Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 10 of 187
Found at i:3586755 original size:18 final size:18
Alignment explanation
Indices: 3586719--3586753 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3586709 GGAAAAACCA
3586719 ATTTATCTTTTTATTTTT
1 ATTTATCTTTTTATTTTT
3586737 ATTTAT-TTTTTATTTTT
1 ATTTATCTTTTTATTTTT
3586754 TAAGAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
ATTTATCTTTTTATTTTT
Found at i:3588012 original size:21 final size:20
Alignment explanation
Indices: 3587979--3588026 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3587969 CAAAATAAAG
3587979 AGGGCCACCCTC-TCTTGCCA
1 AGGGCCACCCTCTTC-TGCCA
*
3587999 AGGGACCACTCTCTTCTGCCA
1 AGGG-CCACCCTCTTCTGCCA
*
3588020 AAGGCCA
1 AGGGCCA
3588027 TTTTTGCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (20 bp):
AGGGCCACCCTCTTCTGCCA
Found at i:3588454 original size:42 final size:43
Alignment explanation
Indices: 3588358--3588454 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 43
3588348 AGTAGGAGAC
*
3588358 ACATGCCCGTGTGGCCGGCCGTGTGCGCCCACACGGCCAGGAG
1 ACATGCCCGTGTGGCCGGCCGTGTGCGCCCACACAGCCAGGAG
* * ** *
3588401 ACACGCCCGTGTGGCCTGCCGTGTG-GCTTACACAGTCAGGAG
1 ACATGCCCGTGTGGCCGGCCGTGTGCGCCCACACAGCCAGGAG
3588443 ACATGCCCGTGT
1 ACATGCCCGTGT
3588455 CTTAGGCCGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 24 0.51
43 23 0.49
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.16
Consensus pattern (43 bp):
ACATGCCCGTGTGGCCGGCCGTGTGCGCCCACACAGCCAGGAG
Found at i:3589424 original size:33 final size:32
Alignment explanation
Indices: 3589387--3589463 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
3589377 TGGCCCTGCC
** * *
3589387 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATCAG-AATGCCATAACCCAGCT
*
3589420 ATGGTCTTATCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAGCT
3589453 ATGGTCTTACA
1 ATGGTCTTACA
3589464 CATGTATCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 32 0.84
34 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAGCT
Found at i:3589511 original size:33 final size:33
Alignment explanation
Indices: 3589469--3589534 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
3589459 TTACACATGT
*
3589469 ATCTATACTGCCATGGTTCAACCATGGTCTTAC
1 ATCTATACTGCCATGGTCCAACCATGGTCTTAC
3589502 ATCTATACTGCCATGGTCCAACCATGGTCTTAC
1 ATCTATACTGCCATGGTCCAACCATGGTCTTAC
3589535 GTTCAATGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (33 bp):
ATCTATACTGCCATGGTCCAACCATGGTCTTAC
Found at i:3589615 original size:105 final size:104
Alignment explanation
Indices: 3589502--3589739 Score: 342
Period size: 105 Copynumber: 2.3 Consensus size: 104
3589492 ATGGTCTTAC
*
3589502 ATCTATACTGCCATGGTCCAACCATGGTCTTACGTTCAATGTGTCATAAGC-CAGTTATGATCAT
1 ATCTATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGTCATAA-CTCAGTTATGATCAT
3589566 TTTATTAAAATGCCATAGCCCAGCTATGGTCTTACACATGT-
65 TTTATTAAAATGCCATAGCCCAGCTATGGTCTT--ACATGTA
* * **
3589607 ATCTATACTGCCATGGTCTAACCATGGTCTTACGTTCAAGGTGTCATAACTCAGTTATGGTGTTT
1 ATCTATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGTCATAACTCAGTTATGATCATT
* *
3589672 TTATTAAAATGCCATGGCCCAGCTATGGTCTTACATTTA
66 TTATTAAAATGCCATAGCCCAGCTATGGTCTTACATGTA
*
3589711 AAC-AT--TGCCATGGTCCAACCATGGTCTTA
1 ATCTATACTGCCATGGTCCAACCATGGTCTTA
3589740 TCAGTCAATT
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
101 23 0.19
103 7 0.06
104 3 0.02
105 89 0.73
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (104 bp):
ATCTATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGTCATAACTCAGTTATGATCATT
TTATTAAAATGCCATAGCCCAGCTATGGTCTTACATGTA
Found at i:3599734 original size:21 final size:21
Alignment explanation
Indices: 3599688--3599736 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3599678 AAATAATAGT
*
3599688 AAAATAGCGAGAAAACAATGA
1 AAAATAGCGAGAAAACAATAA
* *
3599709 GAAATAGC-AGCAAAACAGTAA
1 AAAATAGCGAG-AAAACAATAA
3599730 AAAATAG
1 AAAATAG
3599737 TAAGAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.61, C:0.10, G:0.18, T:0.10
Consensus pattern (21 bp):
AAAATAGCGAGAAAACAATAA
Found at i:3603262 original size:2 final size:2
Alignment explanation
Indices: 3603250--3603280 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3603240 GTGGTGGTGC
3603250 AT AT A- 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
3603281 GTCAATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3620182 original size:21 final size:19
Alignment explanation
Indices: 3620139--3620186 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
3620129 ATATGAAAAT
*
3620139 AAAAATATAAAAAATTTAG
1 AAAAATATAAAAAATCTAG
* *
3620158 AAATATATATAAAATCTAG
1 AAAAATATAAAAAATCTAG
3620177 AAAAATATAA
1 AAAAATATAA
3620187 TTTTTTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAATATAAAAAATCTAG
Found at i:3627773 original size:20 final size:20
Alignment explanation
Indices: 3627732--3627771 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3627722 AATCAATTTT
*
3627732 TTTATATTTAACTATTTAAA
1 TTTATATTTAACTAATTAAA
*
3627752 TTTATATTTTAATTAATTAA
1 TTTATA-TTTAACTAATTAA
3627772 TTAATTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATATTTAACTAATTAAA
Found at i:3627797 original size:16 final size:16
Alignment explanation
Indices: 3627776--3627813 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3627766 AATTAATTAA
3627776 TTGAG-TTATTTTATAT
1 TTGAGTTTA-TTTATAT
3627792 TTGAGTTTATTTATAT
1 TTGAGTTTATTTATAT
*
3627808 ATGAGT
1 TTGAGT
3627814 AATTGAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
TTGAGTTTATTTATAT
Found at i:3630305 original size:14 final size:15
Alignment explanation
Indices: 3630267--3630306 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3630257 ACAATTTTAT
3630267 AACTTAAA--TTCAG
1 AACTTAAATTTTCAG
3630280 AACTTAAATTTTCAG
1 AACTTAAATTTTCAG
*
3630295 TACTT-AATTTTC
1 AACTTAAATTTTC
3630307 TGCATGGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 7 0.29
15 9 0.38
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (15 bp):
AACTTAAATTTTCAG
Found at i:3632280 original size:20 final size:21
Alignment explanation
Indices: 3632255--3632307 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3632245 TAGGAAAATT
*
3632255 TTATAAAAATATATT-ATATA
1 TTATAAAAATATATTAATAGA
*
3632275 TTATAAAAATGTATTAATAGA
1 TTATAAAAATATATTAATAGA
3632296 TTATAAAAATAT
1 TTATAAAAATAT
3632308 GGAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TTATAAAAATATATTAATAGA
Found at i:3632320 original size:17 final size:17
Alignment explanation
Indices: 3632298--3632330 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3632288 TTAATAGATT
*
3632298 ATAAAAATATGGAAAAA
1 ATAAAAATATAGAAAAA
3632315 ATAAAAATATAGAAAA
1 ATAAAAATATAGAAAA
3632331 TGTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
ATAAAAATATAGAAAAA
Found at i:3632417 original size:26 final size:26
Alignment explanation
Indices: 3632388--3632444 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
3632378 TAAATTATGG
3632388 AAAAT-ATGAAATAATTA-TAAAAATCT
1 AAAATAAT-AAAT-ATTATTAAAAATCT
*
3632414 AAAATAAATAAATATTATTAAAAATTT
1 AAAAT-AATAAATATTATTAAAAATCT
3632441 AAAA
1 AAAA
3632445 ATTGATGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.33
27 16 0.59
28 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATAATAAATATTATTAAAAATCT
Found at i:3632511 original size:21 final size:21
Alignment explanation
Indices: 3632485--3632525 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3632475 TGGTGTGATA
*
