Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 130 of 135
Found at i:39673307 original size:24 final size:23
Alignment explanation
Indices: 39673273--39673328 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
39673263 TCCTCCTCCC
*
39673273 ACTTCTTCACCGCCCCCAGTTACA
1 ACTTCTCCACC-CCCCCAGTTACA
*
39673297 ACTTCTCCA--CCCCCAGTTTCA
1 ACTTCTCCACCCCCCCAGTTACA
*
39673318 ACTCCTCCACC
1 ACTTCTCCACC
39673329 TGCTTCTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 19 0.70
24 8 0.30
ACGTcount: A:0.20, C:0.50, G:0.05, T:0.25
Consensus pattern (23 bp):
ACTTCTCCACCCCCCCAGTTACA
Found at i:39673309 original size:21 final size:21
Alignment explanation
Indices: 39673285--39673328 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39673275 TTCTTCACCG
*
39673285 CCCCCAGTTACAACTTCTCCA
1 CCCCCAGTTACAACTCCTCCA
*
39673306 CCCCCAGTTTCAACTCCTCCA
1 CCCCCAGTTACAACTCCTCCA
39673327 CC
1 CC
39673329 TGCTTCTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.52, G:0.05, T:0.23
Consensus pattern (21 bp):
CCCCCAGTTACAACTCCTCCA
Found at i:39673342 original size:15 final size:15
Alignment explanation
Indices: 39673327--39673451 Score: 97
Period size: 15 Copynumber: 8.3 Consensus size: 15
39673317 AACTCCTCCA
* *
39673327 CCTGCTTCTCCACCA
1 CCTGCTACTCCACCT
*
39673342 CCTGCTTCTCCACCT
1 CCTGCTACTCCACCT
* *
39673357 CCCGCTACTCCTCCT
1 CCTGCTACTCCACCT
*
39673372 CCTGCAACTCCACCT
1 CCTGCTACTCCACCT
* *
39673387 CCAGCTTCTCCACCT
1 CCTGCTACTCCACCT
* * * *
39673402 CCAGCCACTCCTCCA
1 CCTGCTACTCCACCT
* *
39673417 CCAGCTTCTCCACCT
1 CCTGCTACTCCACCT
* * *
39673432 CCCGCCACTCCACCA
1 CCTGCTACTCCACCT
39673447 CCTGC
1 CCTGC
39673452 AACCCCACCA
Statistics
Matches: 87, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 87 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.22
Consensus pattern (15 bp):
CCTGCTACTCCACCT
Found at i:39673445 original size:45 final size:45
Alignment explanation
Indices: 39673318--39673433 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 45
39673308 CCCAGTTTCA
* * * *
39673318 ACTCCTCCACCTGCTTCTCCACCACCTGCTTCTCCACCTCCCGCT
1 ACTCCTCCACCTGCTTCTCCACCTCCAGCTTCTCCACCTCCAGCC
* **
39673363 ACTCCTCCTCCTGCAACTCCACCTCCAGCTTCTCCACCTCCAGCC
1 ACTCCTCCACCTGCTTCTCCACCTCCAGCTTCTCCACCTCCAGCC
*
39673408 ACTCCTCCACCAGCTTCTCCACCTCC
1 ACTCCTCCACCTGCTTCTCCACCTCC
39673434 CGCCACTCCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.14, C:0.56, G:0.06, T:0.24
Consensus pattern (45 bp):
ACTCCTCCACCTGCTTCTCCACCTCCAGCTTCTCCACCTCCAGCC
Found at i:39673448 original size:30 final size:30
Alignment explanation
Indices: 39673318--39673448 Score: 136
Period size: 30 Copynumber: 4.4 Consensus size: 30
39673308 CCCAGTTTCA
* * * *
39673318 ACTCCTCCACCTGCTTCTCCACCACCTGCT
1 ACTCCACCACCAGCTTCTCCACCTCCTGCC
* * * * * *
39673348 TCTCCACCTCCCGCTACTCCTCCTCCTGCA
1 ACTCCACCACCAGCTTCTCCACCTCCTGCC
* *
39673378 ACTCCACCTCCAGCTTCTCCACCTCCAGCC
1 ACTCCACCACCAGCTTCTCCACCTCCTGCC
* *
39673408 ACTCCTCCACCAGCTTCTCCACCTCCCGCC
1 ACTCCACCACCAGCTTCTCCACCTCCTGCC
39673438 ACTCCACCACC
1 ACTCCACCACC
39673449 TGCAACCCCA
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.15, C:0.57, G:0.06, T:0.22
Consensus pattern (30 bp):
ACTCCACCACCAGCTTCTCCACCTCCTGCC
Found at i:39673460 original size:30 final size:30
Alignment explanation
Indices: 39673369--39673511 Score: 79
Period size: 30 Copynumber: 4.8 Consensus size: 30
39673359 CGCTACTCCT
* * * ** *
39673369 CCTCCTGCAACTCCACCTCCAGCTTCTCCA
1 CCTCCAGCCACTCCACCACCAGCAACCCCA
* ** *
39673399 CCTCCAGCCACTCCTCCACCAGCTTCTCCA
1 CCTCCAGCCACTCCACCACCAGCAACCCCA
* *
39673429 CCTCCCGCCACTCCACCACCTGCAACCCCA
1 CCTCCAGCCACTCCACCACCAGCAACCCCA
* ** * * * * *
39673459 CCACCAGTAACTCCTCCACCGGCAGCTCCT
1 CCTCCAGCCACTCCACCACCAGCAACCCCA
* * *
39673489 CCTCCTGCTACCCCACCACCAGC
1 CCTCCAGCCACTCCACCACCAGC
39673512 TCCATTGGCT
Statistics
Matches: 87, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.18, C:0.57, G:0.08, T:0.17
Consensus pattern (30 bp):
CCTCCAGCCACTCCACCACCAGCAACCCCA
Found at i:39674734 original size:21 final size:21
Alignment explanation
Indices: 39674701--39674743 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
39674691 GAATCCTTTG
39674701 TTTAATCGATTGA-TTAATTA
1 TTTAATCGATTGATTTAATTA
39674721 TTTAATCTGATTGATTTAATTA
1 TTTAATC-GATTGATTTAATTA
39674743 T
1 T
39674744 CGGTACGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTAATCGATTGATTTAATTA
Found at i:39683402 original size:22 final size:25
Alignment explanation
Indices: 39683356--39683404 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
39683346 TATTTCAGTA
39683356 AAAAATTACATCTATTTTTATTGTT
1 AAAAATTACATCTATTTTTATTGTT
*
39683381 AAAAATTA-GTCT-TTTTTA-TGTT
1 AAAAATTACATCTATTTTTATTGTT
39683403 AA
1 AA
39683405 CATGAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 6 0.26
24 3 0.13
25 8 0.35
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
AAAAATTACATCTATTTTTATTGTT
Found at i:39687057 original size:22 final size:22
Alignment explanation
Indices: 39687015--39687057 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39687005 AACCATCCCT
* *
39687015 AATTTATTTATTTTTATTTAAG
1 AATTTATTTATTTTAAATTAAG
39687037 AATTTAATTT-TTTTAAATTAA
1 AATTT-ATTTATTTTAAATTAA
39687058 TAAAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTATTTATTTTAAATTAAG
Found at i:39687778 original size:21 final size:22
Alignment explanation
Indices: 39687738--39687788 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
39687728 TTGAAATCTG
* *
39687738 AAAATAAAAAGATTAAAATTCTA
1 AAAAT-AAAAGATAAAAATTATA
39687761 AAAATAAAA-ATAAAAATTATA
1 AAAATAAAAGATAAAAATTATA
*
39687782 AATATAA
1 AAAATAA
39687789 CTAAAATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATAAAAGATAAAAATTATA
Found at i:39688108 original size:14 final size:14
Alignment explanation
Indices: 39688052--39688113 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
39688042 TAACAAAATT
39688052 AATAATAA-AATAA
1 AATAATAATAATAA
39688065 AATTTATATAAT-ATCAA
1 AA--TA-ATAATAAT-AA
*
39688082 AATAATAACAATAA
1 AATAATAATAATAA
*
39688096 AATAATAATAATAT
1 AATAATAATAATAA
39688110 AATA
1 AATA
39688114 TTAAAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
13 2 0.05
14 22 0.55
15 6 0.15
16 6 0.15
17 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:39700454 original size:6 final size:6
Alignment explanation
Indices: 39700443--39700467 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39700433 CCAAAGGAAG
39700443 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
39700468 TATAGCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:39702017 original size:21 final size:21
Alignment explanation
Indices: 39701965--39702017 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
39701955 TATAAAAAAT
39701965 ATTATATTAATTATATATTTAA
1 ATTATATT-ATTATATATTTAA
*
39701987 ATAATAATTA-TATATATTTATA
1 ATTAT-ATTATTATATATTTA-A
*
39702009 TTTATATTA
1 ATTATATTA
39702018 AATCACTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATATTATTATATATTTAA
Found at i:39702482 original size:31 final size:31
Alignment explanation
Indices: 39702417--39702486 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
39702407 TGTATGAGTC
* *
39702417 TGGTACTTGAGTTTGGTTTCAATGTTCATCT
1 TGGTACTTGAGTTTAGTTTCAATGTTAATCT
* *
39702448 TGGTACTTGAGTTTAGTTTTAATATTTAAT-T
1 TGGTACTTGAGTTTAGTTTCAAT-GTTAATCT
39702479 TGGTACTT
1 TGGTACTT
39702487 AAATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (31 bp):
TGGTACTTGAGTTTAGTTTCAATGTTAATCT
Found at i:39702903 original size:2 final size:2
Alignment explanation
Indices: 39702896--39702932 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39702886 GGGAGGAGGC
39702896 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39702933 TCTTCAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39707764 original size:59 final size:57
Alignment explanation
Indices: 39707650--39707766 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 57
39707640 CAATTATGAT
39707650 ATCATTCGTGATAAGGATTGCTATATAAGGACTTGGATTTAAACCCAATGCGGCACA
1 ATCATTCGTGATAAGGATTGCTATATAAGGACTTGGATTTAAACCCAATGCGGCACA
* * *
39707707 ATCATT-GTGATAAGGATTGCTATATAAAGAGGACTTTGATTTAAACCCGATGTGGCACA
1 ATCATTCGTGATAAGGATTGCTATAT--A-AGGACTTGGATTTAAACCCAATGCGGCACA
39707766 A
1 A
39707767 CTTTGACTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
56 19 0.35
57 6 0.11
58 1 0.02
59 28 0.52
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (57 bp):
ATCATTCGTGATAAGGATTGCTATATAAGGACTTGGATTTAAACCCAATGCGGCACA
Found at i:39709127 original size:66 final size:66
Alignment explanation
Indices: 39709021--39709176 Score: 258
Period size: 66 Copynumber: 2.4 Consensus size: 66
39709011 AAACAGGCGG
* *
39709021 TTTTCATAGGAGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTACCATGGG
1 TTTTCAGAGGAGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
39709086 A
66 A
* *
39709087 TTTTCAGAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTATCTCTTCTTAACATGGG
1 TTTTCAGAGGAGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
*
39709152 G
66 A
*
39709153 TTTTCAGAGGTGGTTTCCTCCATG
1 TTTTCAGAGGAGGTTTCCTCCATG
39709177 TCCTCCATGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (66 bp):
TTTTCAGAGGAGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
A
