Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006725.1 Hibiscus syriacus cultivar Beakdansim tig00016849_pilon, whole genome shotgun sequence
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: 78624
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2635 original size:91 final size:91
Alignment explanation
Indices: 2476--2655 Score: 315
Period size: 91 Copynumber: 2.0 Consensus size: 91
2466 TCAAAATGAA
* * *
2476 AAAATGACTATTTTAATAATTTAATTGACAAAATTGTTTATTCAGTGTTCATTTTAAAATTAAGA
1 AAAATGACTATTTTAATAATTTAATTGACAAAATTGTTTATTAAGTGGTCATTTTAAAATTAACA
*
2541 CTATAATCTAGTGACCAATAGGAGCT
66 CTATAATCTAATGACCAATAGGAGCT
*
2567 AAAATGACTATTTTAATAATTTAATTGACAAAATTGTTTATTAAGTGGTCGTTTTAAAATTAACA
1 AAAATGACTATTTTAATAATTTAATTGACAAAATTGTTTATTAAGTGGTCATTTTAAAATTAACA
2632 CTATAATCTAATGACCAATAGGAG
66 CTATAATCTAATGACCAATAGGAG
2656 AGTTTAACCT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (91 bp):
AAAATGACTATTTTAATAATTTAATTGACAAAATTGTTTATTAAGTGGTCATTTTAAAATTAACA
CTATAATCTAATGACCAATAGGAGCT
Found at i:3698 original size:15 final size:15
Alignment explanation
Indices: 3678--3718 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
3668 AAAAGCAAAA
3678 GAATGGAAGGAAATG
1 GAATGGAAGGAAATG
3693 GAATGGAAGGAAATG
1 GAATGGAAGGAAATG
*
3708 GATTGGAAGGA
1 GAATGGAAGGA
3719 GATGAGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (15 bp):
GAATGGAAGGAAATG
Found at i:4740 original size:33 final size:33
Alignment explanation
Indices: 4702--4818 Score: 146
Period size: 33 Copynumber: 3.6 Consensus size: 33
4692 CCACGTGGTT
* *
4702 TCCATTTCTTACAACTACATTTTCTAATACTTA
1 TCCATTTCATACAATTACATTTTCTAATACTTA
* *
4735 TCCATTTCATACAATTACATTTTCTAGTATTTA
1 TCCATTTCATACAATTACATTTTCTAATACTTA
* *
4768 TCCATTTCATGCAATTACATTTGCTAATACTT-
1 TCCATTTCATACAATTACATTTTCTAATACTTA
* * *
4800 TTCATCTCAAACAATTACA
1 TCCATTTCATACAATTACA
4819 AACAACGACT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
32 15 0.21
33 57 0.79
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (33 bp):
TCCATTTCATACAATTACATTTTCTAATACTTA
Found at i:12716 original size:20 final size:21
Alignment explanation
Indices: 12691--12729 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12681 TACTATAAAT
12691 TCAAC-TCAAGACAAACTATA
1 TCAACTTCAAGACAAACTATA
*
12711 TCAACTTGAAGACAAACTA
1 TCAACTTCAAGACAAACTA
12730 GTACAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (21 bp):
TCAACTTCAAGACAAACTATA
Found at i:20269 original size:24 final size:24
Alignment explanation
Indices: 20242--20372 Score: 109
Period size: 24 Copynumber: 5.5 Consensus size: 24
20232 AAACGGAGAT
*
20242 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
20266 ATCAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
20290 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* **
20314 ATCACATGTCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* ** *
20338 ATCACATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
20362 ATCAGAAATCA
1 ATCAGAAATCA
20373 GATAAAATAT
Statistics
Matches: 84, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:22798 original size:14 final size:14
Alignment explanation
Indices: 22779--22806 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22769 TGGTCTACGC
22779 CGGTCAACAGTCAA
1 CGGTCAACAGTCAA
22793 CGGTCAACAGTCAA
1 CGGTCAACAGTCAA
22807 TCATTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (14 bp):
CGGTCAACAGTCAA
Found at i:24395 original size:2 final size:2
Alignment explanation
Indices: 24390--24445 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
24380 TGTGTGTGTT
*
24390 GA GA GA TA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24432 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
24446 TTTGCCATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:26731 original size:24 final size:24
Alignment explanation
Indices: 26675--26722 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
26665 TGGAGCAAAA
26675 GCTACTTCCAGGCTTAACAAAGGT
1 GCTACTTCCAGGCTTAACAAAGGT
26699 GCTACTTCCAGGCTTAACAAAGGT
1 GCTACTTCCAGGCTTAACAAAGGT
26723 ATCACTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
GCTACTTCCAGGCTTAACAAAGGT
Found at i:32030 original size:2 final size:2
Alignment explanation
Indices: 32023--32051 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32013 TCTTACTTAT
32023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32052 GAGGAACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32624 original size:19 final size:19
Alignment explanation
Indices: 32600--32638 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
32590 ACGCACACTC
*
32600 GGCGAGACTCGCGTAACTT
1 GGCGAGACTCACGTAACTT
32619 GGCGAGACTCACGTAACTT
1 GGCGAGACTCACGTAACTT
32638 G
1 G
32639 CATTTTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (19 bp):
GGCGAGACTCACGTAACTT
Found at i:33408 original size:17 final size:17
Alignment explanation
Indices: 33378--33410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33368 GTTTTACCGA
33378 TTTTTAAATAATTATGG
1 TTTTTAAATAATTATGG
33395 TTTTATAAAT-ATTATG
1 TTTT-TAAATAATTATG
33411 TGACATCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTTTTAAATAATTATGG
Found at i:37557 original size:60 final size:60
Alignment explanation
Indices: 37487--37614 Score: 195
Period size: 60 Copynumber: 2.1 Consensus size: 60
37477 GCATACACAT
37487 CTTGTAAATATCACTACTCGAAT-CTCAAATCTCTAAGCAAATCAACATTAACTTTTACCG
1 CTTGTAAATATCACTACTCGAATCCT-AAATCTCTAAGCAAATCAACATTAACTTTTACCG
* * * * *
37547 CTTGTAAATATCACTACTCGGATCCTGAATCTCTGAGCAGATCAACATTTACTTTTACCG
1 CTTGTAAATATCACTACTCGAATCCTAAATCTCTAAGCAAATCAACATTAACTTTTACCG
37607 CTTGTAAA
1 CTTGTAAA