3632485 GTTGACATGTCATTTCACATT
1 GTTGACATGACATTTCACATT
*
3632506 GTTGACATGACATTTGACAT
1 GTTGACATGACATTTCACAT
3632526 AAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
GTTGACATGACATTTCACATT
Found at i:3632704 original size:20 final size:21
Alignment explanation
Indices: 3632679--3632729 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
3632669 TAGGAAAATT
*
3632679 TTATAAAAATATATT-ATATA
1 TTATAAAAATATATTAATAGA
*
3632699 TTATAAAAATTTATTAATAGA
1 TTATAAAAATATATTAATAGA
3632720 TTATAAAAAT
1 TTATAAAAAT
3632730 GTGGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATAAAAATATATTAATAGA
Found at i:3632839 original size:27 final size:26
Alignment explanation
Indices: 3632809--3632868 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
3632799 GTAAATTATG
3632809 AAAAATATGAAATAATTA-TAAAAATCT
1 AAAAATAT-AAAT-ATTATTAAAAATCT
* *
3632836 AAAATAAATAAATATTATTAAAAATTT
1 AAAA-ATATAAATATTATTAAAAATCT
3632863 AAAAAT
1 AAAAAT
3632869 TGATGCGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.18
27 20 0.71
28 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAATATAAATATTATTAAAAATCT
Found at i:3632840 original size:19 final size:20
Alignment explanation
Indices: 3632802--3632842 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3632792 ATTATTAGTA
*
3632802 AATTATGAAAAATATGAAAT
1 AATTATGAAAAATATAAAAT
*
3632822 AATTAT-AAAAATCTAAAAT
1 AATTATGAAAAATATAAAAT
3632841 AA
1 AA
3632843 ATAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AATTATGAAAAATATAAAAT
Found at i:3639634 original size:45 final size:45
Alignment explanation
Indices: 3639585--3639673 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
3639575 TTTAGTTGAA
*
3639585 TTTAATAAATT-AATATATCTAAATATTAATTTAGT-AAAAATAAAG
1 TTTAAT-AATTGAA-ATATCTAAATATTAATTAAGTAAAAAATAAAG
*
3639630 TTTAATAATTGCAATATCTAAATATTAATTAAGTAAAAAATAAA
1 TTTAATAATTGAAATATCTAAATATTAATTAAGTAAAAAATAAA
3639674 CATAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 24 0.60
45 16 0.40
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.38
Consensus pattern (45 bp):
TTTAATAATTGAAATATCTAAATATTAATTAAGTAAAAAATAAAG
Found at i:3639684 original size:45 final size:44
Alignment explanation
Indices: 3639599--3639684 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
3639589 ATAAATTAAT
* ** *
3639599 ATATCTAAATATTAATTTAGTAAAAATAAAGTTTAATAATTGCA
1 ATATCTAAATATTAATTAAGTAAAAATAAACATAAATAATTGCA
3639643 ATATCTAAATATTAATTAAGTAAAAAATAAACATAAATAATT
1 ATATCTAAATATTAATTAAGT-AAAAATAAACATAAATAATT
3639685 ATAATACTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.54
45 17 0.46
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (44 bp):
ATATCTAAATATTAATTAAGTAAAAATAAACATAAATAATTGCA
Found at i:3657945 original size:39 final size:39
Alignment explanation
Indices: 3657891--3657976 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
3657881 CAAAGAGAAT
* * * *
3657891 CATTGCTCGGTTATAAAGGTGTCAACAATAGGCTTTAAC
1 CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
*
3657930 CATTGCTCGATTATAAAGATGTCCACAAGAGACTTTAAC
1 CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
*
3657969 TATTGCTC
1 CATTGCTC
3657977 CCTAATACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (39 bp):
CATTGCTCGATTATAAAGATGTCAACAAGAGACTTTAAC
Found at i:3663830 original size:25 final size:25
Alignment explanation
Indices: 3663798--3663852 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
3663788 TAATTTAATC
*
3663798 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
3663822 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
3663847 ATATAT
1 ATATAT
3663853 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:3667399 original size:3 final size:3
Alignment explanation
Indices: 3667391--3667429 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3667381 AATAATTTGA
3667391 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
3667430 GTTTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3667732 original size:15 final size:14
Alignment explanation
Indices: 3667708--3667741 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3667698 TACCTACGTA
*
3667708 TATATGTACATATTT
1 TATATATACATA-TT
3667723 TATATATACATATT
1 TATATATACATATT
3667737 TATAT
1 TATAT
3667742 GTTCTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATATACATATT
Found at i:3669426 original size:38 final size:38
Alignment explanation
Indices: 3669383--3669464 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
3669373 CAAGAAAAGT
3669383 GTTAGTCATATAGTTCTAAATTAATTTCTTGTTAGTTA
1 GTTAGTCATATAGTTCTAAATTAATTTCTTGTTAGTTA
3669421 GTTAGTCATATAGTTCTAAATTAATTTCTTGTTAGTTA
1 GTTAGTCATATAGTTCTAAATTAATTTCTTGTTAGTTA
3669459 GTTAGT
1 GTTAGT
3669465 AGTTTATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (38 bp):
GTTAGTCATATAGTTCTAAATTAATTTCTTGTTAGTTA
Found at i:3676378 original size:23 final size:23
Alignment explanation
Indices: 3676335--3676380 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3676325 TTATTGATTC
* *
3676335 CTATTTTTTTCATTTTCTATTTT
1 CTATTTTTTCCAATTTCTATTTT
3676358 CTATTTTTATCCAATTT-TATTTT
1 CTATTTTT-TCCAATTTCTATTTT
3676381 TAATTATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (23 bp):
CTATTTTTTCCAATTTCTATTTT
Found at i:3679955 original size:16 final size:16
Alignment explanation
Indices: 3679918--3679957 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3679908 TTAATAAAAT
* *
3679918 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3679934 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3679950 TAAAATTA
1 TAAAATTA
3679958 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3680036 original size:59 final size:59
Alignment explanation
Indices: 3679968--3680137 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
3679958 TCAAATTATT
* *
3679968 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAATATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
3680027 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
3680086 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
3680138 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:3680244 original size:22 final size:24
Alignment explanation
Indices: 3680204--3680247 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3680194 AAATAAACTT
3680204 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
3680228 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
3680248 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:3682196 original size:19 final size:20
Alignment explanation
Indices: 3682174--3682215 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3682164 ACTTCATTAA
3682174 ATAAAAATAAATTATTTT-T
1 ATAAAAATAAATTATTTTCT
* *
3682193 AT-AATATAAATTCTTTTCT
1 ATAAAAATAAATTATTTTCT
3682212 ATAA
1 ATAA
3682216 TCATCCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 13 0.68
19 5 0.26
20 1 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAAATAAATTATTTTCT
Found at i:3682203 original size:18 final size:19
Alignment explanation
Indices: 3682180--3682216 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3682170 TTAAATAAAA
3682180 ATAAATTATTTT-TATAAT
1 ATAAATTATTTTCTATAAT
*
3682198 ATAAATTCTTTTCTATAAT
1 ATAAATTATTTTCTATAAT
3682217 CATCCCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAAATTATTTTCTATAAT
Found at i:3683066 original size:23 final size:23
Alignment explanation
Indices: 3683047--3683093 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3683037 TTTAAATTTA
*
3683047 TTAT-TATTTTTTTTGAAAATAT
