Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold553
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: 449280
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 2 of 4
Found at i:140484 original size:22 final size:21
Alignment explanation
Indices: 140445--140490 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
140435 ATTATATAAA
*
140445 TATAAAATAATTTAAATATGAT
1 TATAAAATAATATAAATATG-T
*
140467 TATAAAATAATATGAATATGT
1 TATAAAATAATATAAATATGT
140488 TAT
1 TAT
140491 TATTACTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
TATAAAATAATATAAATATGT
Found at i:140746 original size:21 final size:21
Alignment explanation
Indices: 140708--140749 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
140698 TGATTAAAAA
*
140708 ATTTTTAAAACTTTTTTAATT
1 ATTTTTAAAACTTATTTAATT
140729 ATTTTT-AAACTTAATTTAATT
1 ATTTTTAAAACTT-ATTTAATT
140750 CGATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAACTTATTTAATT
Found at i:140824 original size:125 final size:126
Alignment explanation
Indices: 140687--140917 Score: 340
Period size: 126 Copynumber: 1.8 Consensus size: 126
140677 TTCGTGAGTC
* * * *
140687 GAATCATATAATGATTAAAAAATTTTTAAAA-CTTTTTTAATTATTTTTAAACTTAATTTAA-TT
1 GAATCATATAATGATTAAAAAATTTTTAAAATCTTTTTTAATCATGTTCAAACTTAATTGAACTT
* *
140750 CGATTTAATTTATTTAAATTATTTATATTTACTATTTAAATTTTTTGATCATGGTCACGATT
66 -GATTTAATTTATCTAAATTACTTATATTTACTATTTAAATTTTTTGATCATGGTCACGATT
* * *
140812 GAATCATATAATGATTAAAAAATTTTTAAAATTTTTTTTGATCATGTTCAAATTTAATTGAACTT
1 GAATCATATAATGATTAAAAAATTTTTAAAATCTTTTTTAATCATGTTCAAACTTAATTGAACTT
* *
140877 GATTTGATTTATCTAAATTACTTATATTTATTATTTAAATT
66 GATTTAATTTATCTAAATTACTTATATTTACTATTTAAATT
140918 AATAAAAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
125 31 0.33
126 60 0.65
127 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (126 bp):
GAATCATATAATGATTAAAAAATTTTTAAAATCTTTTTTAATCATGTTCAAACTTAATTGAACTT
GATTTAATTTATCTAAATTACTTATATTTACTATTTAAATTTTTTGATCATGGTCACGATT
Found at i:141534 original size:26 final size:27
Alignment explanation
Indices: 141505--141566 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
141495 TTTTAGTTAA
141505 ATTTTTAG-A-TATG-TATAACTTAATAT
1 ATTTTTAGTATTATGTTATAA-TT-ATAT
141531 ATTTTTTAGTATTTATGTTATAATTATAT
1 A-TTTTTAGTA-TTATGTTATAATTATAT
141560 ATTTTTA
1 ATTTTTA
141567 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 1 0.03
27 7 0.23
28 7 0.23
29 5 0.16
30 6 0.19
31 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (27 bp):
ATTTTTAGTATTATGTTATAATTATAT
Found at i:141570 original size:26 final size:29
Alignment explanation
Indices: 141506--141565 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
141496 TTTAGTTAAA
141506 TTTTTAGA--TATGTATAACTTAATATAT
1 TTTTTAGATTTATGTATAACTTAATATAT
141533 TTTTTAGTATTTATGTTATAA-TT-ATATAT
1 TTTTTAG-ATTTATG-TATAACTTAATATAT
141562 TTTT
1 TTTT
141566 AATTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.24
28 1 0.03
29 10 0.34
30 6 0.21
31 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTTAGATTTATGTATAACTTAATATAT
Found at i:142146 original size:15 final size:15
Alignment explanation
Indices: 142126--142170 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
142116 TGTTAAACCA
142126 ATTATAAATTTTATT
1 ATTATAAATTTTATT
142141 ATTATAATAATTTATATT
1 ATTAT-A-AATTT-TATT
142159 A-TATAAATTTTA
1 ATTATAAATTTTA
142171 AAATATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 2 0.07
17 8 0.30
18 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATAAATTTTATT
Found at i:142150 original size:18 final size:16
Alignment explanation
Indices: 142128--142195 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
142118 TTAAACCAAT
142128 TATAAATTTTATTATTA
1 TATAAATTTTA-TATTA
142145 TA-ATAA-TTTATATTA
1 TATA-AATTTTATATTA
* *
142160 TATAAATTTTAAAATA
1 TATAAATTTTATATTA
* *
142176 TTTAAATATTTTTATTA
1 TATAAAT-TTTATATTA
142193 TAT
1 TAT