37615 ACATTTACTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 60 0.97
61 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (60 bp):
CTTGTAAATATCACTACTCGAATCCTAAATCTCTAAGCAAATCAACATTAACTTTTACCG
Found at i:37622 original size:24 final size:24
Alignment explanation
Indices: 37590--37638 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
37580 TGAGCAGATC
37590 AACATTTACTTTTACCGCTTGTAA
1 AACATTTACTTTTACCGCTTGTAA
37614 AACATTTACTTTTACCGCTTGTAA
1 AACATTTACTTTTACCGCTTGTAA
37638 A
1 A
37639 TATCACTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (24 bp):
AACATTTACTTTTACCGCTTGTAA
Found at i:37706 original size:84 final size:84
Alignment explanation
Indices: 37530--37690 Score: 286
Period size: 84 Copynumber: 1.9 Consensus size: 84
37520 TAAGCAAATC
* * *
37530 AACATTAACTTTTACCGCTTGTAAATATCACTACTCGGATCCTGAATCTCTGAGCAGATCAACAT
1 AACATTTACTTTTACCGCTTGTAAATATCACTACTCGGACCCTGAATCTCTAAGCAGATCAACAT
37595 TTACTTTTACCGCTTGTAA
66 TTACTTTTACCGCTTGTAA
*
37614 AACATTTACTTTTACCGCTTGTAAATATCACTACTCGGACCCTGAATCTCTAAGCAGATCAATAT
1 AACATTTACTTTTACCGCTTGTAAATATCACTACTCGGACCCTGAATCTCTAAGCAGATCAACAT
37679 TTACTTTTACCG
66 TTACTTTTACCG
37691 TTGAGGCCAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (84 bp):
AACATTTACTTTTACCGCTTGTAAATATCACTACTCGGACCCTGAATCTCTAAGCAGATCAACAT
TTACTTTTACCGCTTGTAA
Found at i:37707 original size:18 final size:18
Alignment explanation
Indices: 37684--37737 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
37674 AATATTTACT
37684 TTTACCGTTGAGGCCACC
1 TTTACCGTTGAGGCCACC
*
37702 TTTACCATTGAGGCCACC
1 TTTACCGTTGAGGCCACC
37720 TTTACCGTTGAGGCCACC
1 TTTACCGTTGAGGCCACC
37738 AGATAAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.33, G:0.20, T:0.28
Consensus pattern (18 bp):
TTTACCGTTGAGGCCACC
Found at i:45907 original size:14 final size:14
Alignment explanation
Indices: 45882--45911 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45872 CGCAAAAAGA
*
45882 AATTTCAAAAAATT
1 AATTTAAAAAAATT
45896 AATTTAAAAAAATT
1 AATTTAAAAAAATT
45910 AA
1 AA
45912 AAGAGAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTTAAAAAAATT
Found at i:46249 original size:23 final size:23
Alignment explanation
Indices: 46223--46270 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
46213 ATAAAGTACA
*
46223 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
46246 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
46269 AT
1 AT
46271 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:46705 original size:20 final size:21
Alignment explanation
Indices: 46657--46708 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
46647 AATATAACCA
*
46657 TTACCTATTACATTATATAGGG
1 TTACCTATTACATCATATA-GG
* *
46679 CTACCTATTACATCATAT-GT
1 TTACCTATTACATCATATAGG
46699 TTACCTATTA
1 TTACCTATTA
46709 TATTGAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (21 bp):
TTACCTATTACATCATATAGG
Found at i:47263 original size:407 final size:408
Alignment explanation
Indices: 46390--48006 Score: 3118
Period size: 406 Copynumber: 4.0 Consensus size: 408
46380 ACTTTAACAG
46390 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
46455 GTTTTGATATTTTAT-AAATATTATTTAGAATTTTAAA-TT--TAATAATATATACCGTAACGTA
66 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
46516 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
131 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
46581 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
196 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
46646 CAATATAACCATTACCTATTACATTATAT-AGGGCTACCTATTACATCATATGTTTACCTATTAT
261 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
46710 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGATATGTAATTTATGT
326 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
46774 TTCAATATTTTTTAAGTA
391 TTCAATATTTTTTAAGTA
46792 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
46857 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
66 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
46922 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
131 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
46987 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
196 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
47052 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
261 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
47117 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGATATGTAATTTATGT
326 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
47181 TTCAATATTTTTTAAGTA
391 TTCAATATTTTTTAAGTA
47199 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
47264 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAAT-A-ATATACCGTAACGTA
66 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
47327 AAAAATAAATCATTAGACGCCTATAA-TACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
131 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
47391 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
196 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
47456 CAATA-AACCATTACCTATTACATTATATAAGGGCTACCTATTACAT-ATATGTTTACCTATTAT
261 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
47519 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
326 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
47584 TTCAATATTTTTTAAGTA
391 TTCAATATTTTTTAAGTA
47602 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
47667 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
66 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
47732 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
131 AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