1 TTATGTATTTTTTTTAAAAATAT
*
3683069 TTATGTATTTTTTTTAAAAAAAT
1 TTATGTATTTTTTTTAAAAATAT
3683092 TT
1 TT
3683094 GTTAGAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATGTATTTTTTTTAAAAATAT
Found at i:3690134 original size:44 final size:44
Alignment explanation
Indices: 3690086--3690226 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 44
3690076 TATCACTTGC
*
3690086 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTTATCACTTGT
1 CACTTGTCACTGATCAGATAAGTGTAGCTGAAGTTACCAC-T-T-A----T
* * *
3690137 CACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTATCACTTAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTGAAGTTACCACTTAT
*
3690181 CACTTGTCACTGATCAGATAAGTGTAGCTGAA-TGTACTACTTAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTGAAGT-TACCACTTAT
3690225 CA
1 CA
3690227 AGTCACTGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
44 42 0.52
48 1 0.01
49 1 0.01
50 1 0.01
51 36 0.44
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
CACTTGTCACTGATCAGATAAGTGTAGCTGAAGTTACCACTTAT
Found at i:3690142 original size:51 final size:50
Alignment explanation
Indices: 3690027--3690191 Score: 240
Period size: 51 Copynumber: 3.3 Consensus size: 50
3690017 ATTACGTATG
* * * *
3690027 ATCACTTATCACTTGTCCCTGGTCAGATAAGTGTAGTTAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGTAAAGCTACCACTT
* *
3690077 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAG-TAAAGCTACCACTT
* *
3690128 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAG-TAAAGCTACCACTT
3690179 ATCACTTGTCACT
1 ATCACTTGTCACT
3690192 GATCAGATAA
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 32 0.31
51 71 0.69
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (50 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGTAAAGCTACCACTT
Found at i:3692649 original size:40 final size:40
Alignment explanation
Indices: 3692604--3692690 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
3692594 GCTATGTTTA
3692604 GCACTTAATATGAAATTC-GAGATAGCTTCAGCTATTTATG
1 GCACTTAATATGAAATTCGGA-ATAGCTTCAGCTATTTATG
* * ** * *
3692644 GCACTTAGTGTGCGATTTGGAATAGCTTCGGCTATTTATG
1 GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
*
3692684 ACACTTA
1 GCACTTA
3692691 GTGTGCGAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (40 bp):
GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
Found at i:3692730 original size:41 final size:40
Alignment explanation
Indices: 3692622--3692760 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 40
3692612 TATGAAATTC
**
3692622 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGATTT
1 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
* *
3692662 G-GAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACT
1 GAG-ATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGA-T
* * *
3692703 GAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGAT
1 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
*
3692743 TATGATAGCTTCAGCTAT
1 GA-GATAGCTTCAGCTAT
3692761 ACGATGGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 35 0.41
41 49 0.57
42 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
Found at i:3693084 original size:42 final size:42
Alignment explanation
Indices: 3693027--3693126 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
3693017 CTATATGAAC
3693027 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
* *
3693069 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
3693111 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
3693127 TACCGAGAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
Found at i:3696207 original size:25 final size:25
Alignment explanation
Indices: 3696160--3696209 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3696150 TGTATATATT
* *
3696160 ATATAAAAATAATTATATTTATTTA
1 ATATAAAAATAACTATATGTATTTA
3696185 ATATAAAAATAAACTA-ATGTATTTA
1 ATATAAAAAT-AACTATATGTATTTA
3696210 TTTCTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATAAAAATAACTATATGTATTTA
Found at i:3703417 original size:17 final size:17
Alignment explanation
Indices: 3703378--3703425 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
3703368 TTTTTATGAA
* *
3703378 ATATTTTCAATTAT-AT
1 ATATTTTAAATTTTAAT
*
3703394 ATTTTTTAAATTTTAAT
1 ATATTTTAAATTTTAAT
*
3703411 ATATTTTATATTTTA
1 ATATTTTAAATTTTA
3703426 TTTCAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTTAAATTTTAAT
Found at i:3703445 original size:28 final size:28
Alignment explanation
Indices: 3703388--3703444 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3703378 ATATTTTCAA
3703388 TTATATATTTTTTAAATTTTAATATATT
1 TTATATATTTTTTAAATTTTAATATATT
* *
3703416 TTATAT-TTTATTTCAATTTTTATA-ATT
1 TTATATATTT-TTTAAATTTTAATATATT
3703443 TT
1 TT
3703445 TGGCTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATATATTTTTTAAATTTTAATATATT
Found at i:3716058 original size:71 final size:67
Alignment explanation
Indices: 3715981--3716169 Score: 237
Period size: 63 Copynumber: 2.8 Consensus size: 67
3715971 ACATCATTTG
* * *
3715981 GGTAGTTCGAATGAAACTCATGTTCACAAGTAAAGAAGAAGAGAATTATACTTATATAAAAGGAT
1 GGTAGTTCGAATGAAGCCCAAGTTCACAAGTAAAGAAGAAGAGAATTATA--T-TAT-AAAGGAT
3716046 ATATTC
62 ATATTC
*
3716052 GGTAGTTCGAATGAAGCCCAAGTTCACAAGTAAA-AA-AAGAAGAA--A-ATTATACAGGATATA
1 GGTAGTTCGAATGAAGCCCAAGTTCACAAGTAAAGAAGAAG-AGAATTATATTATAAAGGATATA
3716112 TTC
65 TTC
* *
3716115 GGTAGTTAGAATGAAGCCCAAGTTCACAAGTAAAGAAGACGAGAATTATA-TATAA
1 GGTAGTTCGAATGAAGCCCAAGTTCACAAGTAAAGAAGAAGAGAATTATATTATAA
3716170 CAATTAAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 17
0.81 0.05 0.13
Matches are distributed among these distances:
63 45 0.43
64 9 0.09
65 3 0.03
66 5 0.05
67 2 0.02
68 1 0.01
69 3 0.03
70 6 0.06
71 31 0.30
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (67 bp):
GGTAGTTCGAATGAAGCCCAAGTTCACAAGTAAAGAAGAAGAGAATTATATTATAAAGGATATAT
TC
Found at i:3724024 original size:90 final size:90
Alignment explanation
Indices: 3723922--3724133 Score: 370
Period size: 90 Copynumber: 2.4 Consensus size: 90
3723912 ATTAATGAAA
* *
3723922 ATAAAGGTGATTGCTATGTGTTGATTTCACCGGATACCAATGGTTATATAAGTGATTGTTATGTG
1 ATAAAGGTGATTGCTATGTGCTGATTTCACCGGATACCAATGGTTATATAAGTGATTGCTATGTG
*
3723987 CTGAATTCACCCGGTACCATTGAGT
66 CTGAATTCACCCGGTACCATTAAGT
*
3724012 ATAAAGGTGATTGTTATGTGCTGATTTCACCGGATACCAATGGTTATATAAGTGATTGCTATGTG
1 ATAAAGGTGATTGCTATGTGCTGATTTCACCGGATACCAATGGTTATATAAGTGATTGCTATGTG
*
3724077 CTGAATTCACCTGGTACCATTAAGT
66 CTGAATTCACCCGGTACCATTAAGT
*
3724102 ATAAAGGTGGTTGCTATGTGCTGATTTCACCG
1 ATAAAGGTGATTGCTATGTGCTGATTTCACCG
3724134 AGTACTATTG
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 115 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (90 bp):
ATAAAGGTGATTGCTATGTGCTGATTTCACCGGATACCAATGGTTATATAAGTGATTGCTATGTG
CTGAATTCACCCGGTACCATTAAGT
Found at i:3724123 original size:135 final size:135
Alignment explanation
Indices: 3723891--3724150 Score: 305
Period size: 135 Copynumber: 1.9 Consensus size: 135
3723881 AGGTGGATGC
** * *
3723891 TATGTGCTGATTGCACCGGATATTAATGAAAATAAAGGTGATTGCTATGTGTTGATTTCACCGGA
1 TATGTGCTGATTGCACCGGATACCAATGAAAATAAAGGTGATTGCTATGTGCTGAATTCACCGGA
* * *
3723956 TACCAATGGTTATATAAGTGATTGTTATGTGCTGAATTCACCCG-GTACCATTGAGTATAAAGGT
66 TACCAATAGTTATATAAGTGATTGCTATGTGCTGAATTCA-CCGAGTACCATTGACTATAAAGGT
3724020 GATTGT
130 GATTGT
* ***
3724026 TATGTGCTGATTTCACCGGATACCAATGGTTATATAA-GTGATTGCTATGTGCTGAATTCACCTG
1 TATGTGCTGATTGCACCGGATACCAATGAAAATA-AAGGTGATTGCTATGTGCTGAATTCACC-G
* * * *
