Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 63 of 66
Found at i:24547086 original size:18 final size:19
Alignment explanation
Indices: 24547044--24547086 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
24547034 TCAATTCTGT
*
24547044 CACAGAGCGAAAGCAAAAC
1 CACAGAGCCAAAGCAAAAC
24547063 CACAGAGCCAAAGCAAAA-
1 CACAGAGCCAAAGCAAAAC
24547081 CACAGA
1 CACAGA
24547087 AATGGGGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.53, C:0.28, G:0.19, T:0.00
Consensus pattern (19 bp):
CACAGAGCCAAAGCAAAAC
Found at i:24548300 original size:23 final size:25
Alignment explanation
Indices: 24548255--24548300 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
24548245 TATAAGAAGC
24548255 AAATATGAGTACAACTTACTTAATA
1 AAATATGAGTACAACTTACTTAATA
*
24548280 AAATATG-GTA-AACTTATTTAA
1 AAATATGAGTACAACTTACTTAA
24548301 CTTTGGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (25 bp):
AAATATGAGTACAACTTACTTAATA
Found at i:24563071 original size:31 final size:31
Alignment explanation
Indices: 24563034--24563092 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
24563024 TGGTTTGCTG
* *
24563034 CCCCACATGAAGTTTCAAATCTATCCACTGC
1 CCCCACATGAAGTTTCAAACCCATCCACTGC
24563065 CCCCACATGAAGTTTCAAACCCATCCAC
1 CCCCACATGAAGTTTCAAACCCATCCAC
24563093 GACAAATCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.39, G:0.08, T:0.22
Consensus pattern (31 bp):
CCCCACATGAAGTTTCAAACCCATCCACTGC
Found at i:24564834 original size:14 final size:15
Alignment explanation
Indices: 24564812--24564844 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
24564802 AAGGTTAAAA
24564812 TAATCTTTAATA-AT
1 TAATCTTTAATAGAT
*
24564826 TAATTTTTAATAGAT
1 TAATCTTTAATAGAT
24564841 TAAT
1 TAAT
24564845 AAACGTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
TAATCTTTAATAGAT
Found at i:24564905 original size:18 final size:18
Alignment explanation
Indices: 24564866--24564905 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
24564856 GTATACACAT
* *
24564866 TTAAACACAATAACATGT
1 TTAAACACAATAACACGA
24564884 TTAAACACAATAACACGA
1 TTAAACACAATAACACGA
24564902 TTAA
1 TTAA
24564906 GTAAACATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (18 bp):
TTAAACACAATAACACGA
Found at i:24568224 original size:31 final size:31
Alignment explanation
Indices: 24568175--24568235 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
24568165 TGCCAAAAGG
*
24568175 GTGTTTCCTGCCTAGTGGTAGTCTTGTACAT
1 GTGTTTCATGCCTAGTGGTAGTCTTGTACAT
* *
24568206 GTGTTTCATGCTTGGTGGTAGTCTTGTACA
1 GTGTTTCATGCCTAGTGGTAGTCTTGTACA
24568236 GGCAAAAGCT
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:0.13, C:0.16, G:0.28, T:0.43
Consensus pattern (31 bp):
GTGTTTCATGCCTAGTGGTAGTCTTGTACAT
Found at i:24586869 original size:198 final size:196
Alignment explanation
Indices: 24586531--24586910 Score: 742
Period size: 198 Copynumber: 1.9 Consensus size: 196
24586521 CTTATCATAT
24586531 TTTTTAAAAAAAAAGAAAAGAAAATCAATTAGTTTTAAAAAAATCAATAAGGCATGTTTAAATAA
1 TTTTTAAAAAAAAAGAAAAGAAAATCAATTAGTTTTAAAAAAATCAATAAGGCATGTTTAAATAA
24586596 AAGCAGTTTACACATTTAAAGGAAAAGAGGTAAGGCCAATTATTTTATCACATACGAGGAAGTTA
66 AAGCAGTTTACACATTTAAAGGAAAAGAGGTAAGGCCAATTATTTTATCACATACGAGGAAGTTA
24586661 AAAGTCAGTTTTCATTAATACGTTTAAAGAAAAAAATATAGAGAAGGAAAAAAACAAACCATTTG
131 AAAGTCAGTTTTCATTAATACGTTTAAAGAAAAAAATATAGAGAA-GAAAAAAACAAACCATTTG
24586726 NTA
195 -TA
24586729 TTTTTAAAAAAAAAGAAAAGAAAATCAATTAGTTTTAAAAAAATCAATAAGGCATGTTTAAATAA
1 TTTTTAAAAAAAAAGAAAAGAAAATCAATTAGTTTTAAAAAAATCAATAAGGCATGTTTAAATAA
24586794 AAGCAGTTTACACATTTAAAGGAAAAGAGGTAAGGCCAATTATTTTATCACATACGAGGAAGTTA
66 AAGCAGTTTACACATTTAAAGGAAAAGAGGTAAGGCCAATTATTTTATCACATACGAGGAAGTTA
24586859 AAAGTCAGTTTTCATTAATACGTTTAAAGAAAAAAATATAGAGAAGAAAAAA
131 AAAGTCAGTTTTCATTAATACGTTTAAAGAAAAAAATATAGAGAAGAAAAAA
24586911 CCATTTGGGA
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 7 0.04
198 175 0.96
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (196 bp):
TTTTTAAAAAAAAAGAAAAGAAAATCAATTAGTTTTAAAAAAATCAATAAGGCATGTTTAAATAA
AAGCAGTTTACACATTTAAAGGAAAAGAGGTAAGGCCAATTATTTTATCACATACGAGGAAGTTA
AAAGTCAGTTTTCATTAATACGTTTAAAGAAAAAAATATAGAGAAGAAAAAAACAAACCATTTGT
A
Found at i:24587671 original size:23 final size:24
Alignment explanation
Indices: 24587623--24587671 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
24587613 AAATTTTAGA
* *
24587623 ATTTATAAAAATTCATTGTTAGTT
1 ATTTATAAAAATTCATTCTTACTT
24587647 ATTT-TAAAAATT-ATTCTTGACTT
1 ATTTATAAAAATTCATTCTT-ACTT
24587670 AT
1 AT
24587672 ATTCAACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTATAAAAATTCATTCTTACTT
Found at i:24588342 original size:24 final size:25
Alignment explanation
Indices: 24588294--24588342 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
24588284 TTTTTTGTGA
24588294 AATATGATTTCTGATTTTAAAATATT
1 AATATGATTTCTGA-TTTAAAATATT
* *
24588320 AATATGATTTTTG-TTTAACATAT
1 AATATGATTTCTGATTTAAAATAT
24588343 GCATATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (25 bp):
AATATGATTTCTGATTTAAAATATT
Found at i:24588446 original size:23 final size:23
Alignment explanation
Indices: 24588420--24588474 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
24588410 TACGATATGT
24588420 GTTTTGTGAAAGTGAATATTACG
1 GTTTTGTGAAAGTGAATATTACG
*
24588443 GTTTTGTGAAAGTGAATATTACT
1 GTTTTGTGAAAGTGAATATTACG
24588466 GTTTTGTGA
1 GTTTTGTGA
24588475 GTTTGAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (23 bp):
GTTTTGTGAAAGTGAATATTACG
Found at i:24591413 original size:16 final size:15
Alignment explanation
Indices: 24591372--24591432 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
24591362 TTAAATTATA
* *
24591372 TTAAAATATTGATAT
1 TTAAATTATTAATAT
24591387 TTAAATTATTAATAT
1 TTAAATTATTAATAT
*
24591402 TT---TAATTAAT-T
1 TTAAATTATTAATAT
*
24591413 ATAAATTATTAATAT
1 TTAAATTATTAATAT
24591428 TTAAA
1 TTAAA
24591433 AATAAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 2 0.06
12 7 0.19
14 7 0.19
15 20 0.56
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAAATTATTAATAT
Found at i:24591442 original size:26 final size:26
Alignment explanation
Indices: 24591388--24591443 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
24591378 TATTGATATT
* * *
24591388 TAAATTATTAATATTTTAATTAATTA
1 TAAATTATTAATATTTAAAATAATAA
24591414 TAAATTATTAATATTTAAAAATAA-AA
1 TAAATTATTAATATTT-AAAATAATAA
24591440 TAAA
1 TAAA
24591444 AAAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAATTATTAATATTTAAAATAATAA
Found at i:24600761 original size:41 final size:41
Alignment explanation
Indices: 24600687--24600780 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
24600677 CTTATTGCTT
*
24600687 GACTTGTTATGTTATTAAAAATTTTTTATCTATAAGATTCAA
1 GACTTGTTATGGTATT-AAAATTTTTTATCTATAAGATTCAA
24600729 GACTTGTTATGGTATGT-AAATTTTTTATCTATAAGATTCAA
1 GACTTGTTATGGTAT-TAAAATTTTTTATCTATAAGATTCAA
24600770 GACTTGTTATG
1 GACTTGTTATG
24600781 CTTGACCTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
41 35 0.70
42 14 0.28
43 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (41 bp):
GACTTGTTATGGTATTAAAATTTTTTATCTATAAGATTCAA
Found at i:24645759 original size:44 final size:44
Alignment explanation
Indices: 24645696--24645796 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
24645686 TCTGGACACC
* * *
24645696 ATTGTTGCAAAAAGGAAAAGTAAACAACTTCAGTATCTTAAACT
1 ATTGTTGCAAAAAGGAAAAGGAAACAACTACAATATCTTAAACT
* * *
24645740 ATTGTTGCAAAAAGGAAAAGGAGATAACTACAATATCTTGAACT
1 ATTGTTGCAAAAAGGAAAAGGAAACAACTACAATATCTTAAACT
*
24645784 ACTGTTGCAAAAA
1 ATTGTTGCAAAAA
24645797 CTTGTAACTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.26
Consensus pattern (44 bp):
ATTGTTGCAAAAAGGAAAAGGAAACAACTACAATATCTTAAACT
Found at i:24655777 original size:19 final size:19
Alignment explanation
Indices: 24655753--24655789 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24655743 TTAAACGGTT
*
24655753 TTTCTATACGCATGACAAC
1 TTTCTACACGCATGACAAC
*
24655772 TTTCTACATGCATGACAA
1 TTTCTACACGCATGACAA
24655790 TGGGTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
TTTCTACACGCATGACAAC
Found at i:24661927 original size:17 final size:16
Alignment explanation
Indices: 24661889--24661919 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24661879 TATATTTATG
24661889 TTTTTAAAAATATTTA
1 TTTTTAAAAATATTTA
24661905 TTTTTAAAAA-ATTTA
1 TTTTTAAAAATATTTA
24661920 AATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAAAAATATTTA
Found at i:24665336 original size:2 final size:2
Alignment explanation
Indices: 24665329--24665360 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24665319 TTCAAAGCTC
*
24665329 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24665361 AAGAAAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24672966 original size:3 final size:3
Alignment explanation
Indices: 24672954--24672992 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
24672944 GGAAGAAAAG
24672954 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
24672993 AAAGAATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:24682365 original size:2 final size:2
Alignment explanation
Indices: 24682358--24682388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24682348 TGCTTGGGAG
24682358 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
24682389 CTTGAAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:24685672 original size:36 final size:34
Alignment explanation
Indices: 24685623--24685697 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 34
24685613 CTATAAAATT
24685623 TTTTTATATTATTTTAA-AAATTTAAATAAATTTTTA
1 TTTTTATATTA-TTTAACAAA-TT-AATAAATTTTTA
*
24685659 TTTTTAT-TATATTTAATCAAATTAATATATTTTTA
1 TTTTTATAT-TATTTAA-CAAATTAATAAATTTTTA
24685694 TTTT
1 TTTT
24685698 AAATCAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
35 21 0.60
36 11 0.31
37 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (34 bp):
TTTTTATATTATTTAACAAATTAATAAATTTTTA
Found at i:24685680 original size:27 final size:28
Alignment explanation
Indices: 24685642--24685695 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
24685632 TATTTTAAAA
*
24685642 ATTTAAATAAATT-TTTATTTTTATTAT
1 ATTTAAATAAATTATATATTTTTATTAT
24685669 ATTT-AATCAAATTAATATATTTTTATT
1 ATTTAAAT-AAATT-ATATATTTTTATT
24685696 TTAAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 9 0.39
29 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTAAATAAATTATATATTTTTATTAT
Found at i:24686340 original size:11 final size:11
Alignment explanation
Indices: 24686324--24686348 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24686314 AATTGTTCCA
24686324 AATCCCACATC
1 AATCCCACATC
24686335 AATCCCACATC
1 AATCCCACATC
24686346 AAT
1 AAT
24686349 GGTGCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (11 bp):
AATCCCACATC
Found at i:24686480 original size:4 final size:4
Alignment explanation
Indices: 24686471--24686498 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
24686461 TGCAGCGCGT
24686471 GAAG GAAG GAAG GAAG GAAG GAAG GAAG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG
24686499 AGAAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:24693351 original size:15 final size:17
Alignment explanation
Indices: 24693321--24693352 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24693311 GTTAAAGTCT
24693321 TCTAGTATTCTGTCTTA
1 TCTAGTATTCTGTCTTA
24693338 TCTAGT-TTCT-TCTTA
1 TCTAGTATTCTGTCTTA
24693353 CTACTGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (17 bp):
TCTAGTATTCTGTCTTA
Found at i:24711022 original size:15 final size:15
Alignment explanation
Indices: 24711004--24711036 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24710994 GGTGAAAAAT
24711004 AAAAAGAAAAAAGAG
1 AAAAAGAAAAAAGAG
*
24711019 AAAAAGAAAAAAGGG
1 AAAAAGAAAAAAGAG
24711034 AAA
1 AAA
24711037 GTGGAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAGAG
Found at i:24711686 original size:15 final size:14
Alignment explanation
Indices: 24711648--24711686 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
24711638 AAAGTTATCT
24711648 TTCCAACAATCACA
1 TTCCAACAATCACA
24711662 TTCTCAACAATCACA
1 TTC-CAACAATCACA
24711677 TTCCATACAA
1 TTCCA-ACAA
24711687 AATACCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (14 bp):
TTCCAACAATCACA
Found at i:24712534 original size:14 final size:14
Alignment explanation
Indices: 24712515--24712556 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
24712505 ATAATTTTGA
24712515 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
*
24712529 CCTAAACCTTAAA-
1 CCTAAACCCTAAAT
*
24712542 CCTTAAACCCCAAAT
1 CC-TAAACCCTAAAT
24712557 AGGATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:24714066 original size:3 final size:3
Alignment explanation
Indices: 24714025--24714054 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24714015 AAATGATGTA
24714025 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24714055 GTAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24714319 original size:20 final size:21
Alignment explanation
Indices: 24714291--24714335 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
24714281 ACAAAAGAAG
*
24714291 TAAAGAAATAATGAAAAT-AA
1 TAAAGAAATAATAAAAATAAA
* *
24714311 TAAATAAATAGTAAAAATAAA
1 TAAAGAAATAATAAAAATAAA
24714332 TAAA
1 TAAA
24714336 ACTTTCAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAAGAAATAATAAAAATAAA
Found at i:24715262 original size:21 final size:20
Alignment explanation
Indices: 24715238--24715299 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 20
24715228 TTAGTTTGCT
24715238 AATAAAATAAAGAATAAAATC
1 AATAAAATAAA-AATAAAATC
* *
24715259 AAT-AAATAAAAAT-TAA-G
1 AATAAAATAAAAATAAAATC
*
24715276 AA-AACATAAAAATAAAATC
1 AATAAAATAAAAATAAAATC
24715295 AATAA
1 AATAA
24715300 TTTATACCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
17 11 0.34
18 4 0.12
19 5 0.16
20 9 0.28
21 3 0.09
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (20 bp):
AATAAAATAAAAATAAAATC
Found at i:24719918 original size:40 final size:40
Alignment explanation
Indices: 24719874--24720006 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
24719864 AATTAAAAAG
24719874 TTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATT
1 TTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATT
** * * * **
24719914 TTAAATTTTTATATATAAAAATAATTNTAAA-TTA--AAAAG
1 TTAAAAATTTATAT-TAAAAAGAA-TGTAAATTTATTCAATT
24719953 TTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATT
1 TTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATT
**
24719993 TTAAATTTTTATAT
1 TTAAAAATTTATAT
24720007 ATAATCATAA
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
37 5 0.07
38 11 0.15
39 14 0.19
40 26 0.36
41 11 0.15
42 5 0.07
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (40 bp):
TTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATT
Found at i:24719920 original size:38 final size:38
Alignment explanation
Indices: 24719878--24720000 Score: 133
Period size: 38 Copynumber: 3.2 Consensus size: 38
24719868 AAAAAGTTAA
24719878 AAATTTATATTAAAAAGAATGTAAATTTATTCAATTTT
1 AAATTTATATTAAAAAGAATGTAAATTTATTCAATTTT
* * ** **
24719916 AAATTTTTATATATAAAAATAATTNTAAA-TTA-AAAAGTTAA
1 AAA--TTTATAT-TAAAAAGAA-TGTAAATTTATTCAA-TTTT
24719957 AAATTTATATTAAAAAGAATGTAAATTTATTCAATTTT
1 AAATTTATATTAAAAAGAATGTAAATTTATTCAATTTT
24719995 AAATTT
1 AAATTT
24720001 TTATATATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
37 5 0.08
38 22 0.33
39 9 0.14
40 9 0.14
41 16 0.24
42 5 0.08
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (38 bp):
AAATTTATATTAAAAAGAATGTAAATTTATTCAATTTT
Found at i:24719945 original size:79 final size:78
Alignment explanation
Indices: 24719861--24720019 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 78
24719851 ATTTTAAAGA
24719861 TTAAATTAAAAAGTTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATTTTAAATTTTTAT
1 TTAAATTAAAAAGTTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATTTTAAATTTTTAT
24719926 ATATAAAAATAAT
66 ATATAAAAATAAT
24719939 TNTAAATTAAAAAGTTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATTTTAAATTTTTA
1 T-TAAATTAAAAAGTTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATTTTAAATTTTTA
**
24720004 TATATAATCATAAT
65 TATATAAAAATAAT
24720018 TT
1 TT
24720020 TATAAATTTA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
78 2 0.03
79 76 0.97
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (78 bp):
TTAAATTAAAAAGTTAAAAATTTATATTAAAAAGAATGTAAATTTATTCAATTTTAAATTTTTAT
ATATAAAAATAAT
Found at i:24725294 original size:14 final size:14
Alignment explanation
Indices: 24725275--24725313 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
24725265 TTATATTTGA
*
24725275 TGTTATCATTATTT
1 TGTTATAATTATTT
24725289 TGTTATAATTA-TT
1 TGTTATAATTATTT
24725302 T-TTATAATTATT
1 TGTTATAATTATT
24725314 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 4 0.17