47797 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
196 CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
47862 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
261 CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
47927 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAA-ACTTATGTAATTTAT
326 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGA--TATGTAATTTAT
47991 GTTTCAAT-TTTTTTAA
389 GTTTCAATATTTTTTAA
48007 CAGTGTACTG
Statistics
Matches: 1202, Mismatches: 0, Indels: 20
0.98 0.00 0.02
Matches are distributed among these distances:
402 136 0.11
403 218 0.18
404 111 0.09
405 82 0.07
406 290 0.24
407 271 0.23
408 74 0.06
409 20 0.02
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (408 bp):
TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATATACCGTAACGTA
AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAC
CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTA
CAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
TTCAATATTTTTTAAGTA
Found at i:47948 original size:810 final size:809
Alignment explanation
Indices: 46390--48006 Score: 3136
Period size: 810 Copynumber: 2.0 Consensus size: 809
46380 ACTTTAACAG
46390 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
46455 GTTTTGATATTTTATAAATATTATTTAGAATTTTAAATTTAATAATATATACCGTAACGTAAAAA
66 GTTTTGATATTTTATAAATATTATTTAGAATTTTAAATTTAATAATATATACCGTAACGTAAAAA
46520 ATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTA
131 ATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTA
46585 AATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAAT
196 AATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAAT
46650 ATAACCATTACCTATTACATTATATAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 ATAACCATTACCTATTACATTATATAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
46715 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGATATGTAATTTATGTTTCAAT
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGATATGTAATTTATGTTTCAAT
46780 ATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAA
391 ATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAA
46845 AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATA
456 AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATA
46910 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
521 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
46975 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
586 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
47040 ATAGACACTTTACAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATG
651 ATAGACACTTTACAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATG
47105 TTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGA-T
716 TTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAA-ACT
47168 ATGTAATTTATGTTTCAATATTTTTTAAGTA
780 ATGTAATTTATGTTTCAAT-TTTTTTAAGTA
47199 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
1 TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
47264 GTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATACCGTAACGTAAA
66 GTTTTGATATTTTAT-AAATATTATTTAGAATTTTAAATTTAATAAT-ATATACCGTAACGTAAA
47329 AAATAAATCATTAGACGCCTATAA-TACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
129 AAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
47393 TAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACA
194 TAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACA
47458 ATA-AACCATTACCTATTACATTATATAAGGGCTACCTATTACAT-ATATGTTTACCTATTATAT
259 ATATAACCATTACCTATTACATTATAT-AGGGCTACCTATTACATCATATGTTTACCTATTATAT
47521 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTTT
323 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGATATGTAATTTATGTTT
47586 CAATATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAC
387 CAATATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAC
47651 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAA
452 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAA
47716 TATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
517 TATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
47781 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
582 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
47846 AAGGATAGACACTTTACAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCA
647 AAGGATAGACACTTTACAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCA
47911 TATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAA
712 TATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAA
47976 ACTTATGTAATTTATGTTTCAATTTTTTTAA
777 AC-TATGTAATTTATGTTTCAATTTTTTTAA
48007 CAGTGTACTG
Statistics
Matches: 801, Mismatches: 0, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
809 159 0.20
810 564 0.70
811 58 0.07
812 20 0.02
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (809 bp):
TGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
GTTTTGATATTTTATAAATATTATTTAGAATTTTAAATTTAATAATATATACCGTAACGTAAAAA
ATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTA
AATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAAT
ATAACCATTACCTATTACATTATATAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGATATGTAATTTATGTTTCAAT
ATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAA
AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTAAATTTAATAATAATATA
TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
ATAGACACTTTACAATATAACCATTACCTATTACATTATATAAGGGCTACCTATTACATCATATG
TTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTA
TGTAATTTATGTTTCAATTTTTTTAAGTA
Found at i:48755 original size:184 final size:184
Alignment explanation
Indices: 48446--49156 Score: 1368
