Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 25 of 84
Found at i:5495454 original size:17 final size:17
Alignment explanation
Indices: 5495432--5495464 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5495422 AAGCTTATGC
5495432 TATA-TTAAAAGAATAAA
1 TATATTTAAAA-AATAAA
5495449 TATATTTAAAAAATAA
1 TATATTTAAAAAATAA
5495465 TAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TATATTTAAAAAATAAA
Found at i:5506651 original size:2 final size:2
Alignment explanation
Indices: 5506646--5506674 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5506636 ACACAAAACC
5506646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5506675 ATCTTATGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5510501 original size:2 final size:2
Alignment explanation
Indices: 5510494--5510593 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
5510484 ATATGGTCCT
5510494 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5510536 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5510578 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
5510594 AGCAACTTTC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5525964 original size:31 final size:29
Alignment explanation
Indices: 5525927--5526026 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 29
5525917 ACAATAAAAA
*
5525927 TAAATATCATTTTAATAATTAATTTATAATT
1 TAAATATCATATTAA-AATT-ATTTATAATT
*
5525958 TAAATATCATATTAAAATT-TTTAAAATTT
1 TAAATATCATATTAAAATTATTTATAA-TT
* *
5525987 TAAATATTAAATTAAATATT-TATTATAATT
1 TAAATATCATATTAAA-ATTAT-TTATAATT
*
5526017 TAAAAATCAT
1 TAAATATCAT
5526027 TAATATTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 6 0.10
29 16 0.28
30 17 0.29
31 19 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATATCATATTAAAATTATTTATAATT
Found at i:5526000 original size:29 final size:31
Alignment explanation
Indices: 5525956--5526035 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 31
5525946 TAATTTATAA
* *
5525956 TTTAAATATCATATTAAA-ATTT-TTAAAAT
1 TTTAAATATTAAATTAAATATTTATTAAAAT
*
5525985 TTTAAATATTAAATTAAATATTTATTATAAT
1 TTTAAATATTAAATTAAATATTTATTAAAAT
*
5526016 TTAAAAATCATTAATATTAA
1 TT-TAAAT-ATTAA-ATTAA
5526036 CTCATTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.38
30 4 0.10
31 8 0.19
32 4 0.10
33 5 0.12
34 5 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTAAATATTAAATTAAATATTTATTAAAAT
Found at i:5533200 original size:16 final size:16
Alignment explanation
Indices: 5533179--5533228 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5533169 ATCTTTTTTT
5533179 TTTAATATCAAATTTA
1 TTTAATATCAAATTTA
*
5533195 TTTAAT-TGAAA--TA
1 TTTAATATCAAATTTA
5533208 TTTAA-ATCAAAATTTA
1 TTTAATATC-AAATTTA
5533224 TTTAA
1 TTTAA
5533229 ATATTATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 4 0.14
16 13 0.46
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTAATATCAAATTTA
Found at i:5537899 original size:21 final size:22
Alignment explanation
Indices: 5537825--5537899 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
5537815 AACGTATAGA
*
5537825 TAAATATAAA-TAT-ATTTATTT
1 TAAATATAAATTATAATTTA-AT
*
5537846 TCAAACATAAATTATAATTTAAT
1 T-AAATATAAATTATAATTTAAT
* *
5537869 TATATATAAA-TATAATTTTTAT
1 TAAATATAAATTATAA-TTTAAT
5537891 TAAAT-TAAA
1 TAAATATAAA
5537900 ATATTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 10 0.23
22 24 0.55
23 5 0.11
24 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATATAAATTATAATTTAAT
Found at i:5538249 original size:13 final size:13
Alignment explanation
Indices: 5538233--5538258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5538223 TAAATTAAGC
5538233 TTTTAAATAATAT
1 TTTTAAATAATAT
5538246 TTTTAAATAATAT
1 TTTTAAATAATAT
5538259 ATACAAATAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAATAATAT
Found at i:5538758 original size:19 final size:19
Alignment explanation
Indices: 5538722--5538778 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
5538712 TTTTTTTACA
*
5538722 AAATTTATTAATAA-AAAAT
1 AAATTTAATAA-AATAAAAT
*
5538741 AAATTTAATAAAATAAAAC
1 AAATTTAATAAAATAAAAT
5538760 AAA--TAATAAAAATAAAAT
1 AAATTTAAT-AAAATAAAAT
5538778 A
1 A
5538779 GTGGAGGAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 4 0.12
18 12 0.36
19 17 0.52
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATTTAATAAAATAAAAT
Found at i:5539100 original size:23 final size:23
Alignment explanation
Indices: 5539074--5539118 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5539064 GATGTTAGCT
5539074 AATAATAC-AAAATATTTAATAAA
1 AATAA-ACTAAAATATTTAATAAA
*
5539097 AATAAACTTAAATTATTTAATA
1 AATAAAC-TAAAATATTTAATA
5539119 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 5 0.26
24 12 0.63
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAACTAAAATATTTAATAAA
Found at i:5539141 original size:11 final size:11
Alignment explanation
Indices: 5539135--5539159 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5539125 AAATTAATAA
5539135 ATTATTAAAAT
1 ATTATTAAAAT
5539146 ATTATTAAAAT
1 ATTATTAAAAT
5539157 ATT
1 ATT
5539160 TTTATATCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:5539209 original size:18 final size:19
Alignment explanation
Indices: 5539188--5539228 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5539178 TTTGTTAAAA
*
5539188 ATAATTTTTTA-TTATTTT
1 ATAATTTTTTATTTATTAT
5539206 ATAA-TTTTTATTTATTAT
1 ATAATTTTTTATTTATTAT
5539224 ATAAT
1 ATAAT
5539229 AAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATAATTTTTTATTTATTAT
Found at i:5539221 original size:21 final size:21
Alignment explanation
Indices: 5539190--5539248 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5539180 TGTTAAAAAT
*
5539190 AATTT-TTTATTATTTTATAA
1 AATTTATTTATTATTTAATAA
** *
5539210 TTTTTATTTATTATATAATAA
1 AATTTATTTATTATTTAATAA
5539231 AATTTATTTATTTATTTA
1 AATTTATTTA-TTATTTA
5539249 TTATTTCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTATTTATTATTTAATAA
Found at i:5541419 original size:52 final size:52
Alignment explanation
Indices: 5541321--5541456 Score: 134
Period size: 52 Copynumber: 2.6 Consensus size: 52
5541311 AAACTTGTCC
* * ** * *
5541321 ATTAAGAATCCTTCTCCTCTTAGAATTTTTTTCCTGTAAGTTAAACTTGCCTT
1 ATTAAGAATCCTTCTCCTCTTAGAATTCTTTTACTACAAGTCAAACTT-ACTT
* * * *
5541374 -TTAAGAATCCTTCTCTTTTTATAATTCTTTTATTACAAGTCAAACTTACTT
1 ATTAAGAATCCTTCTCCTCTTAGAATTCTTTTACTACAAGTCAAACTTACTT
5541425 ATTAAGAATCTCATT-T-CTCTTAGAATTCTTTT
1 ATTAAGAATC-C-TTCTCCTCTTAGAATTCTTTT
5541457 TTGCAAGTCT
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
51 3 0.04
52 60 0.90
53 2 0.03
54 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (52 bp):
ATTAAGAATCCTTCTCCTCTTAGAATTCTTTTACTACAAGTCAAACTTACTT
Found at i:5541505 original size:11 final size:11
Alignment explanation
Indices: 5541489--5541528 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
5541479 AGCAATATCT
5541489 AATAAATCTCA
1 AATAAATCTCA
*
5541500 AATAAATCTCT
1 AATAAATCTCA
5541511 AATAAATCTCA
1 AATAAATCTCA
*
5541522 AACAAAT
1 AATAAAT
5541529 TTCTTATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATCTCA
Found at i:5541511 original size:22 final size:22
Alignment explanation
Indices: 5541486--5541528 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5541476 TCAAGCAATA
*
5541486 TCTAATAAATCTCAAATAAATC
1 TCTAATAAATCTCAAACAAATC
5541508 TCTAATAAATCTCAAACAAAT
1 TCTAATAAATCTCAAACAAAT
5541529 TTCTTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (22 bp):
TCTAATAAATCTCAAACAAATC
Found at i:5543559 original size:20 final size:22
Alignment explanation
Indices: 5543519--5543561 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5543509 AAAAAAAAAG
*
5543519 TATTTTATGTTTTAATTAAATT
1 TATTTTATGTTTTAATAAAATT
5543541 TATTTTAT-TTTT-ATAAAATT
1 TATTTTATGTTTTAATAAAATT
5543561 T
1 T
5543562 TGAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTTTATGTTTTAATAAAATT
Found at i:5544052 original size:2 final size:2
Alignment explanation
Indices: 5544045--5544078 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5544035 TGAGAGCTAC
*
5544045 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5544079 GCATCGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5545725 original size:40 final size:40
Alignment explanation
Indices: 5545681--5545760 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5545671 CTTCCTCACA
5545681 TAAATTTTAGAGATGATATATCATTACAAAAATACTATAT
1 TAAATTTTAGAGATGATATATCATTACAAAAATACTATAT
5545721 TAAATTTTAGAGATGATATATCATTACAAAAATACTATAT
1 TAAATTTTAGAGATGATATATCATTACAAAAATACTATAT
5545761 CTAGTAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (40 bp):
TAAATTTTAGAGATGATATATCATTACAAAAATACTATAT
Found at i:5545761 original size:19 final size:19
Alignment explanation
Indices: 5545697--5545761 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
5545687 TTAGAGATGA
5545697 TATATCATTACAAAAATAC
1 TATATCATTACAAAAATAC
* ** * *
5545716 TATATTAAATTTTAGAGATGA-
1 TATA-T-CATTACAAAAAT-AC
5545737 TATATCATTACAAAAATAC
1 TATATCATTACAAAAATAC
5545756 TATATC
1 TATATC
5545762 TAGTAGTATA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 2 0.06
21 11 0.34
22 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
TATATCATTACAAAAATAC
Found at i:5546156 original size:24 final size:24
Alignment explanation
Indices: 5546127--5546172 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5546117 TCTGATTCAC
* *
5546127 TAATAATTTATAAAATTTATACAT
1 TAATAATATATAAAATATATACAT
*
5546151 TAATAATATATTAAATATATAC
1 TAATAATATATAAAATATATAC
5546173 TCTTTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATATATAAAATATATACAT
Found at i:5560083 original size:2 final size:2
Alignment explanation
Indices: 5560076--5560100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5560066 TAAACATGAC
5560076 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5560101 CACACTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5566592 original size:22 final size:22
Alignment explanation
Indices: 5566571--5566611 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5566561 ATAACCTCTA
5566571 ATAAAATTTTGGT-ACCTTTCT
1 ATAAAATTTTGGTAACCTTTCT
* *
5566592 ATACAGTTTTGGTAACCTTT
1 ATAAAATTTTGGTAACCTTT
5566612 ATATTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (22 bp):