Found at i:39710407 original size:16 final size:16
Alignment explanation
Indices: 39710383--39710413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39710373 TTGATGTTTT
39710383 GACTCGTTTCAACTTC
1 GACTCGTTTCAACTTC
*
39710399 GACTTGTTTCAACTT
1 GACTCGTTTCAACTT
39710414 AGTACCGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (16 bp):
GACTCGTTTCAACTTC
Found at i:39715660 original size:45 final size:45
Alignment explanation
Indices: 39715596--39715689 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
39715586 TTTGTCTTTC
* * *
39715596 TTAAATGGCGAGTTTTGTCTGTTTATATGATACGAATACTGTTCA
1 TTAAATAGCGAGTTTTGTCTATTTATATGATACGAATACTATTCA
*
39715641 TTAAATAGCGAGTTTTGTCTATTTATATGATACGAATGCTATTCA
1 TTAAATAGCGAGTTTTGTCTATTTATATGATACGAATACTATTCA
39715686 TTAA
1 TTAA
39715690 TATAATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (45 bp):
TTAAATAGCGAGTTTTGTCTATTTATATGATACGAATACTATTCA
Found at i:39724277 original size:27 final size:28
Alignment explanation
Indices: 39724233--39724288 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
39724223 CATAAGTTTA
39724233 TTGAGAAAAAAAATAAAAATTAAACCAT
1 TTGAGAAAAAAAATAAAAATTAAACCAT
39724261 TTGAG-AAAAAAATAAAAATTAAACCAT
1 TTGAGAAAAAAAATAAAAATTAAACCAT
39724288 T
1 T
39724289 CTTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (28 bp):
TTGAGAAAAAAAATAAAAATTAAACCAT
Found at i:39727880 original size:16 final size:16
Alignment explanation
Indices: 39727859--39727892 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39727849 GAGTAAACGT
39727859 GGAAGAAAG-GAAGAAG
1 GGAAGAAAGTG-AGAAG
39727875 GGAAGAAAGTGAGAAG
1 GGAAGAAAGTGAGAAG
39727891 GG
1 GG
39727893 GCAAAGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (16 bp):
GGAAGAAAGTGAGAAG
Found at i:39730693 original size:76 final size:76
Alignment explanation
Indices: 39730580--39730758 Score: 340
Period size: 76 Copynumber: 2.4 Consensus size: 76
39730570 TGTGAGGACG
*
39730580 GATAAAATTTAAATTTGTGTAATCTAAATATTTTAAAAGTATTTATCATACAATATTTAAAAGGA
1 GATAAAATTTAAATTCGTGTAATCTAAATATTTTAAAAGTATTTATCATACAATATTTAAAAGGA
39730645 GGAAAGGGGAT
66 GGAAAGGGGAT
*
39730656 GATAAAATTTAAATTCGTATAATCTAAATATTTTAAAAGTATTTATCATACAATATTTAAAAGGA
1 GATAAAATTTAAATTCGTGTAATCTAAATATTTTAAAAGTATTTATCATACAATATTTAAAAGGA
39730721 GGAAAGGGGAT
66 GGAAAGGGGAT
39730732 GATAAAATTTAAATTCGTGTAATCTAA
1 GATAAAATTTAAATTCGTGTAATCTAA
39730759 CACATATACA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 100 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (76 bp):
GATAAAATTTAAATTCGTGTAATCTAAATATTTTAAAAGTATTTATCATACAATATTTAAAAGGA
GGAAAGGGGAT
Found at i:39731527 original size:21 final size:19
Alignment explanation
Indices: 39731478--39731531 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
39731468 TAAAAATATT
*
39731478 TAAAAGATTTAAAATAAATA
1 TAAAA-ATTTAAAATAAAAA
*
39731498 TAAATATTTAAAACTAAACAA
1 TAAAAATTTAAAA-TAAA-AA
39731519 TAAAAATTTAAAA
1 TAAAAATTTAAAA
39731532 GTTAATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.28
20 8 0.28
21 13 0.45
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAATTTAAAATAAAAA
Found at i:39735604 original size:22 final size:22
Alignment explanation
Indices: 39735546--39735605 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 22
39735536 GTAATTTAGC
*
39735546 TTTTTTAATTCATTTAATAATCTA
1 TTTTTTAATT-ATTT-ATAATATA
39735570 -TTTTTAA--A--TATAATATA
1 TTTTTTAATTATTTATAATATA
39735587 TTTTTTAATTATTTATAAT
1 TTTTTTAATTATTTATAAT
39735606 TAACATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
20 2 0.07
22 6 0.20
23 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTTAATTATTTATAATATA
Found at i:39748823 original size:18 final size:19
Alignment explanation
Indices: 39748786--39748823 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39748776 TCCCTTATGG
* *
39748786 TCTAGATTTTAAATTGTTT
1 TCTAAATTTCAAATTGTTT
39748805 TCTAAATTTCAAA-TGTTT
1 TCTAAATTTCAAATTGTTT
39748823 T
1 T
39748824 AATTGAGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (19 bp):
TCTAAATTTCAAATTGTTT
Found at i:39757639 original size:27 final size:28
Alignment explanation
Indices: 39757609--39757663 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
39757599 TTAATAGAGT
39757609 TGATGGTTTGCAC-ATATTAAAATATTA
1 TGATGGTTTGCACAATATTAAAATATTA
*
39757636 TGATGGTTTGCACAAATATTAAGATATT
1 TGATGGTTTGCAC-AATATTAAAATATT
39757664 CATTTACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.52
29 12 0.48
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (28 bp):
TGATGGTTTGCACAATATTAAAATATTA
Found at i:39761652 original size:5 final size:5
Alignment explanation
Indices: 39761644--39761685 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
39761634 ACTTTTTCAC
*
39761644 TCATA TCATA TTATA TCATA TCATA TCATA TCATA TCATA TC
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TC
39761686 TCTACTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (5 bp):
TCATA
Found at i:39762622 original size:21 final size:19
Alignment explanation
Indices: 39762598--39762636 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
39762588 TACGTTGTTG
39762598 TAAATGATTCTATTTTTTTTT
1 TAAATGA-TCT-TTTTTTTTT
*
39762619 TAAATTATCTTTTTTTTT
1 TAAATGATCTTTTTTTTT
39762637 ACTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (19 bp):
TAAATGATCTTTTTTTTTT
Found at i:39765739 original size:31 final size:30
Alignment explanation
Indices: 39765695--39765752 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
39765685 TTTTAAATTT
39765695 TTTAAAATATTTAT-ATTATTTTAATTTAATA
1 TTTAAAATATTTATAATT-TTTT-ATTTAATA
39765726 TTTAATAAT-TTTATAATTTTTTATTTA
1 TTTAA-AATATTTATAATTTTTTATTTA
39765753 TTGAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 5 0.20
31 14 0.56
32 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTAAAATATTTATAATTTTTTATTTAATA
Found at i:39770006 original size:17 final size:16
Alignment explanation
Indices: 39769984--39770024 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
39769974 GTAATTTTTA
39769984 TAATAATTTTATCATTT
1 TAATAATTTTAT-ATTT
39770001 TAATAA--TTATATTT
1 TAATAATTTTATATTT
39770015 TAATAATTTT
1 TAATAATTTT
39770025 TAAATGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 2 0.09
17 6 0.27
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATAATTTTATATTT
Found at i:39770532 original size:26 final size:24
Alignment explanation
Indices: 39770503--39770570 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
39770493 ATCATTAATA
39770503 AATAAACGAGAATTTATAAACGAGTC
1 AATAAACGA-AATTT-TAAACGAGTC
* *
39770529 AATAAATGAACTTTTAAACGAGTC
1 AATAAACGAAATTTTAAACGAGTC
**
39770553 AATAAATAAAATTTTAAA
1 AATAAACGAAATTTTAAA
39770571 TGATCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 26 0.68
25 4 0.11
26 8 0.21
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (24 bp):
AATAAACGAAATTTTAAACGAGTC
Found at i:39770551 original size:24 final size:24
Alignment explanation
Indices: 39770513--39770570 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
39770503 AATAAACGAG
*
39770513 AATTTATAAACGAGTCAATAAATGA
1 AATTT-TAAACGAGTCAATAAATAA
*
39770538 ACTTTTAAACGAGTCAATAAATAA
1 AATTTTAAACGAGTCAATAAATAA
39770562 AATTTTAAA
1 AATTTTAAA
39770571 TGATCTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (24 bp):
AATTTTAAACGAGTCAATAAATAA
Found at i:39783132 original size:9 final size:9
Alignment explanation
Indices: 39783082--39783265 Score: 90
Period size: 10 Copynumber: 19.0 Consensus size: 9
39783072 TTTTATGATT
39783082 TTTTTATATA
1 TTTTTATA-A
39783092 CTTTTTATAA
1 -TTTTTATAA
* *
39783102 GCTTATATGAA
1 -TTTTTAT-AA
*
39783113 TTTTAAT-A
1 TTTTTATAA
39783121 TTTTTATAA
1 TTTTTATAA
*
39783130 TTTTGTTATATT
1 -TTT-TTATA-A
*
39783142 TTTTTATGA
1 TTTTTATAA
39783151 TTTTTA-AGA
1 TTTTTATA-A
*
39783160 TTTCTACTACA
1 TTTTTA-TA-A
39783171 TTTTTATAA
1 TTTTTATAA
39783180 TATTTTA-ATA
1 T-TTTTATA-A
39783190 TGTTTTATTATTA
1 T-TTTTA-TA--A
39783203 TTTTT-TAA
1 TTTTTATAA
*
39783211 ATTTTATAA
1 TTTTTATAA
*
39783220 TTTATTAGAA
1 TTT-TTATAA
39783230 TTTTTAT-A
1 TTTTTATAA
39783238 TTTTTATAA
1 TTTTTATAA
*
39783247 TATTTATAA
1 TTTTTATAA
39783256 GTTTTTATAA
1 -TTTTTATAA
39783266 CTTTAAATCA
Statistics
Matches: 135, Mismatches: 21, Indels: 35
0.71 0.11 0.18
Matches are distributed among these distances:
8 20 0.15
9 33 0.24
10 49 0.36
11 25 0.19
12 5 0.04
13 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:39783222 original size:17 final size:18
Alignment explanation
Indices: 39783197--39783262 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
39783187 ATATGTTTTA
*
39783197 TTATTATTTTTTA-AATT
1 TTATAATTTTTTAGAATT
*
39783214 TTATAATTTATTAGAATT
1 TTATAATTTTTTAGAATT
*
39783232 TT-T-ATATTTTTATAATAT
1 TTATAAT-TTTTTAGAAT-T
*
39783250 TTATAAGTTTTTA
1 TTATAATTTTTTA
39783263 TAACTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.05
17 20 0.51
18 9 0.23
19 7 0.18
20 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATAATTTTTTAGAATT
Found at i:39783232 original size:27 final size:27
Alignment explanation
Indices: 39783204--39783270 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
39783194 TTATTATTAT
39783204 TTTTTA-AATTTTATAATTTATTAGAA
1 TTTTTATAATTTTATAATTTATTAGAA
* * *
39783230 TTTTTATATTTTTATAATAT-TTATAA
1 TTTTTATAATTTTATAATTTATTAGAA
*
39783256 GTTTTTATAACTTTA
1 -TTTTTATAATTTTA
