGGCCAGCCCGTGTG
56936940 GAAATGCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.30, G:0.37, T:0.23
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCAGCCCGTGTGTCT
Found at i:56940195 original size:3 final size:3
Alignment explanation
Indices: 56940187--56940222 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
56940177 CTGCACGCAT
56940187 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
56940223 ATCTTCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:56942564 original size:27 final size:27
Alignment explanation
Indices: 56942533--56942584 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
56942523 TTATTGTTAA
56942533 TTTTGTTATTATTTTAAAGGCATTTGT
1 TTTTGTTATTATTTTAAAGGCATTTGT
*
56942560 TTTTGTTATTATTTTAGAGGCATTT
1 TTTTGTTATTATTTTAAAGGCATTT
56942585 ACTTGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.60
Consensus pattern (27 bp):
TTTTGTTATTATTTTAAAGGCATTTGT
Found at i:56942723 original size:11 final size:11
Alignment explanation
Indices: 56942707--56942737 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
56942697 TATATATATT
56942707 TAAAAATTATA
1 TAAAAATTATA
*
56942718 TAAAAATAATA
1 TAAAAATTATA
56942729 TAAAAATTA
1 TAAAAATTA
56942738 ATATGGGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:56942734 original size:12 final size:11
Alignment explanation
Indices: 56942707--56942741 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
56942697 TATATATATT
*
56942707 TAAAAATTATA
1 TAAAAATAATA
56942718 TAAAAATAATA
1 TAAAAATAATA
56942729 TAAAAATTAATA
1 TAAAAA-TAATA
56942741 T
1 T
56942742 GGGCAGGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:56946745 original size:44 final size:44
Alignment explanation
Indices: 56946693--56946850 Score: 208
Period size: 44 Copynumber: 3.4 Consensus size: 44
56946683 TTATCACTTG
* * *
56946693 TCACTTGTCCCTGATCAGATAAGTGAAGCTAAAGCTACCTCTCATTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC---A
56946740 CTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
1 ----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
* *
56946788 TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
56946832 TCACTTGTCACTGATCAGA
1 TCACTTGTCACTGATCAGA
56946851 AGTTCTCAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
44 60 0.59
48 1 0.01
51 40 0.40
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (44 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTCA
Found at i:56946748 original size:51 final size:50
Alignment explanation
Indices: 56946685--56946843 Score: 222
Period size: 51 Copynumber: 3.3 Consensus size: 50
56946675 GATCACATTT
* *
56946685 ATCACTTGTCACTTGTCCCTGATCAGATAAGTGAAGCTAAAGCTACCTCTC
1 ATCACTTGTCACTTGT-CCTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
56946736 ATTACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTC-CTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
56946787 ATCACTTGTCA----T--TGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTC
56946831 ATCACTTGTCACT
1 ATCACTTGTCACT
56946844 GATCAGAAGT
Statistics
Matches: 100, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
44 42 0.42
47 1 0.01
50 1 0.01
51 56 0.56
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (50 bp):
ATCACTTGTCACTTGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:56950790 original size:18 final size:18
Alignment explanation
Indices: 56950764--56950801 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56950754 GTTTCCCAGG
*
56950764 TTAGGATTTTTAAGGTTT
1 TTAGAATTTTTAAGGTTT
*
56950782 TTAGAATTTTTAGGGTTT
1 TTAGAATTTTTAAGGTTT
56950800 TT
1 TT
56950802 GGAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (18 bp):
TTAGAATTTTTAAGGTTT
Found at i:56951200 original size:127 final size:126
Alignment explanation
Indices: 56950917--56951486 Score: 788
Period size: 126 Copynumber: 4.5 Consensus size: 126
56950907 GATAAAAGCA
* * * * * * *
56950917 AAGCAGGATGATTTATAAGAAGAATTTTTTAAAGTCTCGCCCACATGTACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAA-TCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
56950982 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAACAAATAGTTT-AAAAAACACTTC
65 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
56951043 AAGCAGGATGCTTTATGAAAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTAGAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
56951108 TGGTCCTGAAAGAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGAAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
*
56951170 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGAACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
56951235 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGTAAATAGTATAAAACAACGCTGC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
56951296 AAGCAGGATGCTATT-TGAGAAAAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * * *
56951360 TAGGTCCTGGAAAAATAATTTCGACTTGACGTTTTTTAGCAAATAG--TATAAAATCGCTTC
65 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
