Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 26 of 171
Found at i:11906889 original size:26 final size:25
Alignment explanation
Indices: 11906856--11906905 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
11906846 ATTATTTCAA
11906856 TTTAATAT-TTAATAATTTTATATAC
1 TTTAATATATTAA-AATTTTATATAC
11906881 TTTATATATATTAAAATTTTATATA
1 TTTA-ATATATTAAAATTTTATATA
11906906 TAATAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 15 0.65
27 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTAATATATTAAAATTTTATATAC
Found at i:11906899 original size:41 final size:39
Alignment explanation
Indices: 11906836--11906912 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
11906826 TTTAAAAAAA
** *
11906836 ATATATTTATATTATTTCAATTTAATATTTAATAATTTT
1 ATATATTTATATTATTAAAATTTAATATATAATAATTTT
*
11906875 ATATACTTTATATATATTAAAATTTTATATATAATAAT
1 ATATA-TTTATAT-TATTAAAATTTAATATATAATAAT
11906913 CACGAGAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.16
40 7 0.22
41 20 0.62
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (39 bp):
ATATATTTATATTATTAAAATTTAATATATAATAATTTT
Found at i:11907659 original size:13 final size:13
Alignment explanation
Indices: 11907640--11907674 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
11907630 TTAATGAGAT
11907640 AAAAATAAATAACG
1 AAAAATAAATAA-G
11907654 -AAAATAAATAAG
1 AAAAATAAATAAG
11907666 AAAAATAAA
1 AAAAATAAA
11907675 CAAACGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAATAAATAAG
Found at i:11908917 original size:20 final size:20
Alignment explanation
Indices: 11908892--11908936 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
11908882 CCCTAAATTG
11908892 TTTTATTTATAAGA-TTATTA
1 TTTTATTTATAA-ATTTATTA
11908912 TTTTATTTATAAATTTATTA
1 TTTTATTTATAAATTTATTA
11908932 TTTTA
1 TTTTA
11908937 ATAATGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATTTATAAATTTATTA
Found at i:11908946 original size:20 final size:20
Alignment explanation
Indices: 11908906--11908947 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11908896 ATTTATAAGA
* *
11908906 TTATTATTTTATTTATAAAT
1 TTATTATTTTAATAATAAAT
*
11908926 TTATTATTTTAATAATGAAT
1 TTATTATTTTAATAATAAAT
11908946 TT
1 TT
11908948 CATGTTAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTATTTTAATAATAAAT
Found at i:11916519 original size:22 final size:22
Alignment explanation
Indices: 11916494--11916537 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11916484 CAAAGTTAAT
*
11916494 AATTATAAAAAGT-TATAAAAAC
1 AATT-TAAAAAATATATAAAAAC
11916516 AATTTAAAAAATATATAAAAAC
1 AATTTAAAAAATATATAAAAAC
11916538 TTCTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTTAAAAAATATATAAAAAC
Found at i:11917733 original size:26 final size:25
Alignment explanation
Indices: 11917685--11917733 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11917675 TGATGCTGGG
* *
11917685 AAAATGAAAAATATTTGCCTTTAAA
1 AAAATGAAAAATATCTGCATTTAAA
*
11917710 AAAATGAAAAATACTCTGGATTTA
1 AAAATGAAAAATA-TCTGCATTTA
11917734 TTTTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (25 bp):
AAAATGAAAAATATCTGCATTTAAA
Found at i:11917856 original size:2 final size:2
Alignment explanation
Indices: 11917849--11917878 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11917839 AAACATGTGA
11917849 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
11917879 GACACCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11919096 original size:22 final size:22
Alignment explanation
Indices: 11919071--11919114 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11919061 CAAAGTTAAT
*
11919071 AATTATAAAAAGT-TATAAAAAC
1 AATT-TAAAAAATATATAAAAAC
11919093 AATTTAAAAAATATATAAAAAC
1 AATTTAAAAAATATATAAAAAC
11919115 TTCTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTTAAAAAATATATAAAAAC
Found at i:11920172 original size:17 final size:17
Alignment explanation
Indices: 11920150--11920188 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
11920140 CTCTACCTTG
* *
11920150 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
11920167 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
11920184 ACAAG
1 ACAAG
11920189 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:11923258 original size:23 final size:22
Alignment explanation
Indices: 11923232--11923369 Score: 109
Period size: 23 Copynumber: 5.9 Consensus size: 22
11923222 TTACCGTTCA
*
11923232 GCACTGTGTGTGCTTACTGTTTC
1 GCACT-TGTGTGCCTACTGTTTC
11923255 GCACTTTGTGTGCCTACTGTTTC
1 GCAC-TTGTGTGCCTACTGTTTC
11923278 GCACTTCGTGTGCCTACTGATTT-
1 GCACTT-GTGTGCCTACTG-TTTC
* * **
11923301 GCGCTATGTGCGCCTACTAATT-
1 GCACT-TGTGTGCCTACTGTTTC
*
11923323 GCACTGTGTGTGCTTACTGTTTCCCC
1 GCACT-TGTGTGCCTACTGTTT---C
*
11923349 AGCACTTGTGTGCTTACTGTT
1 -GCACTTGTGTGCCTACTGTT
11923370 AAGTACTTCG
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
22 20 0.21
23 50 0.53
24 5 0.05
26 15 0.16
27 5 0.05
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (22 bp):
GCACTTGTGTGCCTACTGTTTC
Found at i:11926342 original size:24 final size:25
Alignment explanation
Indices: 11926293--11926347 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
11926283 AGGAAACTAC
*
11926293 TGAATTAATGCATTAAATTGTTATT
1 TGAATTAATGCATTAAATTGTCATT
*
11926318 TGAATTATATGC-TT-AGTTGTCATT
1 TGAATTA-ATGCATTAAATTGTCATT
11926342 TGAATT
1 TGAATT
11926348 GTTGTCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 14 0.52
25 9 0.33
26 4 0.15
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (25 bp):
TGAATTAATGCATTAAATTGTCATT
Found at i:11932062 original size:40 final size:39
Alignment explanation
Indices: 11931994--11932130 Score: 102
Period size: 40 Copynumber: 3.5 Consensus size: 39
11931984 ACCAGAATGG
* *
11931994 CACCCAGTGCCTCATCGG-ATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCCTAG-CCGAAG-AATAAAGTGA
* *
11932034 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGGCCTAGCCGAAGAATAAAGTGA
* * ** * *
11932071 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG-GCCTAGCCGAAG-AATAA-AGTGA
*
11932112 CACCCAGTGTCTCATCGGC
1 CACCCAGTGCCTCATCGGC
11932131 TCAAGGTCGA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGCCTAGCCGAAGAATAAAGTGA
Found at i:11932126 original size:41 final size:37
Alignment explanation
Indices: 11932026--11932128 Score: 89
Period size: 37 Copynumber: 2.7 Consensus size: 37
11932016 TTCGAAGCAA
* *
11932026 TAAAGTGACACCCAGTGTCTCATCGGCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGACCTAGCCGAAG
* ** ** * *
11932063 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCG-ACCTAGCCGAAG
11932101 TAAAATAATGACACCCAGTGTCTCATCG
1 T--AA-AATGACACCCAGTGTCTCATCG
11932129 GCTCAAGGTC
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.42
38 10 0.20
40 2 0.04
41 17 0.34
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (37 bp):
TAAAATGACACCCAGTGTCTCATCGACCTAGCCGAAG
Found at i:11936197 original size:17 final size:16
Alignment explanation
Indices: 11936165--11936198 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11936155 TGATGTTTTT
11936165 TTTAAAATAAAATATA
1 TTTAAAATAAAATATA
*
11936181 TTTAACATAATAATATA
1 TTTAAAATAA-AATATA
11936198 T
1 T
11936199 AATTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAATAAAATATA
Found at i:11936356 original size:38 final size:38
Alignment explanation
Indices: 11936284--11936356 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
11936274 AAATAGAAAA
* *
11936284 CATGTTTGTTAAGTAAAAACTTAAAAACTTAAAAATAG
1 CATGTTTATTAAGTAAAAACTTAAAAACTAAAAAATAG
* *
11936322 CATGTTTATTAATTAAAAATTTTAAAAA-TAAAAAA
1 CATGTTTATTAAGTAAAAA-CTTAAAAACTAAAAAA
11936357 AATGCTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 23 0.77
39 7 0.23
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (38 bp):
CATGTTTATTAAGTAAAAACTTAAAAACTAAAAAATAG
Found at i:11938558 original size:26 final size:25
Alignment explanation