39783271 AATCAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTTTATAATTTTATAATTTATTAGAA
Found at i:39783236 original size:19 final size:18
Alignment explanation
Indices: 39783204--39783262 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
39783194 TTATTATTAT
39783204 TTTTTA-AA-TTTTATAA
1 TTTTTAGAATTTTTATAA
39783220 TTTATTAGAATTTTTAT-A
1 TTT-TTAGAATTTTTATAA
* *
39783238 TTTTTATAATATTTATAA
1 TTTTTAGAATTTTTATAA
39783256 GTTTTTA
1 -TTTTTA
39783263 TAACTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.08
17 14 0.39
18 7 0.19
19 12 0.33
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTAGAATTTTTATAA
Found at i:39783263 original size:19 final size:17
Alignment explanation
Indices: 39783083--39783270 Score: 68
Period size: 18 Copynumber: 10.3 Consensus size: 17
39783073 TTTATGATTT
39783083 TTTTATATACTTTTTATAA
1 TTTTATA-A-TTTTTATAA
* * *
39783102 GCTTATATGAATTTTAATAT
1 --TTTTAT-AATTTTTATAA
*
39783122 TTTTATAATTTTGTTATATTT
1 TTTTATAA-TTT-TTATA--A
*
39783143 TTTTATGATTTTTA-AGA
1 TTTTATAATTTTTATA-A
39783160 TTTCTACTACATTTTTATAA
1 TTT-TA-TA-ATTTTTATAA
39783180 TATTT-TAATATGTTT-T-A
1 T-TTTATAAT-T-TTTATAA
39783197 TTATTAT--TTTTTA-AA
1 TT-TTATAATTTTTATAA
*
39783212 TTTTATAATTTATTAGAA
1 TTTTATAATTT-TTATAA
39783230 TTTT-TATATTTTTATAA
1 TTTTATA-ATTTTTATAA
39783247 TATTTATAAGTTTTTATAA
1 T-TTTATAA-TTTTTATAA
*
39783266 CTTTA
1 TTTTA
39783271 AATCAATTTT
Statistics
Matches: 132, Mismatches: 11, Indels: 51
0.68 0.06 0.26
Matches are distributed among these distances:
14 7 0.05
15 4 0.03
16 5 0.04
17 22 0.17
18 34 0.26
19 22 0.17
20 20 0.15
21 17 0.13
22 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTATAATTTTTATAA
Found at i:39789109 original size:16 final size:17
Alignment explanation
Indices: 39789088--39789121 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39789078 AATAAGTCCT
*
39789088 CCATTTT-AGTTTTACC
1 CCATTTTAAGTTTCACC
39789104 CCATTTTAAGTTTCACC
1 CCATTTTAAGTTTCACC
39789121 C
1 C
39789122 ACCTACAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.29, G:0.06, T:0.44
Consensus pattern (17 bp):
CCATTTTAAGTTTCACC
Found at i:39790301 original size:21 final size:20
Alignment explanation
Indices: 39790234--39790315 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
39790224 TAAAAAGTTT
39790234 AAATTAAATTATAATTTTTATGA
1 AAATTAAATTA-AATTTTTA--A
* * * *
39790257 TAATAAAAATATAA-TTTTAT
1 AAATTAAATTA-AATTTTTAA
*
39790277 AATTTAAA-TAATATTTTTAA
1 AAATTAAATTAA-ATTTTTAA
39790297 AAATTAAATTAAATTTTTA
1 AAATTAAATTAAATTTTTA
39790316 TTATTTTTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 24 0.51
21 3 0.06
22 5 0.11
23 11 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTAAATTAAATTTTTAA
Found at i:39790317 original size:26 final size:30
Alignment explanation
Indices: 39790288--39790352 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
39790278 ATTTAAATAA
39790288 TATTTTTA-A-AAATTAAATTA-AATTTTTAT
1 TATTTTTAGAGAAATTAAATTATAA--TTTAT
*
39790317 TATTTTTAGAGAGATTAAATTATAA-TT-T
1 TATTTTTAGAGAAATTAAATTATAATTTAT
39790345 TATTTTTA
1 TATTTTTA
39790353 TTAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 9 0.28
29 10 0.31
30 1 0.03
31 10 0.31
32 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
TATTTTTAGAGAAATTAAATTATAATTTAT
Found at i:39791539 original size:17 final size:17
Alignment explanation
Indices: 39791517--39791549 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39791507 TCATCCCAGA
39791517 TGTGATTTGAATTCGAT
1 TGTGATTTGAATTCGAT
39791534 TGTGATTTGAATTCGA
1 TGTGATTTGAATTCGA
39791550 CTCAAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (17 bp):
TGTGATTTGAATTCGAT
Found at i:39792184 original size:20 final size:20
Alignment explanation
Indices: 39792161--39792203 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
39792151 TCAAATGTTG
39792161 GTCCATAAATTGTGGATTTA
1 GTCCATAAATTGTGGATTTA
39792181 GTCCATAAATTGTGGATTTA
1 GTCCATAAATTGTGGATTTA
39792201 GTC
1 GTC
39792204 TCTATCGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (20 bp):
GTCCATAAATTGTGGATTTA
Found at i:39797271 original size:22 final size:22
Alignment explanation
Indices: 39797246--39797296 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
39797236 TTTAGAGTTT
39797246 AATTTTATATTTTATTTTTAAG
1 AATTTTATATTTTATTTTTAAG
* * *
39797268 AATTTATTTGTTTTATTTTTCAG
1 AATTT-TATATTTTATTTTTAAG
39797291 -ATTTTA
1 AATTTTA
39797297 AAATTTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 9 0.38
23 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (22 bp):
AATTTTATATTTTATTTTTAAG
Found at i:39800466 original size:55 final size:55
Alignment explanation
Indices: 39800398--39800587 Score: 238
Period size: 55 Copynumber: 3.5 Consensus size: 55
39800388 AAAAAAATTC
* ** ** *
39800398 TACTCTA-CAAAGTAAAACCTAAATATCAGACACACCTTTATCTACCGCCAACACT
1 TACTCTATC-AAGTAAAACCTAAATATCATACACACCTTCCTCCGCCACCAACACT
* * *
39800453 TACTCTATCAAGTAAAACTTAAATATCATACACACCTCCCTCCGCCACCGACACT
1 TACTCTATCAAGTAAAACCTAAATATCATACACACCTTCCTCCGCCACCAACACT
* *
39800508 TACCCTATCAAGTAAAACCTAAATATCATACACACATTCCTCCGCCACCAACACT
1 TACTCTATCAAGTAAAACCTAAATATCATACACACCTTCCTCCGCCACCAACACT
* * *
39800563 TACTATATTAAGTAAAACTTAAATA
1 TACTCTATCAAGTAAAACCTAAATA
39800588 CATTAAGTAA
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
55 115 0.99
56 1 0.01
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.25
Consensus pattern (55 bp):
TACTCTATCAAGTAAAACCTAAATATCATACACACCTTCCTCCGCCACCAACACT
Found at i:39801312 original size:55 final size:55
Alignment explanation
Indices: 39801227--39801544 Score: 366
Period size: 55 Copynumber: 5.8 Consensus size: 55
39801217 ACACCTCTAC
* **
39801227 TCTCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATGGTACACACCTT
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
* * * * * * * * *
39801282 TCTCTGTCACCAACACTTACTTTATTAAGTAAAACATAAATATGACACAAACCTT
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
* * * * * *
39801337 TATCCGCCGCCAACACTTACTGTATCAAGTAAAACCTAAATATCATATACATCTC
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
* * * * *
39801392 TCTCTGTCGCCAACACTTAGTCTATCAAGTAAAACCTAAATATAATACACGCCTC
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
* * * * * *
39801447 TATTCGCCGCCAACAGTTACTCTATTAAATAAAACCTAAATATAATACACACCTC
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
*
39801502 TATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATAT
1 TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATAT
39801545 CTCAAGTAAA
Statistics
Matches: 220, Mismatches: 43, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 220 1.00
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.28
Consensus pattern (55 bp):
TCTCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTT
Found at i:39801432 original size:110 final size:110
Alignment explanation
Indices: 39801229--39801544 Score: 407
Period size: 110 Copynumber: 2.9 Consensus size: 110
39801219 ACCTCTACTC
* ** * *
39801229 TCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATGGTACACACCTTTCTCTGTCACCA
1 TCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTCTCTCTGTCGCCA
* * * * *
39801294 ACACTTACTTTATTAAGTAAAACATAAATATGACACAAACCTTTA
66 ACACTTACTCTATCAAGTAAAACCTAAATATAACACAAACCTCTA
* * * *
39801339 TCCGCCGCCAACACTTACTGTATCAAGTAAAACCTAAATATCATATACATCTCTCTCTGTCGCCA
1 TCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTCTCTCTGTCGCCA
* * **
39801404 ACACTTAGTCTATCAAGTAAAACCTAAATATAATACACGCCTCTA
66 ACACTTACTCTATCAAGTAAAACCTAAATATAACACAAACCTCTA
* * * * * * *
39801449 TTCGCCGCCAACAGTTACTCTATTAAATAAAACCTAAATATAATACACACCTCTATCCGCCGCCA
1 TCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTCTCTCTGTCGCCA
39801514 ACACTTACTCTATCAAGTAAAACCTAAATAT
66 ACACTTACTCTATCAAGTAAAACCTAAATAT
39801545 CTCAAGTAAA
Statistics
Matches: 177, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 177 1.00
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.28
Consensus pattern (110 bp):
TCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTCTCTCTGTCGCCA
ACACTTACTCTATCAAGTAAAACCTAAATATAACACAAACCTCTA
Found at i:39801508 original size:165 final size:165
Alignment explanation
Indices: 39801226--39801545 Score: 464
Period size: 165 Copynumber: 1.9 Consensus size: 165
39801216 AACACCTCTA
** *
39801226 CTCTCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATGGTACACACCTTTCTCTGTCA
1 CTCTCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTTTCTCTGCCA
* * * *
39801291 CCAACACTTACTTTATTAAGTAAAACATAAATATGACACAAACCTTTATCCGCCGCCAACACTTA
66 CCAACACTTACTCTATTAAATAAAACATAAATATAACACAAACCTCTATCCGCCGCCAACACTTA
*
39801356 CTGTATCAAGTAAAACCTAAATATCATATACATCT
131 CTCTATCAAGTAAAACCTAAATATCATATACATCT
* * *
39801391 CTCTCTGTCGCCAACACTTAGTCTATCAAGTAAAACCTAAATATAATACACGCCTCTAT-TC-GC
1 CTCTCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCT-T-TCTCTGC
* * * * *
39801454 CGCCAACAGTTACTCTATTAAATAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACT
64 CACCAACACTTACTCTATTAAATAAAACATAAATATAACACAAACCTCTATCCGCCGCCAACACT
39801519 TACTCTATCAAGTAAAACCTAAATATC
129 TACTCTATCAAGTAAAACCTAAATATC
39801546 TCAAGTAAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
165 133 0.97
166 3 0.02
167 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.28
Consensus pattern (165 bp):