ATAAAATTTTGGTAACCTTTCT
Found at i:5566647 original size:21 final size:21
Alignment explanation
Indices: 5566623--5566707 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
5566613 TATTAGTTTA
5566623 ATAACTTATGATATAATTTTG
1 ATAACTTATGATATAATTTTG
* * * *
5566644 ATAATTTTTTATAAAATTTTG
1 ATAACTTATGATATAATTTTG
* *
5566665 ATAACCTCT-TTATGTAATTTTG
1 ATAA-CT-TATGATATAATTTTG
5566687 ATAACTATTATGATA-AATTTT
1 ATAAC--TTATGATATAATTTT
5566708 TTGTAATCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 22 0.44
22 23 0.46
23 5 0.10
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (21 bp):
ATAACTTATGATATAATTTTG
Found at i:5566683 original size:22 final size:22
Alignment explanation
Indices: 5566633--5566691 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5566623 ATAACTTATG
* *
5566633 ATATAATTTTGATAA-TTTTTT
1 ATATAATTTTGATAACCTCTTT
*
5566654 ATAAAATTTTGATAACCTCTTT
1 ATATAATTTTGATAACCTCTTT
*
5566676 ATGTAATTTTGATAAC
1 ATATAATTTTGATAAC
5566692 TATTATGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATAATTTTGATAACCTCTTT
Found at i:5566705 original size:22 final size:21
Alignment explanation
Indices: 5566623--5566707 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
5566613 TATTAGTTTA
5566623 ATAAC-TTATGATATAATTTTG
1 ATAACTTTATGATA-AATTTTG
* *
5566644 ATAA-TTTTTTATAAAATTTTG
1 ATAACTTTATGAT-AAATTTTG
5566665 ATAACCTCTTTATG-T-AATTTTG
1 ATAA---CTTTATGATAAATTTTG
5566687 ATAACTATTATGATAAATTTT
1 ATAACT-TTATGATAAATTTT
5566708 TTGTAATCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
19 2 0.04
20 5 0.10
21 21 0.41
22 18 0.35
24 1 0.02
25 4 0.08
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (21 bp):
ATAACTTTATGATAAATTTTG
Found at i:5567010 original size:22 final size:21
Alignment explanation
Indices: 5566982--5567122 Score: 93
Period size: 22 Copynumber: 6.4 Consensus size: 21
5566972 ATTTGATAAT
5566982 TAAATTATTATCGATTTATTAC
1 TAAATTATTAT-GATTTATTAC
* * *
5567004 TATATTATTAGTTATTTACTAC
1 TAAATTATTA-TGATTTATTAC
*
5567026 TAAATTATTAATGATTTATTAA
1 TAAATTATT-ATGATTTATTAC
* * *
5567048 TAAATTATAATTAATTTATAAC
1 TAAATTATTA-TGATTTATTAC
* * *
5567070 TAATTTATAAATGATTTATCAC
1 TAAATTAT-TATGATTTATTAC
* ** **
5567092 TAAGTTACGAATGATTTACCAC
1 TAAATTA-TTATGATTTATTAC
5567114 TAAATTATT
1 TAAATTATT
5567123 GAAAACTTAC
Statistics
Matches: 94, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.01
22 89 0.95
23 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (21 bp):
TAAATTATTATGATTTATTAC
Found at i:5567045 original size:44 final size:44
Alignment explanation
Indices: 5566971--5567094 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 44
5566961 AAGTTATAAA
* * *
5566971 AATTTGATAATTAAATTATT-ATCGATTTATTACTATATTATTAGTT
1 AATTT-ATAACTAAATTATTAAT-GATTTATTACTAAATTA-TAATT
*
5567017 -ATTTACT-ACTAAATTATTAATGATTTATTAATAAATTATAATT
1 AATTTA-TAACTAAATTATTAATGATTTATTACTAAATTATAATT
* * *
5567060 AATTTATAACTAATTTATAAATGATTTATCACTAA
1 AATTTATAACTAAATTATTAATGATTTATTACTAA
5567095 GTTACGAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
43 5 0.08
44 54 0.82
45 7 0.11
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (44 bp):
AATTTATAACTAAATTATTAATGATTTATTACTAAATTATAATT
Found at i:5567046 original size:11 final size:11
Alignment explanation
Indices: 5567030--5567088 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
5567020 TACTACTAAA
*
5567030 TTATTAATGAT
1 TTATTAATAAT
*
5567041 TTATTAATAAA
1 TTATTAATAAT
5567052 TTA-TAATTAAT
1 TTATTAA-TAAT
5567063 TTA-TAACTAAT
1 TTATTAA-TAAT
* *
5567074 TTATAAATGAT
1 TTATTAATAAT
5567085 TTAT
1 TTAT
5567089 CACTAAGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 3 0.08
11 35 0.88
12 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (11 bp):
TTATTAATAAT
Found at i:5567196 original size:22 final size:22
Alignment explanation
Indices: 5567149--5567222 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
5567139 GTTAATGATG
* *
5567149 ATTTATTATAAAGTTAT-AATT
1 ATTTACTACAAAGTTATCAATT
**
5567170 GATTTACTATTAA-TCTATCAATT
1 -ATTTACTACAAAGT-TATCAATT
*
5567193 ATTTGCTACAAAGTTATCAATT
1 ATTTACTACAAAGTTATCAATT
*
5567215 ATTAACTA
1 ATTTACTA
5567223 ATTTATTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.02
22 36 0.86
23 5 0.12
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTACTACAAAGTTATCAATT
Found at i:5567250 original size:22 final size:22
Alignment explanation
Indices: 5567223--5567318 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 22
5567213 TTATTAACTA
5567223 ATTTATTACTAAATTATCATTG
1 ATTTATTACTAAATTATCATTG
*
5567245 ATTTATAACTAAATTATCACTT-
1 ATTTATTACTAAATTATCA-TTG
* * ** * *
5567267 TTTTATAACTATGTTATTAGTG
1 ATTTATTACTAAATTATCATTG
*
5567289 ATTTATTACTAAATTA-CAAATG
1 ATTTATTACTAAATTATC-ATTG
5567311 ATTTATTA
1 ATTTATTA
5567319 TTATGTTCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
21 1 0.02
22 56 0.95
23 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTATTACTAAATTATCATTG
Found at i:5567475 original size:21 final size:22
Alignment explanation
Indices: 5567376--5567472 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
5567366 AATTTTTGAT
5567376 TATTTACTA-TAAACTTATTACA
1 TATTTACTATTAAA-TTATTACA
* * *
5567398 TATTTATTACTAAATTA-TCCA
1 TATTTACTATTAAATTATTACA
* * *
5567419 TGATTCACCATTAAATTATTACT
1 T-ATTTACTATTAAATTATTACA
5567442 TATTTA-TATTAAATTATT-CA
1 TATTTACTATTAAATTATTACA
5567462 TAGTTTACTAT
1 TA-TTTACTAT
5567473 AAAGTTACAG
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.05
21 19 0.32
22 30 0.51
23 7 0.12
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTTACTATTAAATTATTACA
Found at i:5567667 original size:22 final size:22
Alignment explanation
Indices: 5567639--5567695 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
5567629 TTAAAATGAT
* *
5567639 TTACTAAGTTATCA-CTGATTTA
1 TTACTAAGTTAT-ATATGATTAA
*
5567661 TTACTAAATTATATATGATTAA
1 TTACTAAGTTATATATGATTAA
5567683 TTACTAAGTTATA
1 TTACTAAGTTATA
5567696 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (22 bp):
TTACTAAGTTATATATGATTAA
Found at i:5567853 original size:12 final size:12
Alignment explanation
Indices: 5567833--5567862 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5567823 TTATTCAAAT
5567833 TTAAATTTTTTA
1 TTAAATTTTTTA
*
5567845 TTAATTTTTTTA
1 TTAAATTTTTTA
5567857 TTAAAT
1 TTAAAT
5567863 AGGTTCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:5568080 original size:11 final size:11
Alignment explanation
Indices: 5568064--5568125 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
5568054 ATCACAACTT
5568064 TAATTTATGAA
1 TAATTTATGAA
* *
5568075 TAATTTATCAT
1 TAATTTATGAA
*
5568086 TAAGTTATGAA
1 TAATTTATGAA
* ** *
5568097 TGATTTACCAT
1 TAATTTATGAA
*
5568108 TAAGTTATGAA
1 TAATTTATGAA
5568119 TAATTTA
1 TAATTTA
5568126 CTATTAAATT
Statistics
Matches: 35, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (11 bp):
TAATTTATGAA
Found at i:5568093 original size:22 final size:22
Alignment explanation
Indices: 5568063--5568213 Score: 110
Period size: 22 Copynumber: 6.9 Consensus size: 22
5568053 TATCACAACT
* *
5568063 TTAATTTATGAATAATTTATCA
1 TTAAGTTATGAATAATTTACCA
*
5568085 TTAAGTTATGAATGATTTACCA
1 TTAAGTTATGAATAATTTACCA
*
5568107 TTAAGTTATGAATAATTTACTA
1 TTAAGTTATGAATAATTTACCA
* * * *
5568129 TTAAATTGTTG-TTGATTTACCA
1 TTAAGTT-ATGAATAATTTACCA
* **
5568151 TTAAATTATTG-ATAATTTATTA
1 TTAAGTTA-TGAATAATTTACCA
* * *
5568173 TAAAGTTAT-AACTTATTTACTA
1 TTAAGTTATGAA-TAATTTACCA
* *
5568195 CTAATTTATGAATAATTTA
1 TTAAGTTATGAATAATTTA
5568214 TTACAAACTT
Statistics
Matches: 101, Mismatches: 23, Indels: 10
0.75 0.17 0.07
Matches are distributed among these distances:
21 2 0.02
22 95 0.94
23 4 0.04
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (22 bp):
TTAAGTTATGAATAATTTACCA
Found at i:5568258 original size:22 final size:22
Alignment explanation
Indices: 5568163--5568284 Score: 77
Period size: 22 Copynumber: 5.3 Consensus size: 22
5568153 AAATTATTGA
*
5568163 TAATTTATTA-TAAAGTTATAAC
1 TAATTTATTACTAAA-TTATCAC
* * * * *
5568185 TTATTTACTACTAATTTATGAA
1 TAATTTATTACTAAATTATCAC
5568207 TAATTTATTAC-AAACTTATCAATTAAC
1 TAATTTATTACTAAA-TTATC-----AC
5568234 TAATTTATTACTAAATTATCAC
1 TAATTTATTACTAAATTATCAC
* * * *
5568256 TAATTTATAATTAAATTATTAG
1 TAATTTATTACTAAATTATCAC
5568278 TAATTTA
1 TAATTTA
5568285 CTATTATGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
21 2 0.03
22 53 0.68
23 3 0.04
27 17 0.22
28 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATTTATTACTAAATTATCAC
Found at i:5568290 original size:22 final size:22
Alignment explanation
Indices: 5568234--5568384 Score: 144
Period size: 22 Copynumber: 6.9 Consensus size: 22
5568224 ATCAATTAAC
* * * *
5568234 TAATTTATTACTAAATTATCAC
1 TAATTTACTATTAAATTATTAG
5568256 TAATTTA-TAATTAAATTATTAG
1 TAATTTACT-ATTAAATTATTAG
**
5568278 TAATTTACTATTATGTTATTAG
1 TAATTTACTATTAAATTATTAG
* * * *
5568300 TGATTTACTATTAAGTTATCAA
1 TAATTTACTATTAAATTATTAG
* *
5568322 TAATTTACTTTTAAATTATTAA
1 TAATTTACTATTAAATTATTAG
*
5568344 TAATTTACTATTATATTATTATG
1 TAATTTACTATTAAATTATTA-G
*
5568367 T-ATTTACTATTACATTAT
1 TAATTTACTATTAAATTAT
5568385 GATTGGTTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
21 1 0.01
22 106 0.97
23 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (22 bp):
TAATTTACTATTAAATTATTAG
Found at i:5568306 original size:44 final size:44
Alignment explanation
Indices: 5568063--5568384 Score: 170
Period size: 44 Copynumber: 7.2 Consensus size: 44
5568053 TATCACAACT
* * * * * * *
5568063 TTAATTTATGAATAATTTA-TCATTAAGTTATGAATGATTTACCA
1 TTAAATTATTAATAATTTACT-ATTAAATTATTAGTAATTTACTA
* * * * *
5568107 TTAAGTTATGAATAATTTACTATTAAATTGTT-GTTGATTTACCA
1 TTAAATTATTAATAATTTACTATTAAATTATTAG-TAATTTACTA
* * * * *
5568151 TTAAATTATTGATAATTTATTA-TAAAGTTATAACTTATTTACTA
1 TTAAATTATTAATAATTTACTATTAAA-TTATTAGTAATTTACTA
* * * * * * *
5568195 CTAATTTATGAATAATTTATTA-CAAACTTATCAATTAACTAATTTATTA
1 TTAAATTATTAATAATTTACTATTAAA--T-T--ATT-AGTAATTTACTA
* * *
5568244 CTAAATTATCACTAATTTA-TAATTAAATTATTAGTAATTTACTA
1 TTAAATTATTAATAATTTACT-ATTAAATTATTAGTAATTTACTA
** * * * * * *
5568288 TTATGTTATTAGTGATTTACTATTAAGTTATCAATAATTTACTT
1 TTAAATTATTAATAATTTACTATTAAATTATTAGTAATTTACTA
*