Indices: 11938510--11938558 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11938500 TGATGCTGGG
* *
11938510 AAAATGAAAAATATTTGCCTTTAAA
1 AAAATGAAAAATATCTGCATTTAAA
*
11938535 AAAATGAAAAATACTCTGGATTTA
1 AAAATGAAAAATA-TCTGCATTTA
11938559 TTTTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (25 bp):
AAAATGAAAAATATCTGCATTTAAA
Found at i:11938681 original size:2 final size:2
Alignment explanation
Indices: 11938674--11938705 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11938664 AAACATGTGA
11938674 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
11938706 GACACCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11939924 original size:22 final size:22
Alignment explanation
Indices: 11939899--11939942 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11939889 CAAAGTTAAT
*
11939899 AATTATAAAAAGT-TATAAAAAC
1 AATT-TAAAAAATATATAAAAAC
11939921 AATTTAAAAAATATATAAAAAC
1 AATTTAAAAAATATATAAAAAC
11939943 TTCTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTTAAAAAATATATAAAAAC
Found at i:11947936 original size:22 final size:22
Alignment explanation
Indices: 11947890--11947942 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
11947880 TTTTGATCAC
** *
11947890 TTAATTA-TTAATTTTTTCGAT
1 TTAATTATTTAATTTTTTAAAA
11947911 TTAATTATTTAATTTTTTAAAA
1 TTAATTATTTAATTTTTTAAAA
*
11947933 TTAAATATTT
1 TTAATTATTT
11947943 TAATCATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAATTATTTAATTTTTTAAAA
Found at i:11950048 original size:13 final size:13
Alignment explanation
Indices: 11950030--11950054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11950020 TATAAGTATG
11950030 GAAAACTTAAAAA
1 GAAAACTTAAAAA
11950043 GAAAACTTAAAA
1 GAAAACTTAAAA
11950055 TTTTTCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (13 bp):
GAAAACTTAAAAA
Found at i:11964427 original size:24 final size:24
Alignment explanation
Indices: 11964384--11964430 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11964374 TTAAACTTTG
*
11964384 TTTATTTGTTTCAATTAAACTCTA
1 TTTATTTGTTTCAATCAAACTCTA
* *
11964408 TTTATTTGTTTGACTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
11964431 TATTACTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTCTA
Found at i:11967239 original size:23 final size:23
Alignment explanation
Indices: 11967155--11967302 Score: 149
Period size: 23 Copynumber: 6.3 Consensus size: 23
11967145 AGGGACCTTA
*
11967155 GTGTGCTCT-TCGATTAGCACTGT
1 GTGTGCTCTCT-GATTAGCACTTT
* *
11967178 GTGTGCTCTCCGATTAGCACTGT
1 GTGTGCTCTCTGATTAGCACTTT
*
11967201 GTGTGCTCTC-CATTTAGCACTTT
1 GTGTGCTCTCTGA-TTAGCACTTT
*
11967224 GTGTGCTCTCTGTTTAGCACATTT
1 GTGTGCTCTCTGATTAGCAC-TTT
*
11967248 -TGTGCTCTCTGTTATTAGCACTTC
1 GTGTGCTCTCTG--ATTAGCACTTT
* *
11967272 GTGTACTCTCTGATTAACACTTT
1 GTGTGCTCTCTGATTAGCACTTT
*
11967295 ATGTGCTC
1 GTGTGCTC
11967303 AGTACTTTGT
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.01
23 83 0.78
24 5 0.05
25 17 0.16
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (23 bp):
GTGTGCTCTCTGATTAGCACTTT
Found at i:11967342 original size:39 final size:39
Alignment explanation
Indices: 11967267--11967342 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
11967257 TGTTATTAGC
* *
11967267 ACTTCGTGTACTCTCTGATTAACACTTTATGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAACACTGTATGAGCTCAGT
* * *
11967306 ACTTTGTGTACTCTCTGTTTAGCACTGTATGAGCTCA
1 ACTTCGTGTACTCTCTGATTAACACTGTATGAGCTCA
11967343 ATGTTGCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAACACTGTATGAGCTCAGT
Found at i:11968643 original size:20 final size:19
Alignment explanation
Indices: 11968618--11968676 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
11968608 TCGTACTATG
11968618 CTTTTAATAATTTTTATTAT
1 CTTTTAATAATTTTTA-TAT
11968638 CTTTT-ATAATATTTTATAT
1 CTTTTAATAAT-TTTTATAT
*
11968657 -TTTAAAATAATTTTTTATAT
1 CTTT-TAATAA-TTTTTATAT
11968677 ATATATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 22 0.65
21 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
CTTTTAATAATTTTTATAT
Found at i:11976821 original size:25 final size:22
Alignment explanation
Indices: 11976780--11976825 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
11976770 TCCAGCTAGG
*
11976780 ATGAAAAAAATTAAATTATTTTT
1 ATGAAAAAAAATAAATT-TTTTT
11976803 ATGAAAATAAAATACAATTTTTT
1 ATGAAAA-AAAATA-AATTTTTT
11976826 ACCCTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
ATGAAAAAAAATAAATTTTTTT
Found at i:11981682 original size:3 final size:3
Alignment explanation
Indices: 11981674--11981703 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11981664 CATCCCAAAA
11981674 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11981704 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11982777 original size:7 final size:7
Alignment explanation
Indices: 11982754--11982834 Score: 85
Period size: 7 Copynumber: 11.9 Consensus size: 7
11982744 TCAAAAAAAA
*
11982754 GTCAATG
1 GTCAACG
*
11982761 GTCAA-A
1 GTCAACG
11982767 GTCAACG
1 GTCAACG
11982774 GTCAACG
1 GTCAACG
*
11982781 GTCAAAG
1 GTCAACG
11982788 GTCAACG
1 GTCAACG
11982795 GTCAACG
1 GTCAACG
*
11982802 GTCAA-A
1 GTCAACG
11982808 GTCAACG
1 GTCAACG
* *
11982815 ATCAATG
1 GTCAACG
*
11982822 GTCAATG
1 GTCAACG
11982829 GTCAAC
1 GTCAAC
11982835 AGTAAAAGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
6 10 0.16
7 52 0.84
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:11982783 original size:20 final size:20
Alignment explanation
Indices: 11982754--11982826 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
11982744 TCAAAAAAAA
*
11982754 GTCAATGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
11982774 GTCAACGGTCAAAGGTCAACG
1 GTCAACGGTCAAA-GTCAACG
11982795 GTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
* *
11982815 ATCAATGGTCAA
1 GTCAACGGTCAA
11982827 TGGTCAACAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 29 0.59
21 20 0.41
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAACG
Found at i:11982798 original size:34 final size:34
Alignment explanation
Indices: 11982754--11982847 Score: 118
Period size: 34 Copynumber: 2.8 Consensus size: 34
11982744 TCAAAAAAAA
* *
11982754 GTCAATGGTCAA-AGTCAACGGTCAACGGTCAAAG
1 GTCAATGGTCAACAGTCAA-AGTCAACGATCAAAG
* * *
11982788 GTCAACGGTCAACGGTCAAAGTCAACGATCAATG
1 GTCAATGGTCAACAGTCAAAGTCAACGATCAAAG
*
11982822 GTCAATGGTCAACAGTAAAAGTCAAC
1 GTCAATGGTCAACAGTCAAAGTCAAC
11982848 AGTCGGTCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 46 0.90
35 5 0.10
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.18
Consensus pattern (34 bp):
GTCAATGGTCAACAGTCAAAGTCAACGATCAAAG
Found at i:11982799 original size:41 final size:41
Alignment explanation
Indices: 11982754--11982834 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
11982744 TCAAAAAAAA
* *
11982754 GTCAATGGTCAAAGTCAACGGTCAACGGTCAAAGGTCAACG
1 GTCAACGGTCAAAGTCAACGATCAACGGTCAAAGGTCAACG
* *
11982795 GTCAACGGTCAAAGTCAACGATCAATGGTCAATGGTCAAC
1 GTCAACGGTCAAAGTCAACGATCAACGGTCAAAGGTCAAC
11982835 AGTAAAAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (41 bp):
GTCAACGGTCAAAGTCAACGATCAACGGTCAAAGGTCAACG
Found at i:11982858 original size:11 final size:11
Alignment explanation
Indices: 11982842--11982913 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
11982832 AACAGTAAAA
*
11982842 GTCAACAGTCG
1 GTCAACGGTCG
* *
11982853 GTCAACAGTCT
1 GTCAACGGTCG
* *
11982864 ATCAACGGCCG
1 GTCAACGGTCG
* * *
11982875 GTCAATGATCA
1 GTCAACGGTCG
*
11982886 GTCAACGGTTG
1 GTCAACGGTCG
11982897 GTCAACGGTCG
1 GTCAACGGTCG
11982908 GTCAAC
1 GTCAAC
11982914 CGTTTGACTT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:11983336 original size:11 final size:11
Alignment explanation
Indices: 11983320--11983394 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
11983310 AAGTGTGATT
*
11983320 AAAAGAGGAAG