CTCTCCGTCGCCAACACTTACTCTATCAAGTAAAACCTAAATATAATACACACCTTTCTCTGCCA
CCAACACTTACTCTATTAAATAAAACATAAATATAACACAAACCTCTATCCGCCGCCAACACTTA
CTCTATCAAGTAAAACCTAAATATCATATACATCT
Found at i:39801551 original size:20 final size:20
Alignment explanation
Indices: 39801526--39801565 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39801516 ACTTACTCTA
39801526 TCAAGTAAAACCTAAATATC
1 TCAAGTAAAACCTAAATATC
39801546 TCAAGTAAAACCTAAATATC
1 TCAAGTAAAACCTAAATATC
39801566 ATACACACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (20 bp):
TCAAGTAAAACCTAAATATC
Found at i:39801601 original size:75 final size:75
Alignment explanation
Indices: 39801476--39801620 Score: 254
Period size: 75 Copynumber: 1.9 Consensus size: 75
39801466 CTCTATTAAA
39801476 TAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAA
1 TAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAA
39801541 ATATCTCAAG
66 ATATCTCAAG
* * * *
39801551 TAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAATACTTATTCTATCAAGTAAAACCTAA
1 TAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAA
39801616 ATATC
66 ATATC
39801621 ATATACACCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.26
Consensus pattern (75 bp):
TAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAA
ATATCTCAAG
Found at i:39801630 original size:55 final size:55
Alignment explanation
Indices: 39801546--39801674 Score: 177
Period size: 55 Copynumber: 2.3 Consensus size: 55
39801536 CCTAAATATC
* * ** *
39801546 TCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAATACTTATTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACACCA
* * **
39801601 TCAAGTAAAACCTAAATATCATATACACCTTTATTTGCCGCCAACACTTACACCA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACACCA
39801656 TCAAGTAAAACCTAAATAT
1 TCAAGTAAAACCTAAATAT
39801675 TAAAAGTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.39, C:0.29, G:0.05, T:0.27
Consensus pattern (55 bp):
TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACACCA
Found at i:39801649 original size:130 final size:130
Alignment explanation
Indices: 39801416--39801935 Score: 521
Period size: 130 Copynumber: 4.0 Consensus size: 130
39801406 ACTTAGTCTA
* * * * * *
39801416 TCAAGTAAAACCTAAATATAATACACGCCTCTATTCGCCGCCAACAGTTACTCTATTAAATAAAA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAA
*
39801481 CCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATC
66 CCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATC
* * *
39801546 TCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAATACTTATTCTATCAAGTAAAA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAA
* * ** * *
39801611 CCTAAATATCATATACACCTTTATTTGCCGCCAACACTTACACCATCAAGTAAAACCTAAATAT-
66 CCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATC
* * * * *
39801675 TAAAAGTAAAACCTAAATATTATACACATCTTTATCCGCCACCAACACTTACTCTATCAAGTAAA
1 T-CAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAA
* * * ** ** ** ** * * ** * *
39801740 ACCTAAATATTTCAAGAAAAACCTAAATATGATG-C-ACACCTCCCTCT-GCCACCAACA-CTTA
65 ACCTAAATA--TC-ATACACACCTCTATCCGCCGCCAACA-CTTACTCTATCAAGTAAAACCTAA
* * *
39801801 TTCTA
126 ATATC
* * *
39801806 TCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACTCTATCAAGTAAAA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAA
* * *
39801871 CCTAAATATGATACACACCTCCT-TCCGCTGCCAACACTTATTCTATCAAGTAAAACCTAAATAT
66 CCTAAATATCATACACACCT-CTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATAT
39801935 C
130 C
39801936 ATACACACCT
Statistics
Matches: 306, Mismatches: 73, Indels: 22
0.76 0.18 0.05
Matches are distributed among these distances:
127 11 0.04
128 7 0.02
129 9 0.03
130 251 0.82
131 9 0.03
132 7 0.02
133 12 0.04
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (130 bp):
TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAA
CCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAAAACCTAAATATC
Found at i:39801682 original size:75 final size:75
Alignment explanation
Indices: 39801603--39801824 Score: 291
Period size: 75 Copynumber: 3.0 Consensus size: 75
39801593 TTATTCTATC
* * * * *
39801603 AAGTAAAACCTAAATATCATATACACCTTTATTTGCCGCCAACACTTACACCATCAAGTAAAACC
1 AAGTAAAACCTAAATATCATACACACCTTTATCTGCCACCAACACTTACTCTATCAAGTAAAACC
39801668 TAAATATTAA
66 TAAATATTAA
* * *
39801678 AAGTAAAACCTAAATATTATACACATCTTTATCCGCCACCAACACTTACTCTATCAAGTAAAACC
1 AAGTAAAACCTAAATATCATACACACCTTTATCTGCCACCAACACTTACTCTATCAAGTAAAACC
**
39801743 TAAATATTTC
66 TAAATATTAA
* * * *** *
39801753 AAGAAAAACCTAAATATGATGCACACCTCCCTCTGCCACCAACACTTATTCTATCAAGTAAAACC
1 AAGTAAAACCTAAATATCATACACACCTTTATCTGCCACCAACACTTACTCTATCAAGTAAAACC
39801818 TAAATAT
66 TAAATAT
39801825 CACATACACA
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 128 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.27
Consensus pattern (75 bp):
AAGTAAAACCTAAATATCATACACACCTTTATCTGCCACCAACACTTACTCTATCAAGTAAAACC
TAAATATTAA
Found at i:39801683 original size:20 final size:20
Alignment explanation
Indices: 39801658--39801696 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39801648 TTACACCATC
39801658 AAGTAAAACCTAAATATTAA
1 AAGTAAAACCTAAATATTAA
39801678 AAGTAAAACCTAAATATTA
1 AAGTAAAACCTAAATATTA
39801697 TACACATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (20 bp):
AAGTAAAACCTAAATATTAA
Found at i:39801760 original size:20 final size:20
Alignment explanation
Indices: 39801731--39801769 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39801721 ACTTACTCTA
*
39801731 TCAAGTAAAACCTAAATATT
1 TCAAGAAAAACCTAAATATT
39801751 TCAAGAAAAACCTAAATAT
1 TCAAGAAAAACCTAAATAT
39801770 GATGCACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (20 bp):
TCAAGAAAAACCTAAATATT
Found at i:39801848 original size:205 final size:203
Alignment explanation
Indices: 39801469--39801879 Score: 633
Period size: 205 Copynumber: 2.0 Consensus size: 203
39801459 ACAGTTACTC
*
39801469 TATTAAATAAAACCTAAATATAATACACACCTCTATCCGCCGCCAACACTTACTCTATCAAGTAA
1 TATTAAATAAAACCTAAATATAATACACACCTCTATCCGCCACCAACACTTACTCTATCAAGTAA
* * * *
39801534 AACCTAAATATCTCAAGTAAAACCTAAATATCATACACACCTCTCTCCGCCGCCAATACTTATTC
66 AACCTAAATATCTCAAGAAAAACCTAAATATCATACACACCTCCCTCCGCCACCAACACTTATTC
* * * **
39801599 TATCAAGTAAAACCTAAATATCATATACACCTTTATTTGCCGCCAACACTTACACCATCAAGTAA
131 TATCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACACCATCAAGTAA
39801664 AACCTAAA
196 AACCTAAA
* * *
39801672 TATTAAAAGTAAAACCTAAATATTATACACATCTTTATCCGCCACCAACACTTACTCTATCAAGT
1 TATT-AAA-TAAAACCTAAATATAATACACACCTCTATCCGCCACCAACACTTACTCTATCAAGT
* * * *
39801737 AAAACCTAAATATTTCAAGAAAAACCTAAATATGATGCACACCTCCCTCTGCCACCAACACTTAT
64 AAAACCTAAATATCTCAAGAAAAACCTAAATATCATACACACCTCCCTCCGCCACCAACACTTAT
* *
39801802 TCTATCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACTCTATCAAGT
129 TCTATCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACACCATCAAGT
39801867 AAAACCTAAA
194 AAAACCTAAA
39801877 TAT
1 TAT
39801880 GATACACACC
Statistics
Matches: 187, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
203 4 0.02
204 3 0.02
205 180 0.96
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (203 bp):
TATTAAATAAAACCTAAATATAATACACACCTCTATCCGCCACCAACACTTACTCTATCAAGTAA
AACCTAAATATCTCAAGAAAAACCTAAATATCATACACACCTCCCTCCGCCACCAACACTTATTC
TATCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACACCATCAAGTAA
AACCTAAA
Found at i:39801850 original size:55 final size:55
Alignment explanation
Indices: 39801751--39802101 Score: 452
Period size: 55 Copynumber: 6.4 Consensus size: 55
39801741 CCTAAATATT
* * * ** * * *
39801751 TCAAGAAAAACCTAAATATGATGCACACCTCCCTCTGCCACCAACACTTATTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
* * *
39801806 TCAAGTAAAACCTAAATATCACATACACATCTATCCGCCGCCAACACTTACTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
* * *
39801861 TCAAGTAAAACCTAAATATGATACACACCTCCT-TCCGCTGCCAACACTTATTCTA
1 TCAAGTAAAACCTAAATATCATACACACCT-CTATCCGCCGCCAACACTTACTCTA
*
39801916 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGGCAACACTTACTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
* * * *
39801971 TCAAATAAAACTTAAATATGATACACACTTCTATCCGCCGCCAACACTTACTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
* * * *
39802026 TCAAGTAAAACCTAAATATCATACATACCTCTATCCGCCACTAACACCTACTCTA
1 TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
* *
39802081 TCAAAGCAAAATCTAAATATC
1 TC-AAGTAAAACCTAAATATC
39802102 TCAAGTAAAA
Statistics
Matches: 257, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
54 2 0.01
55 237 0.92
56 18 0.07
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (55 bp):
TCAAGTAAAACCTAAATATCATACACACCTCTATCCGCCGCCAACACTTACTCTA
Found at i:39802105 original size:21 final size:20
Alignment explanation
Indices: 39802084--39802121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39802074 TACTCTATCA
*
39802084 AAGCAAAATCTAAATATCTC
1 AAGCAAAACCTAAATATCTC
*
39802104 AAGTAAAACCTAAATATC
1 AAGCAAAACCTAAATATC
39802122 ATACACCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (20 bp):
AAGCAAAACCTAAATATCTC
Found at i:39817822 original size:21 final size:22
Alignment explanation
Indices: 39817776--39817835 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
39817766 AAGCAGTCGC
*
39817776 ATTTTGATTCATCCTTCCGTTAAA
1 ATTTTCATTCAT--TTCCGTTAAA
*
39817800 ATTTTCATTTATTTCCG-TAAA
1 ATTTTCATTCATTTCCGTTAAA