14 10 0.43
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (14 bp):
TGTTATAATTATTT
Found at i:24725308 original size:12 final size:13
Alignment explanation
Indices: 24725275--24725313 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
24725265 TTATATTTGA
*
24725275 TGTTATCATTATTT
1 TGTTATAATTA-TT
24725289 TGTTATAATTATT
1 TGTTATAATTATT
24725302 T-TTATAATTATT
1 TGTTATAATTATT
24725314 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 3 0.12
14 10 0.42
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (13 bp):
TGTTATAATTATT
Found at i:24727644 original size:16 final size:17
Alignment explanation
Indices: 24727623--24727660 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
24727613 CGTCTCGAAC
24727623 TTTAATAAAT-TTATTT
1 TTTAATAAATATTATTT
*
24727639 TTTAATATATATTATTT
1 TTTAATAAATATTATTT
24727656 TTTAA
1 TTTAA
24727661 CAACAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAATAAATATTATTT
Found at i:24727915 original size:17 final size:17
Alignment explanation
Indices: 24727893--24727948 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
24727883 TACAAGTATC
24727893 TAAATATATTTATAATA
1 TAAATATATTTATAATA
*
24727910 TAAATAT-TTCT-T-ATC
1 TAAATATATT-TATAATA
24727925 TAAATATATTTATAATA
1 TAAATATATTTATAATA
24727942 TAAATAT
1 TAAATAT
24727949 TTCTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 10 0.30
16 6 0.18
17 17 0.52
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATATTTATAATA
Found at i:24727918 original size:15 final size:15
Alignment explanation
Indices: 24727898--24727950 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
24727888 GTATCTAAAT
24727898 ATATTTATAATATAA
1 ATATTTATAATATAA
* * *
24727913 ATATTTCTTATCTAAA
1 ATATTTATAATAT-AA
24727929 TATATTTATAATATAA
1 -ATATTTATAATATAA
24727945 ATATTT
1 ATATTT
24727951 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 16 0.53
16 4 0.13
17 10 0.33
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTATAATATAA
Found at i:24727930 original size:32 final size:32
Alignment explanation
Indices: 24727889--24727953 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
24727879 TATTTACAAG
24727889 TATCTAAATATATTTATAATATAAATATTTCT
1 TATCTAAATATATTTATAATATAAATATTTCT
24727921 TATCTAAATATATTTATAATATAAATATTTCT
1 TATCTAAATATATTTATAATATAAATATTTCT
24727953 T
1 T
24727954 TCTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (32 bp):
TATCTAAATATATTTATAATATAAATATTTCT
Found at i:24728029 original size:12 final size:12
Alignment explanation
Indices: 24727984--24728030 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
24727974 TCTCATTCAC
24727984 TTATTATTGTTA-
1 TTATTATT-TTAT
24727996 TTATTATTTT-T
1 TTATTATTTTAT
24728007 TTAATTA-TTTAT
1 TT-ATTATTTTAT
24728019 TTATTATTTTAT
1 TTATTATTTTAT
24728031 AAATACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:24728234 original size:17 final size:17
Alignment explanation
Indices: 24728212--24728259 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
24728202 TGCTTAACTC
24728212 TTTCTTCCCTTTCTTTT
1 TTTCTTCCCTTTCTTTT
* *
24728229 TTTCTTCTCTTTCTCTT
1 TTTCTTCCCTTTCTTTT
*
24728246 TCTC-T-CCTTTCTTT
1 TTTCTTCCCTTTCTTT
24728260 CTCTCGTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 7 0.27
16 1 0.04
17 18 0.69
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTTCCCTTTCTTTT
Found at i:24728244 original size:6 final size:6
Alignment explanation
Indices: 24728220--24728286 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
24728210 TCTTTCTTCC
* *
24728220 CTTTCT TTTTTT C-TTCT CTTTCT CTTTCT CTCCTT-T CTTTCT CTCGTTCT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CT--TTCT CTTTCT CT--TTCT
*
24728270 TTTTCT CTTTCT -TTTCT
1 CTTTCT CTTTCT CTTTCT
24728287 TCTCCTTCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
5 11 0.22
6 28 0.57
7 3 0.06
8 7 0.14
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (6 bp):
CTTTCT
Found at i:24728245 original size:32 final size:34
Alignment explanation
Indices: 24728209--24728282 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 34
24728199 CTTTGCTTAA
* *
24728209 CTCTTTCTTC-CCTTTCTTTTTTTC-TTCTCTTT
1 CTCTTTCTTCTCCTTTCTTTCTCTCGTTCTCTTT
*
24728241 CTCTTTC-TCTCCTTTCTTTCTCTCGTTCTTTTT
1 CTCTTTCTTCTCCTTTCTTTCTCTCGTTCTCTTT
24728274 CTCTTTCTT
1 CTCTTTCTT
24728283 TTCTTCTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 2 0.06
32 19 0.53
33 14 0.39
34 1 0.03
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.66
Consensus pattern (34 bp):
CTCTTTCTTCTCCTTTCTTTCTCTCGTTCTCTTT
Found at i:24728250 original size:12 final size:12
Alignment explanation
Indices: 24728220--24728286 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 12
24728210 TCTTTCTTCC
* *
24728220 CTTTCTTTTTTT
1 CTTTCTCTTTCT
24728232 C-TTCTCTTTCT
1 CTTTCTCTTTCT
24728243 CTTTCTCTCCTT-T
1 CTTTCTCT--TTCT
24728256 CTTTCTCTCGTTCT
1 CTTTCTCT--TTCT
*
24728270 TTTTCTCTTTCT
1 CTTTCTCTTTCT
24728282 -TTTCT
1 CTTTCT
24728287 TCTCCTTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 14 0.30
12 11 0.23
13 12 0.26
14 10 0.21
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (12 bp):
CTTTCTCTTTCT
Found at i:24728274 original size:27 final size:28
Alignment explanation
Indices: 24728224--24728290 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
24728214 TCTTCCCTTT
* *
24728224 CTTTTTTTCTTCTCTTTCTCTTTCTCTC
1 CTTTCTTTCTTCTCGTTCTCTTTCTCTC
24728252 CTTTCTTTC-TCTCGTTCT-TTT-TCT-
1 CTTTCTTTCTTCTCGTTCTCTTTCTCTC
24728276 CTTTCTTTTCTTCTC
1 CTTTC-TTTCTTCTC
24728291 CTTCCTCGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.14
25 7 0.20
26 7 0.20
27 8 0.23
28 8 0.23
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.67
Consensus pattern (28 bp):
CTTTCTTTCTTCTCGTTCTCTTTCTCTC
Found at i:24728959 original size:3 final size:3
Alignment explanation
Indices: 24728951--24728982 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
24728941 AAATTTTTAT
24728951 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24728983 AAAAGGGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:24729331 original size:7 final size:7
Alignment explanation
Indices: 24729319--24729384 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
24729309 AGACACCTCT
24729319 AAAATAA
1 AAAATAA
24729326 AAAAT-A
1 AAAATAA
*
24729332 ATAAT--
1 AAAATAA
*
24729337 AAAATAT
1 AAAATAA
*
24729344 AAAATAT
1 AAAATAA
24729351 AAAATAA
1 AAAATAA
24729358 AATAATTAA
1 AA-AA-TAA
24729367 AAAATTAA
1 AAAA-TAA
24729375 AAAA-AA
1 AAAATAA
24729381 AAAA
1 AAAA
24729385 GAATAGAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.08
6 11 0.21
7 20 0.38
8 12 0.23
9 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAA
Found at i:24729361 original size:27 final size:26
Alignment explanation
Indices: 24729319--24729384 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
24729309 AGACACCTCT
*
24729319 AAAATAAAAAATAATAA-TAAAATAT
1 AAAATAAAAAAAAATAATTAAAATAT
*
24729344 AAAATATAAAATAAAATAATTAAAAAAT
1 AAAATA-AAAA-AAAATAATTAAAATAT
*
24729372 TAAA-AAAAAAAAA
1 AAAATAAAAAAAAA
24729385 GAATAGAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 10 0.29
26 8 0.23
27 7 0.20
28 10 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (26 bp):
AAAATAAAAAAAAATAATTAAAATAT
Found at i:24729754 original size:21 final size:21
Alignment explanation
Indices: 24729728--24729768 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24729718 GTCAGCAGGG
*
24729728 AGAAAGGAGAGAAA-GAGAAGA
1 AGAAA-GAAAGAAAGGAGAAGA
24729749 AGAAAGAAAGAAAGGAGAAG
1 AGAAAGAAAGAAAGGAGAAG
24729769 CCAGCGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAGAAAGGAGAAGA
Found at i:24729828 original size:17 final size:18
Alignment explanation
Indices: 24729788--24729842 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
24729778 GAAAGAAATG
* *
24729788 AGAAGAAAGAAAAAAAAA
1 AGAAGAAAGAGAAAAGAA
24729806 AGAAGAAAGAGAAAAGAA
1 AGAAGAAAGAGAAAAGAA
*
24729824 A-AAGAAAGAGAGAAGAA
1 AGAAGAAAGAGAAAAGAA
24729841 AG
1 AG
24729843 GGGGAGCGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAGAAAAGAA
Found at i:24729842 original size:21 final size:22
Alignment explanation
Indices: 24729779--24729842 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 22
24729769 CCAGCGGGGG
*
24729779 AAAGAAA-TGAGAAGAAAGAAA
1 AAAGAAAGAGAGAAGAAAGAAA
* *
24729800 AAAAAAAGA-AGAAAGAGAAAAGAA
1 AAAGAAAGAGAG-AAGA-AAGA-AA
24729824 AAAGAAAGAGAGAAGAAAG