3724090 G-TACCATTAAG-TATA-AAGGTGGTTGCTATGTGCTGATTTCACCGAGTACTATTGACTATAA
64 GATACCAAT-AGTTATATAA-GTGATTGCTATGTGCTGAATTCACCGAGTACCATTGACTATAA
3724151 GGTTGGTGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
134 5 0.05
135 95 0.90
136 5 0.05
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (135 bp):
TATGTGCTGATTGCACCGGATACCAATGAAAATAAAGGTGATTGCTATGTGCTGAATTCACCGGA
TACCAATAGTTATATAAGTGATTGCTATGTGCTGAATTCACCGAGTACCATTGACTATAAAGGTG
ATTGT
Found at i:3724150 original size:45 final size:45
Alignment explanation
Indices: 3723888--3724133 Score: 270
Period size: 45 Copynumber: 5.5 Consensus size: 45
3723878 TATAGGTGGA
* ** **
3723888 TGCTATGTGCTGATTGCACCGGATATTAATGAAAATAAAGGTGAT
1 TGCTATGTGCTGATTTCACCGGATACCAATGAGTATAAAGGTGAT
*
3723933 TGCTATGTGTTGATTTCACCGGATACCAATG-GTTATATAA-GTGAT
1 TGCTATGTGCTGATTTCACCGGATACCAATGAG-TATA-AAGGTGAT
* * *
3723978 TGTTATGTGCTGAATTCACCCGG-TACCATTGAGTATAAAGGTGAT
1 TGCTATGTGCTGATTTCA-CCGGATACCAATGAGTATAAAGGTGAT
*
3724023 TGTTATGTGCTGATTTCACCGGATACCAATG-GTTATATAA-GTGAT
1 TGCTATGTGCTGATTTCACCGGATACCAATGAG-TATA-AAGGTGAT
* * * *
3724068 TGCTATGTGCTGAATTCACCTGG-TACCATTAAGTATAAAGGTGGT
1 TGCTATGTGCTGATTTCACC-GGATACCAATGAGTATAAAGGTGAT
3724113 TGCTATGTGCTGATTTCACCG
1 TGCTATGTGCTGATTTCACCG
3724134 AGTACTATTG
Statistics
Matches: 172, Mismatches: 18, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
44 10 0.06
45 150 0.87
46 12 0.07
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
TGCTATGTGCTGATTTCACCGGATACCAATGAGTATAAAGGTGAT
Found at i:3736689 original size:31 final size:31
Alignment explanation
Indices: 3736647--3736755 Score: 137
Period size: 31 Copynumber: 3.4 Consensus size: 31
3736637 TATATTTTAA
*
3736647 TATTTTAATTTAAATATTTTAAATACTTTTT
1 TATTTTTATTTAAATATTTTAAATACTTTTT
*
3736678 TATTTTTATTTAAATATTTAAAATACTTTTT
1 TATTTTTATTTAAATATTTTAAATACTTTTT
*
3736709 TATTTTTTATTTTAAAATATTTTAAAATAATTTTT
1 TA-TTTTTA-TTT-AAATATTTT-AAATACTTTTT
*
3736744 AAATTTTTATTT
1 -TATTTTTATTT
3736756 TAAAATAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
31 31 0.46
32 6 0.09
33 3 0.04
34 11 0.16
35 16 0.24
36 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTTTATTTAAATATTTTAAATACTTTTT
Found at i:3736743 original size:35 final size:33
Alignment explanation
Indices: 3736649--3736759 Score: 147
Period size: 35 Copynumber: 3.4 Consensus size: 33
3736639 TATTTTAATA
*
3736649 TTTTAATTTAAATATTTT-AAATACTTTTTTAT
1 TTTTATTTTAAATATTTTAAAATACTTTTTTAT
3736681 TTTTA-TTTAAATA-TTTAAAATACTTTTTTATT
1 TTTTATTTTAAATATTTTAAAATACTTTTTTA-T
* *
3736713 TTTTATTTTAAAATATTTTAAAATAATTTTTAAAT
1 TTTTATTTT-AAATATTTTAAAATACTTTTT-TAT
3736748 TTTTATTTTAAA
1 TTTTATTTTAAA
3736760 ATAATTTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
30 3 0.04
31 21 0.30
32 11 0.15
33 3 0.04
34 8 0.11
35 24 0.34
36 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (33 bp):
TTTTATTTTAAATATTTTAAAATACTTTTTTAT
Found at i:3736777 original size:25 final size:25
Alignment explanation
Indices: 3736726--3736779 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
3736716 TATTTTAAAA
*
3736726 TATTTTAAAATAATTTTTAAATTTT
1 TATTTTAAAATAATTTTTAAATATT
* *
3736751 TATTTTAAAATAATTTTTTAGTATT
1 TATTTTAAAATAATTTTTAAATATT
3736776 TATT
1 TATT
3736780 AAAAAAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTTTAAAATAATTTTTAAATATT
Found at i:3736785 original size:25 final size:25
Alignment explanation
Indices: 3736732--3736785 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
3736722 AAAATATTTT
* **
3736732 AAAATAATTTTTAAATTTTTATTTT
1 AAAATAATTTTTAAATATTTATTAA
* *
3736757 AAAATAATTTTTTAGTATTTATTAA
1 AAAATAATTTTTAAATATTTATTAA
3736782 AAAA
1 AAAA
3736786 ATGAACCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AAAATAATTTTTAAATATTTATTAA
Found at i:3737033 original size:29 final size:29
Alignment explanation
Indices: 3737001--3737086 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
3736991 AATTAGGGTG
*
3737001 AAGTTTTCATTTTGGTCATTTAACTA-AAA
1 AAGTTTTCATTTT-GTCATTGAACTATAAA
* * * *
3737030 AAGTTATAATTTTGTCATTGAATTATTTAA
1 AAGTTTTCATTTTGTCATTGAACTA-TAAA
* *
3737060 AAGTTTTCATTTAAGACATTGAACTAT
1 AAGTTTTCATTT-TGTCATTGAACTAT
3737087 TCAATAGTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
28 10 0.23
29 11 0.25
30 13 0.30
31 10 0.23
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (29 bp):
AAGTTTTCATTTTGTCATTGAACTATAAA
Found at i:3738892 original size:16 final size:16
Alignment explanation
Indices: 3738855--3738902 Score: 80
Period size: 15 Copynumber: 3.1 Consensus size: 16
3738845 TTCGCTGTAT
3738855 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3738871 -GGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
3738886 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
3738902 T
1 T
3738903 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:3738986 original size:39 final size:43
Alignment explanation
Indices: 3738882--3738990 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 43
3738872 GAATAGAGGC
*
3738882 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGGTGTAATAGCAAAT--ACTGTGTGGTTGAAT
* * * *
3738927 GTAATGGAATAGAGGCGTAATAG-TAAT-CT-TGTGTTTGATT
1 GTAATGGAATAGAGGTGTAATAGCAAATACTGTGTGGTTGAAT
3738967 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGTGTAATAGCA
3738991 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.36
40 9 0.16
41 2 0.04
44 3 0.05
45 22 0.39
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (43 bp):
GTAATGGAATAGAGGTGTAATAGCAAATACTGTGTGGTTGAAT
Found at i:3739165 original size:18 final size:16
Alignment explanation
Indices: 3739114--3739157 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3739104 ATTTAATCAT
* *
3739114 ATTTAAACATAATTATT
1 ATTTAAATAT-ATTATA
3739131 A-TTAAATATATTATA
1 ATTTAAATATATTATA
3739146 ATTTAAATATAT
1 ATTTAAATATAT
3739158 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAATATATTATA
Found at i:3739262 original size:120 final size:120
Alignment explanation
Indices: 3739119--3739531 Score: 738
Period size: 120 Copynumber: 3.4 Consensus size: 120
3739109 ATCATATTTA
3739119 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
3739184 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
3739239 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
3739304 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
3739359 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
3739424 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * *
3739479 AAAATAATTAATATTAAATATATT-TTATTTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTT-AAATATATAATTTAATAAAATT
3739532 TAAAATAATT
Statistics
Matches: 283, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 4 0.01
120 279 0.99
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:3739273 original size:16 final size:15
Alignment explanation
Indices: 3739235--3739277 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3739225 ATAAAATATA
3739235 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3739250 TATTAAATATATTAT
1 AATTAAATATATTAT
3739265 AATTTAAATATAT
1 AA-TTAAATATAT
3739278 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3739285 original size:18 final size:16
Alignment explanation
Indices: 3739231--3739277 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3739221 TACTATAAAA
*
3739231 TATAAATTAACATA-AT
1 TATAATTTAA-ATATAT
*
3739247 TATTA-TTAAATATAT
1 TATAATTTAAATATAT
3739262 TATAATTTAAATATAT
1 TATAATTTAAATATAT
3739278 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTTAAATATAT
Found at i:3739404 original size:14 final size:15
Alignment explanation
Indices: 3739355--3739406 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3739345 ATAAAATATA
3739355 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3739370 TATTAAATATATTAT
1 AATTAAATATATTAT
3739385 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3739398 AATTTAATA
1 AATTAAATA
3739407 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3739601 original size:26 final size:28
Alignment explanation
Indices: 3739572--3739632 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3739562 TATGAATTTG
*
3739572 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
3739598 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
3739626 TAAAATT
1 TATAATT
3739633 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:3739630 original size:47 final size:46
Alignment explanation
Indices: 3739579--3739720 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 46
3739569 TTGTATAATT
3739579 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
** * *
3739626 T--AA-AATTATTGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAATTATT-ATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
3739670 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
3739717 TAAA
1 TAAA
3739721 TTTCTTAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 12 0.17
45 13 0.18
46 12 0.17
47 14 0.19
48 9 0.12
49 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:3739633 original size:91 final size:89
Alignment explanation
Indices: 3739538--3739754 Score: 299
Period size: 91 Copynumber: 2.4 Consensus size: 89
3739528 AATTTAAAAT
* * * *
3739538 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
3739603 TTTAATAATAATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
*
3739629 AATTATTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
3739694 TTTAATAATGATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
3739720 ATTTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
3739755 CTAAAATCAA
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
91 89 0.79
92 23 0.21
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (89 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAATAATATATAATTTCATAA
Found at i:3739635 original size:44 final size:43
Alignment explanation
Indices: 3739572--3739714 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 43
3739562 TATGAATTTG
3739572 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAATAATA
* **
3739616 TATAATTTCATAA-AATTATTGA-TAATA-AATTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAATATAA-TTTAATA-AT-AA--TA
* * *
3739663 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAATAATA
3739707 TATAATTT
1 TATAATTT
3739715 CATAAATTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
42 2 0.03
43 8 0.10
44 28 0.36
45 6 0.08
46 5 0.06
47 18 0.23
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATAATA
Found at i:3740735 original size:3 final size:3
Alignment explanation
Indices: 3740714--3740760 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
3740704 GTATATTACT
* *
3740714 TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3740761 GGATATTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3746284 original size:6 final size:6
Alignment explanation
Indices: 3746273--3746303 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3746263 TTTAACCGAC
3746273 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
3746304 ATTCATTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TTAAAA
Found at i:3747180 original size:43 final size:44
Alignment explanation
Indices: 3747132--3747217 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 44
3747122 AGGTTAAATA
* * *
3747132 ATATTAAAATAACTTACATTAAT-AGAGTTTAAGTAAGAAACTG
1 ATATTAAAATAACATACACTAATCAGAGTTTAAGTAAAAAACTG
3747175 ATATTAAAATAACATACACTAATCAGAGTTTAAGTAAAAAACT
1 ATATTAAAATAACATACACTAATCAGAGTTTAAGTAAAAAACT
3747218 AAAAGTAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 21 0.54
44 18 0.46
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (44 bp):
ATATTAAAATAACATACACTAATCAGAGTTTAAGTAAAAAACTG
Found at i:3760000 original size:13 final size:13
Alignment explanation
Indices: 3759982--3760008 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3759972 TATGTTGTCT
3759982 ATATTTATAAATA
1 ATATTTATAAATA
3759995 ATATTTATAAATA
1 ATATTTATAAATA
3760008 A
1 A
3760009 ATGCTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTTATAAATA
Found at i:3772950 original size:6 final size:6
Alignment explanation
Indices: 3772935--3772965 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3772925 AGTAATGGGT
*
3772935 TTTTAA TTTTAG TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
3772966 AAGAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:3773898 original size:12 final size:12
Alignment explanation
Indices: 3773881--3773912 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3773871 ATTGATTATT
3773881 TGTAATTATCAA
1 TGTAATTATCAA
3773893 TGTAATTATCAA
1 TGTAATTATCAA
*
3773905 TCTAATTA
1 TGTAATTA
3773913 CACTCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (12 bp):
TGTAATTATCAA
Found at i:3792607 original size:52 final size:52
Alignment explanation
Indices: 3792545--3792648 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
3792535 TTACAAATTC
*
3792545 TTATAATTCCTAATATTTTTTATAATTTTGTTTAACTTTTAATAACTATTTA
1 TTATAATTCCTAATATTTTTTATAATTTCGTTTAACTTTTAATAACTATTTA
3792597 TTATAATTCCTAATATTTTTTATAATTTCGTTTAACTTTTAATAACTATTTA
1 TTATAATTCCTAATATTTTTTATAATTTCGTTTAACTTTTAATAACTATTTA
3792649 AGAAACAGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (52 bp):
TTATAATTCCTAATATTTTTTATAATTTCGTTTAACTTTTAATAACTATTTA
Found at i:3792767 original size:10 final size:10
Alignment explanation
Indices: 3792752--3792797 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
3792742 TATTTATTAA
3792752 TTTTAATAAT
1 TTTTAATAAT
*
3792762 TTTTAACAAT
1 TTTTAATAAT
*
3792772 TTTTTATAAT
1 TTTTAATAAT
* *
3792782 TCTTAATAGT
1 TTTTAATAAT
3792792 TTTTAA
1 TTTTAA
3792798 ATAAATTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:3802677 original size:53 final size:53
Alignment explanation
Indices: 3802608--3802712 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
3802598 TCTATGCTTA
*
3802608 ATCCAACCGAGTTTCCTATTGAAACTAAGTATTCTCATATCTACCACCCCAAC
1 ATCCAACCGAGCTTCCTATTGAAACTAAGTATTCTCATATCTACCACCCCAAC
* *
3802661 ATCCAACCGAGCTTCCTGTTGAAATTAAGTATTCTCATATCTACCACCCCAA
1 ATCCAACCGAGCTTCCTATTGAAACTAAGTATTCTCATATCTACCACCCCAA
3802713 AGTGTTCTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (53 bp):
ATCCAACCGAGCTTCCTATTGAAACTAAGTATTCTCATATCTACCACCCCAAC
Found at i:3813781 original size:20 final size:21
Alignment explanation
Indices: 3813730--3813781 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
3813720 AAAATTATTA
*
3813730 AAAAATAATTTTAAATTTTTTT
1 AAAAAT-ATTTTAAAGTTTTTT
*
3813752 CAAAAT-TTTT-AAGTTTTTT
1 AAAAATATTTTAAAGTTTTTT
3813771 AAAAATATTTT
1 AAAAATATTTT
3813782 TTAAGAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 13 0.50
20 8 0.31
22 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AAAAATATTTTAAAGTTTTTT
Found at i:3815163 original size:17 final size:17
Alignment explanation
Indices: 3815138--3815175 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3815128 AAAAAAAATT
*
3815138 AATTAAGCCTTTAAAAA
1 AATTAAGCCGTTAAAAA
*
3815155 AATTTAGCCGTTAAAAA
1 AATTAAGCCGTTAAAAA