1 AAAAGAGAAAG
11983331 AAAAGAGAAAAG
1 AAAAGAG-AAAG
11983343 AAAAGAGAAAG
1 AAAAGAGAAAG
11983354 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* * *
11983366 AATGAGAAAAAT
1 AA-AAGAGAAAG
11983378 AAAAGAGAAAG
1 AAAAGAGAAAG
*
11983389 GAAAGA
1 AAAAGA
11983395 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:11983343 original size:12 final size:12
Alignment explanation
Indices: 11983328--11983392 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
11983318 TTAAAAGAGG
11983328 AAGAAAAGAGAA
1 AAGAAAAGAGAA
11983340 AAGAAAAGAG-A
1 AAGAAAAGAGAA
11983351 AAGAAATA-AGAA
1 AAGAAA-AGAGAA
* *
11983363 ATG-AATGAGAAA
1 AAGAAAAGAG-AA
*
11983375 AATAAAAGAGAA
1 AAGAAAAGAGAA
*
11983387 AGGAAA
1 AAGAAA
11983393 GATGAGAGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 13 0.32
12 23 0.56
13 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:11983362 original size:23 final size:23
Alignment explanation
Indices: 11983320--11983392 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
11983310 AAGTGTGATT
*
11983320 AAAAGAGGAAGAAAAGAGAAAAG
1 AAAAGAGAAAGAAAAGAGAAAAG
*
11983343 AAAAGAGAAAGAAATA-AGAAATG
1 AAAAGAGAAAGAAA-AGAGAAAAG
* * * *
11983366 AATGAGAAAAATAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAAGAGAAAAG
11983390 AAA
1 AAA
11983393 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAAGAGAAAAG
Found at i:11991319 original size:3 final size:3
Alignment explanation
Indices: 11991311--11991346 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
11991301 CACCAACTCT
11991311 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GA
11991347 CCTGAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11992521 original size:2 final size:2
Alignment explanation
Indices: 11992510--11992552 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
11992500 ATGAATAATT
*
11992510 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11992551 TA
1 TA
11992553 AAATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11998480 original size:18 final size:20
Alignment explanation
Indices: 11998436--11998481 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
11998426 TTTCTTTGGC
* *
11998436 TTATATTTTTATATATTAAG
1 TTATATATTTATATATGAAG
11998456 TTA-ATATTTA-ATATGAA-
1 TTATATATTTATATATGAAG
11998473 TTATATATT
1 TTATATATT
11998482 CAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.13
18 11 0.48
19 6 0.26
20 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATATATTTATATATGAAG
Found at i:12001382 original size:6 final size:6
Alignment explanation
Indices: 12001371--12001399 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12001361 CTTTCTCCAT
12001371 GCAAAA GCAAAA GCAAAA GCAAAA GCAAA
1 GCAAAA GCAAAA GCAAAA GCAAAA GCAAA
12001400 GATTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
GCAAAA
Found at i:12008695 original size:16 final size:17
Alignment explanation
Indices: 12008666--12008698 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12008656 TTTTTTTATA
*
12008666 AAAGTTATTTTTATAAT
1 AAAGTTATTATTATAAT
12008683 AAAGTT-TTATTATAAT
1 AAAGTTATTATTATAAT
12008699 GATCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
AAAGTTATTATTATAAT
Found at i:12008934 original size:39 final size:39
Alignment explanation
Indices: 12008883--12008972 Score: 180
Period size: 39 Copynumber: 2.3 Consensus size: 39
12008873 CAATAATAAT
12008883 ATTTTGTTTTCATTTATTTAGAAATATATTTGTTATATA
1 ATTTTGTTTTCATTTATTTAGAAATATATTTGTTATATA
12008922 ATTTTGTTTTCATTTATTTAGAAATATATTTGTTATATA
1 ATTTTGTTTTCATTTATTTAGAAATATATTTGTTATATA
12008961 ATTTTGTTTTCA
1 ATTTTGTTTTCA
12008973 ATCTATTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (39 bp):
ATTTTGTTTTCATTTATTTAGAAATATATTTGTTATATA
Found at i:12014851 original size:5 final size:5
Alignment explanation
Indices: 12014841--12014866 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12014831 TTCAAAGTAT
12014841 GGAGA GGAGA GGAGA GGAGA GGAGA G
1 GGAGA GGAGA GGAGA GGAGA GGAGA G
12014867 AGTGTTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:12020002 original size:61 final size:60
Alignment explanation
Indices: 12019917--12020104 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 60
12019907 AAAAACTTGG
* * *
12019917 GGTGTTGGCCATGCAATTGCCGACACACCTTTTTTTGTCAAAAAAAATTTAAAATTTTTTT
1 GGTGTTGGCCATGCAATGGTCGACACACCTTTTTTTCTCAAAAAAAATTTAAAA-TTTTTT
* * * * *
12019978 GGTGTTGGCCAT-CAAATGGTCG--ACATCTCTTTTTCTCGAAAAAAATTT-ACATTTTTG
1 GGTGTTGGCCATGC-AATGGTCGACACACCTTTTTTTCTCAAAAAAAATTTAAAATTTTTT
** * *
12020035 GGTGTTGGCCATTGCAATTATTGACAC-CC-TTTTTTCTCGAGGAAAAAAATTCAAAATTTTTT
1 GGTGTTGGCCA-TGCAATGGTCGACACACCTTTTTTTCTC-A--AAAAAAATTTAAAATTTTTT
*
12020097 AGTGTTGG
1 GGTGTTGG
12020105 TCATCAAATG
Statistics
Matches: 100, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
57 16 0.16
58 16 0.16
59 24 0.24
60 3 0.03
61 27 0.27
62 14 0.14
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (60 bp):
GGTGTTGGCCATGCAATGGTCGACACACCTTTTTTTCTCAAAAAAAATTTAAAATTTTTT
Found at i:12020066 original size:118 final size:118
Alignment explanation
Indices: 12019916--12020164 Score: 283
Period size: 118 Copynumber: 2.1 Consensus size: 118
12019906 AAAAAACTTG
* * *
12019916 GGGTGTTGGCCA-TGCAATTGCCGACACACCTTTTTTTGTC-A-AAAAAAATTTAAAATTTTTTT
1 GGGTGTTGGCCATTGCAATTACCGACACACC-TTTTTTCTCGAGAAAAAAATTCAAAA-TTTTTT
* ** *** * * *
12019978 GGTGTTGGCCATCAAATGGTCGACATCTC-TTTTTCTCGAAAAAAATTTACATTTTT
64 AGTGTTGGCCATCAAATGACCGACATC-CGCCATT-TCAAAAAAAAATTACATTTGT
**
12020034 GGGTGTTGGCCATTGCAATTATTGACAC-CCTTTTTTCTCGAGGAAAAAAATTCAAAATTTTTTA
1 GGGTGTTGGCCATTGCAATTACCGACACACCTTTTTTCTCGA-GAAAAAAATTCAAAATTTTTTA
*
12020098 GTGTTGGTCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
65 GTGTTGGCCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
12020152 GGGTGTTGGCCAT
1 GGGTGTTGGCCAT
12020165 CAAATGGCTG
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
117 8 0.07
118 47 0.42
119 43 0.39
120 13 0.12
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (118 bp):
GGGTGTTGGCCATTGCAATTACCGACACACCTTTTTTCTCGAGAAAAAAATTCAAAATTTTTTAG
TGTTGGCCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
Found at i:12020069 original size:119 final size:118
Alignment explanation
Indices: 12019916--12020164 Score: 272
Period size: 119 Copynumber: 2.1 Consensus size: 118
12019906 AAAAAACTTG
* * * * *
12019916 GGGTGTTGGCCA-TGCAATTGCCGACACACCTTTTT-TTGTCAAAAAAAATTTAAAATTTTTTTG
1 GGGTGTTGGCCATTGCAATTACCGACACACCTTTTTCTCGACAAAAAAAATTCAAAA-TTTTTTA
** *** * * *
12019979 GTGTTGGCCATCAAATGGTCGACATCTC-TTTTTCTCGAAAAAAATTTACATTTTT
65 GTGTTGGCCATCAAATGACCGACATC-CGCCATT-TCAAAAAAAAATTACATTTGT
** **
12020034 GGGTGTTGGCCATTGCAATTATTGACAC-CCTTTTTTCTCGAGGAAAAAAATTCAAAATTTTTTA
1 GGGTGTTGGCCATTGCAATTACCGACACACC-TTTTTCTCGACAAAAAAAATTCAAAATTTTTTA
*
12020098 GTGTTGGTCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
65 GTGTTGGCCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
12020152 GGGTGTTGGCCAT
1 GGGTGTTGGCCAT
12020165 CAAATGGCTG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
118 46 0.42
119 48 0.44
120 15 0.14
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (118 bp):
GGGTGTTGGCCATTGCAATTACCGACACACCTTTTTCTCGACAAAAAAAATTCAAAATTTTTTAG
TGTTGGCCATCAAATGACCGACATCCGCCATTTCAAAAAAAAATTACATTTGT
Found at i:12020189 original size:118 final size:116
Alignment explanation
Indices: 12019954--12020211 Score: 272
Period size: 118 Copynumber: 2.2 Consensus size: 116
12019944 CCTTTTTTTG
* ** *** *
12019954 TCAAAAAAAATTTAAAATTTTTTTGGTGTTGGCCATCAAATGGTCGACATCTCTTTTTCTCGAAA
1 TCAAAAAAAATTTAAAA-TTTTTTAGTGTTGGCCATCAAATGACCGACATCTCCCATTCTCAAAA
* * * * * *
12020019 AAAATTTACATTTTTGGGTGTTGGCCATTGCAATTATTGACACCCTTTTTTC
65 AAAAATTACATTTGTGGGTGTTGGCCATTGCAATGACTGACACCCCTATTTC
* *
12020071 TCGAGGAAAAAAATTCAAAATTTTTTAGTGTTGGTCATCAAATGACCGACATC-CGCCATT-TCA