56951420 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACGGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
56951485 AG
66 AG
56951487 CATGTTTGGG
Statistics
Matches: 394, Mismatches: 46, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
123 2 0.01
124 68 0.17
125 36 0.09
126 204 0.52
127 84 0.21
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
Found at i:56952453 original size:20 final size:20
Alignment explanation
Indices: 56952416--56952453 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56952406 TTTATTTTTA
*
56952416 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
56952436 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
56952454 TTTCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:56953434 original size:51 final size:51
Alignment explanation
Indices: 56953379--56953478 Score: 116
Period size: 51 Copynumber: 2.0 Consensus size: 51
56953369 AATTATTTAA
56953379 AAATA-GGTATTT-AAATGAAATTTAAGAA-AAACTTGAGAGCAAATTGAGATT
1 AAATATGG-ATTTGAAA-GAAATTT-AGAAGAAACTTGAGAGCAAATTGAGATT
* * * *
56953430 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATATGGATTTGAAAGAAATTTAGAAGAAACTTGAGAGCAAATTGAGA
56953479 GGAAATTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
50 3 0.07
51 35 0.83
52 4 0.10
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (51 bp):
AAATATGGATTTGAAAGAAATTTAGAAGAAACTTGAGAGCAAATTGAGATT
Found at i:56953452 original size:11 final size:11
Alignment explanation
Indices: 56953438--56953514 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
56953428 TTAAATATGG
56953438 ATTTGAGAGAA
1 ATTTGAGAGAA
*
56953449 ATTTG-GAAGGA
1 ATTTGAG-AGAA
56953460 ATTTGAGAGCAA
1 ATTTGAGAG-AA
56953472 A-TTGAGAGGAA
1 ATTTGAGA-GAA
56953483 ATTT-AGAGGAA
1 ATTTGAGA-GAA
*
56953494 A-TTGATAGGAA
1 ATTTGAGA-GAA
56953505 ATTTGAGAGA
1 ATTTGAGAGA
56953515 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
10 3 0.05
11 41 0.75
12 11 0.20
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:56953463 original size:22 final size:22
Alignment explanation
Indices: 56953438--56953514 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
56953428 TTAAATATGG
56953438 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAGAGAAA-TTGAG-AGGAA
56953460 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
*
56953483 ATTT-AGAGGAAATTGATAGGAA
1 ATTTGAGA-GAAATTGAGAGGAA
56953505 ATTTGAGAGA
1 ATTTGAGAGA
56953515 GGATTAGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
22 36 0.73
23 13 0.27
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:56953493 original size:33 final size:35
Alignment explanation
Indices: 56953438--56953513 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 35
56953428 TTAAATATGG
* *
56953438 ATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
* *
56953472 A-TTGAGAGGAAATTTAG-AGGAAATTGATAGGAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
56953505 ATTTGAGAG
1 ATTTGAGAG
56953514 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.42, C:0.01, G:0.30, T:0.26
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:56958908 original size:17 final size:18
Alignment explanation
Indices: 56958886--56958919 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56958876 CAAGTGCTTT
56958886 TTTGACAAA-TTGGAACA
1 TTTGACAAATTTGGAACA
56958903 TTTGACAAATTTGGAAC
1 TTTGACAAATTTGGAAC
56958920 TGTATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (18 bp):
TTTGACAAATTTGGAACA
Found at i:56962397 original size:18 final size:20
Alignment explanation
Indices: 56962371--56962412 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
56962361 CATAACTTTT
*
56962371 TAAATTAAAA-AT-TAAAAA
1 TAAAGTAAAATATATAAAAA
56962389 TAAAGTAAAATATATAAAAA
1 TAAAGTAAAATATATAAAAA
56962409 -AAAG
1 TAAAG
56962413 AAGAAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
TAAAGTAAAATATATAAAAA
Found at i:56962877 original size:4 final size:4
Alignment explanation
Indices: 56962868--56962899 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
56962858 TTTATATATT
56962868 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
56962900 CCAAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:56963505 original size:29 final size:29
Alignment explanation
Indices: 56963468--56963541 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
56963458 TCAATTCAAT
* *
56963468 TCAATGAACAAGTTCTTCATTGCGAACTC
1 TCAACGAACAAGTTCTTCATCGCGAACTC
56963497 TCAACGAACAAGTTCTTCATCGCGAACTC
1 TCAACGAACAAGTTCTTCATCGCGAACTC
56963526 TCAACGAACAAGTTCT
1 TCAACGAACAAGTTCT
56963542 CCACCCCTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (29 bp):
TCAACGAACAAGTTCTTCATCGCGAACTC
Found at i:56970686 original size:30 final size:30
Alignment explanation
Indices: 56970642--56970704 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
56970632 ACTTAATAAG
56970642 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
56970672 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
56970702 CAA
1 CAA
56970705 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Done.