Period size: 184 Copynumber: 3.9 Consensus size: 184
48436 TTTTAAATGG
* *
48446 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
48511 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
48576 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
48630 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
48695 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
48760 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
48814 TATGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
48879 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
48944 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
48998 TATGGATATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
49063 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
49128 GATGTGTAAAATGTCGACACTTTTGTAAA
131 GATGTGTAAAATGTCGACACTTTTTTAAA
49157 AAGTGTCCAT
Statistics
Matches: 522, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 522 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:49178 original size:22 final size:22
Alignment explanation
Indices: 49148--49195 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
49138 ATGTCGACAC
*
49148 TTTTGTAAAAAGTG-TCCATACT
1 TTTTATAAAAAG-GATCCATACT
*
49170 TTTTATAAAAAGGATCGATACT
1 TTTTATAAAAAGGATCCATACT
49192 TTTT
1 TTTT
49196 TTAAGATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (22 bp):
TTTTATAAAAAGGATCCATACT
Found at i:50616 original size:3 final size:3
Alignment explanation
Indices: 50608--50678 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
50598 ACTTGTTTGG
* * * ** *
50608 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
50656 TTC ATC GTC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC AT
50679 TGTCATCTTC
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:50685 original size:42 final size:42
Alignment explanation
Indices: 50621--50703 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
50611 ATCATCTTCA
*
50621 TCATCATCATCATCGTCATCATCTTCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
** * *
50663 TCATCATCATCATCATTGTCATCTTCATTGTCAGCTTCATC
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATC
50704 TTCTGCGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
Found at i:50706 original size:6 final size:6
Alignment explanation
Indices: 50612--50706 Score: 50
Period size: 6 Copynumber: 15.3 Consensus size: 6
50602 GTTTGGATCA
* * * * * *
50612 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * *
50663 TCATCA TCATCA TCAT-T GTCATCT TCAT-T GTCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT -TCATCT TCATCT -TCATCT TCATCT TC
50707 TGCGACCGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
5 1 0.01
6 60 0.87
7 2 0.03
8 1 0.01
9 5 0.07
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:53093 original size:394 final size:396
Alignment explanation
Indices: 52160--53963 Score: 3312
Period size: 394 Copynumber: 4.6 Consensus size: 396
52150 TTTAAATTAG
52160 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
52224 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
52289 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
*
52353 AAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
52418 TATAATTGTA-CGGTTAGATTAAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGG
**
52482 GATCGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTA
325 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
52545 AAAAAAA
390 AAAAAAA
*
52552 TATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
52617 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
52682 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
52747 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
52812 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTG
52876 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATT-ATTCT-G
324 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
52939 GAAAAAAA
389 GAAAAAAA
52947 TATCGACACAAAC-TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
53011 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
53076 GACACTTTTTAATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 GACACTTTTT-ATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
53141 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
53206 TATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATTCTTTTGGGTTCGATGATTTTGG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGG
53271 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
325 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
53336 AAAAAAA
390 AAAAAAA
53343 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
53407 ATTGTACCGGTTAGATT-GAAAATTACATATTACATTATTCTTTTGGGTTCGATGATTTTTGGGA
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTTGGGA
53471 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAA
129 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAA
53536 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
194 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
53601 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAT-CTTTTGGGTTCGATGATTTT
259 GTATAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTT
53665 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTCTG
323 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTG
53729 GGAAAAAAA
388 GGAAAAAAA
53738 TATCGACACAAAC-TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
*
53802 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
53867 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAAA
*
53932 AAATATCGACACAAACTATATTAGTATCGACA
196 AAATATCGACACAAACTATATTAGTGTCGACA
53964 TGACCCTTAA
Statistics
Matches: 1377, Mismatches: 19, Indels: 30