3815172 AATT
1 AATT
3815176 CAACCTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (17 bp):
AATTAAGCCGTTAAAAA
Found at i:3824472 original size:3 final size:3
Alignment explanation
Indices: 3824466--3824493 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3824456 AAATTAAGCC
3824466 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3824494 GTTAAAGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3827961 original size:5 final size:5
Alignment explanation
Indices: 3827951--3827987 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
3827941 TAACAAAACC
3827951 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
3827988 AATCTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:3829974 original size:2 final size:2
Alignment explanation
Indices: 3829967--3830002 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3829957 ATGCTTATGA
3829967 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
3830003 TGATAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3830145 original size:22 final size:22
Alignment explanation
Indices: 3830120--3830167 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3830110 GCTTCCTAAA
3830120 AAATTAAAGAAAACAGAACAAT
1 AAATTAAAGAAAACAGAACAAT
3830142 AAATTAAAGAAAACAGAACAAT
1 AAATTAAAGAAAACAGAACAAT
3830164 AAAT
1 AAAT
3830168 GAAAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (22 bp):
AAATTAAAGAAAACAGAACAAT
Found at i:3836914 original size:107 final size:108
Alignment explanation
Indices: 3836720--3836936 Score: 391
Period size: 107 Copynumber: 2.0 Consensus size: 108
3836710 ACTTTGAAGT
*
3836720 TTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
1 TTAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
3836785 CTCGAATTTCCAAACGCAAAATATTGCCTTATTTAG-AAAATC
66 CTCGAATTTCCAAACGCAAAATATTGCCTTATTTAGAAAAATC
*
3836827 TTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
1 TTAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
* *
3836892 CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATC
66 CTCGAATTTCCAAACGCAAAATATTGCCTTATTTAGAAAAATC
3836935 TT
1 TT
3836937 CCTTTTGATG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 97 0.92
108 8 0.08
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (108 bp):
TTAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
CTCGAATTTCCAAACGCAAAATATTGCCTTATTTAGAAAAATC
Found at i:3837592 original size:25 final size:24
Alignment explanation
Indices: 3837559--3837612 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
3837549 TAAGTAAGTC
*
3837559 ATAACAGTAA-TAATAATAATGTAAT
1 ATAATAGTAATTAA-AATAAT-TAAT
3837584 ATAATAGTAATTAAAATAATTAAT
1 ATAATAGTAATTAAAATAATTAAT
*
3837608 CTAAT
1 ATAAT
3837613 GATAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 15 0.58
26 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
ATAATAGTAATTAAAATAATTAAT
Found at i:3837623 original size:29 final size:28
Alignment explanation
Indices: 3837570--3837624 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
3837560 TAACAGTAAT
* *
3837570 AATAATAATGTAATATAATAGTAATTAA
1 AATAATAATCTAATATAATAATAATTAA
3837598 AATAATTAATCTAATGATAA-AATAATT
1 AATAA-TAATCTAAT-ATAATAATAATT
3837625 CTAATAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 14 0.61
30 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (28 bp):
AATAATAATCTAATATAATAATAATTAA
Found at i:3837673 original size:3 final size:3
Alignment explanation
Indices: 3837665--3837695 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3837655 ACAGTTTAAA
3837665 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3837696 CAGATCCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3847273 original size:18 final size:17
Alignment explanation
Indices: 3847248--3847282 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
3847238 CAAATAATTA
3847248 TTAAAAATATAATTTTT
1 TTAAAAATATAATTTTT
3847265 TTAATAAATATAATTTTT
1 TTAA-AAATATAATTTTT
3847283 ATATGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAAATATAATTTTT
Found at i:3848760 original size:30 final size:30
Alignment explanation
Indices: 3848726--3848788 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
3848716 ACTTATTTTA
3848726 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
3848756 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
3848786 TTG
1 TTG
3848789 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:3853995 original size:17 final size:17
Alignment explanation
Indices: 3853951--3853995 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3853941 TTGAGCATCC
3853951 TTTGGTAGAATCATTCA
1 TTTGGTAGAATCATTCA
*
3853968 TGATGG-AGAATCATTCA
1 T-TTGGTAGAATCATTCA
*
3853985 TTTGGTTGAAT
1 TTTGGTAGAAT
3853996 TTATCCAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (17 bp):
TTTGGTAGAATCATTCA
Found at i:3869528 original size:22 final size:20
Alignment explanation
Indices: 3869497--3869546 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
3869487 TTATTAGTTA
3869497 AAAATAATTATAATTTAATTTT
1 AAAATAATTATAATTT--TTTT
*
3869519 AAAATTATTATAATTTTTTT
1 AAAATAATTATAATTTTTTT
3869539 AAAA-AATT
1 AAAATAATT
3869547 GTGTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
22 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTATAATTTTTTT
Found at i:3875077 original size:3 final size:3
Alignment explanation
Indices: 3875069--3875133 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
3875059 CCACTCATTT
3875069 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3875117 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
3875134 CTTATCTCAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3875886 original size:16 final size:16
Alignment explanation
Indices: 3875867--3875902 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3875857 ATTATTTAGT
*
3875867 TAATATAATATTATAA
1 TAATATAATATAATAA
*
3875883 TAATGTAATATAATAA
1 TAATATAATATAATAA
3875899 TAAT
1 TAAT
3875903 TTCTTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATATAATATAATAA
Found at i:3879550 original size:16 final size:17
Alignment explanation
Indices: 3879519--3879551 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3879509 ATTAATTAAA
3879519 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
3879536 TTAACTAAA-TAATTTT
1 TTAACTAAATTAATTTT
3879552 CTAAACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:3879558 original size:17 final size:17
Alignment explanation
Indices: 3879521--3879563 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3879511 TAATTAAATT
*
3879521 AACTAAATTAATTTTTT
1 AACTAAATTAATTTTTA
3879538 AACTAAA-TAATTTTCTA
1 AACTAAATTAATTTT-TA
*
3879555 AACTCAATT
1 AACTAAATT
3879564 TTAATTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 14 0.64
18 1 0.05
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
AACTAAATTAATTTTTA
Found at i:3880682 original size:11 final size:11
Alignment explanation
Indices: 3880666--3880693 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3880656 TATTGTTTAG
3880666 TATTAGTTAAA
1 TATTAGTTAAA
3880677 TATTAGTTAAA
1 TATTAGTTAAA
3880688 TATTAG
1 TATTAG
3880694 ATAACTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (11 bp):
TATTAGTTAAA
Found at i:3881117 original size:111 final size:111
Alignment explanation
Indices: 3880912--3881134 Score: 360
Period size: 111 Copynumber: 2.0 Consensus size: 111
3880902 ACATGCATAA
*
3880912 TTTTGGTTAAGAGTTTATTGTTATAAATATTACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
1 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