1 AAAGAAAGAGAGAAGAAAG
24729843 GGGGAGCGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 8 0.24
22 4 0.12
23 5 0.15
24 14 0.42
25 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AAAGAAAGAGAGAAGAAAGAAA
Found at i:24729868 original size:4 final size:4
Alignment explanation
Indices: 24729859--24729914 Score: 55
Period size: 4 Copynumber: 14.2 Consensus size: 4
24729849 CGGCTAGGAG
*
24729859 AGAA AGAA AGAA AGAA AGTGAA AGAA AGAG AGAA AG-A A-AA AGAA A-AA
1 AGAA AGAA AGAA AGAA A--GAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
24729906 AAAA AGAA A
1 AGAA AGAA A
24729915 AAAAAAGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
3 7 0.16
4 33 0.75
6 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:24729884 original size:22 final size:22
Alignment explanation
Indices: 24729859--24729921 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
24729849 CGGCTAGGAG
**
24729859 AGAAAGAAAGAAAGAAAGTGAA
1 AGAAAGAAAGAAAGAAAAAGAA
*
24729881 AGAAAGAGAGAAAGAAAAAGAA
1 AGAAAGAAAGAAAGAAAAAGAA
* *
24729903 A-AAAAAAAGAAAAAAAAAG
1 AGAAAGAAAGAAAGAAAAAG
24729922 GGAGAAAGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAGAAAGAAAAAGAA
Found at i:24729900 original size:6 final size:6
Alignment explanation
Indices: 24729879--24729920 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
24729869 AAAGAAAGTG
* *
24729879 AAAGAA AGAGAG AAAGAA AAAGAA AAA-AA AAAGAA AAA-AA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
24729921 GGGAGAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:24729900 original size:18 final size:18
Alignment explanation
Indices: 24729861--24729921 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
24729851 GCTAGGAGAG
**
24729861 AAAGAAAGAAAGAAAGTG
1 AAAGAAAGAAAGAAAGAA
*
24729879 AAAGAAAGAGAGAAAGAA
1 AAAGAAAGAAAGAAAGAA
*
24729897 AAAGAAA-AAAAAAAGAA
1 AAAGAAAGAAAGAAAGAA
*
24729914 AAAAAAAG
1 AAAGAAAG
24729922 GGAGAAAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
17 14 0.39
18 22 0.61
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAGAA
Found at i:24729902 original size:10 final size:10
Alignment explanation
Indices: 24729865--24729921 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
24729855 GGAGAGAAAG
24729865 AAAGAAAGAA
1 AAAGAAAGAA
**
24729875 AGTGAAAGAA
1 AAAGAAAGAA
24729885 AGAGAGAAAGAA
1 A-A-AGAAAGAA
*
24729897 AAAGAAAAAAA
1 AAAG-AAAGAA
*
24729908 AAAGAAAAAA
1 AAAGAAAGAA
24729918 AAAG
1 AAAG
24729922 GGAGAAAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 21 0.54
11 10 0.26
12 8 0.21
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:24729911 original size:11 final size:11
Alignment explanation
Indices: 24729895--24729920 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
24729885 AGAGAGAAAG
24729895 AAAAAGAAAAA
1 AAAAAGAAAAA
24729906 AAAAAGAAAAA
1 AAAAAGAAAAA
24729917 AAAA
1 AAAA
24729921 GGGAGAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:24730491 original size:16 final size:16
Alignment explanation
Indices: 24730467--24730508 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
24730457 CAACTTCAGC
* *
24730467 ACTCCAATACTCATTA
1 ACTCAAATAATCATTA
24730483 ACTCAAATAATCATT-
1 ACTCAAATAATCATTA
*
24730498 ACTAAAATAAT
1 ACTCAAATAAT
24730509 AATATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (16 bp):
ACTCAAATAATCATTA
Found at i:24730723 original size:23 final size:23
Alignment explanation
Indices: 24730697--24730770 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
24730687 GATACGTATC
24730697 TAAATAAAAAATAGAAAAAATAA
1 TAAATAAAAAATAGAAAAAATAA
*
24730720 T-AA-AAAAAATA-AATAAATAA
1 TAAATAAAAAATAGAAAAAATAA
** *
24730740 TCCATAAAAAAT-GACAAAATAAA
1 TAAATAAAAAATAGAAAAAAT-AA
*
24730763 TATATAAA
1 TAAATAAA
24730771 TAAGGTGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 9 0.22
21 9 0.22
22 14 0.34
23 9 0.22
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (23 bp):
TAAATAAAAAATAGAAAAAATAA
Found at i:24730725 original size:20 final size:20
Alignment explanation
Indices: 24730702--24730740 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24730692 GTATCTAAAT
24730702 AAAAAATAGAAAAAATAATAA
1 AAAAAATA-AAAAAATAATAA
*
24730723 AAAAAATAAATAAATAAT
1 AAAAAATAAAAAAATAAT
24730741 CCATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAATAAAAAAATAATAA
Found at i:24732620 original size:24 final size:24
Alignment explanation
Indices: 24732588--24732633 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
24732578 CAAGAGTAAA
*
24732588 TATTTATAAATTAATTAATTTATT
1 TATTTATAAAATAATTAATTTATT
24732612 TATTTATAAAATAATTAATTTA
1 TATTTATAAAATAATTAATTTA
24732634 ATTCTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTATAAAATAATTAATTTATT
Found at i:24732641 original size:24 final size:24
Alignment explanation
Indices: 24732588--24732641 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
24732578 CAAGAGTAAA
* *
24732588 TATTTATAAATTAATTAATTTATT
1 TATTTATAAAATAATTAATTTAAT
24732612 TATTTATAAAATAATTAATTTAAT
1 TATTTATAAAATAATTAATTTAAT
*
24732636 TCTTTA
1 TATTTA
24732642 CAACTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTATAAAATAATTAATTTAAT
Found at i:24734474 original size:24 final size:23
Alignment explanation
Indices: 24734447--24734503 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
24734437 ATCTAGTTAG
* *
24734447 ATTAGAATAACAATTCCTAATTTT
1 ATTAGGATAA-AATTCCTAATTAT
* *
24734471 ATTAGGATAAGATTTCTAATTAT
1 ATTAGGATAAAATTCCTAATTAT
24734494 ATTAGGATAA
1 ATTAGGATAA
24734504 GGTTATTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTAGGATAAAATTCCTAATTAT
Found at i:24744996 original size:23 final size:23
Alignment explanation
Indices: 24744966--24745011 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
24744956 TAAAATAACA
*
24744966 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
24744989 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
24745012 GGTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:24748352 original size:2 final size:2
Alignment explanation
Indices: 24748345--24748386 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
24748335 TACAAATTAG
24748345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24748387 GTATGTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24749283 original size:28 final size:28
Alignment explanation
Indices: 24749247--24749514 Score: 194
Period size: 28 Copynumber: 9.9 Consensus size: 28
24749237 TTTTATAATA
* *
24749247 ACGTGTAACAATTAAATTTTTCAACATG
1 ACGTATAACAACTAAATTTTTCAACATG
**
24749275 TTGTATAACAACTAAATTTTT-AACATG
1 ACGTATAACAACTAAATTTTTCAACATG
* * * *
24749302 ACGTGTAACAACTATATTTTTCAATAGG
1 ACGTATAACAACTAAATTTTTCAACATG
* * *
24749330 ACATGTAATAACTAAA--TTTCAACATGG
1 ACGTATAACAACTAAATTTTTCAACAT-G
* * *
24749357 A-GTCTAACAACTACATTTTTCAACATA
1 ACGTATAACAACTAAATTTTTCAACATG
* * *
24749384 ACATGT-A-AACTAAATTTTT-AAAATG
1 ACGTATAACAACTAAATTTTTCAACATG
*
24749409 ACGTGTAACAACTAAATTTTTCAACATG
1 ACGTATAACAACTAAATTTTTCAACATG
** * * *
24749437 ATATGTAATAACTAAA-TTTTGAACATG
1 ACGTATAACAACTAAATTTTTCAACATG
* ** *
24749464 ACGTGTAACAACTAAATTTTAAAATATG
1 ACGTATAACAACTAAATTTTTCAACATG
* * *
24749492 ACATATAAC-ATTACATTTTTCAA
1 ACGTATAACAACTAAATTTTTCAA
24749515 AACTGCCATA
Statistics
Matches: 188, Mismatches: 43, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
25 9 0.05
26 29 0.15
27 72 0.38
28 78 0.41
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (28 bp):
ACGTATAACAACTAAATTTTTCAACATG
Found at i:24749306 original size:55 final size:55
Alignment explanation
Indices: 24749247--24749483 Score: 293
Period size: 55 Copynumber: 4.4 Consensus size: 55
24749237 TTTTATAATA
* *** * *
24749247 ACGTGTAACAATTAAATTTTTCAACATGTTGTATAACAACTAAATTTTTAACATG
1 ACGTGTAACAACTAAATTTTTCAACATGACATGTAATAACTAAATTTTTAACATG
* * * *
24749302 ACGTGTAACAACTATATTTTTCAATAGGACATGTAATAACTAAA-TTTCAACATGG
1 ACGTGTAACAACTAAATTTTTCAACATGACATGTAATAACTAAATTTTTAACAT-G
* * * *
24749357 A-GTCTAACAACTACATTTTTCAACATAACATGT-A-AACTAAATTTTTAAAATG
1 ACGTGTAACAACTAAATTTTTCAACATGACATGTAATAACTAAATTTTTAACATG
* *
24749409 ACGTGTAACAACTAAATTTTTCAACATGATATGTAATAACTAAATTTTGAACATG
1 ACGTGTAACAACTAAATTTTTCAACATGACATGTAATAACTAAATTTTTAACATG
24749464 ACGTGTAACAACTAAATTTT
1 ACGTGTAACAACTAAATTTT
24749484 AAAATATGAC
Statistics
Matches: 154, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
52 9 0.06
53 36 0.23
54 36 0.23
55 73 0.47