1 TC-A--AAAAAAATTTAAAATTTTTTAGTGTTGGCCATCAAATGACCGACATCTC-CCATTCTCA
*
12020134 AAAAAAAATTACATTTGTGGGTGTTGGCCA-T-CAAATGGCTGACACCCCCTATTTC
62 AAAAAAAATTACATTTGTGGGTGTTGGCCATTGC-AATGACTGACA-CCCCTATTTC
*
12020189 TCAAAAAAAATTTGAAATTTTTT
1 TCAAAAAAAATTTAAAATTTTTT
12020212 CTCCAAAAAG
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
115 18 0.15
116 1 0.01
117 12 0.10
118 42 0.36
119 31 0.26
120 13 0.11
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (116 bp):
TCAAAAAAAATTTAAAATTTTTTAGTGTTGGCCATCAAATGACCGACATCTCCCATTCTCAAAAA
AAAATTACATTTGTGGGTGTTGGCCATTGCAATGACTGACACCCCTATTTC
Found at i:12020951 original size:21 final size:20
Alignment explanation
Indices: 12020920--12020984 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
12020910 TATTAATTTG
* *
12020920 AATATAAAAATTAAATATCA
1 AATAAAAAAATTAAAAATCA
*
12020940 AATTAAAAAAATTAAAAATTA
1 AA-TAAAAAAATTAAAAATCA
*
12020961 AAT-AAAAAATAAAAAATTCA
1 AATAAAAAAATTAAAAA-TCA
12020981 AATA
1 AATA
12020985 CTAAATGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.32
20 8 0.22
21 17 0.46
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATTAAAAATCA
Found at i:12020970 original size:28 final size:27
Alignment explanation
Indices: 12020924--12020976 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12020914 AATTTGAATA
* *
12020924 TAAAAATTAAATATCAAATTAAAAAAAT
1 TAAAAATTAAATA-AAAAATAAAAAAAT
12020952 TAAAAATTAAATAAAAAATAAAAAA
1 TAAAAATTAAATAAAAAATAAAAAA
12020977 TTCAAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAAATTAAATAAAAAATAAAAAAAT
Found at i:12020990 original size:20 final size:19
Alignment explanation
Indices: 12020945--12020984 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12020935 TATCAAATTA
*
12020945 AAAAAATTAAAAATTAAAT
1 AAAAAATAAAAAATTAAAT
12020964 AAAAAATAAAAAATTCAAAT
1 AAAAAATAAAAAATT-AAAT
12020984 A
1 A
12020985 CTAAATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAATAAAAAATTAAAT
Found at i:12048702 original size:13 final size:13
Alignment explanation
Indices: 12048684--12048709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12048674 AAAACACAAG
12048684 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
12048697 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
12048710 GAAGGGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:12056628 original size:6 final size:6
Alignment explanation
Indices: 12056613--12056641 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12056603 TTGGATTTTT
12056613 GGAT-G GGATGG GGATGG GGATGG GGATGG
1 GGATGG GGATGG GGATGG GGATGG GGATGG
12056642 CGCCCAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
GGATGG
Found at i:12063412 original size:17 final size:18
Alignment explanation
Indices: 12063374--12063414 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12063364 CTAGAGCATA
*
12063374 CAGATGCACAATCAGAAT
1 CAGATGCACAACCAGAAT
*
12063392 -AGATGCACAACCTG-AT
1 CAGATGCACAACCAGAAT
12063408 CAGATGC
1 CAGATGC
12063415 TGAAGCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (18 bp):
CAGATGCACAACCAGAAT
Found at i:12075720 original size:20 final size:21
Alignment explanation
Indices: 12075695--12075735 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12075685 TGTGTATTTT
12075695 ATATTA-ATTTTTTAAAATTA
1 ATATTATATTTTTTAAAATTA
*
12075715 ATATTATATTTTTTATAATTA
1 ATATTATATTTTTTAAAATTA
12075736 TTTATTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTATATTTTTTAAAATTA
Found at i:12081251 original size:16 final size:17
Alignment explanation
Indices: 12081226--12081262 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12081216 TTATATTATA
12081226 TTATTATTATTGTTGTT
1 TTATTATTATTGTTGTT
*
12081243 TTATT-TTATTTTTGTT
1 TTATTATTATTGTTGTT
12081259 TTAT
1 TTAT
12081263 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (17 bp):
TTATTATTATTGTTGTT
Found at i:12086176 original size:3 final size:3
Alignment explanation
Indices: 12086168--12086192 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12086158 TGCCATGCTA
12086168 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
12086193 CTTTAATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:12092053 original size:25 final size:25
Alignment explanation
Indices: 12092019--12092069 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12092009 CCTGACAGTA
12092019 AAAAAAATAAATATTCTCCAACCTC
1 AAAAAAATAAATATTCTCCAACCTC
12092044 AAAAAAATAAATATTCTCCAACCTC
1 AAAAAAATAAATATTCTCCAACCTC
12092069 A
1 A
12092070 CTCTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAAAATAAATATTCTCCAACCTC
Found at i:12101430 original size:27 final size:28
Alignment explanation
Indices: 12101365--12101439 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
12101355 TGTGATAATA
*
12101365 ATTTATGAAAATTGAATCAAATTAAAATTT
1 ATTTAT-AAAATT-AATAAAATTAAAATTT
* *
12101395 ATGTGTAAAATT-ATAAAATTAAAATTT
1 ATTTATAAAATTAATAAAATTAAAATTT
*
12101422 ATTTATAAATTTAGATAA
1 ATTTATAAAATTA-ATAA
12101440 GATCCAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 23 0.62
29 10 0.27
30 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (28 bp):
ATTTATAAAATTAATAAAATTAAAATTT
Found at i:12119153 original size:81 final size:81
Alignment explanation
Indices: 12119055--12119219 Score: 330
Period size: 81 Copynumber: 2.0 Consensus size: 81
12119045 GCTTTGTCTC
12119055 TATTATGGTCTTCATTGTATATCTTACTCGGCTAATTTGTGGGTTTTACTAACGAATTGTCCCAA
1 TATTATGGTCTTCATTGTATATCTTACTCGGCTAATTTGTGGGTTTTACTAACGAATTGTCCCAA
12119120 TAACTTTATTTTTTCA
66 TAACTTTATTTTTTCA
12119136 TATTATGGTCTTCATTGTATATCTTACTCGGCTAATTTGTGGGTTTTACTAACGAATTGTCCCAA
1 TATTATGGTCTTCATTGTATATCTTACTCGGCTAATTTGTGGGTTTTACTAACGAATTGTCCCAA
12119201 TAACTTTATTTTTTCA
66 TAACTTTATTTTTTCA
12119217 TAT
1 TAT
12119220 CCATCCATAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (81 bp):
TATTATGGTCTTCATTGTATATCTTACTCGGCTAATTTGTGGGTTTTACTAACGAATTGTCCCAA
TAACTTTATTTTTTCA
Found at i:12126885 original size:16 final size:15
Alignment explanation
Indices: 12126867--12126918 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
12126857 TAAATTAAAT
12126867 TATATTTTAATATAA
1 TATATTTTAATATAA
*
12126882 TTATATGTTAAATATAA
1 -TATAT-TTTAATATAA
12126899 TATATTTTTAAT-TAA
1 TATA-TTTTAATATAA
12126914 TATAT
1 TATAT
12126919 GTAAATTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.03
15 7 0.22
16 14 0.44
17 10 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATATTTTAATATAA
Found at i:12126897 original size:17 final size:16
Alignment explanation
Indices: 12126875--12126924 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
12126865 ATTATATTTT
12126875 AATATAATTATATGTTA
1 AATATAA-TATATGTTA
* *
12126892 AATATAATATATTTTT
1 AATATAATATATGTTA
12126908 AAT-TAATATATG-TA
1 AATATAATATATGTTA
12126922 AAT
1 AAT
12126925 TCTTTAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 10 0.34
17 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
AATATAATATATGTTA
Found at i:12139197 original size:58 final size:58
Alignment explanation
Indices: 12139133--12139252 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 58
12139123 AAAAAGAATT
*
12139133 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTAGATTTAAAAATATTTAGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTAGGTTTA
* * * * * * *
12139191 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATTTTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTAGGTTTA
12139249 GTTT
1 GTTT
12139253 GTTGATGGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTAGGTTTA
Found at i:12139266 original size:58 final size:58
Alignment explanation
Indices: 12139157--12139267 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
12139147 TTTAGGAATA
**
12139157 AAATTATATTTAGATTTAAAAATATTTAGGTTTAGTTTATGAGTGTTTTTTAATAATG
1 AAATTATATTTAGATTTAAAAATATTTAGGTTTAGTTTATGAGTGGGTTTTAATAATG
* * * * *