39817821 ATTTTCATTCATTTC
1 ATTTTCATTCATTTC
39817836 TGTCATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.55
22 5 0.15
24 10 0.30
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTTTCATTCATTTCCGTTAAA
Found at i:39820559 original size:6 final size:6
Alignment explanation
Indices: 39820548--39820573 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39820538 ATAAATTGAG
39820548 ATAGTC ATAGTC ATAGTC ATAGTC AT
1 ATAGTC ATAGTC ATAGTC ATAGTC AT
39820574 CATTTGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
ATAGTC
Found at i:39825056 original size:2 final size:2
Alignment explanation
Indices: 39825049--39825073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39825039 TAACCTCTGC
39825049 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39825074 AAAACAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39834400 original size:23 final size:20
Alignment explanation
Indices: 39834345--39834400 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 20
39834335 CGATTAACAT
*
39834345 AAATATTATTATTTATATAAA
1 AAATA-TATTATTTAAATAAA
*
39834366 AAATATA-AATTTAAATACATTA
1 AAATATATTATTTAAATA-A--A
39834388 AAATATATTATTT
1 AAATATATTATTT
39834401 TTTTAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 5 0.18
22 8 0.29
23 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATATTATTTAAATAAA
Found at i:39840706 original size:18 final size:19
Alignment explanation
Indices: 39840669--39840713 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
39840659 GAAGTAGGAC
*
39840669 ACTATCTACTAAATCAAATA
1 ACTA-CTACTAAACCAAATA
39840689 ACTACTAC-AAACCAAATA
1 ACTACTACTAAACCAAATA
*
39840707 ACAACTA
1 ACTACTA
39840714 TTTGACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 15 0.65
19 4 0.17
20 4 0.17
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (19 bp):
ACTACTACTAAACCAAATA
Found at i:39843584 original size:21 final size:21
Alignment explanation
Indices: 39843559--39843598 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39843549 AAAATAACAT
39843559 TACAAT-ATTCAATTTCATCAC
1 TACAATAATT-AATTTCATCAC
39843580 TACAATAATTAATTTCATC
1 TACAATAATTAATTTCATC
39843599 GTTGTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (21 bp):
TACAATAATTAATTTCATCAC
Found at i:39847553 original size:29 final size:29
Alignment explanation
Indices: 39847498--39847554 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
39847488 AAAATTATAT
** *
39847498 TTAATATAATAAATGTTTATTTGTATTTG
1 TTAATATAATAAACATTTATTTATATTTG
39847527 TTAATATAATAAAACATTTA-TTATATTT
1 TTAATATAAT-AAACATTTATTTATATTT
39847555 ATGGTAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAATATAATAAACATTTATTTATATTTG
Found at i:39848452 original size:24 final size:24
Alignment explanation
Indices: 39848425--39848470 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39848415 ATAAAAAAGA
39848425 TAAA-TTAGTTTTTCCAATAAAAAC
1 TAAACTTA-TTTTTCCAATAAAAAC
*
39848449 TAAACTTATTTTTCCTATAAAA
1 TAAACTTATTTTTCCAATAAAA
39848471 GCACATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAACTTATTTTTCCAATAAAAAC
Found at i:39848680 original size:16 final size:16
Alignment explanation
Indices: 39848656--39848686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39848646 AATATTTTTA
39848656 AAATAAAAAATAAAAG
1 AAATAAAAAATAAAAG
*
39848672 AAATTAAAAATAAAA
1 AAATAAAAAATAAAA
39848687 TAAAACAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAAAAG
Found at i:39850904 original size:21 final size:21
Alignment explanation
Indices: 39850864--39850904 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39850854 AGGGTAATAA
* *
39850864 GGTGGAGGCGGGTAAGCGCCT
1 GGTGGAGGAGGGTAACCGCCT
*
39850885 GGTGGAGGAGGGTATCCGCC
1 GGTGGAGGAGGGTAACCGCC
39850905 ATATGGGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.51, T:0.15
Consensus pattern (21 bp):
GGTGGAGGAGGGTAACCGCCT
Found at i:39851381 original size:23 final size:23
Alignment explanation
Indices: 39851332--39851385 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
39851322 TAAATTATTT
**
39851332 ATTTATTATCTAAAAAAAATATC
1 ATTTATTATCTAAAAAAAATAAA
* * *
39851355 ATTTATTATTTAACAAAATTAAA
1 ATTTATTATCTAAAAAAAATAAA
39851378 ATTT-TTAT
1 ATTTATTAT
39851386 AATTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTATTATCTAAAAAAAATAAA
Found at i:39860001 original size:28 final size:28
Alignment explanation
Indices: 39859970--39860026 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
39859960 AAAGAAGATG
39859970 AAAGA-AAAAAATGAAAAAAAATAAAAAT
1 AAAGAGAAAAAAT-AAAAAAAATAAAAAT
* * *
39859998 AAAGAGAGAAAATAAAAGAATTAAAAAT
1 AAAGAGAAAAAATAAAAAAAATAAAAAT
39860026 A
1 A
39860027 TTTTTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (28 bp):
AAAGAGAAAAAATAAAAAAAATAAAAAT
Found at i:39860379 original size:3 final size:3
Alignment explanation
Indices: 39860371--39860412 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39860361 AGTGCAATTA
39860371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39860413 TAACCTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39863077 original size:15 final size:15
Alignment explanation
Indices: 39863057--39863090 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39863047 CATGTTATAT
*
39863057 TAATTTAATATTTAA
1 TAATTTAATATTAAA
*
39863072 TAATTTTATATTAAA
1 TAATTTAATATTAAA
39863087 TAAT
1 TAAT
39863091 ATATTCTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTAATATTAAA
Found at i:39868895 original size:57 final size:57
Alignment explanation
Indices: 39868807--39868937 Score: 190
Period size: 57 Copynumber: 2.3 Consensus size: 57
39868797 CTGTCCACTT
* *
39868807 CCACCCCCGCCTCCCCCTCCTGTACCAAAATGTACACTTCCCCCACCTCCTCCGCCA
1 CCACCCCCGCCTCCGCCTCCTGTACCAAAATGTACACTTCCCCCACCTCCACCGCCA
* * * *
39868864 CCACCTCCGCCTCCGCCTCCTGTACCAAAATGTACATTTCCTCCACCTCCACCGCCG
1 CCACCCCCGCCTCCGCCTCCTGTACCAAAATGTACACTTCCCCCACCTCCACCGCCA
* *
39868921 CCTCCCCCGCCACCGCC
1 CCACCCCCGCCTCCGCC
39868938 GCCTCCACCG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.16, C:0.57, G:0.09, T:0.18
Consensus pattern (57 bp):
CCACCCCCGCCTCCGCCTCCTGTACCAAAATGTACACTTCCCCCACCTCCACCGCCA
Found at i:39868930 original size:12 final size:12
Alignment explanation
Indices: 39868930--39868955 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39868920 GCCTCCCCCG
39868930 CCACCGCCGCCT
1 CCACCGCCGCCT
39868942 CCACCGCCGCCT
1 CCACCGCCGCCT
39868954 CC
1 CC
39868956 CCCACCTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.69, G:0.15, T:0.08
Consensus pattern (12 bp):
CCACCGCCGCCT
Found at i:39868933 original size:18 final size:18
Alignment explanation
Indices: 39868903--39868949 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
39868893 ATGTACATTT
*
39868903 CCTCCACCTCCACCGCCG
1 CCTCCACCGCCACCGCCG
*
39868921 CCTCCCCCGCCACCGCCG
1 CCTCCACCGCCACCGCCG
39868939 CCTCCACCGCC
1 CCTCCACCGCC
39868950 GCCTCCCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.70, G:0.13, T:0.09
Consensus pattern (18 bp):
CCTCCACCGCCACCGCCG
Found at i:39880455 original size:20 final size:19
Alignment explanation
Indices: 39880430--39880482 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
39880420 TTTTTTTATT
39880430 TTTTAAAAATATTTATATAA
1 TTTTAAAAATATTTA-ATAA
*
39880450 TTTTAATTCAATATTTAATAA
1 TTTTAA--AAATATTTAATAA
39880471 -TTT-AAAATATTT
1 TTTTAAAAATATTT
39880483 TTCTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 7 0.24
19 1 0.03
20 9 0.31
21 4 0.14
22 8 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATATTTAATAA
Found at i:39886486 original size:18 final size:17
Alignment explanation
Indices: 39886465--39886499 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39886455 TATTTCATTC
*
39886465 AATATTTAAAAATTAAAT
1 AATATATAAAAA-TAAAT
39886483 AATATATAAAAATAAAT
1 AATATATAAAAATAAAT
39886500 GAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATATAAAAATAAAT
Found at i:39910659 original size:24 final size:24
Alignment explanation
Indices: 39910598--39910660 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
39910588 TAGACTAATA
* *
39910598 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
* *
39910622 AGAGTTTAATTGAAATAATTAAAC
1 AGAGTTTAACTGAAATAAATAAAC
39910646 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
39910661 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAATAAATAAAC
Found at i:39911387 original size:25 final size:23
Alignment explanation
Indices: 39911342--39911398 Score: 55
Period size: 25 Copynumber: 2.4 Consensus size: 23
39911332 AATTTATACT
*
39911342 AAATTTATTCTAATTCTAATGGATA
1 AAATTTATTATAATTCTAAT-GA-A
*
39911367 AAATTTA-TATAATTGTAAATGAA
1 AAATTTATTATAATTCT-AATGAA
39911390 AAA-TTATTA
1 AAATTTATTA
39911399 GATGGACCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 6 0.21
24 9 0.32
25 10 0.36
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (23 bp):
AAATTTATTATAATTCTAATGAA
Found at i:39912057 original size:20 final size:19
Alignment explanation
Indices: 39912015--39912057 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
39912005 GTTGAAGAAA
*
39912015 ATGATTGATGTGACATAAT
1 ATGATTGATGGGACATAAT
39912034 ATGATTGAATGGGATCAT-AT
1 ATGATTG-ATGGGA-CATAAT
39912054 ATGA
1 ATGA
39912058 GATGATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (19 bp):
ATGATTGATGGGACATAAT