5568332 TTAAATTATTAATAATTTACTATTATATTATTATGT-ATTTACTA
1 TTAAATTATTAATAATTTACTATTAAATTATTA-GTAATTTACTA
*
5568376 TTACATTAT
1 TTAAATTAT
5568385 GATTGGTTTA
Statistics
Matches: 216, Mismatches: 49, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
43 4 0.02
44 169 0.78
45 7 0.03
46 1 0.00
47 1 0.00
48 4 0.02
49 27 0.12
50 3 0.01
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.49
Consensus pattern (44 bp):
TTAAATTATTAATAATTTACTATTAAATTATTAGTAATTTACTA
Found at i:5568326 original size:66 final size:66
Alignment explanation
Indices: 5568099--5568378 Score: 199
Period size: 66 Copynumber: 4.2 Consensus size: 66
5568089 GTTATGAATG
* * * ** * * *
5568099 ATTTACCATTAAGTTATGAATAATTTACTATTAAATTGTTGTTGATTTACCATTAAATTATTGAT
1 ATTTACTATTAAGTTATCAATAATTTACTATTAAATTATTAATAATTTACTATTATATTATT-AT
*
5568164 -A
65 GT
* * * * * * * ** *
5568165 ATTTATTATAAAGTTAT-AACTTATTTACTACTAATTTATGAATAATTTATTACAAACTTATCAA
1 ATTTACTATTAAGTTATCAA-TAATTTACTATTAAATTATTAATAATTTACTA-TTA--TAT-TA
**
5568229 TTAACT
61 TTATGT
* * * * * *
5568235 AATTTATTACTAAATTATCACTAATTTA-TAATTAAATTATTAGTAATTTACTATTATGTTATTA
1 -ATTTACTATTAAGTTATCAATAATTTACT-ATTAAATTATTAATAATTTACTATTATATTATTA
5568299 -GT
64 TGT
*
5568301 GATTTACTATTAAGTTATCAATAATTTACTTTTAAATTATTAATAATTTACTATTATATTATTAT
1 -ATTTACTATTAAGTTATCAATAATTTACTATTAAATTATTAATAATTTACTATTATATTATTAT
5568366 GT
65 GT
5568368 ATTTACTATTA
1 ATTTACTATTA
5568379 CATTATGATT
Statistics
Matches: 161, Mismatches: 42, Indels: 22
0.72 0.19 0.10
Matches are distributed among these distances:
65 2 0.01
66 102 0.63
67 8 0.05
68 2 0.01
69 3 0.02
70 5 0.03
71 38 0.24
72 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (66 bp):
ATTTACTATTAAGTTATCAATAATTTACTATTAAATTATTAATAATTTACTATTATATTATTATG
T
Found at i:5568513 original size:43 final size:42
Alignment explanation
Indices: 5568443--5568569 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 42
5568433 AATTTTCTAC
* ** *
5568443 TAAATTATCCATGATTCACTACCAAGTTATAATTGATTTA-TAT
1 TAAATTATCCAT-ATTTACTATTAAGTTAT-ATTGATTTACAAT
*
5568486 TAAATTATCCATATTTTACTATTAAGTTATTATTGATTAACAAT
1 TAAATTATCCATA-TTTACTATTAAGTTA-TATTGATTTACAAT
* * * *
5568530 TAAGTTATCAATAATTTATTATTAATTTATATTGATTTAC
1 TAAATTATCCAT-ATTTACTATTAAGTTATATTGATTTAC
5568570 TTTTAAGTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.01
43 42 0.60
44 26 0.37
45 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (42 bp):
TAAATTATCCATATTTACTATTAAGTTATATTGATTTACAAT
Found at i:5568553 original size:22 final size:22
Alignment explanation
Indices: 5568478--5568612 Score: 78
Period size: 22 Copynumber: 6.2 Consensus size: 22
5568468 GTTATAATTG
* *
5568478 ATTTA-TATTAAATTATCCATA
1 ATTTACTATTAAGTTATCAATA
* * * *
5568499 TTTTACTATTAAGTTATTATTG
1 ATTTACTATTAAGTTATCAATA
* *
5568521 ATTAACAATTAAGTTATCAATA
1 ATTTACTATTAAGTTATCAATA
* * * *
5568543 ATTTATTATTAATTTAT-ATTG
1 ATTTACTATTAAGTTATCAATA
* * *
5568564 ATTTACTTTTAAGTCT-CCTATA
1 ATTTACTATTAAGT-TATCAATA
* * *
5568586 ATTAACTATTAAATTATCAATT
1 ATTTACTATTAAGTTATCAATA
5568608 ATTTA
1 ATTTA
5568613 TTTCTAAATT
Statistics
Matches: 78, Mismatches: 32, Indels: 7
0.67 0.27 0.06
Matches are distributed among these distances:
21 18 0.23
22 60 0.77
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCAATA
Found at i:5568576 original size:43 final size:43
Alignment explanation
Indices: 5568278--5568577 Score: 153
Period size: 44 Copynumber: 6.9 Consensus size: 43
5568268 AAATTATTAG
* *
5568278 TAATTTACTATTATGTTATTAGTGATTTACTATTAAGTTATCAA
1 TAATTTACTATTAAGTTA-TATTGATTTACTATTAAGTTATCAA
* * * * *
5568322 TAATTTACTTTTAAATTATTAATAATTTACTATTATA-TTAT-TA
1 TAATTTACTATTAAGTTA-TATTGATTTACTATTA-AGTTATCAA
* * * * **
5568365 TGTATTTACTATTACA-TTATGATTGGTTTACAACTTAA-TTTTTTA
1 T-AATTTACTATTA-AGTTAT-ATTGATTTACTA-TTAAGTTATCAA
* * * ** * * * *
5568410 TTATTTGCTA-CAAGATTATCATCAATTTTCTACTAAATTATCCA
1 TAATTTACTATTAAG-TTAT-ATTGATTTACTATTAAGTTATCAA
* * ** * *
5568454 TGATTCACTACCAAGTTATAATTGATTTA-TATTAAATTATCCA
1 TAATTTACTATTAAGTTAT-ATTGATTTACTATTAAGTTATCAA
* * *
5568497 TATTTTACTATTAAGTTATTATTGATTAACAATTAAGTTATCAA
1 TAATTTACTATTAAGTTA-TATTGATTTACTATTAAGTTATCAA
* * *
5568541 TAATTTATTATTAATTTATATTGATTTACTTTTAAGT
1 TAATTTACTATTAAGTTATATTGATTTACTATTAAGT
5568578 CTCCTATAAT
Statistics
Matches: 196, Mismatches: 48, Indels: 25
0.73 0.18 0.09
Matches are distributed among these distances:
42 1 0.01
43 57 0.29
44 126 0.64
45 12 0.06
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (43 bp):
TAATTTACTATTAAGTTATATTGATTTACTATTAAGTTATCAA
Found at i:5568715 original size:22 final size:22
Alignment explanation
Indices: 5568690--5568754 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
5568680 AAACTAAAGC
*
5568690 TAATTTACTATTAAATTATTAG
1 TAATTTATTATTAAATTATTAG
* * *
5568712 TAATTTATTATTAACTTATCAT
1 TAATTTATTATTAAATTATTAG
*
5568734 TAATTTATTATTAAGTTATTA
1 TAATTTATTATTAAATTATTA
5568755 ACGATTAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (22 bp):
TAATTTATTATTAAATTATTAG
Found at i:5568721 original size:11 final size:11
Alignment explanation
Indices: 5568690--5568754 Score: 76
Period size: 11 Copynumber: 5.9 Consensus size: 11
5568680 AAACTAAAGC
*
5568690 TAATTTACTAT
1 TAATTTATTAT
* *
5568701 TAAATTATTAG
1 TAATTTATTAT
5568712 TAATTTATTAT
1 TAATTTATTAT
* *
5568723 TAACTTATCAT
1 TAATTTATTAT
5568734 TAATTTATTAT
1 TAATTTATTAT
*
5568745 TAAGTTATTA
1 TAATTTATTA
5568755 ACGATTAACT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 44 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (11 bp):
TAATTTATTAT
Found at i:5568875 original size:22 final size:22
Alignment explanation
Indices: 5568866--5568907 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5568856 GAGTTGTCTA
5568866 TGATTAACTATTAAGTTATTAC
1 TGATTAACTATTAAGTTATTAC
*
5568888 TTATTAACTATTAAGTTATT
1 TGATTAACTATTAAGTTATT
5568908 GATGAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
TGATTAACTATTAAGTTATTAC
Found at i:5570818 original size:153 final size:153
Alignment explanation
Indices: 5570535--5570835 Score: 541
Period size: 153 Copynumber: 2.0 Consensus size: 153
5570525 TCAAATTTCT
5570535 TTAGGTGATAAGTGAACAATTAAGTATACAATGAATAGGCAAAGATGATAAAACTTAACTCAACT
1 TTAGGTGATAAGTGAACAATTAAGTATACAATGAATAGGCAAAGATGATAAAACTTAACTCAACT
5570600 TAATTGATTGTTGATCTTAAGTTTAAAATCCAACTCAAAATTATGAAAAGTCAAAATTCAAAATA
66 TAATTGATTGTTGATCTTAAGTTTAAAATCCAACTCAAAATTATGAAAAGTCAAAATTCAAAATA
*
5570665 TCTTAATTATTAAATACATTTGC
131 TCTTAAATATTAAATACATTTGC
* * *
5570688 TTAGGTGATAAGTGAATAATTGAGTATACAATGAATAGGCATAGATGATAAAACTTAACTCAACC
1 TTAGGTGATAAGTGAACAATTAAGTATACAATGAATAGGCAAAGATGATAAAACTTAACTCAA-C
*
5570753 TT-ATTGATTGTTGATCTTAAGTTTAAAATCCAACTCAAAATTATGAAAAGTCAAAATTCAGAAT
65 TTAATTGATTGTTGATCTTAAGTTTAAAATCCAACTCAAAATTATGAAAAGTCAAAATTCAAAAT
5570817 ATCTTAAATATTAAATACA
130 ATCTTAAATATTAAATACA
5570836 CAATTAAGTA
Statistics
Matches: 142, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
153 139 0.98
154 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (153 bp):
TTAGGTGATAAGTGAACAATTAAGTATACAATGAATAGGCAAAGATGATAAAACTTAACTCAACT
TAATTGATTGTTGATCTTAAGTTTAAAATCCAACTCAAAATTATGAAAAGTCAAAATTCAAAATA
TCTTAAATATTAAATACATTTGC
Found at i:5572362 original size:783 final size:770
Alignment explanation
Indices: 5571301--5572706 Score: 1897
Period size: 767 Copynumber: 1.8 Consensus size: 770
5571291 TTTATTTAAT
** *
5571301 ATTTTTATTATATAAAACTATTACAATACATAATTTTAAAAATAAAAATAAAATAAAGTGAAAGG
1 ATTTTTATTATATAAAAAAATTACAATACATAATTCTAAAAATAAAAATAAAATAAA--GAAAGG
* * *
5571366 ATTTAATTAATTTATCTTTTGAATTATTTAAAAGGACTAAAAGGATTTAATAATGTTATCAATGA
64 ATTTAATTAATTTATCTTTTGAATTATTTAAAAGGAATAAAAGAATTTAATAATATTATCAATGA
* * * *
5571431 TCAAATCATCACCTAATAAAATATACAAACAATAAAATCATTAATATACATATATAGTTAGTAAA
129 TCAAATCATCAACTAATAAAATATACAAACAATAAAACCATTAACATACATATATAATTAGTAAA
* * *
5571496 TCCATTAAAAAAAATTGAAAGGGAAAAATAAAAAAAAATAAATATACTTCAATGACTTAATTATA
194 TCCATTAAAAAAAACTGAAAGGAAAAAATAAAAAAAAATAAATATACTACAATGACTTAATTATA
* *
5571561 AAAAAAGGAGTATAATAAT-AACAAAATTCATTTAAATTAAAATTGATAAAAAAAATTTACTATG
259 AAAAAAGGAGTATAATAATAAAAAAAAATCATTTAAATT-AAA---AT--------TTTACTATG
* * *
5571625 GTATTTTAATAAAT-CATTTTTAACA-TTTTGGAATTAAAATTTT-TTTAAGAGTATTTTAACTA
312 GTACTTTAATAAATAC-TTTTTAACATTTTTGGAATTAAAATTTTATTT-AGAATATTTTAACCA
* * *
5571687 ATCACTTTTAGCACTTTTTTTTATTGTGATTA-TAAAAAAGTAA-TCTAATAATAAAAAAGAAAT
375 ATCACTTTTAGCAC---TTTTAAGTGTAATTATTAAAAAAG-AAGTCTAATAAT----AA-AAAT
* * * * *
5571750 TTTATTTAAATTAAAATTTAT-AAAAAATTTACAAAGAATATTTTAGTCAATTATTTTTAATGCT
431 ATTATTTAAAATAAAATTTATAAAAAAAATTACAAAGAATATTTTAGTAAATTATTTTTAATACT
*
5571814 TGCGGTATTAAAATTTCAAAATTTTAAATAGTTTAATTTCACATAAACTCTATTTTAAATTTTAG
496 TGCGGTATTAAAATTTCAAAATTTTAAATAGTTTAATTTCACATAAACTATATTTTAAATTTTAG
* *
5571879 TTAATTTCTTTTAAACTTGAATAAATTAATAAAAATTATATACTTAAGAATAAATTTGTTAAATT
561 TTAATTTATTTTAAACTTAAAT-AATTAATAAAAATTATATACTTAAGAATAAATTTGTTAAATT
5571944 AAAAATTCATAGAGGTATTTAGGTCTTTTTTTTTTTTTTGCTTAAGATAATTTGTAGTTGGTGCT
625 AAAAATTCATAGAGGTATTTAGGTCTTTTTTTTTTTTTTGCTTAAGATAATTTGTAGTTGGTGCT
5572009 TCCATCAATTAAGTGTAATTGTAAATTTTACCAATTTAAAACTTAAATTTTCTTTTATTTAAAAA
690 TCCATCAATTAAGTGTAATTGTAAATTTTACCAATTTAAAACTTAAATTTTCTTTTATTTAAAAA
5572074 AATTTATTATACATAA
755 AATTTATTATACATAA
* * *
5572090 ATTTTTATTATATAAAAAAATTACAATATATAATTCTAAAAATTAAAATGAAAT-AA-AAA-GAT
1 ATTTTTATTATATAAAAAAATTACAATACATAATTCTAAAAATAAAAATAAAATAAAGAAAGGAT
* ** * * ** *
5572152 TTATTTAATTTCA-CTTTTGAATT-TTTTCAAGGAATTAAAGAATTTATTTGTATTATCATTGAT
66 TTAATTAATTT-ATCTTTTGAATTATTTAAAAGGAATAAAAGAATTTAATAATATTATCAATGAT
** * * *
5572215 CATGTGATCAACTCATAAAATATACAAATAATAAAACCATTAACATACATATATAATTAGTAAAT
130 CAAATCATCAACTAATAAAATATACAAACAATAAAACCATTAACATACATATATAATTAGTAAAT
* * * *
5572280 CCATTAAAACAAAAAACTGAAAGGAAAAAAT-AGAGAAAA-AAATTTACTACAATGTCTTAATTA
195 CCATT--AA-AAAAAACTGAAAGGAAAAAATAAAAAAAAATAAATATACTACAATGACTTAATTA
*
5572343 T-AAAAAAGGAGTCTAATAATAAAAAAAAATCATTTAAATTAAAATTTTACTATGGTACTTTAAT
257 TAAAAAAAGGAGTATAATAATAAAAAAAAATCATTTAAATTAAAATTTTACTATGGTACTTTAAT
* ** *
5572407 CAATACTTTTTAACATTTTTGGAATTAAAATTTTATTTAGAATATTTTAACCAATCTTTTTTATC
322 AAATACTTTTTAACATTTTTGGAATTAAAATTTTATTTAGAATATTTTAACCAATCACTTTTAGC