12139215 AAATTATATTTGGGTTTAAAAATTTTTGGGTTTAGTTTGTTGA-TGGGTTTTAA
1 AAATTATATTTAGATTTAAAAATATTTAGGTTTAGTTT-ATGAGTGGGTTTTAA
12139268 ATATTAGGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 42 0.93
59 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (58 bp):
AAATTATATTTAGATTTAAAAATATTTAGGTTTAGTTTATGAGTGGGTTTTAATAATG
Found at i:12139404 original size:9 final size:9
Alignment explanation
Indices: 12139390--12139418 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12139380 TAATATATTT
12139390 TTATTCGAA
1 TTATTCGAA
12139399 TTATTCGAA
1 TTATTCGAA
12139408 TTATTCGAA
1 TTATTCGAA
12139417 TT
1 TT
12139419 CGAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:12139506 original size:23 final size:23
Alignment explanation
Indices: 12139462--12139507 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12139452 AAAAAAAATT
**
12139462 TAACTCGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
12139485 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
12139508 ATTTGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:12143411 original size:2 final size:2
Alignment explanation
Indices: 12143404--12143433 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12143394 AGGAAAACGA
*
12143404 AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12143434 CACGCGTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12173195 original size:31 final size:31
Alignment explanation
Indices: 12173157--12173223 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
12173147 AATTTAATTT
12173157 TTTTTTTCAATTAGTGCCATTAGTGCCATTG
1 TTTTTTTCAATTAGTGCCATTAGTGCCATTG
12173188 TTTTTTTCAATTAGTGCCATTAGTGCCATTG
1 TTTTTTTCAATTAGTGCCATTAGTGCCATTG
12173219 TTTTT
1 TTTTT
12173224 AATATCACCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTTTTCAATTAGTGCCATTAGTGCCATTG
Found at i:12176690 original size:2 final size:2
Alignment explanation
Indices: 12176683--12176707 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12176673 AGTATGATTC
12176683 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12176708 GTAATTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12181608 original size:18 final size:17
Alignment explanation
Indices: 12181585--12181619 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12181575 TCTCAATCAT
*
12181585 AAAAATGAATAAAATTTA
1 AAAAATAAAT-AAATTTA
12181603 AAAAATAAATAAATTTA
1 AAAAATAAATAAATTTA
12181620 CTCTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAATAAATAAATTTA
Found at i:12184514 original size:2 final size:2
Alignment explanation
Indices: 12184507--12184552 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12184497 CACCTTAAGC
12184507 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12184549 CT CT
1 CT CT
12184553 TTTCTTCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12188439 original size:30 final size:29
Alignment explanation
Indices: 12188384--12188441 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
12188374 ATAATTTCTT
* *
12188384 AATAAATTATATATTATTTCGATAAAAAA
1 AATAAACTATATATTATTACGATAAAAAA
12188413 AATAAACTATACTATTATATAC-ATAAAAA
1 AATAAACTATA-TATTAT-TACGATAAAAA
12188442 TATATCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (29 bp):
AATAAACTATATATTATTACGATAAAAAA
Found at i:12199140 original size:25 final size:24
Alignment explanation
Indices: 12199104--12199162 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
12199094 GCTATACTCA
*
12199104 TTTTTCTATTTTGGTA-TTTAATT
1 TTTTTCTATTTTGGTACTTGAATT
12199127 TTTTATCTCATTTTGGTACTTGAATT
1 TTTT-TCT-ATTTTGGTACTTGAATT
12199153 TTGTTT-TATT
1 TT-TTTCTATT
12199163 ACCCGTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.13
24 6 0.19
25 10 0.32
26 9 0.29
27 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.66
Consensus pattern (24 bp):
TTTTTCTATTTTGGTACTTGAATT
Found at i:12209336 original size:2 final size:2
Alignment explanation
Indices: 12209329--12209362 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12209319 GTGAAGAAAA
12209329 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
12209363 GATGTGTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12209574 original size:46 final size:46
Alignment explanation
Indices: 12209522--12209635 Score: 201
Period size: 46 Copynumber: 2.5 Consensus size: 46
12209512 CTCTCTATTA
* *
12209522 TTAGCACTGTGTGTGCTCTCTTATCAGTACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGT
12209568 TTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGT
*
12209614 TTAGCACTTTGTCTGCTCTCTG
1 TTAGCACTTTGTGTGCTCTCTG
12209636 TTGCCCAGCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (46 bp):
TTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGT
Found at i:12209636 original size:23 final size:23
Alignment explanation
Indices: 12209465--12209637 Score: 161
Period size: 23 Copynumber: 7.4 Consensus size: 23
12209455 ACACTAGCGC
* * *
12209465 GCTCTCAGATTAGCACTATGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
12209488 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
* *
12209511 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTCT-GT-TTAGCACTTTGTGT
* *
12209536 GCTCTCT-TATCAGTACTTTGTGT
1 GCTCTCTGT-TTAGCACTTTGTGT
*
12209559 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
12209582 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
12209605 ACTCTCTGTTTAGCACTTTGTCT
1 GCTCTCTGTTTAGCACTTTGTGT
12209628 GCTCTCTGTT
1 GCTCTCTGTT
12209638 GCCCAGCACT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
23 100 0.82
24 6 0.05
25 16 0.13
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:12212863 original size:20 final size:20
Alignment explanation
Indices: 12212838--12212879 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12212828 TTTCATTTAT
**
12212838 TAAAATAACAATTTTATAAA
1 TAAAATAACAATACTATAAA
*
12212858 TAAAATAATAATACTATAAA
1 TAAAATAACAATACTATAAA
12212878 TA
1 TA
12212880 TGAATTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAACAATACTATAAA
Found at i:12214166 original size:14 final size:13
Alignment explanation
Indices: 12214147--12214187 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
12214137 TAATTTAAAT
12214147 TATTTATTATTTAA
1 TATTTA-TATTTAA
*
12214161 TATTTAT-TTTGA
1 TATTTATATTTAA
12214173 TATTTATATTTAA
1 TATTTATATTTAA
12214186 TA
1 TA
12214188 AGTGAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 7 0.29
14 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:12221707 original size:2 final size:2
Alignment explanation
Indices: 12221702--12221765 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
12221692 TTTTATTCGA
12221702 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
12221744 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
12221766 CAAAACCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12256046 original size:3 final size:3
Alignment explanation
Indices: 12256038--12256069 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12256028 ATTAACTAGG
12256038 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12256070 AAACTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12269397 original size:14 final size:14
Alignment explanation
Indices: 12269375--12269413 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
12269365 CTTTTAATTG
*
12269375 TATACAAATATATA
1 TATATAAATATATA
12269389 TATATAAATATATA
1 TATATAAATATATA
*
12269403 TATATCAATAT
1 TATATAAATAT
12269414 GATAGACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TATATAAATATATA
Found at i:12269666 original size:2 final size:2
Alignment explanation
Indices: 12269659--12269687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12269649 TCTATCTATC
12269659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12269688 CTAGAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12272748 original size:15 final size:15
Alignment explanation