* * * *
3880977 CACTGTGCTTAAAAATACTTTTTTGTAAAC-AGATTTTTCCAACAGT
66 CACCGTGCTTAAAAACACTATTTTATAAACTA-ATTTTTCCAACAGT
3881023 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAATA-CTCGATTTTAAGAAACTTTTTAAACTT
1 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAA-AGCTCGATTTTAAGAAACTTTTTAAACTT
*
3881087 TTACCGTGCTTAAAAACACTATTTTATAAACTAATTTTTCCAACAGT
65 TCACCGTGCTTAAAAACACTATTTTATAAACTAATTTTTCCAACAGT
3881134 T
1 T
3881135 AGGTCCATTC
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
111 102 0.98
112 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (111 bp):
TTTTGGTTAAGAGTTTATTGTTATAAATATCACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
CACCGTGCTTAAAAACACTATTTTATAAACTAATTTTTCCAACAGT
Found at i:3888897 original size:34 final size:35
Alignment explanation
Indices: 3888853--3888919 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3888843 TAGTAAAATG
*
3888853 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
3888887 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
3888920 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:3890172 original size:24 final size:24
Alignment explanation
Indices: 3890140--3890185 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3890130 GGTGAAGAGA
3890140 GTGAAGAGAGGAACTGTGGAAAGG
1 GTGAAGAGAGGAACTGTGGAAAGG
*
3890164 GTGAAGAGAGGAGCTGTGGAAA
1 GTGAAGAGAGGAACTGTGGAAA
3890186 TGGTTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (24 bp):
GTGAAGAGAGGAACTGTGGAAAGG
Found at i:3905049 original size:119 final size:120
Alignment explanation
Indices: 3904837--3905075 Score: 462
Period size: 119 Copynumber: 2.0 Consensus size: 120
3904827 GTTTTATGAG
3904837 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
*
3904902 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTAAGTTTTATGCTTGTT
3904957 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATT-AATTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
3905021 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTAAGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTAAGTTTTATGCTTGTT
3905076 GTATACATGC
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
119 84 0.71
120 34 0.29
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.43
Consensus pattern (120 bp):
TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTAAGTTTTATGCTTGTT
Found at i:3906995 original size:20 final size:20
Alignment explanation
Indices: 3906975--3907012 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3906965 ATAAAAAACT
3906975 TTTCATTAT-TTTATTTTAC
1 TTTCATTATATTTATTTTAC
*
3906994 TTTCATTTTATTTATTTTA
1 TTTCATTATATTTATTTTA
3907013 TTTACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTCATTATATTTATTTTAC
Found at i:3907003 original size:11 final size:9
Alignment explanation
Indices: 3906984--3907026 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
3906974 TTTTCATTAT
3906984 TTTATTTTA
1 TTTATTTTA
3906993 CTTTCATTTTA
1 -TTT-ATTTTA
3907004 TTTATTTTA
1 TTTATTTTA
*
3907013 TTTACTTTTG
1 TTTA-TTTTA
3907023 TTTA
1 TTTA
3907027 GTTAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 10 0.33
10 14 0.47
11 6 0.20
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3914515 original size:3 final size:3
Alignment explanation
Indices: 3914507--3914548 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
3914497 TGACGCTTTC
* * *
3914507 TAT TAT TAT TAT TAT TAT TGT TGT TGT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3914549 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3924991 original size:24 final size:24
Alignment explanation
Indices: 3924964--3925012 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3924954 AAAAGTTTTC
* *
3924964 TTAACAATAATTCTAAAAAAGAAA
1 TTAAAAATAAATCTAAAAAAGAAA
* *
3924988 TTAAAAATAAATCTTAAAAATAAA
1 TTAAAAATAAATCTAAAAAAGAAA
3925012 T
1 T
3925013 ACAAATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
TTAAAAATAAATCTAAAAAAGAAA
Found at i:3925004 original size:13 final size:13
Alignment explanation
Indices: 3924962--3925012 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
3924952 AAAAAAGTTT
* *
3924962 TCTTAACAATAAT
1 TCTTAAAAATAAA
* *
3924975 TCTAAAAAAGAAA
1 TCTTAAAAATAAA
3924988 --TTAAAAATAAA
1 TCTTAAAAATAAA
3924999 TCTTAAAAATAAA
1 TCTTAAAAATAAA
3925012 T
1 T
3925013 ACAAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 9 0.30
13 21 0.70
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (13 bp):
TCTTAAAAATAAA
Found at i:3925042 original size:20 final size:19
Alignment explanation
Indices: 3925015--3925059 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3925005 AAATAAATAC
*
3925015 AAATTA-TTAAAATTATTAA
1 AAATTATTTAAAA-AATTAA
3925034 AAATATATTTAAAAAATTAA
1 AAAT-TATTTAAAAAATTAA
3925054 AAATTA
1 AAATTA
3925060 CGTTAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATTTAAAAAATTAA
Found at i:3925065 original size:20 final size:20
Alignment explanation
Indices: 3925029--3925067 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3925019 TATTAAAATT
*
3925029 ATTAAAAATATATTTAAAAA
1 ATTAAAAATATAGTTAAAAA
3925049 ATTAAAAAT-TACGTTAAAA
1 ATTAAAAATATA-GTTAAAA
3925068 CAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTAAAAATATAGTTAAAAA
Found at i:3925328 original size:15 final size:15
Alignment explanation
Indices: 3925296--3925338 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3925286 ATTTTGAATT
*
3925296 TTTAGAATTTTT-TA
1 TTTAAAATTTTTATA
*
3925310 TTTAAAATTTTTATG
1 TTTAAAATTTTTATA
3925325 TTTAAAATATTTTA
1 TTTAAAAT-TTTTA
3925339 ACCTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTAAAATTTTTATA
Found at i:3931285 original size:30 final size:30
Alignment explanation
Indices: 3931249--3931313 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3931239 ATATTTTAAA
3931249 AAAAATTAT-AA-AATATATAGAAAATTATTT
1 AAAAATTATCAAGAAT-TATA-AAAATTATTT
* *
3931279 AAAAATTATCAAGAATTATAATAATTTTTT
1 AAAAATTATCAAGAATTATAAAAATTATTT
3931309 AAAAA
1 AAAAA
3931314 AGTATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 22 0.71
31 6 0.19
32 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATTATCAAGAATTATAAAAATTATTT
Found at i:3937014 original size:13 final size:13
Alignment explanation
Indices: 3936975--3937024 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3936965 TCTTCATTGT
3936975 TTTTGAAAAGTG-
1 TTTTGAAAAGTGC
* *
3936987 TTCTGAAAAAATGC
1 TTTTG-AAAAGTGC
*
3937001 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
3937014 TTTTGAAAAGT
1 TTTTGAAAAGT
3937025 TTAGTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:3938941 original size:111 final size:108
Alignment explanation
Indices: 3938795--3939005 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 108
3938785 ATGTCAATAA
*
3938795 AATATAATAATAAAGAATAAAAGATATTTCTATCAATTCATATGCATATCATATAATAATAAATA
1 AATATAATAATAAACAATAAAAGATATTTCTATCAATTCATATGCATAT--TAT-ATAATAAAT-
*
3938860 TTACAT-CGAATAAGTACTTCAATTATTTTATATAAAAAACTCTAATG
62 TTACATAC-AATAAGCACTTCAATTATTTTATATAAAAAACTCTAATG
*
3938907 AATATAATAA-AAACAATAAAATATATTT-TCATCAATTCATATGCATATTATATAATAAATTTA
1 AATATAATAATAAACAATAAAAGATATTTCT-ATCAATTCATATGCATATTATATAATAAATTTA
* * *
3938970 CATACAATGAGCATTTTAATTATTTTATATAAAAAA
65 CATACAATAAGCACTTCAATTATTTTATATAAAAAA
3939006 TCCCTATTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
107 33 0.36
108 10 0.11
109 3 0.03
110 1 0.01
111 34 0.37
112 10 0.11
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (108 bp):