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (55 bp):
ACGTGTAACAACTAAATTTTTCAACATGACATGTAATAACTAAATTTTTAACATG
Found at i:24749398 original size:107 final size:108
Alignment explanation
Indices: 24749284--24749483 Score: 305
Period size: 107 Copynumber: 1.9 Consensus size: 108
24749274 GTTGTATAAC
* * *
24749284 AACTAAATTTTTAACATGACGTGTAACAACTATATTTTTCAATAGGACATGTAATAACTAAA-TT
1 AACTAAATTTTTAAAATGACGTGTAACAACTAAATTTTTCAACAGGACATGTAATAACTAAATTT
*
24749348 TCAACATGGA-GTCTAACAACTACATTTTTCAACATAACATGTA
66 TCAACAT-GACGTCTAACAACTAAATTTTTCAACATAACATGTA
* *
24749391 AACTAAATTTTTAAAATGACGTGTAACAACTAAATTTTTCAACATGATATGTAATAACTAAATTT
1 AACTAAATTTTTAAAATGACGTGTAACAACTAAATTTTTCAACAGGACATGTAATAACTAAATTT
* *
24749456 TGAACATGACGTGTAACAACTAAATTTT
66 TCAACATGACGTCTAACAACTAAATTTT
24749484 AAAATATGAC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
107 59 0.71
108 24 0.29
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (108 bp):
AACTAAATTTTTAAAATGACGTGTAACAACTAAATTTTTCAACAGGACATGTAATAACTAAATTT
TCAACATGACGTCTAACAACTAAATTTTTCAACATAACATGTA
Found at i:24756076 original size:12 final size:13
Alignment explanation
Indices: 24756044--24756081 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
24756034 TTATATTTGA
*
24756044 TGTTATTATTATT
1 TGTTATAATTATT
24756057 TGTTATAATTATT
1 TGTTATAATTATT
24756070 T-TTATAATTATT
1 TGTTATAATTATT
24756082 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (13 bp):
TGTTATAATTATT
Found at i:24756246 original size:37 final size:36
Alignment explanation
Indices: 24756186--24756256 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
24756176 AATCGTTTAA
24756186 TTGTATTTACTAATCGCGTCATGTCATATAAAAATTT
1 TTGTATTTACTAATCGCGTCATGTCATA-AAAAATTT
* * * *
24756223 TTGTGTTTATTAATCGTGTCATGTTATAAAAAAT
1 TTGTATTTACTAATCGCGTCATGTCATAAAAAAT
24756257 CATAACACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 6 0.20
37 24 0.80
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (36 bp):
TTGTATTTACTAATCGCGTCATGTCATAAAAAATTT
Found at i:24757540 original size:20 final size:19
Alignment explanation
Indices: 24757515--24757554 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24757505 TTCATTGAAA
*
24757515 TTGACAAAATATAATAATTC
1 TTGAC-AAATAAAATAATTC
*
24757535 TTGACAATTAAAATAATTC
1 TTGACAAATAAAATAATTC
24757554 T
1 T
24757555 AAAATCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
TTGACAAATAAAATAATTC
Found at i:24767080 original size:21 final size:20
Alignment explanation
Indices: 24767051--24767100 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
24767041 ATTTTTACTA
*
24767051 TTAAGATTTAAGATTCA-GAG
1 TTAAAATTTAAGATT-ATGAG
*
24767071 TTTAAAATTTAGGATTATGAG
1 -TTAAAATTTAAGATTATGAG
24767092 TTAAAATTT
1 TTAAAATTT
24767101 TATTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (20 bp):
TTAAAATTTAAGATTATGAG
Found at i:24784420 original size:27 final size:29
Alignment explanation
Indices: 24784388--24784461 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
24784378 AGTATTAAAG
*
24784388 TGTAACAA-AATATTTTT-AAATATAGTG
1 TGTAACAACAATATTTTTGAAATATAGTA
* *
24784415 TTTAACAACAATATTTTTGTAATATAGTA
1 TGTAACAACAATATTTTTGAAATATAGTA
* *
24784444 TGTAGCAATAATATTTTT
1 TGTAACAACAATATTTTT
24784462 TTTTCAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 7 0.18
28 9 0.23
29 23 0.59
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (29 bp):
TGTAACAACAATATTTTTGAAATATAGTA
Found at i:24784488 original size:26 final size:26
Alignment explanation
Indices: 24784452--24784515 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
24784442 TATGTAGCAA
*
24784452 TAATATTTTTTTTTCAA-CATAACGTG
1 TAATAATTTTTTTT-AACCATAACGTG
*
24784478 TAATAATTTTTTTTAACCATGACGTG
1 TAATAATTTTTTTTAACCATAACGTG
24784504 TAATATATTTTT
1 TAATA-ATTTTT
24784516 ATACATGGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 2 0.06
26 26 0.76
27 6 0.18
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (26 bp):
TAATAATTTTTTTTAACCATAACGTG
Found at i:24802940 original size:23 final size:26
Alignment explanation
Indices: 24802877--24802941 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
24802867 AAAATAAATC
24802877 TAATTT-TTTTATAAATATTAAAAAA
1 TAATTTATTTTATAAATATTAAAAAA
*
24802902 TAAATTA-TTTATAAAT-TTAAAAAA
1 TAATTTATTTTATAAATATTAAAAAA
24802926 T-ATTTATTTTA-AAATA
1 TAATTTATTTTATAAATA
24802942 CTTTTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
23 8 0.23
24 13 0.37
25 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTTATTTTATAAATATTAAAAAA
Found at i:24803481 original size:30 final size:30
Alignment explanation
Indices: 24803445--24803512 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
24803435 AATTATAAGG
24803445 ACTTATTTGAATT-AAAATAAAAATATAAAA
1 ACTTATTTG-ATTCAAAATAAAAATATAAAA
*
24803475 ATTTATTTGATTCAAAATAAAAATATAAAA
1 ACTTATTTGATTCAAAATAAAAATATAAAA
24803505 ACTTATTT
1 ACTTATTT
24803513 AAATGCAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (30 bp):
ACTTATTTGATTCAAAATAAAAATATAAAA
Found at i:24803522 original size:29 final size:29
Alignment explanation
Indices: 24803445--24803533 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
24803435 AATTATAAGG
**
24803445 ACTTATTTGAATTAAAATAAAAATATAAAA
1 ACTTATTT-AATGCAAATAAAAATATAAAA
* * *
24803475 ATTTATTTGATTCAAAATAAAAATATAAAA
1 ACTTATTTAATGC-AAATAAAAATATAAAA
*
24803505 ACTTATTTAAATGC-AATAAAACTATAAAA
1 ACTTATTT-AATGCAAATAAAAATATAAAA
24803534 GTTGATTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 17 0.34
30 30 0.60
31 3 0.06
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (29 bp):
ACTTATTTAATGCAAATAAAAATATAAAA
Found at i:24833643 original size:23 final size:21
Alignment explanation
Indices: 24833601--24833643 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
24833591 TATAAAAAAA
* *
24833601 ATTATTTATATATTTACAAAC
1 ATTATATATATATTAACAAAC
24833622 ATTATATATATATATAATCAAA
1 ATTATATATATAT-TAA-CAAA
24833644 TGTGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 2 0.11
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATATATATATTAACAAAC
Found at i:24835946 original size:49 final size:50
Alignment explanation
Indices: 24835882--24835996 Score: 151
Period size: 49 Copynumber: 2.3 Consensus size: 50
24835872 TTATCTTGAT
*
24835882 ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTT-CGACTTA
1 ATCTTGATTACGAACACTTCATATCTTCGCTTCAAGAGTCTTACGACTTA
* * * * * *
24835931 ATCTTGATCACGAACACTTGATATCTTCTCTTGAAGGGTCTTCACGACTTG
1 ATCTTGATTACGAACACTTCATATCTTCGCTTCAAGAGTCTT-ACGACTTA
24835982 ATCTTGATTACGAAC
1 ATCTTGATTACGAAC
24835997 TTCGCTTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 36 0.64
51 20 0.36
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (50 bp):
ATCTTGATTACGAACACTTCATATCTTCGCTTCAAGAGTCTTACGACTTA
Found at i:24835956 original size:79 final size:80
Alignment explanation
Indices: 24835803--24836198 Score: 252
Period size: 79 Copynumber: 5.0 Consensus size: 80
24835793 GCACAACTTA
* * * * * * ** *
24835803 ATCTTGATCATGAACACTTGATATTTTCGCTTTAAGGGTCTTCACGACTTGATCTTGAAAACAAA
1 ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTT-ACGACTTAATCTTGATCACGAA
24835868 CACTT--TATCTTGAT
65 CACTTGATATCTTGAT
24835882 ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTT-CGACTTAATCTTGATCACGAAC
1 ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTTACGACTTAATCTTGATCACGAAC
24835946 ACTTGATATC-T--T
66 ACTTGATATCTTGAT
* * * ** * * * *
24835958 CTCTTGAAGGGTCTTCACGACTT--GATCTT-GATT-ACGA-ACTT-CG-CTTGATATCTTGATC
1 ATCTTG-A--TTATGAAC-ACTTCATATCTTCGCTTCAAGAGTCTTACGACTT-A-ATCTTGATC
** * *
24836016 ACGAAGTTCGTGGACT-TGTTGCCACTT
60 ACGAA-CAC-TTGA-TATCTTG--A--T
* * * * *
24836043 GATCTTGATTACGAACACTTGATATCTTTGCTTCAAAAGTCTTCACGACTTGATCTTGATCACGA
1 -ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTT-ACGACTTAATCTTGATCACGA
*
24836108 ACACTT--TATCTTTAT
64 ACACTTGATATCTTGAT
*
24836123 ATCTTGATTATGAACACTTCATATCTTCACTTC-A-AGTCTTCACGACTTAATCTTGATCACGAA
1 ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTT-ACGACTTAATCTTGATCACGAA
24836186 CACTTGATATCTT
65 CACTTGATATCTT
24836199 CGCTTTAAGG
Statistics
Matches: 243, Mismatches: 44, Indels: 60
0.70 0.13 0.17
Matches are distributed among these distances:
74 3 0.01
75 6 0.02
76 23 0.09
77 60 0.25
78 11 0.05
79 82 0.34
80 5 0.02
82 5 0.02
83 4 0.02
84 8 0.03
85 5 0.02
86 8 0.03
87 4 0.02
88 14 0.06
89 2 0.01