Found at i:39926597 original size:10 final size:10
Alignment explanation
Indices: 39926582--39926606 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39926572 TTTAACTGTT
39926582 TTAAAAAAAA
1 TTAAAAAAAA
39926592 TTAAAAAAAA
1 TTAAAAAAAA
39926602 TTAAA
1 TTAAA
39926607 TTGTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAAAAAAA
Found at i:39927851 original size:21 final size:21
Alignment explanation
Indices: 39927804--39927851 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
39927794 AATCAATTTG
* *
39927804 ATTAAATTATTATGTAAAATA
1 ATTAAAATATTATATAAAATA
* **
39927825 AATAAAATATTATATAATGTA
1 ATTAAAATATTATATAAAATA
39927846 ATTAAA
1 ATTAAA
39927852 TCAAATCAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTAAAATATTATATAAAATA
Found at i:39936362 original size:61 final size:60
Alignment explanation
Indices: 39936167--39936452 Score: 307
Period size: 61 Copynumber: 4.8 Consensus size: 60
39936157 AAAAATTTAA
** * * *
39936167 AAATTTTGGGGTGTTGGCCATCAAATGGTCGACACCCCCTATT-TC-A-AAAAAAAATT-
1 AAATTTTTTGGTGTTGGCCATGAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATTC
** * * * * * *
39936223 GTATTTTTGGGTGCTGGCCATGCAATGGCCGACACCCTCTATT-TCCA-AAAAAAAATTTC
1 AAATTTTTTGGTGTTGGCCATGAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAA-TTC
* * *
39936282 AAATTTTTTGGTCTTGGCCATGTAATAGCCGACACCCCCTGTTCTCGAGAAAAAAAATTC
1 AAATTTTTTGGTGTTGGCCATGAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATTC
*
39936342 AAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCCTGTTCTCGAG-AAAAAAATTC
1 AAA-TTTTTTGGTGTTGGCCATGAAATGGCCGACA-CCCCCTGTTCTCGAGAAAAAAAATTC
* * *
39936403 AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACATCCCTTGTTCTCGAG
1 AAA-TTTTTTGGTGTTGGCCATGAAATGGCCGACACCCCCTGTTCTCGAG
39936453 CACCCCCTGT
Statistics
Matches: 198, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
56 37 0.19
57 9 0.05
58 2 0.01
59 34 0.17
60 22 0.11
61 79 0.40
62 15 0.08
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (60 bp):
AAATTTTTTGGTGTTGGCCATGAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATTC
Found at i:39936449 original size:122 final size:118
Alignment explanation
Indices: 39936106--39936452 Score: 362
Period size: 122 Copynumber: 2.9 Consensus size: 118
39936096 AAAAAAAAAA
* * *
39936106 TTTGGGTGTTGGCCATGCAATGGCCTACACCCACCTCCTTTTTGTCAGGAAAAAAATTTAAAAAT
1 TTTGGGTGTTGGCCATGCAATGGCCGACA-CC-CC-CC-TATT-TCA-GAAAAAAATTT-CAAAT
** * * **
39936171 TTTGGGGTGTTGGCCATCAAATGGTCGACACCCCCTATT-TC-A-AAAAAAAATTGTATT
59 TTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATTAAATT
* * *
39936228 TTTGGGTGCTGGCCATGCAATGGCCGACA-CCCTCTATTTCCAAAAAAAAATTTCAAATTTTTTG
1 TTTGGGTGTTGGCCATGCAATGGCCGACACCCCCCTATTT-CAGAAAAAAATTTCAAATTTTTTG
* ** *
39936292 GTCTTGGCCATGTAATAGCCGACACCCCCTGTTCTCGAGAAAAAAAATTCAAATTT
65 GTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATT-AAA-TT
* *
39936348 TTTTGGTGTTGGCCATGCAATGGCCGACACCCCCCTGTTCTCGAGAAAAAAA-TTCAAATTTTTT
1 TTTGGGTGTTGGCCATGCAATGGCCGACACCCCCCTATT-TC-AGAAAAAAATTTCAAA-TTTTT
* *
39936412 TGGTGTTGGCCATCAAATGGCCGACATCCCTTGTTCTCGAG
63 TGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAG
39936453 CACCCCCTGT
Statistics
Matches: 188, Mismatches: 27, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
115 35 0.19
116 13 0.07
117 6 0.03
118 11 0.06
119 3 0.02
120 30 0.16
121 14 0.07
122 76 0.40
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (118 bp):
TTTGGGTGTTGGCCATGCAATGGCCGACACCCCCCTATTTCAGAAAAAAATTTCAAATTTTTTGG
TGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAATTAAATT
Found at i:39937678 original size:37 final size:37
Alignment explanation
Indices: 39937630--39937704 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
39937620 TTGTACGAAT
39937630 TTTGTTTTTATACTTTTTCCTATAACATATTTCTCAA
1 TTTGTTTTTATACTTTTTCCTATAACATATTTCTCAA
39937667 TTTGTTTTTATACTTTTTCCTATAACATATTTCTCAA
1 TTTGTTTTTATACTTTTTCCTATAACATATTTCTCAA
39937704 T
1 T
39937705 GTAAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.57
Consensus pattern (37 bp):
TTTGTTTTTATACTTTTTCCTATAACATATTTCTCAA
Found at i:39942368 original size:31 final size:31
Alignment explanation
Indices: 39942311--39942381 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
39942301 TAAGTCAATC
* *
39942311 TCTAAACTTGACAAATTTTTCCATATTCGAG-
1 TCTAAACTTGACAAATTATCCCATATT-GAGA
39942342 TCTAAACTTGAC-AATTATCCCTATATTGAGA
1 TCTAAACTTGACAAATTATCCC-ATATTGAGA
*
39942373 TTTAAACTT
1 TCTAAACTT
39942382 CAGAGCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (31 bp):
TCTAAACTTGACAAATTATCCCATATTGAGA
Found at i:39942775 original size:5 final size:5
Alignment explanation
Indices: 39942765--39942798 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
39942755 GAAGTGGAGG
39942765 CTGGT CTGGT CTGGT CTGGT CTGGT CTGGT CTGG
1 CTGGT CTGGT CTGGT CTGGT CTGGT CTGGT CTGG
39942799 ATTCCAGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.41, T:0.38
Consensus pattern (5 bp):
CTGGT
Found at i:39945862 original size:55 final size:55
Alignment explanation
Indices: 39945772--39946038 Score: 295
Period size: 55 Copynumber: 4.7 Consensus size: 55
39945762 ATATTACTTT
* * * * *
39945772 TTTTCAATTGATTGTTTTTATGTTTGAATTGATTGTTATGTTGAAATACTGCTTC
1 TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGTTGGAATACTGCTTC
* ** * *
39945827 TTTTGAATTTATTGTTTATACATTTAAATCA-ATTGTTATGGTGGAATACTACTTC
1 TTTTGAATTGATTGTTTATATGTTTAAAT-AGATTGTTATGTTGGAATACTGCTTC
* *
39945882 TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGGTGGAATATTGTTTATTCTTC
1 TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGTTGGAATACTG------CTTC
* * ** *
39945943 TTTTGAATCGTTTGTTTATATGTTTAAATCTATTGTTATGTTGGAATATTGCTT-
1 TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGTTGGAATACTGCTTC
39945997 TTCTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGT
1 TT-TTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGT
39946039 AGCATGTCTA
Statistics
Matches: 179, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
54 3 0.02
55 126 0.70
61 50 0.28
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.54
Consensus pattern (55 bp):
TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGTTGGAATACTGCTTC
Found at i:39945978 original size:116 final size:109
Alignment explanation
Indices: 39945761--39946037 Score: 331
Period size: 116 Copynumber: 2.5 Consensus size: 109
39945751 ATTTCTCAAA
* * * * *
39945761 AATATTACTTTTTTTCAATTGATTGTTTTTATGTTTGAATTGATTGTTATGTTGAAATACTGCTT
1 AATATTAC-TTTTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGGTGAAATACTGCTT
*
39945826 CTTTTGAATTTATTGTTTATACATTTAAATCAATTGTTATGGTGG
65 CTTTTGAATGTATTGTTTATACATTTAAATCAATTGTTATGGTGG
* * *
39945871 AATACTACTTCTTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGGTGGAATATTGTTT
1 AATATTACTT-TTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGGTGAAATACTG---
** * *
39945936 ATTCTTCTTTTGAATCGT-TTGTTTATATGTTTAAATCTATTGTTATGTTGG
62 ---CTTCTTTTGAAT-GTATTGTTTATACATTTAAATCAATTGTTATGGTGG
*
39945987 AATATTGCTTTTCTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATG
1 AATATTACTTTT-TTGAATTGATTGTTTATATGTTTAAATAGATTGTTATG
39946038 TAGCATGTCT
Statistics
Matches: 143, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
109 2 0.01
110 51 0.36
115 2 0.01
116 87 0.61
117 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (109 bp):
AATATTACTTTTTTGAATTGATTGTTTATATGTTTAAATAGATTGTTATGGTGAAATACTGCTTC
TTTTGAATGTATTGTTTATACATTTAAATCAATTGTTATGGTGG
Found at i:39947672 original size:9 final size:9
Alignment explanation
Indices: 39947658--39947689 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39947648 AGGTTGCTTT
*
39947658 TAAAAGTCA
1 TAAAAGTAA
39947667 TAAAAGTAA
1 TAAAAGTAA
39947676 TAAAAGTAA
1 TAAAAGTAA
39947685 TAAAA
1 TAAAA
39947690 TATCAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.66, C:0.03, G:0.09, T:0.22
Consensus pattern (9 bp):
TAAAAGTAA
Found at i:39954568 original size:82 final size:82
Alignment explanation
Indices: 39954431--39954594 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
39954421 TTAAGTTTGA
39954431 TTTTTGAATTCGAACTTGAGTACGAAAATTGTATCTTGAACCAAGCTCAAGCTTAGAAATAGAAG
1 TTTTTGAATTCGAACTTGAGTACGAAAATTGTATCTTGAACCAAGCTCAAGCTTAGAAATAGAAG
39954496 TTCAACAAAGCTCAAGC
66 TTCAACAAAGCTCAAGC
39954513 TTTTTGAATTCGAACTTGAGTACGAAAATTGTATCTTGAACCAAGCTCAAGCTTAGAAATAGAAG
1 TTTTTGAATTCGAACTTGAGTACGAAAATTGTATCTTGAACCAAGCTCAAGCTTAGAAATAGAAG
39954578 TTCAACAAAGCTCAAGC
66 TTCAACAAAGCTCAAGC
39954595 AGAGTACGGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (82 bp):
TTTTTGAATTCGAACTTGAGTACGAAAATTGTATCTTGAACCAAGCTCAAGCTTAGAAATAGAAG
TTCAACAAAGCTCAAGC
Found at i:39965335 original size:25 final size:24
Alignment explanation
Indices: 39965305--39965400 Score: 83
Period size: 25 Copynumber: 4.0 Consensus size: 24
39965295 ATTTTTTGTA
39965305 ATATTTTTAAAATTTTTATATACTT
1 ATATTTTTAAAATTTTTATATA-TT
* *
39965330 ATATTTTTATAATTTTTAGTTTATT
1 ATATTTTTAAAATTTTTA-TATATT
* *
39965355 TTATATTTT-AAATTTTTATGTATT
1 ATAT-TTTTAAAATTTTTATATATT
*
39965379 -T-TCTTTT-AAATTTTTAAATATT
1 ATAT-TTTTAAAATTTTTATATATT
39965401 TTATAAGTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.30
23 1 0.02
24 5 0.08
25 30 0.49
26 7 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATTTTTAAAATTTTTATATATT
Found at i:39965339 original size:8 final size:8
Alignment explanation
Indices: 39965305--39965373 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
39965295 ATTTTTTGTA
39965305 ATATTTTT
1 ATATTTTT
*
39965313 AAAATTTTT
1 -ATATTTTT
**
39965322 ATATACTT
1 ATATTTTT
39965330 ATATTTTT
1 ATATTTTT
39965338 ATAATTTTT
1 AT-ATTTTT
*
39965347 AGTTTATTTT
1 A-TAT-TTTT
39965357 ATA-TTTT
1 ATATTTTT
*
39965364 AAATTTTT
1 ATATTTTT
39965372 AT
1 AT
39965374 GTATTTTCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
7 6 0.13
8 18 0.39
9 16 0.35
10 6 0.13
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (8 bp):
ATATTTTT
Found at i:39965400 original size:22 final size:22
Alignment explanation
Indices: 39965360--39965402 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39965350 TTATTTTATA
**
39965360 TTTTAAATTTTTATGTATTTTC
1 TTTTAAATTTTTAAATATTTTC
39965382 TTTTAAATTTTTAAATATTTT
1 TTTTAAATTTTTAAATATTTT
39965403 ATAAGTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAAATTTTTAAATATTTTC
Found at i:39965514 original size:24 final size:26
Alignment explanation
Indices: 39965478--39965530 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
39965468 TATAATTAAG
*
39965478 TATAAACACATAT-AATATTATT-TA
1 TATAAACACATATAAATAATATTGTA
* *
39965502 TATAAATATATATAAATAATATTGTA
1 TATAAACACATATAAATAATATTGTA
39965528 TAT
1 TAT
39965531 TGTACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 8 0.33
26 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
TATAAACACATATAAATAATATTGTA
Found at i:39976439 original size:12 final size:12
Alignment explanation
Indices: 39976422--39976455 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39976412 ACGGAAGGAA
39976422 AGCCACGGCCAC
1 AGCCACGGCCAC
*
39976434 AGCCACAGCCAC
1 AGCCACGGCCAC
*
39976446 AGCCATGGCC
1 AGCCACGGCC
39976456 TCCGTCGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.47, G:0.24, T:0.03
Consensus pattern (12 bp):
AGCCACGGCCAC
Found at i:39984432 original size:20 final size:21
Alignment explanation
Indices: 39984407--39984452 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
39984397 AGTGAATAAC
39984407 ATTTTTAATA-AAAAAAATTA
1 ATTTTTAATAGAAAAAAATTA
39984427 ATTTTTAATAGAAAAAAATTA
1 ATTTTTAATAGAAAAAAATTA
39984448 ATTTT
1 ATTTT
39984453 CTCTTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTTTAATAGAAAAAAATTA
Found at i:39989185 original size:332 final size:334
Alignment explanation
Indices: 39988600--39989206 Score: 783
Period size: 332 Copynumber: 1.8 Consensus size: 334
39988590 GACAGTACAT
* * * *
39988600 TGTGTATATTAAAATAAAAATGTATAGAATATATTAAAATGAAATTTTGGTTGAGTGGTAAATTT
1 TGTGAATAGTAAAATAAAAATGCATAAAATATATTAAAATGAAATTTTGGTTGAGTGGTAAATTT
* * * ** * *
39988665 AAAATTTTATTTAATGCAATTGGTGTAAGTTCAGTTTTCACCTTATGCAAATTTTTTTTGGTTTT
66 AAAATTTTATCTAATGCAATTAGTGCAAGTTCAG-AATCACCTTATGCAAATTTTTATTGATTTT
*** * * * * *
39988730 TGTTAAAATGAAATGCCTAAGATATCCTCGAATAATATGGGTTATCTTAATTACGAAAGAATATT
130 TGTTAAAATGAAAAAACTAAAATACCCTCAAATAATATGAGTTATCTTAATTACAAAAGAATATT
** * * *
39988795 TTTTTAATTTTTTAACCGAGTTGATGTTTGGTTGACTTGTGACACCAACTCAGTTAGAGATTTTA
195 TTCATAAATTTTTAACCGAGTTGATGCTTGGTTGACTCGTGACACCAACTCAGTTAGAGATTTTA
*
39988860 TTAAAATTAAGTATACGTAGATGTACTTTCTAAAAAAAAGTATATGTATAAATACAATCGGTGAA
260 TTAAAAGTAAGTATACGTAGATGTACTTTCTAAAAAAAAGTATATGTATAAATACAATCGGTGAA
39988925 GATAATAAAA
325 GATAATAAAA
* * *
39988935 TGTGAATAGTAAAATAAAAATGCATAAAATATATTAAAATGAAGTTTTGGTTTAGTGGTGAATTT
1 TGTGAATAGTAAAATAAAAATGCATAAAATATATTAAAATGAAATTTTGGTTGAGTGGTAAATTT
* **
39989000 AAAATTTTA-CTAATGCAATTATTGCGGGTTCA-AATC-CCTCTATGCAAATTTTTATTGATTTT
66 AAAATTTTATCTAATGCAATTAGTGCAAGTTCAGAATCACCT-TATGCAAATTTTTATTGATTTT
* * *
39989062 TGTTAAAATGAAAAAATTAAAATACCCTCAAATAATATGATTTA-CTTTAATTACAAAAGGGA-A
130 TGTTAAAATGAAAAAACTAAAATACCCTCAAATAATATGAGTTATC-TTAATTACAAAA-GAATA
* * * **
39989125 TTTTCATAAATTTTTAATCGAGTTGGTGCTTGGTTGACTCGTGATACTGACTCAGTTAGAGATTT
193 TTTTCATAAATTTTTAACCGAGTTGATGCTTGGTTGACTCGTGACACCAACTCAGTTAGAGATTT
*
39989190 TATTAATAGTAAGTATA
258 TATTAAAAGTAAGTATA
39989207 GATATAGATA
Statistics
Matches: 229, Mismatches: 40, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
331 4 0.02
332 139 0.61
333 2 0.01
334 17 0.07
335 67 0.29
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (334 bp):
TGTGAATAGTAAAATAAAAATGCATAAAATATATTAAAATGAAATTTTGGTTGAGTGGTAAATTT
AAAATTTTATCTAATGCAATTAGTGCAAGTTCAGAATCACCTTATGCAAATTTTTATTGATTTTT
GTTAAAATGAAAAAACTAAAATACCCTCAAATAATATGAGTTATCTTAATTACAAAAGAATATTT
TCATAAATTTTTAACCGAGTTGATGCTTGGTTGACTCGTGACACCAACTCAGTTAGAGATTTTAT
TAAAAGTAAGTATACGTAGATGTACTTTCTAAAAAAAAGTATATGTATAAATACAATCGGTGAAG
ATAATAAAA
Found at i:39991207 original size:23 final size:23
Alignment explanation
Indices: 39991172--39991230 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
39991162 CAATTAAACT
*
39991172 AAAATATTAAA-ATATGAAAAATAA
1 AAAAAATTAAATAT-TGAAAAAT-A
*
39991196 AAAAAATTAAATATTTAAAAATA
1 AAAAAATTAAATATTGAAAAATA
*
39991219 TAAAAATTAAAT
1 AAAAAATTAAAT
39991231 TTCAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.39
24 17 0.55
25 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAATTAAATATTGAAAAATA
Found at i:39994465 original size:17 final size:17
Alignment explanation
Indices: 39994447--39994518 Score: 80
Period size: 17 Copynumber: 4.5 Consensus size: 17
39994437 TTAAATTGAT
39994447 TTTAAATTT-GTTTAAA
1 TTTAAATTTAGTTTAAA
*
39994463 TTTAAATTTATTTTAAA
1 TTTAAATTTAGTTTAAA
*
39994480 TTTAAATTTA-ATT--A
1 TTTAAATTTAGTTTAAA
* *
39994494 TTTAAATTTACTTTGAA
1 TTTAAATTTAGTTTAAA
39994511 TTTAAATT
1 TTTAAATT
39994519 AAATAAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 25 0.51
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAGTTTAAA
Found at i:39994541 original size:7 final size:6
Alignment explanation
Indices: 39994457--39994545 Score: 76
Period size: 6 Copynumber: 14.8 Consensus size: 6
39994447 TTTAAATTTG
* *
39994457 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAATTA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA
* ** *
39994505 TTTGAA TTTAAA -TTAAA TAAAAA TTAAAA TATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA
39994546 CATTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
5 13 0.19
6 44 0.65
7 5 0.07
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:39996698 original size:30 final size:30
Alignment explanation
Indices: 39996376--39996681 Score: 344
Period size: 30 Copynumber: 10.2 Consensus size: 30
39996366 TTTGACATTG
*
39996376 AAACTTTTCCAAAATTATATTTTGACCCTA
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* *
39996406 AAACTTTTCCAAAATTACATTTTAACCCCA
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* * *
39996436 AAA-TGTTCTTAATATTATATTTTGACCCCA
1 AAACTTTTC-CAAAATTATATTTTGACCCCA
* *
39996466 AAACTTTTCCAAAATTACATTTTGACCCTA
1 AAACTTTTCCAAAATTATATTTTGACCCCA
*
39996496 AAACTTTTCCAAAATTATATTTTGACCCCG
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* * * * * *
39996526 AGACTTTACCGAAATTACATTTTAACCCCG
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* * *
39996556 AAACTTTTCTAAAATCATATTTCGACCCCA
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* * ***
39996586 AAACTTTTCCATAATTATATTTTAACCTTG
1 AAACTTTTCCAAAATTATATTTTGACCCCA
* * ***
39996616 AAACTTTTCCAAAATTACATTTTGGCCTTG
1 AAACTTTTCCAAAATTATATTTTGACCCCA
39996646 AAACTTTTCCAAAATTATATTTTGACCCCA
1 AAACTTTTCCAAAATTATATTTTGACCCCA
39996676 AAACTT
1 AAACTT
39996682 CTAAAAATTA
Statistics
Matches: 227, Mismatches: 47, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
29 4 0.02
30 219 0.96
31 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (30 bp):
AAACTTTTCCAAAATTATATTTTGACCCCA
Found at i:39996698 original size:90 final size:89
Alignment explanation
Indices: 39996352--39996699 Score: 374
Period size: 90 Copynumber: 3.9 Consensus size: 89
39996342 CCCTAAATTA
*** *
39996352 TCCAGAAATTACATTTTGACATTGAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCA
1 TCCA-AAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCA
* * *
39996417 AAATTACATTTTAACCCCAAAATGT
65 AAATTACATTTTAACCCGAAACTTT
* * * * * *
39996442 TCTTAATATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCA
1 TC-CAAAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCA
* * *
39996507 AAATTATATTTTGACCCCGAGACTTT
65 AAATTACATTTT-AACCCGAAACTTT
* * * * * * *
39996533 ACCGAAATTACATTTTAACCCCGAAACTTTTCTAAAATCATATTTCGACCCCAAAACTTTTCCAT
1 TCCAAAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAA
* *
39996598 AATTATATTTTAACCTTGAAACTTT
66 AATTACATTTTAACC-CGAAACTTT
* ** * *
39996623 TCCAAAATTACATTTTGGCCTTGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTCT-AAA
1 TCCAAAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAA
39996687 AATTACCATTTTA
66 AATTA-CATTTTA
39996700 CCCCTGAACT
Statistics
Matches: 211, Mismatches: 43, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
89 9 0.04
90 192 0.91
91 10 0.05
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (89 bp):
TCCAAAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAA
AATTACATTTTAACCCGAAACTTT
Found at i:39999848 original size:2 final size:2
Alignment explanation
Indices: 39999841--39999883 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39999831 TTTTAGTTTT
*
39999841 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39999883 T