5572472 ACTTTTAAGTGTAATTATTAAAAAAGAAGTCTAATAATAAAAATATTATTTAAAATAAAATTTAT
387 ACTTTTAAGTGTAATTATTAAAAAAGAAGTCTAATAATAAAAATATTATTTAAAATAAAATTTAT
** **
5572537 AAAAAAAATTAGTAAGAATATTTTAGTAAATTATTTTTAATACTTTTGGTATTAAAATTTCAAAA
452 AAAAAAAATTACAAAGAATATTTTAGTAAATTATTTTTAATACTTGCGGTATTAAAATTTCAAAA
*
5572602 TTTTAAGTAGTTTAATTTCACATAAACTATATTTTAAATTTTAGTTAATTTATTTTAAACTTAAA
517 TTTTAAATAGTTTAATTTCACATAAACTATATTTTAAATTTTAGTTAATTTATTTTAAACTTAAA
*
5572667 TAATTAATAAAAATTATATATTTAAGAATAAATTTGTTAA
582 TAATTAATAAAAATTATATACTTAAGAATAAATTTGTTAA
5572707 TTTTAAATTA
Statistics
Matches: 546, Mismatches: 60, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
766 61 0.11
767 121 0.22
770 14 0.03
771 17 0.03
772 30 0.05
773 43 0.08
774 3 0.01
780 2 0.00
783 112 0.21
784 62 0.11
785 12 0.02
786 19 0.03
788 2 0.00
789 48 0.09
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (770 bp):
ATTTTTATTATATAAAAAAATTACAATACATAATTCTAAAAATAAAAATAAAATAAAGAAAGGAT
TTAATTAATTTATCTTTTGAATTATTTAAAAGGAATAAAAGAATTTAATAATATTATCAATGATC
AAATCATCAACTAATAAAATATACAAACAATAAAACCATTAACATACATATATAATTAGTAAATC
CATTAAAAAAAACTGAAAGGAAAAAATAAAAAAAAATAAATATACTACAATGACTTAATTATAAA
AAAAGGAGTATAATAATAAAAAAAAATCATTTAAATTAAAATTTTACTATGGTACTTTAATAAAT
ACTTTTTAACATTTTTGGAATTAAAATTTTATTTAGAATATTTTAACCAATCACTTTTAGCACTT
TTAAGTGTAATTATTAAAAAAGAAGTCTAATAATAAAAATATTATTTAAAATAAAATTTATAAAA
AAAATTACAAAGAATATTTTAGTAAATTATTTTTAATACTTGCGGTATTAAAATTTCAAAATTTT
AAATAGTTTAATTTCACATAAACTATATTTTAAATTTTAGTTAATTTATTTTAAACTTAAATAAT
TAATAAAAATTATATACTTAAGAATAAATTTGTTAAATTAAAAATTCATAGAGGTATTTAGGTCT
TTTTTTTTTTTTTGCTTAAGATAATTTGTAGTTGGTGCTTCCATCAATTAAGTGTAATTGTAAAT
TTTACCAATTTAAAACTTAAATTTTCTTTTATTTAAAAAAATTTATTATACATAA
Found at i:5572925 original size:17 final size:17
Alignment explanation
Indices: 5572903--5572936 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5572893 CAGAAACTTG
5572903 CCTTTTTCCTTATTCTT
1 CCTTTTTCCTTATTCTT
*
5572920 CCTTTTTCCTTGTTCTT
1 CCTTTTTCCTTATTCTT
5572937 TGTTCCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.65
Consensus pattern (17 bp):
CCTTTTTCCTTATTCTT
Found at i:5572944 original size:14 final size:15
Alignment explanation
Indices: 5572918--5572953 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
5572908 TTCCTTATTC
5572918 TTCCTTT-TTCCTTG
1 TTCCTTTGTTCCTTG
5572932 TT-CTTTGTTCCTTG
1 TTCCTTTGTTCCTTG
5572946 TTCCTTTG
1 TTCCTTTG
5572954 ATTCTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.00, C:0.25, G:0.11, T:0.64
Consensus pattern (15 bp):
TTCCTTTGTTCCTTG
Found at i:5573577 original size:4 final size:4
Alignment explanation
Indices: 5573570--5573624 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
5573560 TTCTTTATAT
* * *
5573570 ATAG ATAG ATAG AT-G ATAG AT-G AAAT ATAG ATAG ATAA ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
5573616 AT-G ATAG AT
1 ATAG ATAG AT
5573625 GAAATATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 8 0.19
4 34 0.81
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:5573589 original size:11 final size:11
Alignment explanation
Indices: 5573573--5573624 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
5573563 TTTATATATA
5573573 GATAGATAGAT
1 GATAGATAGAT
*
5573584 GATAGATGAAAT
1 GATAGAT-AGAT
5573596 -ATAGATAGAT
1 GATAGATAGAT
*
5573606 AAATAGATAGAT
1 -GATAGATAGAT
5573618 GATAGAT
1 GATAGAT
5573625 GAAATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 3 0.09
11 19 0.54
12 13 0.37
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (11 bp):
GATAGATAGAT
Found at i:5573590 original size:15 final size:14
Alignment explanation
Indices: 5573570--5573626 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
5573560 TTCTTTATAT
5573570 ATAGATAGATAGATG
1 ATAGAT-GATAGATG
5573585 ATAGATGA-A-AT-
1 ATAGATGATAGATG
*
5573596 ATAGATAGATAAATAG
1 ATAGAT-GATAGAT-G
5573612 ATAGATGATAGATG
1 ATAGATGATAGATG
5573626 A
1 A
5573627 AATATATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 2 0.06
14 6 0.17
15 12 0.33
16 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (14 bp):
ATAGATGATAGATG
Found at i:5573597 original size:26 final size:27
Alignment explanation
Indices: 5573568--5573619 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
5573558 TCTTCTTTAT
*
5573568 ATATAGATAGATAGAT-GATAGATGAA
1 ATATAGATAGATAAATAGATAGATGAA
5573594 ATATAGATAGATAAATAGATAGATGA
1 ATATAGATAGATAAATAGATAGATGA
5573620 TAGATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (27 bp):
ATATAGATAGATAAATAGATAGATGAA
Found at i:5573604 original size:30 final size:31
Alignment explanation
Indices: 5573565--5573632 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 31
5573555 CAATCTTCTT
*
5573565 TATATATAG-ATAGATAGATGATAGATGAAA
1 TATAGATAGAATAGATAGATGATAGATGAAA
5573595 TATAGATAGATAAATAGATAGATGATAGATGAAA
1 TATAGATAG---AATAGATAGATGATAGATGAAA
5573629 TATA
1 TATA
5573633 TAAGTAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 8 0.24
34 25 0.76
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.29
Consensus pattern (31 bp):
TATAGATAGAATAGATAGATGATAGATGAAA
Found at i:5574873 original size:16 final size:16
Alignment explanation
Indices: 5574847--5574920 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
5574837 ATCAAACCTG
5574847 AATTGCAAAATAATTTA
1 AATT-CAAAATAATTTA
*
5574864 AATTCAAAATGATTTA
1 AATTCAAAATAATTTA
*
5574880 AAGTT-GAAATAATTTA
1 AA-TTCAAAATAATTTA
* * * *
5574896 GATCCAAAATGATTTT
1 AATTCAAAATAATTTA
5574912 AA-TCAAAAT
1 AATTCAAAAT
5574921 GACTTGGAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
15 7 0.16
16 32 0.71
17 6 0.13
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (16 bp):
AATTCAAAATAATTTA
Found at i:5576395 original size:16 final size:16
Alignment explanation
Indices: 5576375--5576416 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5576365 ATTTAATTTC
*
5576375 GAAATAATTCAAATTT
1 GAAATAATTCAAAATT
* *
5576391 TAAATAAATCAAAATT
1 GAAATAATTCAAAATT
5576407 GAAATAATTC
1 GAAATAATTC
5576417 GAATATGAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (16 bp):
GAAATAATTCAAAATT
Found at i:5582871 original size:2 final size:2
Alignment explanation
Indices: 5582864--5582895 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5582854 ATAGGTTTAG
5582864 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
5582896 TACAATAGAT
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:5583257 original size:2 final size:2
Alignment explanation
Indices: 5583252--5583280 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5583242 TGTGTGTGTG
5583252 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
5583281 GTCATAGTAA
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:5586145 original size:2 final size:2
Alignment explanation
Indices: 5586138--5586170 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5586128 TGTTAATTAA
5586138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5586171 AACAAATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5588399 original size:20 final size:22
Alignment explanation
Indices: 5588347--5588400 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
5588337 GTATCTTCCA
5588347 AAAAAGTGTAATTGAATTTAGTC
1 AAAAAGT-TAATTGAATTTAGTC
5588370 AAGTATAAGTTAATTG-ATTTAGT-
1 AA--A-AAGTTAATTGAATTTAGTC
5588393 AAAAAGTT
1 AAAAAGTT
5588401 TGAGTTCACT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 5 0.18
21 1 0.04
23 4 0.14
24 7 0.25
25 7 0.25
26 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (22 bp):
AAAAAGTTAATTGAATTTAGTC
Found at i:5589740 original size:40 final size:40
Alignment explanation
Indices: 5589695--5589773 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
5589685 TTAAGAAGGA
*
5589695 TCAAACTCAATTAATAAGAAAAAAGAACTTTAAACTAATG
1 TCAAACTCAATTAACAAGAAAAAAGAACTTTAAACTAATG
5589735 TCAAACTCAATTAACAAGAAAAAAGAACTTTAAACTAAT
1 TCAAACTCAATTAACAAGAAAAAAGAACTTTAAACTAAT
5589774 TTTTTTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (40 bp):
TCAAACTCAATTAACAAGAAAAAAGAACTTTAAACTAATG
Found at i:5591196 original size:28 final size:28
Alignment explanation
Indices: 5591163--5591218 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5591153 AGCTTGTATG
5591163 TACTAAAATTGATCTTGGTCG-TTGTCGT
1 TACTAAAATTGATCTTGGT-GATTGTCGT
5591191 TACTAAAATTGATCTTGGTGATTGTCGT
1 TACTAAAATTGATCTTGGTGATTGTCGT
5591219 ATTGTTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.43
Consensus pattern (28 bp):
TACTAAAATTGATCTTGGTGATTGTCGT
Found at i:5592876 original size:196 final size:196
Alignment explanation
Indices: 5592542--5592940 Score: 771
Period size: 196 Copynumber: 2.0 Consensus size: 196
5592532 ACTCCTGAAG
*
5592542 TTGATAGCTCTTTATGTTTCTGAGTTTATATTTGACTTGACAATTTGCTATGATATTTTTGTTTA
1 TTGATAGCTCTTTATGTTTCTGAGTTTATACTTGACTTGACAATTTGCTATGATATTTTTGTTTA
*
5592607 TCACAGAGGTAGTTAACTTCAATTCAAAAAGCAACATTTCTTTTTGATGCAGAAAGTTGCATCTT
66 TCACAGAAGTAGTTAACTTCAATTCAAAAAGCAACATTTCTTTTTGATGCAGAAAGTTGCATCTT
*
5592672 CTTTCTGCATTTAACAAGTCTGCTTTAATTTCCACTTGAAAGTGCAAAATGCAAAGGACGTGCCA
131 CTTTCTGCATTTAACAAGTCTGCTTTAATTTCCACTTGAAAGTGCAAAATGCAAACGACGTGCCA
5592737 T
196 T
5592738 TTGATAGCTCTTTATGTTTCTGAGTTTATACTTGACTTGACAATTTGCTATGATATTTTTGTTTA
1 TTGATAGCTCTTTATGTTTCTGAGTTTATACTTGACTTGACAATTTGCTATGATATTTTTGTTTA
5592803 TCACAGAAGTAGTTAACTTCAATTCAAAAAGCAACATTTCTTTTTGATGCAGAAAGTTGCATCTT
66 TCACAGAAGTAGTTAACTTCAATTCAAAAAGCAACATTTCTTTTTGATGCAGAAAGTTGCATCTT
5592868 CTTTCTGCATTTAACAAGTCTGCTTTAATTTCCACTTGAAAGTGCAAAATGCAAACGACGTGCCA
131 CTTTCTGCATTTAACAAGTCTGCTTTAATTTCCACTTGAAAGTGCAAAATGCAAACGACGTGCCA
5592933 T
196 T
5592934 TTGATAG
1 TTGATAG
5592941 AGTAATTGTT
Statistics
Matches: 200, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 200 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (196 bp):
TTGATAGCTCTTTATGTTTCTGAGTTTATACTTGACTTGACAATTTGCTATGATATTTTTGTTTA
TCACAGAAGTAGTTAACTTCAATTCAAAAAGCAACATTTCTTTTTGATGCAGAAAGTTGCATCTT
CTTTCTGCATTTAACAAGTCTGCTTTAATTTCCACTTGAAAGTGCAAAATGCAAACGACGTGCCA
T
Found at i:5597511 original size:60 final size:59
Alignment explanation
Indices: 5597370--5597765 Score: 397
Period size: 58 Copynumber: 6.7 Consensus size: 59
5597360 AATTTCAAGA
* * * * *
5597370 AAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTC
1 AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* * * * * * *
5597428 CAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCTATTTTTTTTAAAAATAAAATTTC
1 AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* * * * *
5597486 AAAAAAGATTTTTTTTAAGGAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAGAGTTTTC
1 AAAAAA-ATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATA-AATTTTC
* * * *
5597547 -AAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* * * * * * *
5597604 AAAAAAGGTTTTTTTTTAGGATAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCC
1 AAAAAA-ATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAA-TTTTC
* * * * *
5597665 AAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTT
1 AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* *
5597723 AAAAAAGGTTTCTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
1 AAAAAA-ATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
5597766 TCTGTACAAA
Statistics
Matches: 271, Mismatches: 57, Indels: 18
0.78 0.16 0.05
Matches are distributed among these distances:
57 6 0.02
58 97 0.36
59 59 0.22
60 94 0.35
61 15 0.06
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (59 bp):
AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
Found at i:5597700 original size:119 final size:118
Alignment explanation
Indices: 5597387--5597765 Score: 605
Period size: 118 Copynumber: 3.2 Consensus size: 118
5597377 TATTTTTGGA
* *
5597387 GAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTAGGGAAAAGT
1 GAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTGGGGAAAAGT
* ** * *
5597452 TGAAAGTATCTATTTTTTTTAAAAATAAAATTTCAAAAAAGATTTTTTTTAAG
66 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTAAG
* * *
5597505 GAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAGAGTTTTCAAAAAATATTTTTGGAGAAAAGT
1 GAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTGGGGAAAAGT
*
5597570 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTTAG
66 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTAAG
*
5597623 GATAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCCAAAAAAATATTTTTGGGGAAAAG
1 GAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCC-AAAAAATATTTTTGGGGAAAAG
* * *
5597688 TTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTAAAAAAGGTTTCTTTTGAG
65 TTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTAAG
*
5597742 GAAAAGTTGAAAGTATCAATTTTT
1 GAAAAGTTGAAAGTATCAAATTTT
5597766 TCTGTACAAA
Statistics
Matches: 240, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
118 146 0.61
119 94 0.39
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (118 bp):
GAAAAGTTGAAAGTATCAAATTTTCTCGAAATTAAAGTTTCCAAAAAATATTTTTGGGGAAAAGT
TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTAAG
Found at i:5602573 original size:30 final size:30
Alignment explanation
Indices: 5602539--5602622 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
5602529 ATCAACAATG
*
5602539 GATGAAAAATGAGAAAAAAAAAAAG-AAAAT
1 GATGAAAAATGA-AAAAAAAAAAAGAAAAAA
*
5602569 GATGACAAA-GAAATAAAAAAAAAAGAAAAAA
1 GATGAAAAATG-AA-AAAAAAAAAAGAAAAAA
*
5602600 AATGAGAAAATGAAAAAAAAAAA
1 GATGA-AAAATGAAAAAAAAAAA
5602623 GATTCAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
29 2 0.04
30 20 0.44
31 17 0.38
32 5 0.11
33 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.08
Consensus pattern (30 bp):
GATGAAAAATGAAAAAAAAAAAAGAAAAAA
Found at i:5602590 original size:23 final size:19
Alignment explanation
Indices: 5602543--5602622 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 19
5602533 ACAATGGATG
5602543 AAAAATGAGAAAAAAAAAA
1 AAAAATGAGAAAAAAAAAA
5602562 AGAAAATGATGACAAAGAAATAAA
1 A-AAAATGA-GA-AAA-AAA-AAA
* *
5602586 AAAAA-AAGAAAAAAAATGA
1 AAAAATGAGAAAAAAAA-AA
*
5602605 GAAAATGA-AAAAAAAAAA
1 AAAAATGAGAAAAAAAAAA
5602623 GATTCAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.04
19 17 0.35
20 11 0.22
21 4 0.08
22 4 0.08
23 7 0.14
24 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAATGAGAAAAAAAAAA
Found at i:5604563 original size:85 final size:82
Alignment explanation
Indices: 5604419--5604762 Score: 340
Period size: 85 Copynumber: 4.1 Consensus size: 82
5604409 ATGATTGTTA
* * *
5604419 AGGAGTAATTTATTTTTCAAAGTCGTGGTTGCCTCT-ATTTAGAGGAGTAATTT-GCTTTTCAAA
1 AGGAGCAATTTATTTTTCAAAGTCGTGG-AGCCTCTGA-TTAGAGGAGCAATTTAG-TTTTCAAA
5604482 GTCG-TGAGGTACCTCTGTTTAG
63 GTCGTTGA-G--CCTCTGTTTAG
* *
5604504 AGGAGCAATTTACTTTTCAAAGTCGTGGTTGCCTCT-ATTTAGAGGAGCAATTTAGTTTTCCAAA
1 AGGAGCAATTTATTTTTCAAAGTCGTGG-AGCCTCTGA-TTAGAGGAGCAATTTAGTTTT-CAAA
5604568 GTTTCGTT--GCCTCTGTTTAG
63 G--TCGTTGAGCCTCTGTTTAG
** * * * * *
5604588 ATAAACAATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTATTTATTTTTCAAAGTC
1 AGGAGCAATTTATTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTAGTTTTCAAAGTC
*
5604653 GTTGAGCCTCTGATTAG
66 GTTGAGCCTCTGTTTAG
* * * *
5604670 AGGAACCATTTATTTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTATGTTTCTCA
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGAGCCTCTGATTAGAGGAGC--AATTTA-GTTT-TCA
*
5604735 AAGTCGTTGAGCCTCTGCTTAG
61 AAGTCGTTGAGCCTCTGTTTAG
5604757 AGGAGC
1 AGGAGC
5604763 TTTAATCAAA
Statistics
Matches: 226, Mismatches: 20, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
80 5 0.02
82 31 0.14
83 53 0.23
84 34 0.15
85 60 0.27
86 10 0.04
87 29 0.13
88 3 0.01
89 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (82 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTAGTTTTCAAAGTC
GTTGAGCCTCTGTTTAG
Found at i:5604766 original size:45 final size:41
Alignment explanation
Indices: 5604426--5604763 Score: 310
Period size: 42 Copynumber: 8.0 Consensus size: 41
5604416 TTAAGGAGTA
* *
5604426 ATTTATTTTTCAAAGTCGTGGTTGCCTCT-ATTTAGAGGAG-T
1 ATTTATTTTTCAAAGTCGTTG-AGCCTCTGA-TTAGAGGAGCT
** * *
5604467 AATTTGCTTTTCAAAGTCG-TGAGGTACCTCTGTTTAGAGGAGCA
1 -ATTTATTTTTCAAAGTCGTTGA-G--CCTCTGATTAGAGGAGCT
* * * *
5604511 ATTTACTTTTCAAAGTCGTGGTTGCCTCT-ATTTAGAGGAGCA
1 ATTTATTTTTCAAAGTCGTTG-AGCCTCTGA-TTAGAGGAGCT
* * ** * *
5604553 ATTTAGTTTTCCAAAGTTTCGTT--GCCTCTGTTTAGATAAACA
1 ATTTA-TTTTTCAAAG--TCGTTGAGCCTCTGATTAGAGGAGCT
*
5604595 ATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
* *
5604636 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAACC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
5604677 ATTTATTTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
1 ATTTATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC--T
*
5604721 ATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGCT
1 ATTTAT-TTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
5604764 TTAATCAAAA
Statistics
Matches: 247, Mismatches: 30, Indels: 37
0.79 0.10 0.12
Matches are distributed among these distances:
39 4 0.02
41 74 0.30
42 84 0.34
43 40 0.16
44 8 0.03
45 35 0.14
46 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (41 bp):
ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
Found at i:5604881 original size:99 final size:102
Alignment explanation
Indices: 5604708--5604977 Score: 307
Period size: 99 Copynumber: 2.6 Consensus size: 102
5604698 GAGCCTCTGA
* * * * *
5604708 TTAGAGGAGCTTTATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGCTTTAATCAAA
1 TTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTCTACTTAGAGAAGCTTTAATCAAA
*
5604773 ATTTT-AAAAA-AAAAATA-AAAAAAATTACCTCTAT
66 ATTTTAAAAAATAAAAAAATAAAAAAATTACCTCTAT
* * *
5604807 TTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTTTACTTAGAGAAGTTTTGATC-AA
1 TTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTCTACTTAGAGAAGCTTTAATCAAA
*
5604871 ATTTTAAAAAAAAATAAAAAAATAAAAAAATTACCTCTGT
66 ATTTT---AAAAAATAAAAAAATAAAAAAATTACCTCTAT
* * * ** * *
5604911 TTAGAAGAGCTTTGTTTATTTTTTGTCAAAGTTGTTGAGTATCTGCTTAGA-AGAGCTTTAATAA
1 TTAGAAGAGCTTTGTTTA-TATTTCTCAAAGTCGTTGAGCCTCTACTTAGAGA-AGCTTTAATCA
5604975 AAA
64 AAA
5604978 AAATTTGCCT
Statistics
Matches: 142, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
98 7 0.05
99 54 0.38
102 5 0.04
103 6 0.04
104 35 0.25
105 32 0.23
106 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (102 bp):
TTAGAAGAGCTTTGTTTATATTTCTCAAAGTCGTTGAGCCTCTACTTAGAGAAGCTTTAATCAAA
ATTTTAAAAAATAAAAAAATAAAAAAATTACCTCTAT
Found at i:5605037 original size:79 final size:80
Alignment explanation
Indices: 5604894--5605056 Score: 213
Period size: 79 Copynumber: 2.0 Consensus size: 80
5604884 ATAAAAAAAT
* * * * *
5604894 AAAAAAATTACCTCTGTTTAGAAGAGCTTTGTTTATTTTTTGTCAAAGTTGTTGAGTATCTGCTT
1 AAAAAAATTACCTCTATTTAGAAGAGCTTTATTTATTTTTTCTCAAAGTCGTTGAGCATCTGCTT
5604959 AGAAGAGCTTTAATA
66 AGAAGAGCTTTAATA
* * *
5604974 AAAAAAATTTGCCTCTATTTAGAGGAGCTTTATTTA-TTTTTCT-AAAGTCGTTGAGCCTCTGCT
1 AAAAAAA-TTACCTCTATTTAGAAGAGCTTTATTTATTTTTTCTCAAAGTCGTTGAGCATCTGCT
* *
5605037 TAGAGGAGCTTTAATC
65 TAGAAGAGCTTTAATA
5605053 AAAA
1 AAAA
5605057 TTAAAAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
79 35 0.49
80 13 0.18
81 24 0.33
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (80 bp):
AAAAAAATTACCTCTATTTAGAAGAGCTTTATTTATTTTTTCTCAAAGTCGTTGAGCATCTGCTT
AGAAGAGCTTTAATA
Found at i:5607585 original size:121 final size:119
Alignment explanation
Indices: 5607460--5607739 Score: 427
Period size: 121 Copynumber: 2.3 Consensus size: 119
5607450 TAATTTTAAG
* *
5607460 AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAATTTTCAAAAAAA
1 AAAAAAATATTTTTAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
*
5607525 G-TTTTTTCTGAGGAAAAGTTGAAAGTATCAATTTCTCTCAAAATTAAAGTTTTC
66 GTTTTTTTCTGAGAAAAAGTTGAAAGTATCAATTTCTCTCAAAATTAAAG-TTTC
* * *
5607579 AAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCTATTTTTCTTAAAAATAAATTTTCAAAAAAG
1 AAAAAAATATTTTTAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
* * * *
5607644 GTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
66 G-TTTTTTTCTGAGAAAAAGTTGAAAGTATCAATTTCTCTCAAAATTAAAGTTT-C
*
5607700 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTAGAAAAAAGTTGAAAGTATCAATTTT
5607740 CTCTGTACAA
Statistics
Matches: 146, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 62 0.42
120 3 0.02
121 81 0.55
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (119 bp):
AAAAAAATATTTTTAGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAA
GTTTTTTTCTGAGAAAAAGTTGAAAGTATCAATTTCTCTCAAAATTAAAGTTTC