90 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (80 bp):
ATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTTACGACTTAATCTTGATCACGAAC
ACTTGATATCTTGAT
Found at i:24836167 original size:77 final size:78
Alignment explanation
Indices: 24836044--24836190 Score: 233
Period size: 77 Copynumber: 1.9 Consensus size: 78
24836034 TTGCCACTTG
* ** *
24836044 ATCTTGATTACGAACACTTGATATCTTTGCTTCAAAAGTCTTCACGACTTGATCTTGATCACGAA
1 ATCTTGATTACGAACACTTCATATCTTCACTTC-AAAGTCTTCACGACTTAATCTTGATCACGAA
24836109 CACTTTATCTTTAT
65 CACTTTATCTTTAT
*
24836123 ATCTTGATTATGAACACTTCATATCTTCACTTC-AAGTCTTCACGACTTAATCTTGATCACGAAC
1 ATCTTGATTACGAACACTTCATATCTTCACTTCAAAGTCTTCACGACTTAATCTTGATCACGAAC
24836187 ACTT
66 ACTT
24836191 GATATCTTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 34 0.54
79 29 0.46
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (78 bp):
ATCTTGATTACGAACACTTCATATCTTCACTTCAAAGTCTTCACGACTTAATCTTGATCACGAAC
ACTTTATCTTTAT
Found at i:24836187 original size:49 final size:50
Alignment explanation
Indices: 24836123--24836235 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 50
24836113 TTATCTTTAT
* *
24836123 ATCTTGATTATGAACACTTCATATCTTCACTTCAA-GTCTTCACGACTTA
1 ATCTTGATCACGAACACTTCATATCTTCACTTCAAGGTCTTCACGACTTA
* * * * *
24836172 ATCTTGATCACGAACACTTGATATCTTCGCTTTAAGGGTCTTCACGGCTTG
1 ATCTTGATCACGAACACTTCATATCTTCACTTCAA-GGTCTTCACGACTTA
24836223 ATCTTGATCACGA
1 ATCTTGATCACGA
24836236 CTTAATCTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 30 0.55
51 25 0.45
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (50 bp):
ATCTTGATCACGAACACTTCATATCTTCACTTCAAGGTCTTCACGACTTA
Found at i:24836226 original size:241 final size:241
Alignment explanation
Indices: 24835798--24836235 Score: 693
Period size: 241 Copynumber: 1.8 Consensus size: 241
24835788 GGTCTGCACA
* * **
24835798 ACTTAATCTTGATCATGAACACTTGATATTTTCGCTTTAAGGGTCTTCACGACTTGATCTTGAAA
1 ACTTAATCTTGATCACGAACACTTGATATTTTCGCTTCAAAAGTCTTCACGACTTGATCTTGAAA
*
24835863 ACAAACACTTTATCTTGATATCTTGATTATGAACACTTCATATCTTCGCTTCAAGAGTCTTCGAC
66 ACAAACACTTTATCTTGATATCTTGATTATGAACACTTCATATCTTCACTTCAAGAGTCTTCGAC
* *
24835928 TTAATCTTGATCACGAACACTTGATATCTTCTCTTGAAGGGTCTTCACGACTTGATCTTGATTAC
131 TTAATCTTGATCACGAACACTTGATATCTTCGCTTGAAGGGTCTTCACGACTTGATCTTGATCAC
24835993 GAACTTCGCTTGATATCTTGATCACGAAGTTCGTGGACTTGTTGCC
196 GAACTTCGCTTGATATCTTGATCACGAAGTTCGTGGACTTGTTGCC
* * *
24836039 ACTTGATCTTGATTACGAACACTTGATATCTTT-GCTTCAAAAGTCTTCACGACTTGATCTTGAT
1 ACTTAATCTTGATCACGAACACTTGATAT-TTTCGCTTCAAAAGTCTTCACGACTTGATCTTGAA
* * *
24836103 CACGAACACTTTATCTTTATATCTTGATTATGAACACTTCATATCTTCACTTC-A-AGTCTTCAC
65 AACAAACACTTTATCTTGATATCTTGATTATGAACACTTCATATCTTCACTTCAAGAGTCTT--C
* *
24836166 GACTTAATCTTGATCACGAACACTTGATATCTTCGCTTTAAGGGTCTTCACGGCTTGATCTTGAT
128 GACTTAATCTTGATCACGAACACTTGATATCTTCGCTTGAAGGGTCTTCACGACTTGATCTTGAT
24836231 CACGA
193 CACGA
24836236 CTTAATCTTG
Statistics
Matches: 179, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
239 6 0.03
240 1 0.01
241 169 0.94
242 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (241 bp):
ACTTAATCTTGATCACGAACACTTGATATTTTCGCTTCAAAAGTCTTCACGACTTGATCTTGAAA
ACAAACACTTTATCTTGATATCTTGATTATGAACACTTCATATCTTCACTTCAAGAGTCTTCGAC
TTAATCTTGATCACGAACACTTGATATCTTCGCTTGAAGGGTCTTCACGACTTGATCTTGATCAC
GAACTTCGCTTGATATCTTGATCACGAAGTTCGTGGACTTGTTGCC
Found at i:24836243 original size:17 final size:17
Alignment explanation
Indices: 24836213--24836249 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
24836203 TTAAGGGTCT
* *
24836213 TCACGGCTTGATCTTGA
1 TCACGACTTAATCTTGA
24836230 TCACGACTTAATCTTGA
1 TCACGACTTAATCTTGA
24836247 TCA
1 TCA
24836250 TGAACACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (17 bp):
TCACGACTTAATCTTGA
Found at i:24836329 original size:31 final size:31
Alignment explanation
Indices: 24836291--24836367 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
24836281 TCACAACTTC
*
24836291 ATCTTGATCATGAACTTCACTTGATATCTTA
1 ATCTTGATCACGAACTTCACTTGATATCTTA
* * *
24836322 ATCTTGATCACGAATTTCGCTTGATATCTTG
1 ATCTTGATCACGAACTTCACTTGATATCTTA
24836353 ATCTTGATCACGAAC
1 ATCTTGATCACGAAC
24836368 ACTTTATCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (31 bp):
ATCTTGATCACGAACTTCACTTGATATCTTA
Found at i:24836329 original size:68 final size:68
Alignment explanation
Indices: 24836162--24836300 Score: 233
Period size: 68 Copynumber: 2.0 Consensus size: 68
24836152 CTTCAAGTCT
* * ** *
24836162 TCACGACTTAATCTTGATCACGAACACTTGATATCTTCGCTTTAAGGGTCTTCACGGCTTGATCT
1 TCACGACTTAATCTTGATCATGAACACTTGATATCTTCACTTTAAGGGTCTTCACAACTTCATCT
24836227 TGA
66 TGA
24836230 TCACGACTTAATCTTGATCATGAACACTTGATATCTTCACTTTAAGGGTCTTCACAACTTCATCT
1 TCACGACTTAATCTTGATCATGAACACTTGATATCTTCACTTTAAGGGTCTTCACAACTTCATCT
24836295 TGA
66 TGA
24836298 TCA
1 TCA
24836301 TGAACTTCAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (68 bp):
TCACGACTTAATCTTGATCATGAACACTTGATATCTTCACTTTAAGGGTCTTCACAACTTCATCT
TGA
Found at i:24836619 original size:51 final size:50
Alignment explanation
Indices: 24836507--24836624 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 50
24836497 TTTATCTTGA
* * * *
24836507 TATCTTGATTACGAACACTTTATATCTTTACTTCAATGGTCTTCATTGCT
1 TATCTTGATCACGAACACTTGATATCTTGACTTCAAGGGTCTTCATTGCT
* * *
24836557 TAGTCTGGATCAGGAACACTTGATATCTTCGA-TTTAAGGGTCTTCA-TGACT
1 TA-TCTTGATCACGAACACTTGATATCTT-GACTTCAAGGGTCTTCATTG-CT
24836608 TGATCTTGATCACGAAC
1 T-ATCTTGATCACGAAC
24836625 TTCGCTTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
50 4 0.07
51 49 0.89
52 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (50 bp):
TATCTTGATCACGAACACTTGATATCTTGACTTCAAGGGTCTTCATTGCT
Found at i:24836641 original size:31 final size:31
Alignment explanation
Indices: 24836606--24836840 Score: 177
Period size: 31 Copynumber: 7.7 Consensus size: 31
24836596 GTCTTCATGA
*
24836606 CTTGATCTTGATCACGAACTTCGCTTGATAT
1 CTTGATCTTGATCACAAACTTCGCTTGATAT
*
24836637 CTTGATCTTGATCACGAACTTCGCTTGATAT
1 CTTGATCTTGATCACAAACTTCGCTTGATAT
*
24836668 CTTGATCTTGATCATAAACTTCGCTTGATAT
1 CTTGATCTTGATCACAAACTTCGCTTGATAT
* **
24836699 ACGAACACTTTATCTTGATCACAAACTTCG-TTG-TCG
1 -------CTTGATCTTGATCACAAACTTCGCTTGATAT
* * * *
24836735 CTTGATCTTAATCACAAACTTC-ATTGCT-G
1 CTTGATCTTGATCACAAACTTCGCTTGATAT
* *
24836764 CTTGATCTTGATCACGAA-GT-GCTTG--AT
1 CTTGATCTTGATCACAAACTTCGCTTGATAT
* ** *
24836791 CTTGATCATGATCATGAACTTCG-TT-ACTGT
1 CTTGATCTTGATCACAAACTTCGCTTGA-TAT
24836821 -TTGATCTTGATCACAAACTT
1 CTTGATCTTGATCACAAACTT
24836841 TGCTGCTACT
Statistics
Matches: 168, Mismatches: 20, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
27 16 0.10
28 7 0.04
29 58 0.35
30 2 0.01
31 60 0.36
36 1 0.01
37 3 0.02
38 21 0.12
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (31 bp):
CTTGATCTTGATCACAAACTTCGCTTGATAT
Found at i:24836853 original size:29 final size:29
Alignment explanation
Indices: 24836710--24836854 Score: 134
Period size: 29 Copynumber: 5.1 Consensus size: 29
24836700 CGAACACTTT
24836710 ATCTTGATCACAAACTTCGTTG-TCGCTTG
1 ATCTTGATCACAAACTTCGTTGCT-GCTTG
* *
24836739 ATCTTAATCACAAACTTCATTGCTGCTTG
1 ATCTTGATCACAAACTTCGTTGCTGCTTG
* * * *
24836768 ATCTTGATCACGAAGTGC-TTGAT-CTTG
1 ATCTTGATCACAAACTTCGTTGCTGCTTG
* ** * *
24836795 ATCATGATCATGAACTTCGTTACTGTTTG
1 ATCTTGATCACAAACTTCGTTGCTGCTTG
* * *
24836824 ATCTTGATCACAAACTTTGCTGCTACTTG
1 ATCTTGATCACAAACTTCGTTGCTGCTTG
24836853 AT
1 AT
24836855 TTTCATTTTA
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
27 18 0.20
28 7 0.08
29 65 0.71
30 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (29 bp):
ATCTTGATCACAAACTTCGTTGCTGCTTG
Found at i:24836923 original size:18 final size:18
Alignment explanation
Indices: 24836900--24836934 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
24836890 TGAAATGTTC
24836900 TCAATCTTCGAATGCTTG
1 TCAATCTTCGAATGCTTG
24836918 TCAATCTTCGAATGCTT
1 TCAATCTTCGAATGCTT
24836935 TTGAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (18 bp):
TCAATCTTCGAATGCTTG
Found at i:24837315 original size:82 final size:80
Alignment explanation
Indices: 24837209--24837413 Score: 268
Period size: 82 Copynumber: 2.5 Consensus size: 80
24837199 AATATAATTA
*
24837209 TTAGAGATAAATTAAATGACCAATAATTTAATTTTGATTGGTAAAAAATATGAATATTATCTCTA
1 TTAGAGAAAAATT-AATGACCAATAATTTAATTTTGATTGGTAAAAAATATGAATATTATCTCTA
*
24837274 AATTATCTTGATTTAT
65 AATTACCTTGATTTAT
* * * * * *
24837290 TTCGAGACAAAATTATATGAGCAATAATTAAATTTTAATTGGTCAAAAATATGAATATTATCTTT