0.97 0.01 0.02
Matches are distributed among these distances:
392 52 0.04
393 232 0.17
394 514 0.37
395 132 0.10
396 311 0.23
397 136 0.10
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (396 bp):
TATCGACACAAACATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGA
AAAAAA
Found at i:53283 original size:592 final size:596
Alignment explanation
Indices: 52160--53963 Score: 3318
Period size: 592 Copynumber: 3.0 Consensus size: 596
52150 TTTAAATTAG
52160 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
52224 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
52289 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
*
52353 AAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
52418 TATAATTGTA-CGGTTAGATTAAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
52481 GGATCGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGT
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
* *
52544 AAAAAAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
390 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
*
52609 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
455 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
52674 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATT
520 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATT
52739 CTGGGAAAAAAA
585 CTGGGAAAAAAA
52751 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
52816 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
52880 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATT-ATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
52943 AAAATATCGACACAAAC-TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
196 AAAATATCGACACAAACATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
53007 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* *
53072 GATCGACACTTTTTAATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GATCGACACTTTTT-ATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
53137 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
390 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
*
53202 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATTCTTTTGGGTTCGATGAT
455 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
53266 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATT
520 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATT
53331 CTGGGAAAAAAA
585 CTGGGAAAAAAA
53343 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
53407 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATTCTTTTGGGTTCGATGATTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTTGGGA
53471 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAA
53536 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAAC-ATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
53601 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAT-CTTTTGGGTTCGATGATTTT
259 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
53665 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTCTG
324 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTG
53729 GGAAAAAAATATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAA
389 GGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAA
53792 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
454 ACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA
53857 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCAT
519 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCAT
*
53922 TCTGGAAAAAAAA
584 TCTGGGAAAAAAA
*
53935 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
53964 TGACCCTTAA
Statistics
Matches: 1180, Mismatches: 18, Indels: 28
0.96 0.01 0.02
Matches are distributed among these distances:
588 56 0.05
589 23 0.02
590 97 0.08
591 229 0.19
592 392 0.33
593 206 0.17
594 53 0.04
595 36 0.03
596 88 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (596 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAATATCGACACAAACATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG
AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTC
TGGGAAAAAAA
Found at i:53883 original size:790 final size:787
Alignment explanation
Indices: 52160--53963 Score: 3368
Period size: 790 Copynumber: 2.3 Consensus size: 787
52150 TTTAAATTAG
52160 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
52224 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
64 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
52289 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
129 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
*
52353 AAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
194 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
52418 TATAATTGTACGGTTAGATTAAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGG
259 TATAATTGTACGGTTAGATTAAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGG
*
52483 ATCGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGTAAAA
324 ATCGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
52548 AAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
389 AAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
52613 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
454 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
52678 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
519 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
52743 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
584 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
52808 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
649 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
52873 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTATTCT
714 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTATTCT
52938 GGAAAAAAA
779 GGAAAAAAA
52947 TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAAT
1 TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAAT
53012 TGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
66 TGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
53077 ACACTTTTTAATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
131 ACACTTTTT-ATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
53142 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
* *
53207 ATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATTCTTTTGGGTTCGATGATTTTGGG
260 ATAATTGTA-CGGTTAGATTAAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGG
*
53272 ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGA
324 ATCGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
53337 AAAAAATATCGACACA-ACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
387 AAAAAATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
* *
53401 GGTATAATTGTACCGGTTAGATT-GAAAATTACATATTACATTATTCTTTTGGGTTCGATGATTT
452 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TT
53465 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTC
516 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTC
53530 TGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
581 TGGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATA
53595 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTAT-CTTTTGGGTTCGAT
646 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
53659 GATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTC
711 GA-TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATT-
53723 ATTCTGGGAAAAAAA
774 ATTCT-GGAAAAAAA
53738 TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAAT
1 TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAAT
*
53803 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
66 TGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
* * *
53868 ACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
131 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAA
*
53933 AATATCGACACAAACTATATTAGTATCGACA
196 AATATCGACACAAACTATATTAGTGTCGACA
53964 TGACCCTTAA
Statistics
Matches: 995, Mismatches: 12, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
785 38 0.04
786 82 0.08
787 17 0.02
788 128 0.13
789 121 0.12
790 397 0.40
791 212 0.21
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (787 bp):
TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAAT
TGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
TAATTGTACGGTTAGATTAAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
AATATCGACACAGACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGA
AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTATTCTGG
AAAAAAA
Found at i:54071 original size:19 final size:19
Alignment explanation
Indices: 54044--54084 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
54034 ATTCACATAA
54044 AAAAATATAAATCGTATAC
1 AAAAATATAAATCGTATAC
* *
54063 AAAATTATAAATCTTATAC
1 AAAAATATAAATCGTATAC
54082 AAA
1 AAA
54085 TTAACTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATAAATCGTATAC
Found at i:56938 original size:17 final size:18
Alignment explanation
Indices: 56916--56957 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
56906 ATATATCCGG
*
56916 TATCATTTTA-CCGGTTT
1 TATCATTTTATACGGTTT
56933 TATCATTTTATTACGGTTT
1 TATCATTTTA-TACGGTTT
56952 TATCAT
1 TATCAT
56958 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (18 bp):
TATCATTTTATACGGTTT
Found at i:56965 original size:19 final size:18
Alignment explanation
Indices: 56921--56965 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 18
56911 TCCGGTATCA
56921 TTTTACCGGTTTTATCATT
1 TTTTA-CGGTTTTATCATT
56940 TTATTACGGTTTTATCATAT
1 TT-TTACGGTTTTATCAT-T
56960 TTTTAC
1 TTTTAC
56966 CTGTTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (18 bp):
TTTTACGGTTTTATCATT
Found at i:58637 original size:16 final size:16
Alignment explanation
Indices: 58616--58650 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
58606 TTCGGTAAAA
*
58616 GAGCTTAATGAGCAAC
1 GAGCTTAACGAGCAAC
58632 GAGCTTAACGAGCAAC
1 GAGCTTAACGAGCAAC
58648 GAG
1 GAG
58651 TTGAGCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.14
Consensus pattern (16 bp):
GAGCTTAACGAGCAAC
Found at i:60933 original size:2 final size:2
Alignment explanation
Indices: 60920--60950 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
60910 ATAGATAGCA
*
60920 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60951 AGTTAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:61407 original size:60 final size:61
Alignment explanation
Indices: 61280--61420 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 61
61270 ATATAAGTAC
* * * **
61280 AGTTT-GGGATGAAATCGAAATGCTCAAAAAGTTTGGGGACTAATTTAGAAAGAGGGTCAT
1 AGTTTAGGGATGAAATTGAAATGCTCAAAAACTTTGAGGACTAATTTAGAAAGAGACTCAT
* * ** *
61340 AGCTTAGGGATGAAATTGAAATGTTC-AAAACTTTGAGGACTAATTTAGATCGATACTCAT
1 AGTTTAGGGATGAAATTGAAATGCTCAAAAACTTTGAGGACTAATTTAGAAAGAGACTCAT
*
61400 AGTTTAGGAATGAAATTGAAA
1 AGTTTAGGGATGAAATTGAAA
61421 CATTAATAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 50 0.74
61 18 0.26
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (61 bp):
AGTTTAGGGATGAAATTGAAATGCTCAAAAACTTTGAGGACTAATTTAGAAAGAGACTCAT
Found at i:63092 original size:22 final size:22
Alignment explanation
Indices: 63066--63118 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
63056 TTCCATTTCA
*
63066 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTATACAGTTGT
*
63088 TGTTGCGATAGTATACAGTTGT