Found at i:5607605 original size:59 final size:58
Alignment explanation
Indices: 5607460--5607739 Score: 328
Period size: 59 Copynumber: 4.7 Consensus size: 58
5607450 TAATTTTAAG
* *
5607460 AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAATTTTC
1 AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* * *
5607518 AAAAAAAGT-TTTTTCTGAGGAAAAGTTGAAAGTATCAATTTCTCTCAAAATTAAAGTTTTC
1 AAAAAAA-TATTTTT-TGA-AAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAA-TTTTC
* * *
5607579 AAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCTATTTTTCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
* * * * * *
5607637 AAAAAAGGTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
1 AAAAAA---ATATTTTTTGA-AAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAA-TTTTC
* *
5607700 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTT
5607740 CTCTGTACAA
Statistics
Matches: 187, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
58 23 0.12
59 58 0.31
60 40 0.21
61 24 0.13
62 32 0.17
63 10 0.05
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (58 bp):
AAAAAAATATTTTTTGAAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAATTTTC
Found at i:5608499 original size:19 final size:20
Alignment explanation
Indices: 5608475--5608518 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5608465 TGTTTGAAGA
5608475 TTTTTTTGAG-ATTTTTAAG
1 TTTTTTTGAGAATTTTTAAG
*
5608494 -TTTTTTGGGCAATTTTTAAG
1 TTTTTTTGAG-AATTTTTAAG
5608514 TTTTT
1 TTTTT
5608519 ACAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.18, C:0.02, G:0.16, T:0.64
Consensus pattern (20 bp):
TTTTTTTGAGAATTTTTAAG
Found at i:5608885 original size:12 final size:11
Alignment explanation
Indices: 5608867--5608944 Score: 66
Period size: 12 Copynumber: 6.5 Consensus size: 11
5608857 AGGTATTCCC
5608867 TTTTATTTTTT
1 TTTTATTTTTT
5608878 TGTTTATTTTCTGT
1 T-TTTATTTT-T-T
*
5608892 TTTGATTTTTTT
1 TTTTA-TTTTTT
5608904 TTGTTATTTTATT
1 TT-TTATTTT-TT
5608917 TTTTATTTTTT
1 TTTTATTTTTT
* *
5608928 TATATATTATTT
1 T-TTTATTTTTT
5608940 TTTTA
1 TTTTA
5608945 CATTTACATT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 7 0.13
12 31 0.56
13 11 0.20
14 6 0.11
ACGTcount: A:0.14, C:0.01, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:5608910 original size:26 final size:26
Alignment explanation
Indices: 5608872--5608928 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
5608862 TTCCCTTTTA
*
5608872 TTTTTTTGTTTATTTTCTGTTTTGATT
1 TTTTTTTGTTTATTTTAT-TTTTGATT
*
5608899 TTTTTTTG-TTATTTTATTTTTTATT
1 TTTTTTTGTTTATTTTATTTTTGATT
5608924 TTTTT
1 TTTTT
5608929 ATATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 12 0.43
26 8 0.29
27 8 0.29
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (26 bp):
TTTTTTTGTTTATTTTATTTTTGATT
Found at i:5608937 original size:22 final size:19
Alignment explanation
Indices: 5608897--5608943 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
5608887 TCTGTTTTGA
5608897 TTTTTTTTTGTTATTTTAT
1 TTTTTTTTTGTTATTTTAT
*
5608916 TTTTTATTTTTTTATATATTAT
1 TTTTT-TTTTGTTAT-T-TTAT
5608938 TTTTTT
1 TTTTTT
5608944 ACATTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 8 0.33
21 2 0.08
22 9 0.38
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTTTTGTTATTTTAT
Found at i:5609014 original size:3 final size:3
Alignment explanation
Indices: 5609006--5609045 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
5608996 TAAGAAAAGA
5609006 ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
5609046 TGCATAACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:5609195 original size:3 final size:3
Alignment explanation
Indices: 5609183--5609220 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
5609173 TATATTTGCT
5609183 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5609221 ATTCATGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5609283 original size:13 final size:15
Alignment explanation
Indices: 5609251--5609287 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
5609241 TATTGTATGG
5609251 TAATTTT-TTCATTA
1 TAATTTTATTCATTA
5609265 TAATTTTATTCATT-
1 TAATTTTATTCATTA
5609279 T-ATTTTATT
1 TAATTTTATT
5609288 TGAGTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 8 0.36
15 6 0.27
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTATTCATTA
Found at i:5612386 original size:46 final size:45
Alignment explanation
Indices: 5612316--5612491 Score: 179
Period size: 46 Copynumber: 4.0 Consensus size: 45
5612306 TTTTAAACTA
* * *
5612316 TGGATGTGAATCTC-TAATCTTTTGAATATGAATCTTTAAAATTT
1 TGGATGTGAATCTCACAATTTTTTGAATGTGAATCTTTAAAATTT
* *
5612360 TGGATGTGAATCTTCACAATTTTTTGAATGT-AAACTTTTGAAATTT
1 TGGATGTGAATC-TCACAATTTTTTGAATGTGAATC-TTTAAAATTT
*
5612406 TGGA--TG---CT-AAAATTTTTTGAATGTGAATCTTTAAAATTT
1 TGGATGTGAATCTCACAATTTTTTGAATGTGAATCTTTAAAATTT
* * * *
5612445 TGGATATGAATCTTTACAATTTTTGGAATGTGAATCTCTAAAATTT
1 TGGATGTGAATC-TCACAATTTTTTGAATGTGAATCTTTAAAATTT
5612491 T
1 T
5612492 TCAAATATGA
Statistics
Matches: 110, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
39 28 0.25
40 4 0.04
41 3 0.03
44 15 0.14
45 6 0.05
46 54 0.49
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (45 bp):
TGGATGTGAATCTCACAATTTTTTGAATGTGAATCTTTAAAATTT
Found at i:5612390 original size:24 final size:23
Alignment explanation
Indices: 5612319--5612390 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
5612309 TAAACTATGG
* *
5612319 ATGTGAATC-TCTAATCTTTTGA
1 ATGTGAATCTTCAAATATTTTGA
* * *
5612341 ATATGAATCTTTAAA-ATTTTGG
1 ATGTGAATCTTCAAATATTTTGA
*
5612363 ATGTGAATCTTCACAATTTTTTGA
1 ATGTGAATCTTCA-AATATTTTGA
5612387 ATGT
1 ATGT
5612391 AAACTTTTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
22 24 0.63
23 5 0.13
24 9 0.24
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (23 bp):
ATGTGAATCTTCAAATATTTTGA
Found at i:5612440 original size:24 final size:24
Alignment explanation
Indices: 5612413--5612561 Score: 162
Period size: 24 Copynumber: 6.3 Consensus size: 24
5612403 TTTTGGATGC
5612413 TAAAATTTTTTGAATGTGAATCTT
1 TAAAATTTTTTGAATGTGAATCTT
* *
5612437 TAAAA--TTTTGGATATGAATCTT
1 TAAAATTTTTTGAATGTGAATCTT
* * *
5612459 TACAATTTTTGGAATGTGAATCTC
1 TAAAATTTTTTGAATGTGAATCTT
** *
5612483 TAAAATTTTTCAAATATGAATCTT
1 TAAAATTTTTTGAATGTGAATCTT
*
5612507 TAAAA--TTTTGGATGTGAATCTT
1 TAAAATTTTTTGAATGTGAATCTT
* *
5612529 TAAAATTTTTCGAATGTGAATTTT
1 TAAAATTTTTTGAATGTGAATCTT
5612553 TGAAAATTT
1 T-AAAATTT
5612562 GGATGCAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
22 37 0.37
24 57 0.56
25 7 0.07
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (24 bp):
TAAAATTTTTTGAATGTGAATCTT
Found at i:5612489 original size:85 final size:85
Alignment explanation
Indices: 5612335--5612491 Score: 235
Period size: 85 Copynumber: 1.8 Consensus size: 85
5612325 ATCTCTAATC
* * * *
5612335 TTTTGAATATGAATCTTTAAAATTTTGGATGTGAATCTTCACAATTTTTTGAATGTAAACTTTTG
1 TTTTGAATATGAATCTTTAAAATTTTGGATATGAATCTTCACAATTTTTGGAATGTAAACTTCTA
5612400 AAATTTTGGATGCTAAAATT
66 AAATTTTGGATGCTAAAATT
* * *
5612420 TTTTGAATGTGAATCTTTAAAATTTTGGATATGAATCTTTACAATTTTTGGAATGTGAA-TCTCT
1 TTTTGAATATGAATCTTTAAAATTTTGGATATGAATCTTCACAATTTTTGGAATGTAAACT-TCT
5612484 AAAATTTT
65 AAAATTTT
5612492 TCAAATATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 1 0.02
85 63 0.98
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (85 bp):
TTTTGAATATGAATCTTTAAAATTTTGGATATGAATCTTCACAATTTTTGGAATGTAAACTTCTA
AAATTTTGGATGCTAAAATT
Found at i:5612508 original size:70 final size:70
Alignment explanation
Indices: 5612412--5612549 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 70
5612402 ATTTTGGATG
** * * *
5612412 CTAAAATTTTTTGAATGTGAATCTTTAAAATTTTGGATATGAATCTTTACAATTTTTGGAATGTG
1 CTAAAATTTTTCAAATATGAATCTTTAAAATTTTGGATATGAATCTTTAAAATTTTTCGAATGTG
5612477 AATCT
66 AATCT
*
5612482 CTAAAATTTTTCAAATATGAATCTTTAAAATTTTGGATGTGAATCTTTAAAATTTTTCGAATGTG
1 CTAAAATTTTTCAAATATGAATCTTTAAAATTTTGGATATGAATCTTTAAAATTTTTCGAATGTG
5612547 AAT
66 AAT
5612550 TTTTGAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (70 bp):
CTAAAATTTTTCAAATATGAATCTTTAAAATTTTGGATATGAATCTTTAAAATTTTTCGAATGTG
AATCT
Found at i:5612522 original size:46 final size:46
Alignment explanation
Indices: 5612420--5612566 Score: 183
Period size: 46 Copynumber: 3.2 Consensus size: 46
5612410 TGCTAAAATT
* * *
5612420 TTTTGAATGTGAATCTTTAAAA-TTTT-GGATATGAATCTTTACAAT
1 TTTTGGATGTGAATCTTTAAAATTTTTCGAATATGAATCTTTA-AAA
* *
5612465 TTTTGGAATGTGAATCTCTAAAATTTTTCAAATATGAATCTTTAAAA
1 TTTTGG-ATGTGAATCTTTAAAATTTTTCGAATATGAATCTTTAAAA
* *
5612512 TTTTGGATGTGAATCTTTAAAATTTTTCGAATGTGAATTTTTGAAAA
1 TTTTGGATGTGAATCTTTAAAATTTTTCGAATATGAATCTTT-AAAA
5612559 -TTTGGATG
1 TTTTGGATG
5612567 CAAAATTCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
45 5 0.06
46 55 0.62
47 16 0.18
48 13 0.15
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (46 bp):
TTTTGGATGTGAATCTTTAAAATTTTTCGAATATGAATCTTTAAAA
Found at i:5612623 original size:21 final size:22
Alignment explanation
Indices: 5612599--5612645 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5612589 TGATAATTTT
5612599 TGAAATTTT-AAATTTTGAATG
1 TGAAATTTTAAAATTTTGAATG
**
5612620 TGAAATTTTAAAATTTTTTATG
1 TGAAATTTTAAAATTTTGAATG
5612642 TGAA
1 TGAA
5612646 TCTCTACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
TGAAATTTTAAAATTTTGAATG
Found at i:5613125 original size:35 final size:36
Alignment explanation
Indices: 5613064--5613171 Score: 137
Period size: 36 Copynumber: 3.0 Consensus size: 36
5613054 TTGGAACCTA
* * *
5613064 TGTGAAACTTGAAACCTTTACAAATCTTGAAATTTT
1 TGTGAATCTTAAAACCTTTACGAATCTTGAAATTTT
** * *
5613100 TGTGAAT-TTAAAATTTTTACGAATCTTAAAATCTT
1 TGTGAATCTTAAAACCTTTACGAATCTTGAAATTTT
*
5613135 TGTGAATCTTGAAACCTTTACGAATCTTGAAATTTT
1 TGTGAATCTTAAAACCTTTACGAATCTTGAAATTTT
5613171 T
1 T
5613172 TAGAACCTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 29 0.49
36 30 0.51
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (36 bp):
TGTGAATCTTAAAACCTTTACGAATCTTGAAATTTT
Found at i:5613128 original size:18 final size:18
Alignment explanation
Indices: 5613080--5613171 Score: 87
Period size: 18 Copynumber: 5.2 Consensus size: 18
5613070 ACTTGAAACC
*
5613080 TTTACAAATCTTGAAATT