1 TTAGAGA-AAAATTA-ATGACCAATAATTTAATTTTGATTGGTAAAAAATATGAATATTATCTCT
24837355 AAATTACCTTGATTTAT
64 AAATTACCTTGATTTAT
* *
24837372 TTAGAGATAAATTGAATGACCAATAA-TTAAGTTTTGAGTGGT
1 TTAGAGAAAAATT-AATGACCAATAATTTAA-TTTTGATTGGT
24837414 CCAATTTAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.03
81 31 0.29
82 72 0.68
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (80 bp):
TTAGAGAAAAATTAATGACCAATAATTTAATTTTGATTGGTAAAAAATATGAATATTATCTCTAA
ATTACCTTGATTTAT
Found at i:24842947 original size:2 final size:2
Alignment explanation
Indices: 24842940--24842972 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
24842930 TCGTGAAGCA
*
24842940 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
24842973 AACTTGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:24844926 original size:21 final size:22
Alignment explanation
Indices: 24844884--24844929 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
24844874 TATCATATCT
*
24844884 ATTATAAAAAAAATTGTTTATATA
1 ATTATAAAAAAAA-T-TATATATA
24844908 ATTATAAAAAAAA-TATATATA
1 ATTATAAAAAAAATTATATATA
24844929 A
1 A
24844930 GAAAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
24 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTATAAAAAAAATTATATATA
Found at i:24845512 original size:10 final size:10
Alignment explanation
Indices: 24845482--24845540 Score: 54
Period size: 9 Copynumber: 6.3 Consensus size: 10
24845472 AAACACCTAA
24845482 AAAATA-AAT
1 AAAATATAAT
* *
24845491 AAAAAAT-TT
1 AAAATATAAT
*
24845500 AAATTATAAT
1 AAAATATAAT
*
24845510 AAAATAAAAT
1 AAAATATAAT
24845520 AAAATATAA-
1 AAAATATAAT
24845529 AAAATA-AAT
1 AAAATATAAT
24845538 AAA
1 AAA
24845541 GACAATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
8 2 0.05
9 20 0.51
10 17 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAATATAAT
Found at i:24858547 original size:29 final size:30
Alignment explanation
Indices: 24858497--24858563 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
24858487 AGAATTTTTT
* *
24858497 TTTAAAAAAAGAGAGAACAAAATTATAAAA
1 TTTAAAAAAAGAGAAAAAAAAATTATAAAA
* *
24858527 TTTAAAAAAA-ATAAAAAAAAATTATTAAA
1 TTTAAAAAAAGAGAAAAAAAAATTATAAAA
*
24858556 TTTTAAAA
1 TTTAAAAA
24858564 GTTTAGGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (30 bp):
TTTAAAAAAAGAGAAAAAAAAATTATAAAA
Found at i:24865092 original size:65 final size:65
Alignment explanation
Indices: 24865012--24865142 Score: 183
Period size: 65 Copynumber: 2.0 Consensus size: 65
24865002 TTATATCGAA
* * *
24865012 TTATTCTTAGTATTAAAT-AAGAGTGAAAGAAAAACAAAATGGAAGTGAAAGATATGGAGAATAT
1 TTATTCTTAGCATTAAATGAA-AGTGAAAGAAAAAAAAAATGAAAGTGAAAGATATGGAGAATAT
24865076 T
65 T
* * * *
24865077 TTATTCTTAGCATTAAATGAAAGTGAACGAAAAAAAAAATGAAAGTGGAAGATTTGGAGTATATT
1 TTATTCTTAGCATTAAATGAAAGTGAAAGAAAAAAAAAATGAAAGTGAAAGATATGGAGAATATT
24865142 T
1 T
24865143 AAACAGCAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 56 0.97
66 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (65 bp):
TTATTCTTAGCATTAAATGAAAGTGAAAGAAAAAAAAAATGAAAGTGAAAGATATGGAGAATATT
Found at i:24889365 original size:18 final size:18
Alignment explanation
Indices: 24889325--24889366 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24889315 CTTATAAAAA
*
24889325 ATTAAATATTTAAATTTT
1 ATTAAATATTTAAATATT
*
24889343 ATTAATTATTTAAATGATT
1 ATTAAATATTTAAAT-ATT
24889362 -TTAAA
1 ATTAAA
24889367 AATTATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTAAATATTTAAATATT
Found at i:24889800 original size:22 final size:22
Alignment explanation
Indices: 24889775--24889817 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24889765 GTGTGTGTAT
24889775 ATAAATATATATA-TTATAATTA
1 ATAAATATATA-AGTTATAATTA
* *
24889797 ATAATTTTATAAGTTATAATT
1 ATAAATATATAAGTTATAATT
24889818 TTTATAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAAATATATAAGTTATAATTA
Found at i:24889822 original size:16 final size:15
Alignment explanation
Indices: 24889788--24889825 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
24889778 AATATATATA
24889788 TTATAATTAATAATT
1 TTATAATTAATAATT
24889803 TTATAAGTT-ATAATTT
1 TTATAA-TTAATAA-TT
24889819 TTATAAT
1 TTATAAT
24889826 ACTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTAATAATT
Found at i:24889875 original size:15 final size:15
Alignment explanation
Indices: 24889855--24889885 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24889845 TAAATATATT
*
24889855 TATATTTAAAGTATA
1 TATATTAAAAGTATA
24889870 TATATTAAAAGTATA
1 TATATTAAAAGTATA
24889885 T
1 T
24889886 TAGTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
TATATTAAAAGTATA
Found at i:24890224 original size:2 final size:2
Alignment explanation
Indices: 24890217--24890254 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24890207 ATTTAAAGTG
24890217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24890255 NAATCATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24890470 original size:273 final size:273
Alignment explanation
Indices: 24889978--24890497 Score: 681
Period size: 273 Copynumber: 1.9 Consensus size: 273
24889968 GTTAATTAAT
* * *
24889978 AATCATAGTTTCATTAATTAATTTAATAAATTATATGAGTTTATTCTTAATTACATGAAATTAAA
1 AATCATAGTTTCATGAATTAATTTAATAAATTATATGAGTTTATCCTTAATTACATAAAATTAAA
* ** ** * *
24890043 AAAATAACTGAGTTTCAAAACTATTCTAATTTCATAATTTCTTTTTAGATAATTAAGTTTATATA
66 AAAATAACAGAGACTCAAAACTATTCTAACCTCACAACTTC-TTTT--ATAA-TAAGTTTATATA
* * ***
24890108 TTATAAATTTATATAAACAAATATATATATTGTAATTAATAATTTTGTAAGTTATAATTTTTATA
127 TTACAAATTTATATAAACAAATATATATATTATAATTAATAATTTCACAAGTTATAATTTTTATA
*
24890173 ATGTTAACATAAAACAGAAAGTAAATATATTTATATTTAAAGTGTATATATATATATATATATAT
192 ATGTTAACATAAAACAGAAAGTAAATATATTTATATTTAAAGTATATATATATATATATATATAT
24890238 ATATATATATATATATA
257 ATATATATATATATATA
* * *
24890255 NAATCATAGTTTTATGAATTAATTTAATTAATTATATGAGTTTGTCCTTAATTACATAAAATTAC
1 -AATCATAGTTTCATGAATTAATTTAATAAATTATATGAGTTTATCCTTAATTACATAAAATTA-
* * *
24890320 AAAAAATAACA-AGGACTCAAAACTATTCTTACCTCACAACTTC-TTT-T-A-AGGTTTGTATAT
64 AAAAAATAACAGA-GACTCAAAACTATTCTAACCTCACAACTTCTTTTATAATAAGTTTATATAT
* * *
24890380 TACAAGTTTATATAAATAAAGGTATATATATTATAATTAATAATTTCACAAGTTATAATTTTTGT
128 TACAAATTTATATAAACAAA--TATATATATTATAATTAATAATTTCACAAGTTATAATTTTTAT
* *
24890445 AATGTTAATATAAAATAGAAAGTAAATATATTTATATTTAAAGTATATATATA
191 AATGTTAACATAAAACAGAAAGTAAATATATTTATATTTAAAGTATATATATA
24890498 CTAAAAGTAT
Statistics
Matches: 211, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
271 27 0.13
273 89 0.42
274 1 0.00
277 3 0.01
278 58 0.27
279 33 0.16
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (273 bp):
AATCATAGTTTCATGAATTAATTTAATAAATTATATGAGTTTATCCTTAATTACATAAAATTAAA
AAAATAACAGAGACTCAAAACTATTCTAACCTCACAACTTCTTTTATAATAAGTTTATATATTAC
AAATTTATATAAACAAATATATATATTATAATTAATAATTTCACAAGTTATAATTTTTATAATGT
TAACATAAAACAGAAAGTAAATATATTTATATTTAAAGTATATATATATATATATATATATATAT
ATATATATATATA
Found at i:24890497 original size:17 final size:17
Alignment explanation
Indices: 24890467--24890517 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
24890457 AAATAGAAAG
*
24890467 TAAA-TATATTTATATT
1 TAAAGTATATATATATT
*
24890483 TAAAGTATATATATACT
1 TAAAGTATATATATATT
*
24890500 AAAAGTATTAGTATATAT
1 TAAAGTA-TA-TATATAT
24890518 GATATAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 2 0.07
19 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (17 bp):
TAAAGTATATATATATT
Found at i:24892627 original size:31 final size:33
Alignment explanation
Indices: 24892589--24892651 Score: 103
Period size: 31 Copynumber: 1.9 Consensus size: 33
24892579 GCTTAAAGCT
24892589 TATTATTTTTGGTTTTAT-TTT-TTTTGAAAGG
1 TATTATTTTTGGTTTTATATTTCTTTTGAAAGG
24892620 TATTATTTTTGGTTTTATACTTTCTTTTGAAA
1 TATTATTTTTGGTTTTATA-TTTCTTTTGAAA
24892652 TTAAACGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 18 0.62
33 3 0.10
34 8 0.28
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.63
Consensus pattern (33 bp):
TATTATTTTTGGTTTTATATTTCTTTTGAAAGG
Found at i:24894937 original size:25 final size:23
Alignment explanation
Indices: 24894893--24894938 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
24894883 TGTATGACGT
*
24894893 TTGGCTATTTATTGATGTGAGGC
1 TTGGCTATTAATTGATGTGAGGC
24894916 TTGGCTAATTAATTGGATGTGAG
1 TTGGCT-ATTAATT-GATGTGAG
24894939 AAAGGAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (23 bp):
TTGGCTATTAATTGATGTGAGGC