AATATAATAATAAACAATAAAAGATATTTCTATCAATTCATATGCATATTATATAATAAATTTAC
ATACAATAAGCACTTCAATTATTTTATATAAAAAACTCTAATG
Found at i:3942947 original size:18 final size:20
Alignment explanation
Indices: 3942922--3942963 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3942912 TTTCAACAAC
*
3942922 ATTTTTTTTTCAAATTTT-T
1 ATTTTTTTCTCAAATTTTAT
3942941 ATTTTTTTCTCAAATTTTAT
1 ATTTTTTTCTCAAATTTTAT
3942961 ATT
1 ATT
3942964 AAAAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTTCTCAAATTTTAT
Found at i:3943113 original size:19 final size:20
Alignment explanation
Indices: 3943069--3943113 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3943059 TTTTTTTCAT
*
3943069 ATATTTTTTAAAATTTTTAG
1 ATATTTTATAAAATTTTTAG
*
3943089 AT-TTTTATGAAATTTTTA-
1 ATATTTTATAAAATTTTTAG
3943107 ATATTTT
1 ATATTTT
3943114 GGAAATTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATATTTTATAAAATTTTTAG
Found at i:3943118 original size:18 final size:19
Alignment explanation
Indices: 3943079--3943120 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3943069 ATATTTTTTA
*
3943079 AAATTTTTAGATTTTTATG
1 AAATTTTTAGATTTTTAGG
3943098 AAATTTTTA-ATATTTT-GG
1 AAATTTTTAGAT-TTTTAGG
3943116 AAATT
1 AAATT
3943121 CTTATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
AAATTTTTAGATTTTTAGG
Found at i:3943239 original size:11 final size:11
Alignment explanation
Indices: 3943223--3943248 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3943213 TTTTAGAATT
3943223 TTTTAGAAACA
1 TTTTAGAAACA
3943234 TTTTAGAAACA
1 TTTTAGAAACA
3943245 TTTT
1 TTTT
3943249 TATAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (11 bp):
TTTTAGAAACA
Found at i:3943249 original size:12 final size:12
Alignment explanation
Indices: 3943222--3943250 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3943212 CTTTTAGAAT
3943222 TTTTTAGAAACA
1 TTTTTAGAAACA
3943234 -TTTTAGAAACA
1 TTTTTAGAAACA
3943245 TTTTTA
1 TTTTTA
3943251 TAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTTTAGAAACA
Found at i:3947203 original size:22 final size:22
Alignment explanation
Indices: 3947144--3947203 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
3947134 TCATTCTATG
* *
3947144 TTAAAAATACATAA-TTATAAA
1 TTAATAATAAATAATTTATAAA
* * *
3947165 TTAATAATATATGATTTATAAT
1 TTAATAATAAATAATTTATAAA
*
3947187 TTACTAATAAATAATTT
1 TTAATAATAAATAATTT
3947204 TGTTTATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATAATAAATAATTTATAAA
Found at i:3954155 original size:17 final size:20
Alignment explanation
Indices: 3954115--3954161 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
3954105 AAATTAAAAA
3954115 TAATAAT-ATAACTTTTAAG
1 TAATAATAATAACTTTTAAG
3954134 TAATAATAATAAC-TTT-AG
1 TAATAATAATAACTTTTAAG
3954152 -AATAATAATA
1 TAATAATAATA
3954162 CACAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.37
18 2 0.07
19 10 0.37
20 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAATAATAACTTTTAAG
Found at i:3955150 original size:20 final size:20
Alignment explanation
Indices: 3955122--3955168 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3955112 TTTAACTTTT
*
3955122 TCTTT-ATATTTTAAGTAAC
1 TCTTTCATATTTTAAATAAC
*
3955141 TCTTTCATATTTTAAATAAT
1 TCTTTCATATTTTAAATAAC
3955161 TCTTTCAT
1 TCTTTCAT
3955169 GTATTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.55
Consensus pattern (20 bp):
TCTTTCATATTTTAAATAAC
Found at i:3956469 original size:21 final size:21
Alignment explanation
Indices: 3956443--3956484 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3956433 CAAAAAGAAC
3956443 AGTGATATAGCGATGTAGTCG
1 AGTGATATAGCGATGTAGTCG
3956464 AGTGATATAGCGATGTAGTCG
1 AGTGATATAGCGATGTAGTCG
3956485 TGGCTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (21 bp):
AGTGATATAGCGATGTAGTCG
Found at i:3956847 original size:3 final size:3
Alignment explanation
Indices: 3956805--3956953 Score: 68
Period size: 3 Copynumber: 49.0 Consensus size: 3
3956795 ATTTCGGTAG
* * * * * ** *
3956805 TAT TAT CAT TAT TGT TAC TAT TAT TTT TAA TAT TGC TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
3956853 CGTGT TAT TAT TAT TAT TACT TAC T-T TAT TAT TAT CAT TAT CAT TAT
1 --TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
3956900 TTT TTT TAT TAC TAA TAT TAT TAT T-T CTAT TTT TAC TAC TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
3956945 TAT TAT TAT
1 TAT TAT TAT
3956954 ACATTGTTAT
Statistics
Matches: 105, Mismatches: 35, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
2 2 0.02
3 98 0.93
4 4 0.04
5 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3957121 original size:23 final size:24
Alignment explanation
Indices: 3957078--3957131 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3957068 TATCTTACTA
3957078 TTTTATTATTTCATCA-TTTTTGC
1 TTTTATTATTTCATCATTTTTTGC
* * *
3957101 TTTTATTGTTT-ATCTTATTTTTGT
1 TTTTATTATTTCATCAT-TTTTTGC
3957125 TTTTATT
1 TTTTATT
3957132 CTTATTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 10 0.38
24 13 0.50
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTTATTATTTCATCATTTTTTGC
Found at i:3960962 original size:17 final size:16
Alignment explanation
Indices: 3960930--3960965 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3960920 GAACCGACTG
*
3960930 TTCTTTTTCTTTTTCT
1 TTCTTTTTCTTCTTCT
3960946 TTCTTTTTCCTTCTTCT
1 TTCTTTTT-CTTCTTCT
3960963 TTC
1 TTC
3960966 AACTCAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTTTTTCTTCTTCT
Found at i:3961082 original size:11 final size:11
Alignment explanation
Indices: 3961052--3961117 Score: 64
Period size: 11 Copynumber: 5.7 Consensus size: 11
3961042 CCCTCATATC
3961052 TTTTCTCCTCTT
1 TTTTCT-CTCTT
3961064 TCTCTTCTCTCTT
1 T-T-TTCTCTCTT
*
3961077 CTTTCTCT-TT
1 TTTTCTCTCTT
3961087 TTTTCTTCTCTT
1 TTTTC-TCTCTT
3961099 TTCTTC-CTCTT
1 TT-TTCTCTCTT
3961110 TTTTCTCT
1 TTTTCTCT
3961118 TCCCGTTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
10 9 0.20
11 18 0.39
12 6 0.13
13 9 0.20
14 4 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:3961083 original size:9 final size:9
Alignment explanation
Indices: 3961053--3961119 Score: 54
Period size: 9 Copynumber: 8.0 Consensus size: 9
3961043 CCTCATATCT
*
3961053 TTTCTCCTC
1 TTTCTCTTC
3961062 TTTCTCTTC
1 TTTCTCTTC
3961071 --TCTCTTC
1 TTTCTCTTC
3961078 TTTCTCTT-
1 TTTCTCTTC
*
3961086 TTTTTCTTC
1 TTTCTCTTC
*
3961095 --TCTTTTC
1 TTTCTCTTC
* *
3961102 TTCCTCTTT
1 TTTCTCTTC
3961111 TTTCTCTTC
1 TTTCTCTTC
3961120 CCGTTTTGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
7 12 0.27
8 7 0.16
9 25 0.57
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTCTCTTC
Found at i:3961095 original size:13 final size:13
Alignment explanation
Indices: 3961079--3961119 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3961069 TCTCTCTTCT
3961079 TTCTCTTTTTTTC
1 TTCTCTTTTTTTC
*
3961092 TTCTCTTTTCTTC
1 TTCTCTTTTTTTC
3961105 --CTCTTTTTTCTC
1 TTCTCTTTTTT-TC
3961117 TTC
1 TTC
3961120 CCGTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 12 0.52
14 1 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTCTTTTTTTC
Found at i:3961102 original size:24 final size:25
Alignment explanation
Indices: 3961062--3961119 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
3961052 TTTTCTCCTC
*
3961062 TTTCTCTTCTCTCTTCTTTCTCTTT
1 TTTCTCTTCTCTCTTCTTCCTCTTT
*
3961087 TTT-TCTTCTCTTTTCTTCCTCTTT
1 TTTCTCTTCTCTCTTCTTCCTCTTT
3961111 TTTCTCTTC
1 TTTCTCTTC
3961120 CCGTTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTCTCTTCTCTCTTCTTCCTCTTT
Done.