1 T
39999884 TATTTAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40003563 original size:43 final size:43
Alignment explanation
Indices: 40003505--40003603 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
40003495 TTTATGCGGG
* *
40003505 AAAGCGCCGCCAAAGGCCATGTTCTTTAGCGGCACTTTCTCCA
1 AAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCACTTTCTCCA
*
40003548 TAAA-CGCCGCTAAAGGCCATGTTCTTTAACGGCGCTTTCTCCA
1 -AAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCACTTTCTCCA
40003591 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
40003604 TATAACAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 3 0.06
43 45 0.88
44 3 0.06
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCACTTTCTCCA
Found at i:40003692 original size:15 final size:15
Alignment explanation
Indices: 40003672--40003700 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40003662 CTTGTAAATT
40003672 CAAATCCAACCAATG
1 CAAATCCAACCAATG
40003687 CAAATCCAACCAAT
1 CAAATCCAACCAAT
40003701 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:40003926 original size:21 final size:21
Alignment explanation
Indices: 40003901--40003974 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
40003891 CTTGTAGCCT
*
40003901 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTTCCTCCGCTTGCCTCG
* *
40003922 CTGCTGCCTCCACTTGCCTCG
1 CTGCTTCCTCCGCTTGCCTCG
40003943 CTG-TTGCCTCCGCTTGCCTCG
1 CTGCTT-CCTCCGCTTGCCTCG
*
40003964 CTGCTGCCTCC
1 CTGCTTCCTCC
40003975 ACTTTAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.01, C:0.46, G:0.20, T:0.32
Consensus pattern (21 bp):
CTGCTTCCTCCGCTTGCCTCG
Found at i:40003931 original size:11 final size:11
Alignment explanation
Indices: 40003915--40003973 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
40003905 TTCCTTCGCT
40003915 TGCCTCGCTGC
1 TGCCTCGCTGC
*
40003926 TGCCTC-C-AC
1 TGCCTCGCTGC
*
40003935 TTGCCTCGCTGT
1 -TGCCTCGCTGC
40003947 TGCCTC-C-GC
1 TGCCTCGCTGC
40003956 TTGCCTCGCTGC
1 -TGCCTCGCTGC
40003968 TGCCTC
1 TGCCTC
40003974 CACTTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
9 2 0.05
10 14 0.37
11 20 0.53
12 2 0.05
ACGTcount: A:0.02, C:0.46, G:0.22, T:0.31
Consensus pattern (11 bp):
TGCCTCGCTGC
Found at i:40005078 original size:15 final size:15
Alignment explanation
Indices: 40005058--40005088 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40005048 AACTTTTTCT
40005058 TTCAGGCTGGTTAGG
1 TTCAGGCTGGTTAGG
40005073 TTCAGGCTGGTTAGG
1 TTCAGGCTGGTTAGG
40005088 T
1 T
40005089 ATGTGTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.39, T:0.35
Consensus pattern (15 bp):
TTCAGGCTGGTTAGG
Found at i:40008062 original size:41 final size:41
Alignment explanation
Indices: 40008005--40008252 Score: 270
Period size: 41 Copynumber: 6.0 Consensus size: 41
40007995 ATAGATTAAT
*
40008005 TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGTGCCGCTAA
1 TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGCGCCGCTAA
* *
40008046 TGATCCTACCTTTAGCGGCGCTTGAGGTAAAGCGTCGCTAA
1 TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGCGCCGCTAA
*
40008087 TGATCCTACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAA
1 TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGCGCCGCTAA
* * ** * * *
40008128 TTA-CCATACCTTTAGCGGCGCTTCACCCACAAGCACTGCTAA
1 TGATCC-TACCTTTAGCGGCGCTTGA-GGAAAAGCGCCGCTAA
* * *
40008170 TGA-CCTGACCTTTAGCGGCGCTTG-TGATTAAGCGCCACTAA
1 TGATCCT-ACCTTTAGCGGCGCTTGAGGA-AAAGCGCCGCTAA
* * **
40008211 TGACCCGACCTTTAGCGGCGCTTG-GGTTAAGCGCCGCTAA
1 TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGCGCCGCTAA
40008251 TG
1 TG
40008253 CTTTACCATT
Statistics
Matches: 177, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
40 17 0.10
41 128 0.72
42 32 0.18
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (41 bp):
TGATCCTACCTTTAGCGGCGCTTGAGGAAAAGCGCCGCTAA
Found at i:40008539 original size:8 final size:8
Alignment explanation
Indices: 40008526--40008557 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
40008516 ATTTTAGACG
40008526 TAAAAAAA
1 TAAAAAAA
40008534 TAAAAAAAA
1 T-AAAAAAA
40008543 TAAAAAAA
1 TAAAAAAA
40008551 TAAAAAA
1 TAAAAAA
40008558 TAAGGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:40008541 original size:9 final size:9
Alignment explanation
Indices: 40008527--40008557 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
40008517 TTTTAGACGT
40008527 AAAAAAATA
1 AAAAAAATA
40008536 AAAAAAAT-
1 AAAAAAATA
40008544 AAAAAAATA
1 AAAAAAATA
40008553 AAAAA
1 AAAAA
40008558 TAAGGACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:40009894 original size:6 final size:6
Alignment explanation
Indices: 40009883--40009913 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40009873 GTTTACCAAA
40009883 ACATTC ACATTC ACATTC ACATTC ACATTC A
1 ACATTC ACATTC ACATTC ACATTC ACATTC A
40009914 TTTAGGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATTC
Found at i:40011159 original size:22 final size:22
Alignment explanation
Indices: 40011134--40011176 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40011124 AAATAATAAG
40011134 GATGACAT-GAAATCACAGTTTC
1 GATGACATAG-AATCACAGTTTC
*
40011156 GATGATATAGAATCACAGTTT
1 GATGACATAGAATCACAGTTT
40011177 TATACAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (22 bp):
GATGACATAGAATCACAGTTTC
Found at i:40014264 original size:29 final size:30
Alignment explanation
Indices: 40014230--40014293 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
40014220 TTGACTTTGA
40014230 GACTAAATTGATC-AATT-TAATGATAGAGG
1 GACTAAATTGATCTAATTCT-ATGATAGAGG
* *
40014259 GACTAATTTGATCTAATTCCTATTATAGAGG
1 GACTAAATTGATCTAATT-CTATGATAGAGG
40014290 GACT
1 GACT
40014294 TAGTAGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 13 0.43
32 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (30 bp):
GACTAAATTGATCTAATTCTATGATAGAGG
Found at i:40016279 original size:77 final size:77
Alignment explanation
Indices: 40016152--40016308 Score: 287
Period size: 77 Copynumber: 2.0 Consensus size: 77
40016142 TCCTTTCTAT
40016152 TTTATTTCTATAACTAGTGACGGGATTCGAGTCACATAACTCTAACAATTTTAGTACTTGAAGAT
1 TTTATTTCTATAACTAGTGACGGGATTCGAGTCACATAACTCTAACAATTTTAGTACTTGAAGAT
40016217 TATAGGGTAAAC
66 TATAGGGTAAAC
* * *
40016229 TTTATTTCTATAACTAGTGATGGGATTCGGGTCACATAACTCTAATAATTTTAGTACTTGAAGAT
1 TTTATTTCTATAACTAGTGACGGGATTCGAGTCACATAACTCTAACAATTTTAGTACTTGAAGAT
40016294 TATAGGGTAAAC
66 TATAGGGTAAAC
40016306 TTT
1 TTT
40016309 TTAGTGTTAG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (77 bp):
TTTATTTCTATAACTAGTGACGGGATTCGAGTCACATAACTCTAACAATTTTAGTACTTGAAGAT
TATAGGGTAAAC
Found at i:40019513 original size:40 final size:36
Alignment explanation
Indices: 40019463--40019555 Score: 89
Period size: 40 Copynumber: 2.4 Consensus size: 36
40019453 AATTTGATTT
*
40019463 TATTTCTAAAAAAATCA-AATAAGTATATAAAAGTACATAAA
1 TATTT-TAAAAAAAT-AGAATAA--ATATAAAAATA-AT-AA
40019504 TATTTTAAAAAATATAGTAATAAATATAAAAATAATAA
1 TATTTTAAAAAA-ATAG-AATAAATATAAAAATAATAA
40019542 TATTGTTAAAAAAA
1 TATT-TTAAAAAAA
40019556 ATATTAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
38 7 0.15
39 10 0.21
40 18 0.38
41 7 0.15
42 5 0.11
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (36 bp):
TATTTTAAAAAAATAGAATAAATATAAAAATAATAA
Found at i:40019551 original size:39 final size:40
Alignment explanation
Indices: 40019487--40019568 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 40
40019477 TCAAATAAGT
* *
40019487 ATATAAAAGTACATAAATATTTTAAAAAATATAGTAATAA
1 ATATAAAAATACATAAATATTTTAAAAAAAATAGTAATAA
*
40019527 ATATAAAAATA-AT-AATATTGTTAAAAAAAATATTAATAA
1 ATATAAAAATACATAAATATT-TTAAAAAAAATAGTAATAA
40019566 ATA
1 ATA
40019569 AAATTCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 6 0.16
39 22 0.58
40 10 0.26
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (40 bp):
ATATAAAAATACATAAATATTTTAAAAAAAATAGTAATAA
Found at i:40019582 original size:18 final size:18
Alignment explanation
Indices: 40019561--40019603 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
40019551 AAAAAATATT
* * *
40019561 AATAAATAAAATTCAAAG
1 AATAAATAAAAATAAAAA
*
40019579 AATATATAAAAATAAAAA
1 AATAAATAAAAATAAAAA
40019597 AATAAAT
1 AATAAAT
40019604 TCAAAAAAAA
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:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAATAAAAATAAAAA
Found at i:40019681 original size:27 final size:26
Alignment explanation
Indices: 40019631--40019691 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
40019621 ATTTAACTTA
* *
40019631 ATTATTATATTTTTTTGAAAATATTT
1 ATTATTATATATTTTTGAAAATATAT
*
40019657 ATTTTTATATATTTTT-AAATTATATAT
1 ATTATTATATATTTTTGAAA--ATATAT
40019684 ATTATTAT
1 ATTATTAT
40019692 TTCTTATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 14 0.48
27 12 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTATTATATATTTTTGAAAATATAT
Found at i:40023253 original size:31 final size:31
Alignment explanation
Indices: 40023216--40023276 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
40023206 TAACAGTCCA
*
40023216 ATGACTTAAATAAAAACTTTTGAATAATTCG
1 ATGACTTAAATAAAAACTTTCGAATAATTCG
* *
40023247 ATGACTTAAATGAAAACTTTCGAATTATTC
1 ATGACTTAAATAAAAACTTTCGAATAATTC
40023277 AGTGACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (31 bp):
ATGACTTAAATAAAAACTTTCGAATAATTCG
Done.