Indices: 12272730--12272761 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12272720 CAGTTTCTTC
12272730 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
*
12272745 AAAAAGAAAAAGGAA
1 AAAAAGAAAAAAGAA
12272760 AA
1 AA
12272762 CAGAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAGAA
Found at i:12274868 original size:12 final size:12
Alignment explanation
Indices: 12274851--12274876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12274841 CTTGGATAAC
12274851 TATGTATAAAAT
1 TATGTATAAAAT
12274863 TATGTATAAAAT
1 TATGTATAAAAT
12274875 TA
1 TA
12274877 ATATCATACA
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:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TATGTATAAAAT
Found at i:12278304 original size:20 final size:21
Alignment explanation
Indices: 12278276--12278317 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12278266 CTAATAACAT
*
12278276 CAATCCAAAATT-AAACAGAA
1 CAATACAAAATTCAAACAGAA
*
12278296 CAATACAAAATTCAAACCGAA
1 CAATACAAAATTCAAACAGAA
12278317 C
1 C
12278318 CAAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.57, C:0.24, G:0.05, T:0.14
Consensus pattern (21 bp):
CAATACAAAATTCAAACAGAA
Found at i:12279575 original size:12 final size:12
Alignment explanation
Indices: 12279558--12279589 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12279548 ATATAAAAAT
12279558 CATAAATTTTGA
1 CATAAATTTTGA
12279570 CATAAATTTTGA
1 CATAAATTTTGA
12279582 -AT-AATTTT
1 CATAAATTTT
12279590 CAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.30
11 2 0.10
12 12 0.60
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (12 bp):
CATAAATTTTGA
Found at i:12286497 original size:43 final size:43
Alignment explanation
Indices: 12286436--12286517 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
12286426 CCTTGGAAGC
12286436 TTTCAAAGTTTCGATCCTTATTTGGTAAGCTCAATTAAGTTTT
1 TTTCAAAGTTTCGATCCTTATTTGGTAAGCTCAATTAAGTTTT
* * *
12286479 TTTCAAAGTTTTGGTCCTTATTTGGTAAGTTCAATTAAG
1 TTTCAAAGTTTCGATCCTTATTTGGTAAGCTCAATTAAG
12286518 CTCAACTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (43 bp):
TTTCAAAGTTTCGATCCTTATTTGGTAAGCTCAATTAAGTTTT
Found at i:12297973 original size:18 final size:18
Alignment explanation
Indices: 12297935--12297976 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12297925 AGTATTTTTT
12297935 AAAAGCACTTTTGACATA
1 AAAAGCACTTTTGACATA
* *
12297953 AAAAGTACTTTTGA-ATC
1 AAAAGCACTTTTGACATA
12297970 AAAAGCA
1 AAAAGCA
12297977 ATACTAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGACATA
Found at i:12298405 original size:13 final size:14
Alignment explanation
Indices: 12298363--12298410 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
12298353 TAAACCAAGC
12298363 TTTTCAAAAGT-AC-
1 TTTTCAAAA-TCACT
12298376 TTTTCAAAATCACT
1 TTTTCAAAATCACT
12298390 TTTTCAAAA-CA-T
1 TTTTCAAAATCACT
*
12298402 TTTTTAAAA
1 TTTTCAAAA
12298411 GTAATACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 10 0.31
13 13 0.41
14 9 0.28
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44
Consensus pattern (14 bp):
TTTTCAAAATCACT
Found at i:12316986 original size:29 final size:31
Alignment explanation
Indices: 12316951--12317028 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
12316941 GTTTAAATAA
**
12316951 AAAAATATAGGGACTAAATTCCTAA-A-ATT
1 AAAAATATAGGGACTAAATTCCTAATACACC
* *
12316980 AAAAATA-GGAGGACTAAATTCTTAATACACC
1 AAAAATATAG-GGACTAAATTCCTAATACACC
*
12317011 AAAAGTATAGGGACTAAA
1 AAAAATATAGGGACTAAA
12317029 ACATGTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 21 0.54
30 1 0.03
31 15 0.38
32 1 0.03
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (31 bp):
AAAAATATAGGGACTAAATTCCTAATACACC
Found at i:12320362 original size:27 final size:28
Alignment explanation
Indices: 12320332--12320399 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
12320322 TTTATTGGTT
12320332 TTTTATAATTTTTA--ATATTTAAT-AATA
1 TTTTATAATTTTTATGAT-TTTAATGAA-A
12320359 TTTT-TATATTTTTATGATTTTAATGAAA
1 TTTTATA-ATTTTTATGATTTTAATGAAA
*
12320387 TTTTATTATTTTT
1 TTTTATAATTTTT
12320400 TATAAGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 17 0.49
29 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTATAATTTTTATGATTTTAATGAAA
Found at i:12320439 original size:21 final size:21
Alignment explanation
Indices: 12320396--12320439 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12320386 ATTTTATTAT
* *
12320396 TTTTTATAAGTTTTTTTAGAA
1 TTTTTATAAGTTTTTATAAAA
*
12320417 TTTTTATATGTTTTTATAAAA
1 TTTTTATAAGTTTTTATAAAA
12320438 TT
1 TT
12320440 ATATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTATAAGTTTTTATAAAA
Found at i:12320540 original size:32 final size:32
Alignment explanation
Indices: 12320504--12320573 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
12320494 TATTAATTTT
* *
12320504 ATAATTTTTATAAT-TTATTTTTTATTAAAT-AA
1 ATAATTTTTA-AATATTA-TTTATATCAAATAAA
12320536 ATAATTTTTAAATATTATTTATATCAAATAAA
1 ATAATTTTTAAATATTATTTATATCAAATAAA
12320568 ATAATT
1 ATAATT
12320574 ATTTTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
ATAATTTTTAAATATTATTTATATCAAATAAA
Found at i:12326358 original size:16 final size:16
Alignment explanation
Indices: 12326325--12326358 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12326315 CAAAATTGCG
* *
12326325 TTTAAAAGGTTTACTA
1 TTTAAAAGGATTAATA
12326341 TTTAAAAGGATTAATA
1 TTTAAAAGGATTAATA
12326357 TT
1 TT
12326359 ACATTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTAAAAGGATTAATA
Found at i:12332807 original size:105 final size:106
Alignment explanation
Indices: 12332614--12332812 Score: 292
Period size: 105 Copynumber: 1.9 Consensus size: 106
12332604 AAAACAATAG
* * * * *
12332614 GAATACTAAGTACATGTTGGGCATCAATCAGAGACAACAACTCTTTAACAAGGCTAATGTTCCAA
1 GAATACTAAGCACATGTTGGGCATCAACCAGAGACAACAACCCCTTAACAAGGCTAATGTCCCAA
*
12332679 AAACAACCATTTGTCACCGAAGAGATCATCCAAGCGGTAAA
66 AAACAACCATCTGTCACCGAAGAGATCATCCAAGCGGTAAA
* *
12332720 GAATA-TAAGCACATGTTGGGCATCAGCCGGAGACAACAACCCCTTAACAAGGCTAATGTCCCAA
1 GAATACTAAGCACATGTTGGGCATCAACCAGAGACAACAACCCCTTAACAAGGCTAATGTCCCAA
* * *
12332784 GAACAGCCATCTGTCACTGAAGAGATCAT
66 AAACAACCATCTGTCACCGAAGAGATCAT
12332813 TAACCTTCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
105 77 0.94
106 5 0.06
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (106 bp):
GAATACTAAGCACATGTTGGGCATCAACCAGAGACAACAACCCCTTAACAAGGCTAATGTCCCAA
AAACAACCATCTGTCACCGAAGAGATCATCCAAGCGGTAAA
Found at i:12342198 original size:2 final size:2
Alignment explanation
Indices: 12342193--12342231 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12342183 ATATATATAT
*
12342193 AG AG AG AG AG AG AG AG AG AG AC 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 AG A
12342232 ACAGTTTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12344094 original size:18 final size:18
Alignment explanation
Indices: 12344059--12344094 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12344049 TCAGTACAAA
*
12344059 TTTTTTATTACTCGAAAT
1 TTTTTTATTACTCAAAAT
*
12344077 TTTTTTATTACTTAAAAT
1 TTTTTTATTACTCAAAAT
12344095 AATAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTTTATTACTCAAAAT
Found at i:12345453 original size:25 final size:25
Alignment explanation
Indices: 12345400--12345452 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
12345390 TACACTTATC
*
12345400 AAAATTTAAATGAAAAAGTAAAAAT
1 AAAATTTAAATAAAAAAGTAAAAAT
*
12345425 AAAATTTAACTAAAAAAG-AAAAAT
1 AAAATTTAAATAAAAAAGTAAAAAT
12345449 AAAA
1 AAAA
12345453 AAATACGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAATTTAAATAAAAAAGTAAAAAT
Found at i:12346272 original size:20 final size:19
Alignment explanation
Indices: 12346249--12346335 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 19
12346239 GTAAGAGTTA
12346249 ATTTTAAATTTTTTTATATT
1 ATTTT-AATTTTTTTATATT
*