1 TTTACGAATCTTGAAATT
** *
5613098 TTTGTGAAT-TTAAAATT
1 TTTACGAATCTTGAAATT
* *
5613115 TTTACGAATCTTAAAATC
1 TTTACGAATCTTGAAATT
** **
5613133 TTTGTGAATCTTGAAACC
1 TTTACGAATCTTGAAATT
5613151 TTTACGAATCTTGAAATT
1 TTTACGAATCTTGAAATT
5613169 TTT
1 TTT
5613172 TAGAACCTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
17 14 0.24
18 44 0.76
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTACGAATCTTGAAATT
Found at i:5613182 original size:36 final size:34
Alignment explanation
Indices: 5613069--5613191 Score: 122
Period size: 36 Copynumber: 3.5 Consensus size: 34
5613059 ACCTATGTGA
*
5613069 AACTTGAAACCTTTACAAATCTTGAAATTTTTGTG
1 AACTTGAAACCTTTACGAATCTTGAAATTTTT-TG
* * ** * *
5613104 AATTTAAAATTTTTACGAATCTTAAAATCTTTGTG
1 AACTTGAAACCTTTACGAATCTTGAAAT-TTTTTG
5613139 AATCTTGAAACCTTTACGAATCTTGAAATTTTTTAG
1 AA-CTTGAAACCTTTACGAATCTTGAAATTTTTT-G
5613175 AACCTTG-AACCATTTAC
1 AA-CTTGAAACC-TTTAC
5613192 CAACTTTTGG
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
35 34 0.49
36 36 0.51
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (34 bp):
AACTTGAAACCTTTACGAATCTTGAAATTTTTTG
Found at i:5613584 original size:11 final size:12
Alignment explanation
Indices: 5613566--5613602 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
5613556 CCAACAAGAA
5613566 ATTTTTAATTTT
1 ATTTTTAATTTT
5613578 A-TTTTAATTTT
1 ATTTTTAATTTT
5613589 ATTGTTTAATTTT
1 ATT-TTTAATTTT
5613602 A
1 A
5613603 CTTGTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 2 0.09
13 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (12 bp):
ATTTTTAATTTT
Found at i:5614582 original size:14 final size:13
Alignment explanation
Indices: 5614560--5614594 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
5614550 TTCCCTTTTC
*
5614560 TTTTTTTTGTTTA
1 TTTTTTTTGTTGA
5614573 TTTTTCTTTGTTGA
1 TTTTT-TTTGTTGA
5614587 TTTTTTTT
1 TTTTTTTT
5614595 CATATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.06, C:0.03, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTTTTTGTTGA
Found at i:5614607 original size:14 final size:13
Alignment explanation
Indices: 5614586--5614632 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5614576 TTCTTTGTTG
5614586 ATTT-TTTTTCAT
1 ATTTATTTTTCAT
*
5614598 ATATTATTTTTCAC
1 AT-TTATTTTTCAT
*
5614612 ATTTATATTTTAAT
1 ATTTAT-TTTTCAT
5614626 ATTTATT
1 ATTTATT
5614633 ATGTTAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 20 0.69
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTATTTTTCAT
Found at i:5614854 original size:19 final size:19
Alignment explanation
Indices: 5614786--5614854 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
5614776 TTTTGCACAA
*
5614786 TTGCATGATTATATT-TAA
1 TTGCATGATTATATTATAT
* *
5614804 TTGCATGATAATTAATATAT
1 TTGCATGATTA-TATTATAT
* * *
5614824 TTACATGCTTATATTATTT
1 TTGCATGATTATATTATAT
5614843 TTGCATGATTAT
1 TTGCATGATTAT
5614855 TATATTGCAC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
18 10 0.26
19 19 0.49
20 10 0.26
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (19 bp):
TTGCATGATTATATTATAT
Found at i:5614918 original size:15 final size:14
Alignment explanation
Indices: 5614888--5614915 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5614878 TTATTGCATG
5614888 ATAATTTTTGTATT
1 ATAATTTTTGTATT
5614902 ATAATTTTTGTATT
1 ATAATTTTTGTATT
5614916 TATTTATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
ATAATTTTTGTATT
Found at i:5618747 original size:20 final size:19
Alignment explanation
Indices: 5618722--5618761 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5618712 TTTTGATAAT
*
5618722 ATCTTATGAAAGTTTAGATA
1 ATCTTAT-AAAATTTAGATA
*
5618742 ATCTTATAAAATTTGGATA
1 ATCTTATAAAATTTAGATA
5618761 A
1 A
5618762 CCTTCTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
ATCTTATAAAATTTAGATA
Found at i:5618775 original size:21 final size:21
Alignment explanation
Indices: 5618745--5618874 Score: 120
Period size: 21 Copynumber: 6.2 Consensus size: 21
5618735 TTAGATAATC
* *
5618745 TTATAAAATTTGGATAACCTT
1 TTATATAATTTTGATAACCTT
*
5618766 CTATATAATTTTGATAACC-T
1 TTATATAATTTTGATAACCTT
* *
5618786 TTATATTAGTTTGATAA-CTT
1 TTATATAATTTTGATAACCTT
* * **
5618806 ATAATATAATTTTAATAATTTT
1 -TTATATAATTTTGATAACCTT
*
5618828 TTATAAAATTTTGATAACCTCT
1 TTATATAATTTTGATAACCT-T
* *
5618850 TTATGTAATTTTGGTAACCTT
1 TTATATAATTTTGATAACCTT
5618871 TTAT
1 TTAT
5618875 GAGATAATTT
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 16 0.19
21 49 0.57
22 20 0.23
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (21 bp):
TTATATAATTTTGATAACCTT
Found at i:5618790 original size:41 final size:40
Alignment explanation
Indices: 5618745--5618871 Score: 112
Period size: 41 Copynumber: 3.0 Consensus size: 40
5618735 TTAGATAATC
*
5618745 TTATAAAATTTGGATAACCTTCTATATAATTTTGATAACCT
1 TTATAAAATTT-GATAACCTTATATATAATTTTGATAACCT
* * * **
5618786 TTATATTAGTTTGATAA-CTTATAATATAATTTTAATAATTTT
1 TTATA-AAATTTGATAACCTTAT-ATATAATTTTGATAA-CCT
* * *
5618828 TTATAAAATTTTGATAACCTCTTTATGTAATTTTGGTAACCT
1 TTATAAAA-TTTGATAACCT-TATATATAATTTTGATAACCT
5618870 TT
1 TT
5618872 TATGAGATAA
Statistics
Matches: 66, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
40 4 0.06
41 25 0.38
42 21 0.32
43 14 0.21
44 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (40 bp):
TTATAAAATTTGATAACCTTATATATAATTTTGATAACCT
Found at i:5618885 original size:24 final size:22
Alignment explanation
Indices: 5618834--5618875 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5618824 TTTTTTATAA
*
5618834 AATTTTGATAACCTCTTTATGT
1 AATTTTGGTAACCTCTTTATGT
5618856 AATTTTGGTAACCT-TTTATG
1 AATTTTGGTAACCTCTTTATG
5618876 AGATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (22 bp):
AATTTTGGTAACCTCTTTATGT
Found at i:5619523 original size:22 final size:22
Alignment explanation
Indices: 5619498--5619624 Score: 100
Period size: 22 Copynumber: 5.9 Consensus size: 22
5619488 TTTATTACCT
* *
5619498 AATTTTTAATTATTTACTATAA
1 AATTATTAATGATTTACTATAA
* *
5619520 AATTATTACAT-ATTTATTATTA
1 AATTATTA-ATGATTTACTATAA
* * *
5619542 AATTATCT-ATGATTCACCATTA
1 AATTAT-TAATGATTTACTATAA
*
5619564 AATTATTACTGATTTA-TATAA
1 AATTATTAATGATTTACTATAA
* *
5619585 AATTATTCATAATTTACTATAA
1 AATTATTAATGATTTACTATAA
* *
5619607 AATTA-CAATGATTAACTA
1 AATTATTAATGATTTACTA
5619625 ATAAGTTATC
Statistics
Matches: 83, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
21 28 0.34
22 52 0.63
23 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTATTAATGATTTACTATAA
Found at i:5619731 original size:22 final size:22
Alignment explanation
Indices: 5619537--5619748 Score: 64
Period size: 22 Copynumber: 9.6 Consensus size: 22
5619527 ACATATTTAT
*
5619537 TATTAAATTATC-TATGATTCAC
1 TATTAAATTATCAT-TGATTAAC
* * * *
5619559 CATTAAATTATTACTGATTTA-
1 TATTAAATTATCATTGATTAAC
* * *
5619580 TATAAAATTATTCA-TAATTTAC
1 TATTAAATTA-TCATTGATTAAC
* *
5619602 TATAAAATTA-CAATGATTAAC
1 TATTAAATTATCATTGATTAAC
* * *
5619623 TAATAAGTTATCGATT-ATAATATATA
1 TATTAAATTATC-ATTGAT--TA-A-C
* *
5619649 TATTAAATTATTGA-TGATTTAC
1 TATTAAATTA-TCATTGATTAAC
* *
5619671 TACTAAATTA-GATTGA-TATAC
1 TATTAAATTATCATTGATTA-AC
* * *
5619692 TTTTAAGTT-TCTAATGATTAAC
1 TATTAAATTATC-ATTGATTAAC
* *
5619714 TATTAAATTATCATTGATTTAT
1 TATTAAATTATCATTGATTAAC
*
5619736 TACTAAATTATCA
1 TATTAAATTATCA
5619749 ATTAATTATG
Statistics
Matches: 139, Mismatches: 33, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
20 5 0.04
21 38 0.27
22 72 0.52
23 7 0.05
24 3 0.02
25 2 0.01
26 11 0.08
27 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAAATTATCATTGATTAAC
Found at i:5619764 original size:22 final size:22
Alignment explanation
Indices: 5619715--5619764 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5619705 ATGATTAACT
* *
5619715 ATTAAATTATCATTGATTTATT
1 ATTAAATTATCATTGAATTATG
*
5619737 ACTAAATTATCAATT-AATTATG
1 ATTAAATTATC-ATTGAATTATG
5619759 ATTAAA
1 ATTAAA
5619765 GTGAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTAAATTATCATTGAATTATG
Found at i:5620146 original size:22 final size:22
Alignment explanation
Indices: 5620105--5620198 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 22
5620095 ATAAAAAAGT
*
5620105 TTATCAATAA-TTAATAATTAAA
1 TTATCAATAATTTACT-ATTAAA
* **
5620127 TTATCATTAATTTACTATTATG
1 TTATCAATAATTTACTATTAAA
* *
5620149 TTAGT-ACTAATTTACTATTAAG
1 TTA-TCAATAATTTACTATTAAA
* * * *
5620171 CTATCAATGATTTAATACTAAA
1 TTATCAATAATTTACTATTAAA
5620193 TTATCA
1 TTATCA
5620199 CTACTCTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.02
22 50 0.89
23 5 0.09
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (22 bp):
TTATCAATAATTTACTATTAAA
Found at i:5620322 original size:22 final size:22
Alignment explanation
Indices: 5620238--5620335 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
5620228 AAATTGTTAT
*
5620238 TAATTTATTACTAAGTTATTG-A
1 TAATTTATTACAAAGTTA-TGAA
*
5620260 TAATTTATTATAAAGTTAT-AA
1 TAATTTATTACAAAGTTATGAA
* * * *
5620281 CTTATTTACTACTAATTTATGAA
1 -TAATTTATTACAAAGTTATGAA
* *
5620304 TAATTTATTACAAAATTATCAA
1 TAATTTATTACAAAGTTATGAA
*
5620326 TAATTAATTA
1 TAATTTATTA
5620336 ATTTACTGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.03
22 56 0.93
23 2 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
TAATTTATTACAAAGTTATGAA
Found at i:5620417 original size:44 final size:44
Alignment explanation
Indices: 5620369--5620706 Score: 151
Period size: 44 Copynumber: 7.7 Consensus size: 44
5620359 TTAATTTATA
* * * * *
5620369 ATTAAGTTATTAGTAATTTACTACTACATTATTAGTGATTTACT
1 ATTAAGTTATCAATAATTTACTACTAAATTATCAATGATTTACT
**
5620413 ATTAAGTTATCAATAATTTACTTTTAAATTATCAATGATTTACT
1 ATTAAGTTATCAATAATTTACTACTAAATTATCAATGATTTACT
** * * * * *
5620457 ATTGCGTTAT-AATTGATTTACAATTTAATATT-T-GATTATTTACT
1 ATTAAGTTATCAA-TAATTTACTA-CTAA-ATTATCAATGATTTACT
** * * * *
5620501 ACAAAATTATCATTGATTTACTACTAAATTATTC-ATGA-TTCCTT
1 ATTAAGTTATCAATAATTTACTACTAAATTA-TCAATGATTTAC-T
* * * * *
5620545 ACTAAGTTAT-AACTAATTTA-TATTAAATTATCTATAATTTATT
1 ATTAAGTTATCAA-TAATTTACTACTAAATTATCAATGATTTACT
* * * * *
5620588 ATTAAGTTATCACTGA-TTAGC-ATTTAAGTTATCAATAATTTACT
1 ATTAAGTTATCAATAATTTA-CTA-CTAAATTATCAATGATTTACT
* * * * *
5620632 ATTAATTTAT-ATTAATTTACTTA-TAAGTCT-TCAATAATTAACT