1 CGTTGCGATAGTATACAGTTGT
63110 CGTTGCGAT
1 CGTTGCGAT
63119 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTATACAGTTGT
Found at i:63834 original size:21 final size:21
Alignment explanation
Indices: 63808--63860 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
63798 GAAATGGAAA
63808 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
63829 ATCGCAA-ACGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
*
63849 ATCACAACGCGA
1 ATCGCAACGCGA
63861 AATGGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:63878 original size:20 final size:20
Alignment explanation
Indices: 63853--63924 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
63843 TCAATTATCA
63853 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
* ** *
63873 CAACGCGAACTAAAAAATCA
1 CAACGCGAAATGGAAAATCG
*
63893 CAATGCGAAAT-GAAAACTCG
1 CAACGCGAAATGGAAAA-TCG
63913 CAACGCGAAATG
1 CAACGCGAAATG
63925 CAACGTGAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.11
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCG
Found at i:65255 original size:19 final size:18
Alignment explanation
Indices: 65206--65256 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
65196 CTCAAAATAT
65206 TATTATTTTATATATTTTA
1 TATTATTTTA-ATATTTTA
* *
65225 TATTAATATAATATTTTA
1 TATTATTTTAATATTTTA
65243 GTATTATTTTAATA
1 -TATTATTTTAATA
65257 AAATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTATTTTAATATTTTA
Found at i:65547 original size:42 final size:42
Alignment explanation
Indices: 65518--65609 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
65508 TTATTATTAT
*
65518 TATTATTATTATTTTAATAAGTAATTAATATAATTAATAATA
1 TATTATTATTATTTTAATAAATAATTAATATAATTAATAATA
*
65560 TATTATTATTATTTTAATAAATAATTAAAATAATTAATAATA
1 TATTATTATTATTTTAATAAATAATTAATATAATTAATAATA
65602 -ATT-TTATT
1 TATTATTATT
65610 TTAATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 5 0.10
41 3 0.06
42 40 0.83
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
TATTATTATTATTTTAATAAATAATTAATATAATTAATAATA
Found at i:66154 original size:43 final size:44
Alignment explanation
Indices: 66106--66218 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 44
66096 CCATTTTTTA
*
66106 AATCTTATTTTTTATCTTTAAAATT-AAGGTCT-TAATATTATTC
1 AATCTTACTTTTTATCTTTAAAATTGAA-GTCTCTAATATTATTC
* * *
66149 AATCTTACTTTTTATCTTTATAATTGAAGTCTCTAATTTTTTTC
1 AATCTTACTTTTTATCTTTAAAATTGAAGTCTCTAATATTATTC
* *
66193 AATC--ACTTTCTTACCTTTATAATTGA
1 AATCTTACTTT-TTATCTTTAAAATTGA
66219 GACCCCTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 5 0.08
43 42 0.68
44 15 0.24
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (44 bp):
AATCTTACTTTTTATCTTTAAAATTGAAGTCTCTAATATTATTC
Found at i:66196 original size:44 final size:44
Alignment explanation
Indices: 66146--66388 Score: 184
Period size: 43 Copynumber: 5.7 Consensus size: 44
66136 CTTAATATTA
* * *
66146 TTCAATCTTACTTTTTATCTTTATAATTGAAGTCTCTAATTTTT
1 TTCAATCTCACTTTTTACCTTTATAATTGAAGTCCCTAATTTTT
*
66190 TTCAA--TCACTTTCTTACCTTTATAATTG-AGACCCCTAA-TTTT
1 TTCAATCTCACTTT-TTACCTTTATAATTGAAG-TCCCTAATTTTT
* * * *
66232 GT-AATCTCAC-TTTTAACTTTATAATTG-AGACCCCTAAGTTTT
1 TTCAATCTCACTTTTTACCTTTATAATTGAAG-TCCCTAATTTTT
* * *
66274 TTCAATCTCAATTTATACCTTTATAATTG-AGATTCCTAA-TTTT
1 TTCAATCTCACTTTTTACCTTTATAATTGAAG-TCCCTAATTTTT
* * * * * * *
66317 TT-AATCTCACTTTCTAACTTTCTAATCGAGGCCCCTAAGTTTT
1 TTCAATCTCACTTTTTACCTTTATAATTGAAGTCCCTAATTTTT
* * *
66360 TTCGATCTCA-ATTATACCTTTATAATTGA
1 TTCAATCTCACTTTTTACCTTTATAATTGA
66389 GGCCTCTATT
Statistics
Matches: 163, Mismatches: 26, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
41 26 0.16
42 46 0.28
43 57 0.35
44 34 0.21
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (44 bp):
TTCAATCTCACTTTTTACCTTTATAATTGAAGTCCCTAATTTTT
Found at i:66238 original size:85 final size:85
Alignment explanation
Indices: 66149--66389 Score: 283
Period size: 85 Copynumber: 2.8 Consensus size: 85
66139 AATATTATTC
* * * * * * *
66149 AATCTTACTTTTTATCTTTATAATTGA-AGTCTCTAATTTTTTTCAA-TCACTTTCTTACCTTTA
1 AATCTCACTTTTTAACTTTATAATTGAGA-CCCCTAAGTTTTTTCAACTCAATTT-ATACCTTTA
66212 TAATTGAGACCCCTAATTTTGT
64 TAATTGAGACCCCTAATTTTGT
66234 AATCTCAC-TTTTAACTTTATAATTGAGACCCCTAAGTTTTTTCAATCTCAATTTATACCTTTAT
1 AATCTCACTTTTTAACTTTATAATTGAGACCCCTAAGTTTTTTCAA-CTCAATTTATACCTTTAT
** *
66298 AATTGAGATTCCTAATTTTTT
65 AATTGAGACCCCTAATTTTGT
* * * * *
66319 AATCTCACTTTCTAACTTTCTAATCGAGGCCCCTAAGTTTTTTCGATCTCAA-TTATACCTTTAT
1 AATCTCACTTTTTAACTTTATAATTGAGACCCCTAAGTTTTTTC-AACTCAATTTATACCTTTAT
66383 AATTGAG
65 AATTGAG
66390 GCCTCTATTT
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
84 31 0.23
85 62 0.46
86 42 0.31
87 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (85 bp):
AATCTCACTTTTTAACTTTATAATTGAGACCCCTAAGTTTTTTCAACTCAATTTATACCTTTATA
ATTGAGACCCCTAATTTTGT
Found at i:66296 original size:128 final size:127
Alignment explanation
Indices: 66146--66451 Score: 293
Period size: 128 Copynumber: 2.4 Consensus size: 127
66136 CTTAATATTA
* * * *
66146 TTCAATCTTACTTTTTATCTTTATAATTGAAGTCTCTAATTTTTTTCAATCACTTTCTTACCTTT
1 TTCAATC-TAATTTATACCTTTATAATTGAAGTCTCTAATTTTTTTCAATCACTTTC-TAACTTT
* * *
66211 ATAATTGAGACCCCTAA-TTTTGT-AATCTCACTTTTAACTTTATAATTGAGACCCCTAAGTTTT
64 ATAATCGAGACCCCTAAGTTTTGTCAATCTCAATTATAACTTTATAATTGAGACCCCT-AGTTTT
*
66274 TTCAATCTCAATTTATACCTTTATAATTGAGATTC-CTAA-TTTTTT-AATCTCACTTTCTAACT
1 TTCAATCT-AATTTATACCTTTATAATTGA-AGTCTCTAATTTTTTTCAA--TCACTTTCTAACT
* * * * * * * *
66336 TTCTAATCGAGGCCCCTAAGTTTTTTCGATCTCAATTATACCTTTATAATTGAGGCCTCTATTTT
62 TTATAATCGAGACCCCTAAGTTTTGTCAATCTCAATTATAACTTTATAATTGAGACCCCTAGTTT
66401 T
127 T
* * * *
66402 TTAAATATAGATTTCTACCTTTATAATT-AATGCCTCT-ATTTTTTTACAAT