12346269 A-TTTAATTTTTATTTTATTTTT
1 ATTTTAA--TTT-TTTTA-TATT
*
12346291 ATAATTTAATTGTTTTTA-ATA
1 AT--TTTAATT-TTTTTATATT
12346312 ATATTTAA-TTTTTTATATT
1 AT-TTTAATTTTTTTATATT
12346331 ATTTT
1 ATTTT
12346336 TATAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
18 11 0.20
19 8 0.15
20 10 0.19
21 8 0.15
22 4 0.07
23 7 0.13
24 1 0.02
25 5 0.09
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (19 bp):
ATTTTAATTTTTTTATATT
Found at i:12346274 original size:25 final size:25
Alignment explanation
Indices: 12346246--12346355 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 25
12346236 ATGGTAAGAG
*
12346246 TTAATTTTAAATTTT-TTTATATTAT
1 TTAATTTT-AATTTTATTTATATAAT
* *
12346271 TTAATTTTTATTTTATTTTTATAAT
1 TTAATTTTAATTTTATTTATATAAT
* *
12346296 TTAATTGT--TTTTA-ATA-AT-AT
1 TTAATTTTAATTTTATTTATATAAT
* * *
12346316 TTAATTTTTTATATTATTTTTATAAT
1 TTAA-TTTTAATTTTATTTATATAAT
*
12346342 TTAA-TTAAATTTTA
1 TTAATTTTAATTTTA
12346356 ATATTTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.09
21 5 0.08
22 1 0.02
23 9 0.14
24 13 0.20
25 25 0.38
26 6 0.09
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (25 bp):
TTAATTTTAATTTTATTTATATAAT
Found at i:12346278 original size:18 final size:18
Alignment explanation
Indices: 12346255--12346334 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 18
12346245 GTTAATTTTA
12346255 AATTTTTTTATATTATTT
1 AATTTTTTTATATTATTT
*
12346273 AATTTTTATTTTATTTTTATAATTT
1 AA--TTT-TTTTA----TATTATTT
*
12346298 AATTGTTTTTAATAATATTT
1 AATT-TTTTT-ATATTATTT
12346318 AA-TTTTTTATATTATTT
1 AATTTTTTTATATTATTT
12346335 TTATAATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 19
0.68 0.06 0.26
Matches are distributed among these distances:
17 8 0.16
18 7 0.14
19 1 0.02
20 11 0.22
21 5 0.10
23 6 0.12
24 2 0.04
25 9 0.18
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (18 bp):
AATTTTTTTATATTATTT
Found at i:12346317 original size:45 final size:44
Alignment explanation
Indices: 12346255--12346347 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 44
12346245 GTTAATTTTA
* *
12346255 AATTTTTTTATATTATTTAA-TTTTTATTTTATTTTTATAATTT
1 AATTTTTTTATAATATTTAATTTTTTATATTATTTTTATAATTT
12346298 AATTGTTTTTAATAATATTTAATTTTTTATATTATTTTTATAATTT
1 AATT-TTTTT-ATAATATTTAATTTTTTATATTATTTTTATAATTT
12346344 AATT
1 AATT
12346348 AAATTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 4 0.09
44 5 0.11
45 10 0.22
46 26 0.58
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (44 bp):
AATTTTTTTATAATATTTAATTTTTTATATTATTTTTATAATTT
Found at i:12348747 original size:30 final size:31
Alignment explanation
Indices: 12348713--12348784 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
12348703 GTTATGTGTA
* * * *
12348713 ACAAAACAGTCACTCAACTT-TGAAAATGTG
1 ACAAAACAGTCACTAAAATTATCAAAAAGTG
*
12348743 ACAAAACAGTTACTAAAATTATCAAAAAGTG
1 ACAAAACAGTCACTAAAATTATCAAAAAGTG
*
12348774 ACAAAATAGTC
1 ACAAAACAGTC
12348785 CTCTTGTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCAAAAAGTG
Found at i:12350152 original size:30 final size:31
Alignment explanation
Indices: 12350088--12350159 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
12350078 ACAACAAGAG
* * * *
12350088 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
*
12350119 GACTGTTTTGTCACATTTCCA-AAGTTGAGT
1 GACTGTTTTGTCACATTTCCATAACTTGAGT
12350149 GACTGTTTTGT
1 GACTGTTTTGT
12350160 TACACGTAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTCCATAACTTGAGT
Found at i:12356779 original size:15 final size:15
Alignment explanation
Indices: 12356745--12356785 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12356735 GTTTTTTACT
12356745 AAAATAATAT-TAAA
1 AAAATAATATATAAA
**
12356759 AAAATAATATATATC
1 AAAATAATATATAAA
12356774 AAAATAATATAT
1 AAAATAATATAT
12356786 TCTCCCCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAATATATAAA
Found at i:12357953 original size:10 final size:10
Alignment explanation
Indices: 12357938--12357962 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12357928 AAGTCATGGC
12357938 AAGCACAAGA
1 AAGCACAAGA
12357948 AAGCACAAGA
1 AAGCACAAGA
12357958 AAGCA
1 AAGCA
12357963 AAAAAAGAGT
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:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGCACAAGA
Found at i:12358039 original size:17 final size:17
Alignment explanation
Indices: 12357991--12358038 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
12357981 GAGATTATTT
* *
12357991 TATTTAATTCATTTGATA
1 TATTTAAAT-ATTTTATA
12358009 TATTTAAATATTTTATA
1 TATTTAAATATTTTATA
12358026 TA-TTAAATATTTT
1 TATTTAAATATTTT
12358039 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.39
17 9 0.32
18 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTAAATATTTTATA
Found at i:12358058 original size:12 final size:13
Alignment explanation
Indices: 12358030--12358057 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12358020 TTTATATATT
12358030 AAATATTTTTTAA
1 AAATATTTTTTAA
12358043 AAATATTTTTTAA
1 AAATATTTTTTAA
12358056 AA
1 AA
12358058 TGAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:12360477 original size:6 final size:6
Alignment explanation
Indices: 12360466--12360524 Score: 84
Period size: 6 Copynumber: 9.8 Consensus size: 6
12360456 GGCCATTAAA
* *
12360466 TATGTT TATGTT TATGTT TATTTT TATGTT TATGTT TATGTT CT-TATT
1 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT
12360514 TATGTT TATGT
1 TATGTT TATGT
12360525 ATGCAAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.96
7 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.14, T:0.68
Consensus pattern (6 bp):
TATGTT
Found at i:12360653 original size:26 final size:26
Alignment explanation
Indices: 12360597--12360673 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
12360587 TGCTAAACCT
*
12360597 AATTAAATAAATTCAAACATAAAAAT
1 AATTAAATAAATTCAAACATAAAAAG
* ** *
12360623 TATTAAATAAATTCAAATTTAAATAG
1 AATTAAATAAATTCAAACATAAAAAG
* *
12360649 AATTAATTCCAAATTCAATCATAAA
1 AATTAAAT--AAATTCAAACATAAA
12360674 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (26 bp):
AATTAAATAAATTCAAACATAAAAAG
Found at i:12363517 original size:25 final size:25
Alignment explanation
Indices: 12363483--12363532 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12363473 TTTGCTTCCT
12363483 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
*
12363508 TTCCTTCTTCAAAAATTTGCTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
12363533 AACAGATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (25 bp):
TTCCTTCTTCAAAAATTTACTGTTA
Found at i:12363727 original size:58 final size:58
Alignment explanation
Indices: 12363665--12363787 Score: 135
Period size: 58 Copynumber: 2.1 Consensus size: 58
12363655 TATAAAAGTG
* ** *
12363665 TATTATTTTTTATATTTAAAT-TTCTCTTATATTA-TTATTGTAAAAATCTAGAGATTAT
1 TATTATTTTTGATAAATAAATATTCTCTTATATTATTTATT-TAAAAATATAGAG-TTAT
* * *
12363723 TATTA-TTTTGATAAATAAATATTTTTTTATATTATTTATTTAAAAATATTGAGTTAT
1 TATTATTTTTGATAAATAAATATTCTCTTATATTATTTATTTAAAAATATAGAGTTAT
*
12363780 TCTTATTT
1 TATTATTT
12363788 AATATTTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
57 20 0.37
58 29 0.54
59 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (58 bp):
TATTATTTTTGATAAATAAATATTCTCTTATATTATTTATTTAAAAATATAGAGTTAT
Found at i:12363996 original size:27 final size:27
Alignment explanation
Indices: 12363966--12364055 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
12363956 CTTGATAGAA
* *
12363966 AGGCACCATTGGTGCCGCCTGACAGGT
1 AGGCACCACTGGTGCCGCCTGTCAGGT
*
12363993 AGGCACCACTGGTGCTGCCTGTCAGGT
1 AGGCACCACTGGTGCCGCCTGTCAGGT
12364020 AGGCACCACTGGTGCCGCCTGTCAGGT
1 AGGCACCACTGGTGCCGCCTGTCAGGT
12364047 AGGCACCAC
1 AGGCACCAC
12364056 CCATTTATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.18, C:0.32, G:0.32, T:0.18
Consensus pattern (27 bp):
AGGCACCACTGGTGCCGCCTGTCAGGT