Found at i:24913768 original size:19 final size:18
Alignment explanation
Indices: 24913746--24913792 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
24913736 AATTATTTAT
24913746 TTTAAAAATTAA-TAAATTA
1 TTTAAAAATTAATTAAA--A
*
24913765 TTTAAAATTTTAATTAAAA
1 TTTAAAA-ATTAATTAAAA
24913784 TTTAAAAAT
1 TTTAAAAAT
24913793 GTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 4 0.17
21 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAAAATTAATTAAAA
Found at i:24914186 original size:17 final size:17
Alignment explanation
Indices: 24914164--24914203 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
24914154 ATTTCAAACA
24914164 ATGCTTTGAATGTGCCC
1 ATGCTTTGAATGTGCCC
*
24914181 ATGCTTTGAATGTTCCC
1 ATGCTTTGAATGTGCCC
24914198 A-GCTTT
1 ATGCTTT
24914204 TTCGTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (17 bp):
ATGCTTTGAATGTGCCC
Found at i:24934838 original size:6 final size:6
Alignment explanation
Indices: 24934827--24934878 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
24934817 GACACCCATT
*
24934827 AAATAA AAATAA AAAT-- AAATAA ATCTAATAA AAATAA AAATAA AAAGAA
1 AAATAA AAATAA AAATAA AAATAA A---AATAA AAATAA AAATAA AAATAA
24934876 AAA
1 AAA
24934879 GAAGAGTCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 4 0.10
6 30 0.75
9 6 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:24936004 original size:23 final size:24
Alignment explanation
Indices: 24935962--24936007 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
24935952 AGAAAATCAA
*
24935962 AATAAAAAAAATAATGATAGTAAT
1 AATAAAAAAAATAATAATAGTAAT
*
24935986 AATAATAAAAA-AATAATAGTAA
1 AATAAAAAAAATAATAATAGTAA
24936008 AGATGCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (24 bp):
AATAAAAAAAATAATAATAGTAAT
Found at i:24947466 original size:30 final size:30
Alignment explanation
Indices: 24947430--24947490 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
24947420 ACCAACTGAG
24947430 TGACAACCTAAAGAAAGATGAAGCAGTTTA
1 TGACAACCTAAAGAAAGATGAAGCAGTTTA
24947460 TGACAACCTAAAGAAAGATGAAGCAGTTTA
1 TGACAACCTAAAGAAAGATGAAGCAGTTTA
24947490 T
1 T
24947491 CTTTCCAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (30 bp):
TGACAACCTAAAGAAAGATGAAGCAGTTTA
Found at i:24948117 original size:2 final size:2
Alignment explanation
Indices: 24948110--24948165 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
24948100 GTTCAATGCA
24948110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
24948152 AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT
24948166 GCATATATGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24948171 original size:6 final size:6
Alignment explanation
Indices: 24948113--24948176 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
24948103 CAATGCAATA
* * * * * *
24948113 TATATA TATATA TATATA TATATA TATATA TATATA TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
24948161 TATATG CATATATG TA
1 TATATG --TATATG TA
24948177 AAATAACACC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
6 49 0.89
8 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:24953856 original size:22 final size:21
Alignment explanation
Indices: 24953830--24953925 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
24953820 ATATCTTTTG
24953830 TAATATTTTATTAATTATATAA
1 TAATATTTTATT-ATTATATAA
* *
24953852 TAATATTTAATATCTTTTTTATAA
1 TAATATTT--TAT-TATTATATAA
* * **
24953876 AAAAATTTTGATT-TTAT-TTG
1 TAATATTTT-ATTATTATATAA
*
24953896 TAATATTTTATTAATTATGTAA
1 TAATATTTTATT-ATTATATAA
24953918 TAATATTT
1 TAATATTT
24953926 AATATTTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.05
20 8 0.14
21 7 0.12
22 19 0.34
23 2 0.04
24 16 0.29
25 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (21 bp):
TAATATTTTATTATTATATAA
Found at i:24953953 original size:66 final size:66
Alignment explanation
Indices: 24953826--24953954 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 66
24953816 CTAAATATCT
**
24953826 TTTGTAATATTTTATTAATTATATAATAATATTTAATATCTTTTTTATAAAAAAATTTTGATTTT
1 TTTGTAATATTTTATTAATTATATAATAATATTTAATATCTTTTTTATAAAAAAACCTTGATTTT
24953891 A
66 A
* *
24953892 TTTGTAATATTTTATTAATTATGTAATAATATTTAATATTTTTTTTATAAAAAAACCTTGATT
1 TTTGTAATATTTTATTAATTATATAATAATATTTAATATCTTTTTTATAAAAAAACCTTGATT
24953955 CTATGTGGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (66 bp):
TTTGTAATATTTTATTAATTATATAATAATATTTAATATCTTTTTTATAAAAAAACCTTGATTTT
A
Found at i:24954379 original size:12 final size:12
Alignment explanation
Indices: 24954362--24954388 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24954352 TAGAGTATAG
24954362 AAACAAACTAAT
1 AAACAAACTAAT
24954374 AAACAAACTAAT
1 AAACAAACTAAT
24954386 AAA
1 AAA
24954389 AGCTAGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACAAACTAAT
Found at i:24954616 original size:2 final size:2
Alignment explanation
Indices: 24954611--24954638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24954601 TTTTTTAATA
24954611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24954639 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24958662 original size:26 final size:27
Alignment explanation
Indices: 24958615--24958669 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
24958605 GCCAAAAGGG
*
24958615 AACTCTCAACTTTACATCAAGGAGATT
1 AACTCTCAACTTGACATCAAGGAGATT
* *
24958642 AACTCT-AACTTGATATGAAGGAGATT
1 AACTCTCAACTTGACATCAAGGAGATT
24958668 AA
1 AA
24958670 TTCAACCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (27 bp):
AACTCTCAACTTGACATCAAGGAGATT
Found at i:24958799 original size:50 final size:49
Alignment explanation
Indices: 24958739--24959007 Score: 159
Period size: 50 Copynumber: 5.3 Consensus size: 49
24958729 GGGTCAAGAA
* *
24958739 ATGAGCGATAAAGCTTGCGGCCAATAGCATAACATCATTACAGCCAAATT
1 ATGAGCGATAAAGCTTGCGGCCAATAGAATAA-ATCATTACAGCCAAAAT
* * * * ** *
24958789 ATGAGTGATAAAGCTAGCAGCTGAAATATGAAT-AATCAATTATGGTCAAAGA-
1 ATGAGCGATAAAGCTTGCGGC--CAATA-GAATAAATC-ATTACAGCCAAA-AT
* * * *
24958841 ATAAGCGATAAAGCTTGCGACCAATAGAAAAATATCATTGCAGCCAAAAT
1 ATGAGCGATAAAGCTTGCGGCCAATAGAATAA-ATCATTACAGCCAAAAT
* * * * * * *
24958891 ATGAGTGGTAAAGCTTGCGGCTGAAGTAAGAAT-AATGAACTACGGTCAAAGA-
1 ATGAGCGATAAAGCTTGCGGC-CAA-T-AGAATAAAT-CATTACAGCCAAA-AT
* * * * *
24958943 ATGTGCGATAAAGCTTGCGACCAATAGTATAATATAATTACAACCAAAAT
1 ATGAGCGATAAAGCTTGCGGCCAATAGAATAA-ATCATTACAGCCAAAAT
*
24958993 ATAAGCGATAAAGCT
1 ATGAGCGATAAAGCT
24959008 AGTAGTTGAA
Statistics
Matches: 160, Mismatches: 43, Indels: 32
0.68 0.18 0.14
Matches are distributed among these distances:
49 9 0.06
50 72 0.45
51 14 0.09
52 57 0.36
53 8 0.05
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (49 bp):
ATGAGCGATAAAGCTTGCGGCCAATAGAATAAATCATTACAGCCAAAAT
Found at i:24958914 original size:102 final size:102
Alignment explanation
Indices: 24958719--24959009 Score: 350
Period size: 102 Copynumber: 2.9 Consensus size: 102
24958709 AATTTGTGAG
* * * * * *
24958719 TAATAAACTAGGGTC-AAGAAATGAGCGATAAAGCTTGCGGCCAATAGCATAACATCATTACAGC
1 TAATCAACTACGGTCAAAG-AATAAGCGATAAAGCTTGCGACCAATAGAATAATATCATTACAGC
* *
24958783 CAAATTATGAGTGATAAAGCTAGCAGCTGAAATATGAA
65 CAAAATATGAGTGATAAAGCTAGCAGCTGAAATAAGAA
* * * *
24958821 TAATCAATTATGGTCAAAGAATAAGCGATAAAGCTTGCGACCAATAGAAAAATATCATTGCAGCC
1 TAATCAACTACGGTCAAAGAATAAGCGATAAAGCTTGCGACCAATAGAATAATATCATTACAGCC
* * * *
24958886 AAAATATGAGTGGTAAAGCTTGCGGCTGAAGTAAGAA
66 AAAATATGAGTGATAAAGCTAGCAGCTGAAATAAGAA
* ** * * *
24958923 TAATGAACTACGGTCAAAGAATGTGCGATAAAGCTTGCGACCAATAGTATAATATAATTACAACC
1 TAATCAACTACGGTCAAAGAATAAGCGATAAAGCTTGCGACCAATAGAATAATATCATTACAGCC
* *
24958988 AAAATATAAGCGATAAAGCTAG
66 AAAATATGAGTGATAAAGCTAG
24959010 TAGTTGAATA
Statistics
Matches: 159, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
102 156 0.98
103 3 0.02
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (102 bp):
TAATCAACTACGGTCAAAGAATAAGCGATAAAGCTTGCGACCAATAGAATAATATCATTACAGCC
AAAATATGAGTGATAAAGCTAGCAGCTGAAATAAGAA
Found at i:24960186 original size:29 final size:29
Alignment explanation
Indices: 24960154--24960225 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
24960144 GAAAATAGGT
* *
24960154 GTACAAGAATAGGTATAAGAGAAGAAGCC
1 GTACAAGAATAGGTACAAAAGAAGAAGCC
* *
24960183 GTACGAGAATAGGTACAAAAGAAGAAGCT
1 GTACAAGAATAGGTACAAAAGAAGAAGCC
* *
24960212 ATACATGAATAGGT
1 GTACAAGAATAGGT
24960226 GTACAAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (29 bp):
GTACAAGAATAGGTACAAAAGAAGAAGCC
Done.