1 ATTAAGTTATCAATAATTTAC-TACTAAAT-TATCAATGATTTACT
* * * *
5620675 ATTAAATTATCAATTATTTACTATTAAGTTAT
1 ATTAAGTTATCAATAATTTACTACTAAATTAT
5620707 TATTTATAGT
Statistics
Matches: 227, Mismatches: 45, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
42 8 0.04
43 67 0.30
44 142 0.63
45 7 0.03
46 3 0.01
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (44 bp):
ATTAAGTTATCAATAATTTACTACTAAATTATCAATGATTTACT
Found at i:5620454 original size:66 final size:65
Alignment explanation
Indices: 5620384--5620641 Score: 172
Period size: 66 Copynumber: 3.9 Consensus size: 65
5620374 GTTATTAGTA
*
5620384 ATTTACTACTACATTATTAGTGATTTACTA-TTAAGTTATCAATAATTTACTTTTAAATTATCAA
1 ATTTACTACTACATTATTA-TGA-TTACTATTTAAGTTATCAATAATTTACTATTAAATTATCAA
5620448 TG
64 TG
* * * * * ** * **
5620450 ATTTACTATTGCGTTATAATTGATTTACAATTTAA--TATTTGATTATTTACTACAAAATTATCA
1 ATTTACTACTACATTATTA-TGA-TTACTATTTAAGTTA-TCAATAATTTACTATTAAATTATCA
*
5620513 TTG
63 ATG
* * * *
5620516 ATTTACTACTAAATTATTCATGATTCCT-TACTAAGTTAT-AACTAATTTA-TATTAAATTATCT
1 ATTTACTACTACATTATT-ATGATTACTAT-TTAAGTTATCAA-TAATTTACTATTAAATTATCA
*
5620578 ATA
63 ATG
* * * *
5620581 ATTTATTATTA-AGTTATCACTGATTAGC-ATTTAAGTTATCAATAATTTACTATTAATTTAT
1 ATTTACTACTACA-TTATTA-TGATTA-CTATTTAAGTTATCAATAATTTACTATTAAATTAT
5620642 ATTAATTTAC
Statistics
Matches: 145, Mismatches: 34, Indels: 26
0.71 0.17 0.13
Matches are distributed among these distances:
64 3 0.02
65 53 0.37
66 82 0.57
67 7 0.05
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (65 bp):
ATTTACTACTACATTATTATGATTACTATTTAAGTTATCAATAATTTACTATTAAATTATCAATG
Found at i:5620605 original size:65 final size:64
Alignment explanation
Indices: 5620547--5620706 Score: 159
Period size: 65 Copynumber: 2.5 Consensus size: 64
5620537 GATTCCTTAC
*
5620547 TAAGTTAT-AACTAATTTA-TATTAAATTATCTATAATTTA-TTATTAAGTTATCACTGATTAGC
1 TAAGTTATCAA-TAATTTACTATTAAATTATAT-TAATTTACTTA-TAAGTTATCACTGATTA-C
5620609 ATT
62 ATT
* * *
5620612 TAAGTTATCAATAATTTACTATTAATTTATATTAATTTACTTATAAGTCT-TCAATAATTA-ACT
1 TAAGTTATCAATAATTTACTATTAAATTATATTAATTTACTTATAAGT-TATCACTGATTACA-T
5620675 AT
64 -T
* * *
5620677 TAAATTATCAATTATTTACTATTAAGTTAT
1 TAAGTTATCAATAATTTACTATTAAATTAT
5620707 TATTTATAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
63 1 0.01
64 1 0.01
65 63 0.77
66 17 0.21
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (64 bp):
TAAGTTATCAATAATTTACTATTAAATTATATTAATTTACTTATAAGTTATCACTGATTACATT
Found at i:5620646 original size:10 final size:11
Alignment explanation
Indices: 5620623--5620652 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
5620613 AAGTTATCAA
5620623 TAATTTACTAT
1 TAATTTACTAT
5620634 TAATTTA-TAT
1 TAATTTACTAT
5620644 TAATTTACT
1 TAATTTACT
5620653 TATAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTTACTAT
Found at i:5620713 original size:22 final size:22
Alignment explanation
Indices: 5620354--5620710 Score: 123
Period size: 22 Copynumber: 16.3 Consensus size: 22
5620344 TTAAATTATA
5620354 TATTATTAATTTA-TAATTAAGT
1 TATTATTAATTTACT-ATTAAGT
* *
5620376 TATTAGTAATTTACTACTACA-T
1 TATTATTAATTTACTATTA-AGT
* *
5620398 TATTAGTGATTTACTATTAAGT
1 TATTATTAATTTACTATTAAGT
* * * *
5620420 TATCAATAATTTACTTTTAAAT
1 TATTATTAATTTACTATTAAGT
* * * **
5620442 TATCAATGATTTACTATTGCGT
1 TATTATTAATTTACTATTAAGT
* * *
5620464 TATAATTGATTTACAATTTAA--
1 TATTATTAATTTACTA-TTAAGT
** *
5620485 TATTTGATT-ATTTACTACAAAAT
1 TA-TT-ATTAATTTACTATTAAGT
* * * *
5620508 TATCATTGATTTACTACTAAAT
1 TATTATTAATTTACTATTAAGT
* * *
5620530 TATTCA-TGA-TTCCTTACTAAGT
1 TATT-ATTAATTTAC-TATTAAGT
* * *
5620552 TATAACTAATTTA-TATTAAAT
1 TATTATTAATTTACTATTAAGT
*
5620573 TATCTA-TAATTTATTATTAAGT
1 TAT-TATTAATTTACTATTAAGT
* * *
5620595 TATCACTGA-TTAGC-ATTTAAGT
1 TATTATTAATTTA-CTA-TTAAGT
* * *
5620617 TATCAATAATTTACTATTAATT
1 TATTATTAATTTACTATTAAGT
5620639 TA-TATTAATTTACT-TATAAGT
1 TATTATTAATTTACTAT-TAAGT
* * * *
5620660 CT-TCAATAATTAACTATTAAAT
1 -TATTATTAATTTACTATTAAGT
*
5620682 TATCAATT-ATTTACTATTAAGT
1 TAT-TATTAATTTACTATTAAGT
5620704 TATTATT
1 TATTATT
5620711 TATAGTATAA
Statistics
Matches: 256, Mismatches: 53, Indels: 53
0.71 0.15 0.15
Matches are distributed among these distances:
20 1 0.00
21 51 0.20
22 185 0.72
23 19 0.07
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (22 bp):
TATTATTAATTTACTATTAAGT
Found at i:5620780 original size:22 final size:21
Alignment explanation
Indices: 5620755--5620810 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
5620745 TATTAATTAA
5620755 TTACTATTCAACTAAAACTAAT
1 TTACTATT-AACTAAAACTAAT
* **
5620777 TTACTATTAAGTTATCACTAAT
1 TTACTATTAA-CTAAAACTAAT
5620799 TTACTATTAACT
1 TTACTATTAACT
5620811 TGTCATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (21 bp):
TTACTATTAACTAAAACTAAT
Found at i:5620803 original size:44 final size:44
Alignment explanation
Indices: 5620755--5620852 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
5620745 TATTAATTAA
*
5620755 TTACTATTCAAC-TAAAACTAATTTACTATTAAGTTATCACTAAT
1 TTACTATT-AACTTAAAACTAATTTACTATTAAGTTATCAATAAT
*** * *
5620799 TTACTATTAACTTGTCATTAATTTATTATTAAGTTATCAATAAT
1 TTACTATTAACTTAAAACTAATTTACTATTAAGTTATCAATAAT
*
5620843 TAACTATTAA
1 TTACTATTAA
5620853 GTTATCACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (44 bp):
TTACTATTAACTTAAAACTAATTTACTATTAAGTTATCAATAAT
Found at i:5620820 original size:22 final size:22
Alignment explanation
Indices: 5620773--5620859 Score: 120
Period size: 22 Copynumber: 4.0 Consensus size: 22
5620763 CAACTAAAAC
*
5620773 TAATTTACTATTAAGTTATCAC
1 TAATTTACTATTAAGTTATCAA
* * *
5620795 TAATTTACTATTAACTTGTCAT
1 TAATTTACTATTAAGTTATCAA
*
5620817 TAATTTATTATTAAGTTATCAA
1 TAATTTACTATTAAGTTATCAA
*
5620839 TAATTAACTATTAAGTTATCA
1 TAATTTACTATTAAGTTATCA
5620860 CTTATTTTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
TAATTTACTATTAAGTTATCAA
Found at i:5620976 original size:142 final size:142
Alignment explanation
Indices: 5620821--5621109 Score: 542
Period size: 142 Copynumber: 2.0 Consensus size: 142
5620811 TGTCATTAAT
*
5620821 TTATTATTAAGTTATCAATAATTAACTATTAAGTTATCACTTATTTTCATTAAATTCTTTTTTAT
1 TTATTATTAAGTTATCAATAATTAACTATTAAGTTATCACTTATTTTCATTAAATTATTTTTTAT
* *
5620886 TTATTACTTTATTGTTATGTATTTACAATTATATTATAATTGGTTTACTACTAAATTATTATACA
66 TTATTACTCTATTGTTATGTATTTACAATTATATTATAATTGATTTACTACTAAATTATTATACA
5620951 TTTATTATTATG
131 TTTATTATTATG
*
5620963 TTATTATTAAGTTATCAATAATTAACTATTAGGTTATCACTTATTTTCATTAAATTATTTTTTAT
1 TTATTATTAAGTTATCAATAATTAACTATTAAGTTATCACTTATTTTCATTAAATTATTTTTTAT
5621028 TTATTACTCTATTGTTATGTATTTACAATTATATTATAATTGATTTACTACTAAATTATTATACA
66 TTATTACTCTATTGTTATGTATTTACAATTATATTATAATTGATTTACTACTAAATTATTATACA
5621093 TTTATTATTATG
131 TTTATTATTATG
5621105 TTATT
1 TTATT
5621110 GCTAATTTAT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 143 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (142 bp):
TTATTATTAAGTTATCAATAATTAACTATTAAGTTATCACTTATTTTCATTAAATTATTTTTTAT
TTATTACTCTATTGTTATGTATTTACAATTATATTATAATTGATTTACTACTAAATTATTATACA
TTTATTATTATG
Found at i:5621152 original size:22 final size:22
Alignment explanation
Indices: 5621068--5621153 Score: 57
Period size: 22 Copynumber: 3.9 Consensus size: 22
5621058 ATATTATAAT
*
5621068 TGATTTACTACTAAATTA-TTA
1 TGATTTATTACTAAATTATTTA
* * ** **
5621089 TACATTTATTATTATGTTATTGC
1 T-GATTTATTACTAAATTATTTA
* * *
5621112 TAATTTATTACTGAGTTATTTA
1 TGATTTATTACTAAATTATTTA
*
5621134 TGATTTATTATTAAATTATT
1 TGATTTATTACTAAATTATT
5621154 ACTTATTAAC
Statistics
Matches: 46, Mismatches: 17, Indels: 3
0.70 0.26 0.05
Matches are distributed among these distances:
21 1 0.02
22 43 0.93
23 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.55
Consensus pattern (22 bp):
TGATTTATTACTAAATTATTTA
Found at i:5622190 original size:2 final size:2
Alignment explanation
Indices: 5622183--5622209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5622173 GTTGACATCA
5622183 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5622210 CCTTCTGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5624831 original size:26 final size:27
Alignment explanation
Indices: 5624766--5624832 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 27
5624756 AAGTCTAATA
5624766 ATAAAAAATTTTATTTAAATTAAAATTT
1 ATAAAAAATTTTATTTAAATT-AAATTT
5624794 ATAAAAAATTTTATTTAAATT-AATTT
1 ATAAAAAATTTTATTTAAATTAAATTT
*
5624820 ATAAAAATTTTTA
1 ATAAAAAATTTTA
5624833 ATAAGAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 17 0.45
28 21 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAAAAAATTTTATTTAAATTAAATTT
Found at i:5624846 original size:26 final size:26
Alignment explanation
Indices: 5624766--5624846 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
5624756 AAGTCTAATA
* *
5624766 ATAAAAAATTTTATTTAAATTAAAATTT
1 ATAAAAAATTTTATATAAA--ATAATTT
* *
5624794 ATAAAAAATTTTATTTAAATTAATTT
1 ATAAAAAATTTTATATAAAATAATTT
* *
5624820 ATAAAAATTTTTA-ATAAGAATATTTT
1 ATAAAAAATTTTATATAA-AATAATTT
5624846 A
1 A
5624847 GTCAATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.07
26 24 0.52
28 19 0.41
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
ATAAAAAATTTTATATAAAATAATTT
Found at i:5624964 original size:21 final size:22
Alignment explanation
Indices: 5624915--5624964 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
5624905 TTAATTTCAC
*
5624915 ATAAATTCTATTTTAAATTTTA
1 ATAAATTCTATTTTAAATTTAA
* *
5624937 GTTAATT-TATTTTAAATTTAA
1 ATAAATTCTATTTTAAATTTAA
5624958 ATAAATT
1 ATAAATT
5624965 AATAAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATAAATTCTATTTTAAATTTAA
Found at i:5626980 original size:72 final size:72
Alignment explanation
Indices: 5626870--5627013 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
5626860 CACATACATA
5626870 TATATATATATATGTACACCAACACACACACTTCATAGTGGATGGTAGTCTATTAATATTGGATG
1 TATATATATATATGTACACCAACACACACACTTCATAGTGGATGGTAGTCTATTAATATTGGATG
5626935 ATATATG
66 ATATATG
*
5626942 TATATATATGTATGTACACCAACACACACACTTCATAGTGGATGGTAGTCTATTAATATTGGATG
1 TATATATATATATGTACACCAACACACACACTTCATAGTGGATGGTAGTCTATTAATATTGGATG
5627007 ATATATG
66 ATATATG
5627014 AAAAATATGA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (72 bp):
TATATATATATATGTACACCAACACACACACTTCATAGTGGATGGTAGTCTATTAATATTGGATG
ATATATG
Done.