Found at i:12379998 original size:96 final size:96
Alignment explanation
Indices: 12379868--12380155 Score: 524
Period size: 96 Copynumber: 3.0 Consensus size: 96
12379858 CCAAGCTAGA
*
12379868 ATTGTTGATAAAAGGGGTT-GGATATTTATATAAAATATACATGTTTAAAAAGCCAAGCCAACTT
1 ATTGTTGATAAAAGGGGTTGGGATATTTATATAAAATATACATGTTTAAAGAGCCAAGCCAACTT
12379932 TCAGTAAGTATTTTTAAATTTGGATGAATCT
66 TCAGTAAGTATTTTTAAATTTGGATGAATCT
*
12379963 ATTGTTGATAAAAGGGGTTGGGATATTTATATAAAATATACATATTTAAAGAGCCAAGCCAACTT
1 ATTGTTGATAAAAGGGGTTGGGATATTTATATAAAATATACATGTTTAAAGAGCCAAGCCAACTT
* *
12380028 ACAATAAGTATTTTTAAATTTGGATGAATCT
66 TCAGTAAGTATTTTTAAATTTGGATGAATCT
*
12380059 ATTGTTGATAAAAGGGGTTGAGATATTTATATAAAATATACATGTTTAAAGAGCCAAGCCAACTT
1 ATTGTTGATAAAAGGGGTTGGGATATTTATATAAAATATACATGTTTAAAGAGCCAAGCCAACTT
12380124 TCAGTAAGTATTTTTAAATTTGGATGAATCT
66 TCAGTAAGTATTTTTAAATTTGGATGAATCT
12380155 A
1 A
12380156 ATGTGATGGC
Statistics
Matches: 184, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 19 0.10
96 165 0.90
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (96 bp):
ATTGTTGATAAAAGGGGTTGGGATATTTATATAAAATATACATGTTTAAAGAGCCAAGCCAACTT
TCAGTAAGTATTTTTAAATTTGGATGAATCT
Found at i:12380466 original size:9 final size:9
Alignment explanation
Indices: 12380454--12380478 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12380444 CTACTATTAC
12380454 TAATAATAT
1 TAATAATAT
12380463 TAATAATAT
1 TAATAATAT
12380472 TAATAAT
1 TAATAAT
12380479 GATTCAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATAATAT
Found at i:12386088 original size:22 final size:21
Alignment explanation
Indices: 12386049--12386107 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
12386039 TAATTTTAAA
* *
12386049 TATATATATATATATAATATTT
1 TATAAATATAAATATAAT-TTT
*
12386071 TATAAATATAAATGTAATTTT
1 TATAAATATAAATATAATTTT
* *
12386092 T-TTAATATAATTATAA
1 TATAAATATAAATATAA
12386108 AATAATATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 15 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATAAATATAAATATAATTTT
Found at i:12386277 original size:15 final size:15
Alignment explanation
Indices: 12386248--12386280 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12386238 ATTATCTTTG
12386248 AAATAATAAATAAAT
1 AAATAATAAATAAAT
12386263 AAATATATAAA-AAAT
1 AAATA-ATAAATAAAT
12386278 AAA
1 AAA
12386281 ATCATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:12386544 original size:15 final size:14
Alignment explanation
Indices: 12386508--12386534 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12386498 CTTCTCTCCC
12386508 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
12386522 TTTTTTTATTTTT
1 TTTTTTTATTTTT
12386535 TCATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:12386887 original size:15 final size:15
Alignment explanation
Indices: 12386858--12386890 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12386848 ATTATCTTTG
12386858 AAATAATAAATAAAT
1 AAATAATAAATAAAT
12386873 AAATATATAAA-AAAT
1 AAATA-ATAAATAAAT
12386888 AAA
1 AAA
12386891 ATCATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:12387347 original size:607 final size:609
Alignment explanation
Indices: 12386148--12387382 Score: 2388
Period size: 607 Copynumber: 2.0 Consensus size: 609
12386138 TTGACAAGAT
*
12386148 ACACATAAATATTAGAACTCGAATCTCTTAAAATGATAATCATATTTTTTTTACTGAAATCACTT
1 ACACATAAATATTAAAACTCGAATCTCTTAAAATGATAATCATATTTTTTTTACTGAAATCACTT
12386213 GTTAAATTCAAATATAAATATAATTATTATCTTTGAAATAATAAATAAATAAATATATAAAAAAT
66 GTTAAATTCAAATATAAATATAATTATTATCTTTGAAATAATAAATAAATAAATATATAAAAAAT
12386278 AAAATCATCTAAATTTTGGTAAATGTTATTTTTTATTTTTATTTTCCTCTCTTGACGTTTAACTT
131 AAAATCATCTAAATTTTGGTAAATGTTATTTTTTATTTTTATTTTCCTCTCTTGACGTTTAACTT
12386343 TTTATTCATTCTAGCTTTTCATCATGTGTAACACTAATTTTTTATTTTTTTAATTCATCTCTTTT
196 TTTATTCATTCTAGCTTTTCATCATGTGTAACACTAATTTTTTATTTTTTTAATTCATCTCTTTT
12386408 GACTTTTGCCATCATCTTCATCTGCTCTTCACCTGCACCTGACACTGCTTCTCTCTTTTCTCTAA
261 GACTTTTGCCATCATCTTCATCTGCTCTTCACCTGCACCTGACACTGCTTCTCTCTTTTCTCTAA
12386473 CAGCGGCCTTCTGCATGTCTATCTTCTTCTCTCCCTTTTTTTATTTTTATTTTTTTATTTTTTCA
326 CAGCGGCCTTCTGCATGTCTATCTTCTTCTCTCCCTTTTTTTATTTTTATTTTTTTATTTTTTCA
12386538 TTTTTTAACTTTAGAAAAGCTTAAAAAGTGGAATTGCCGGCCGTTATTCACCGCTATACCGATTC
391 TTTTTTAACTTTAGAAAAGCTTAAAAAGTGGAATTGCCGGCCGTTATTCACCGCTATACCGATTC
12386603 TTGCAGCCGTTATTCTCTGCTTCTTGTGATTTACAATCACACCCGTTTTCCTTCCTATAGCGGTG
456 TTGCAGCCGTTATTCTCTGCTTCTTGTGATTTACAATCACACCCGTTTTCCTTCCTATAGCGGTG
12386668 GCGGCCGGTGGCGCATCGCTGATAACACAATAATTTTTTTTTAAATATACTGATATAATTATATA
521 GCGGCCGGTGGCGCATCGCTGATAACACAATAATTTTTTTTTAAATATACTGATATAATTATATA
12386733 ATAATATTTATTTATATTTTTTTC
586 ATAATATTTATTTATATTTTTTTC
*
12386757 ACACATAAATATTAAAATTCGAATCTCTTAAAATGATAATCATATTTTTTTTTACTGAAATCACT
1 ACACATAAATATTAAAACTCGAATCTCTTAAAATGATAATCATA-TTTTTTTTACTGAAATCACT
12386822 TGTTAAATTCAAATATAAATATAATTATTATCTTTGAAATAATAAATAAATAAATATATAAAAAA
65 TGTTAAATTCAAATATAAATATAATTATTATCTTTGAAATAATAAATAAATAAATATATAAAAAA
*
12386887 TAAAATCATCTAAATTTTGGTAAATGTTATTTTTTATTTTTATTTTCCTCTCTTGACTTTTAACT
130 TAAAATCATCTAAATTTTGGTAAATGTTATTTTTTATTTTTATTTTCCTCTCTTGACGTTTAACT
12386952 TTTTATTCATTCTAGCTTTTCATCATGTGTAACACTAATTTTTTTATTTTTTTAATTCATCTCTT
195 TTTTATTCATTCTAGCTTTTCATCATGTGTAACACTAA-TTTTTTATTTTTTTAATTCATCTCTT
12387017 TTGACTTTTGCCATCATCTTCATCTGCTCTTCACCTGCACCTGACACTGCTTCTCTCTTTTCTCT
259 TTGACTTTTGCCATCATCTTCATCTGCTCTTCACCTGCACCTGACACTGCTTCTCTCTTTTCTCT
12387082 AACAGCGGCCTTCTGCATGTCTATCTTCTTCTCTCCC-TTTTTT-TTTTT-TTTTTTT-TTTTTT
324 AACAGCGGCCTTCTGCATGTCTATCTTCTTCTCTCCCTTTTTTTATTTTTATTTTTTTATTTTTT
12387143 CATTTTTTAACTTTAGAAAAGCTTAAAAAGTGGAATTGCCGGCCGTTATTCACCGCTATACCGAT
389 CATTTTTTAACTTTAGAAAAGCTTAAAAAGTGGAATTGCCGGCCGTTATTCACCGCTATACCGAT
12387208 TCTTGCAGCCGTTATTCTCTGCTTCTTGTGATTTACAATCACACCCGTTTTCCTTCCTATAGCGG
454 TCTTGCAGCCGTTATTCTCTGCTTCTTGTGATTTACAATCACACCCGTTTTCCTTCCTATAGCGG
12387273 TGGCGGCCGGTGGCGCATCGCTGATAACACAATAATTTTTTTTTAAATATACTGATATAATTATA
519 TGGCGGCCGGTGGCGCATCGCTGATAACACAATAATTTTTTTTTAAATATACTGATATAATTATA
12387338 TAATAATATTTATTTATATTTTTTTC
584 TAATAATATTTATTTATATTTTTTTC
*
12387364 ACACATAAATATTTAAACT
1 ACACATAAATATTAAAACT
12387383 TGAAATTTTT
Statistics
Matches: 619, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
607 244 0.39
608 7 0.01
609 47 0.08
610 193 0.31
611 128 0.21
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (609 bp):
ACACATAAATATTAAAACTCGAATCTCTTAAAATGATAATCATATTTTTTTTACTGAAATCACTT
GTTAAATTCAAATATAAATATAATTATTATCTTTGAAATAATAAATAAATAAATATATAAAAAAT
AAAATCATCTAAATTTTGGTAAATGTTATTTTTTATTTTTATTTTCCTCTCTTGACGTTTAACTT
TTTATTCATTCTAGCTTTTCATCATGTGTAACACTAATTTTTTATTTTTTTAATTCATCTCTTTT
GACTTTTGCCATCATCTTCATCTGCTCTTCACCTGCACCTGACACTGCTTCTCTCTTTTCTCTAA
CAGCGGCCTTCTGCATGTCTATCTTCTTCTCTCCCTTTTTTTATTTTTATTTTTTTATTTTTTCA
TTTTTTAACTTTAGAAAAGCTTAAAAAGTGGAATTGCCGGCCGTTATTCACCGCTATACCGATTC
TTGCAGCCGTTATTCTCTGCTTCTTGTGATTTACAATCACACCCGTTTTCCTTCCTATAGCGGTG
GCGGCCGGTGGCGCATCGCTGATAACACAATAATTTTTTTTTAAATATACTGATATAATTATATA
ATAATATTTATTTATATTTTTTTC
Found at i:12393131 original size:11 final size:11
Alignment explanation
Indices: 12393104--12393138 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12393094 ATTTAATTTG
12393104 ATTAAATAAATT
1 ATTAAA-AAATT
*
12393116 GTTAAAAAATT
1 ATTAAAAAATT
12393127 ATTAAAAAATT
1 ATTAAAAAATT
12393138 A
1 A
12393139 ATATAAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:12394690 original size:34 final size:35
Alignment explanation
Indices: 12394634--12394702 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
12394624 TTATTTTTTA
12394634 TTTCAAAAAATTTAATCTTTTTATTTTTTAAAATT
1 TTTCAAAAAATTTAATCTTTTTATTTTTTAAAATT
12394669 TTTCAAAAAATTTAATC-TTTTATTTTTTAAAATT
1 TTTCAAAAAATTTAATCTTTTTATTTTTTAAAATT
12394703 AAAAAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTCAAAAAATTTAATCTTTTTATTTTTTAAAATT
Done.