1 TTCAATCTA-ATTTATACCTTTATAATTGAA-GTCTCTAATTTTTTT-CAAT
66452 TTCATAAAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
126 3 0.02
127 31 0.21
128 79 0.54
129 30 0.21
130 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (127 bp):
TTCAATCTAATTTATACCTTTATAATTGAAGTCTCTAATTTTTTTCAATCACTTTCTAACTTTAT
AATCGAGACCCCTAAGTTTTGTCAATCTCAATTATAACTTTATAATTGAGACCCCTAGTTTT
Found at i:66417 original size:86 final size:86
Alignment explanation
Indices: 66204--66428 Score: 269
Period size: 85 Copynumber: 2.6 Consensus size: 86
66194 ATCACTTTCT
* * * * *
66204 TACCTTTATAATTGAGACCCCTAATTTTGTAATCTCACTTT-TAACTTTATAATTGAGACCCCTA
1 TACCTTTATAATTGAGACTCCTAATTTTTTAATATCAATTTCTAACTTTATAATCGAGACCCCTA
66268 AGTTTTTTCAATCTCAATTTA
66 AGTTTTTTCAATCTCAATTTA
* * * * *
66289 TACCTTTATAATTGAGATTCCTAATTTTTTAATCTCACTTTCTAACTTTCTAATCGAGGCCCCTA
1 TACCTTTATAATTGAGACTCCTAATTTTTTAATATCAATTTCTAACTTTATAATCGAGACCCCTA
*
66354 AGTTTTTTCGATCTCAA-TTA
66 AGTTTTTTCAATCTCAATTTA
* * *
66374 TACCTTTATAATTGAGGC-CTCTATTTTTTTAAATAT-AGATTTCTACCTTTATAAT
1 TACCTTTATAATTGAGACTC-CTAATTTTTT-AATATCA-ATTTCTAACTTTATAAT
66429 TAATGCCTCT
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 67 0.55
86 54 0.44
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (86 bp):
TACCTTTATAATTGAGACTCCTAATTTTTTAATATCAATTTCTAACTTTATAATCGAGACCCCTA
AGTTTTTTCAATCTCAATTTA
Found at i:68396 original size:10 final size:10
Alignment explanation
Indices: 68381--68422 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
68371 TTAAATCAAT
*
68381 ATATTTTATA
1 ATATTTAATA
68391 ATATTTAATA
1 ATATTTAATA
68401 ATATTTAAT-
1 ATATTTAATA
68410 A-ATTTAATA
1 ATATTTAATA
68419 ATAT
1 ATAT
68423 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.24
9 2 0.07
10 20 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATTTAATA
Found at i:68428 original size:13 final size:13
Alignment explanation
Indices: 68412--68436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68402 TATTTAATAA
68412 TTTAATAATATAT
1 TTTAATAATATAT
68425 TTTAATAATATA
1 TTTAATAATATA
68437 AAAATAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAATAATATAT
Found at i:68430 original size:10 final size:9
Alignment explanation
Indices: 68378--68433 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 9
68368 ATGTTAAATC
68378 AATATATTTT
1 AATA-ATTTT
68388 -ATAATATTT
1 AATAAT-TTT
68397 AATAATATTT
1 AATAAT-TTT
68407 AATAATTTAAT
1 AATAATTT--T
68418 AATATATTTT
1 AATA-ATTTT
68428 AATAAT
1 AATAAT
68434 ATAAAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.05
9 10 0.24
10 20 0.49
11 5 0.12
12 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATAATTTT
Found at i:68430 original size:18 final size:18
Alignment explanation
Indices: 68389--68422 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
68379 ATATATTTTA
68389 TAAT-ATTTAATAATATT
1 TAATAATTTAATAATATT
68406 TAATAATTTAATAATAT
1 TAATAATTTAATAATAT
68423 ATTTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTAATAATATT
Found at i:68433 original size:41 final size:41
Alignment explanation
Indices: 68334--68435 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 41
68324 TATATTTTAG
*
68334 AATAATATATTTGTAAT--TATTTATTATATTTAAAATGTTA
1 AATAATATATTT-TAATAATATTTATAATATTTAAAATGTTA
68374 AATCAATATATTTT-ATAATATTTAATAATATTTAATAAT-TT-
1 AAT-AATATATTTTAATAATATTT-ATAATATTTAA-AATGTTA
68415 AATAATATATTTTAATAATAT
1 AATAATATATTTTAATAATAT
68436 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
39 2 0.04
40 14 0.25
41 24 0.44
42 12 0.22
43 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
AATAATATATTTTAATAATATTTATAATATTTAAAATGTTA
Found at i:68437 original size:18 final size:18
Alignment explanation
Indices: 68378--68437 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 18
68368 ATGTTAAATC
68378 AATATATTTT-ATAATATTT
1 AATATATTTTAATAATA--T
68397 AATA-ATATTTAATAATTTAAT
1 AATATAT-TTTAATAA--T-AT
68418 AATATATTTTAATAATAT
1 AATATATTTTAATAATAT
68436 AA
1 AA
68438 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 4 0.11
21 13 0.37
22 3 0.09
23 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATATTTTAATAATAT
Found at i:70589 original size:2 final size:2
Alignment explanation
Indices: 70582--70666 Score: 53
Period size: 2 Copynumber: 47.0 Consensus size: 2
70572 GAAAATATTT
* * *
70582 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
70618 TA TA TA TA TA TA TA -A T- TA -A TA TA AA AA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70657 TA TA TA TA TA
1 TA TA TA TA TA
70667 ATAGGGGAGG
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
1 9 0.14
2 57 0.86
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:70668 original size:35 final size:35
Alignment explanation
Indices: 70600--70664 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
70590 ATTAATATAA
*
70600 AATATATAAAATATTACATATATATATATATAATT
1 AATATATAAAATATAACATATATATATATATAATT
70635 AATATA-AAAATATAA-ATATATATATATATA
1 AATATATAAAATATAACATATATATATATATA
70665 TAATAGGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 15 0.52
34 8 0.28
35 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATATAAAATATAACATATATATATATATAATT
Found at i:74318 original size:26 final size:25
Alignment explanation
Indices: 74268--74319 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
74258 ATCTCATAAT
* *
74268 TTTATTTATTTTTAATTTTTTAAAA
1 TTTATTTATTTTTAATTATTAAAAA
74293 TTTATTTACTTTTTGAA-TATTAAAAA
1 TTTATTTA-TTTTT-AATTATTAAAAA
74319 T
1 T
74320 GATATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 8 0.35
26 13 0.57
27 2 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTATTTATTTTTAATTATTAAAAA
Done.