142196 CATATTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
15 9 0.22
16 19 0.47
17 12 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAAATTTTATATTA
Found at i:142163 original size:17 final size:17
Alignment explanation
Indices: 142132--142164 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
142122 ACCAATTATA
142132 AATTTTATTATTATAAT
1 AATTTTATTATTATAAT
142149 AATTTATATTA-TATAA
1 AATTT-TATTATTATAA
142165 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTATTATTATAAT
Found at i:148594 original size:23 final size:23
Alignment explanation
Indices: 148568--148614 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
148558 TACGTTCATG
* *
148568 TTTGATGTGTATTTCGATACAGA
1 TTTGACGTGTATATCGATACAGA
148591 TTTGACGTGTATATCGATACAGA
1 TTTGACGTGTATATCGATACAGA
148614 T
1 T
148615 ATAAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (23 bp):
TTTGACGTGTATATCGATACAGA
Found at i:148957 original size:17 final size:17
Alignment explanation
Indices: 148935--148986 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
148925 TGAATATCTG
*
148935 ATAATTTTAAAAATAAT
1 ATAATTATAAAAATAAT
*
148952 ATAATTATATAATATAA-
1 ATAATTATA-AAAATAAT
*
148969 ATAAATATAAAAATAAT
1 ATAATTATAAAAATAAT
148986 A
1 A
148987 ATTAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTATAAAAATAAT
Found at i:151112 original size:7 final size:7
Alignment explanation
Indices: 151092--151122 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
151082 ATAATATGTT
151092 ATAAATA
1 ATAAATA
151099 TATAAATA
1 -ATAAATA
151107 ATAAATA
1 ATAAATA
151114 ATAAATA
1 ATAAATA
151121 AT
1 AT
151123 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATAAATA
Found at i:151134 original size:18 final size:19
Alignment explanation
Indices: 151111--151165 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
151101 TAAATAATAA
151111 ATAATAAATAATTTTTATT
1 ATAATAAATAATTTTTATT
** *
151130 A-AATATGTGATTTTT-TT
1 ATAATAAATAATTTTTATT
*
151147 ATAATTAAATAATTCTTAT
1 ATAA-TAAATAATTTTTAT
151166 GTAATACATA
Statistics
Matches: 26, Mismatches: 7, Indels: 5
0.68 0.18 0.13
Matches are distributed among these distances:
17 3 0.12
18 13 0.50
19 9 0.35
20 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATAATAAATAATTTTTATT
Found at i:156571 original size:2 final size:2
Alignment explanation
Indices: 156564--156606 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
156554 CTGGAAAATG
* *
156564 CA CA CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CG CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
156606 C
1 C
156607 CCTGCACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:161961 original size:17 final size:19
Alignment explanation
Indices: 161940--161980 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
161930 AAAAAAATTT
161940 AATTTTTTA-TAA-TTTAA
1 AATTTTTTATTAAGTTTAA
*
161957 TATTTTTTATTAAGTTTAA
1 AATTTTTTATTAAGTTTAA
161976 AATTT
1 AATTT
161981 AAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTTTTTATTAAGTTTAA
Found at i:162069 original size:26 final size:27
Alignment explanation
Indices: 162040--162097 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
162030 TTTTTATATG
* *
162040 ATAAAAATTACTTAATA-TATAAAAAT
1 ATAAAAATTAATAAATATTATAAAAAT
* *
162066 AT-AAAATTAATAAATATTATATAATT
1 ATAAAAATTAATAAATATTATAAAAAT
162092 ATAAAA
1 ATAAAA
162098 TAAGTGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.46
26 11 0.42
27 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAAAAATTAATAAATATTATAAAAAT
Found at i:162073 original size:25 final size:26
Alignment explanation
Indices: 162043--162098 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
162033 TTATATGATA
* *
162043 AAAATTACTTAATA-TATAAAAATAT
1 AAAATTAATAAATATTATAAAAATAT
* *
162068 AAAATTAATAAATATTATATAATTAT
1 AAAATTAATAAATATTATAAAAATAT
162094 AAAAT
1 AAAAT
162099 AAGTGAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATTAATAAATATTATAAAAATAT
Found at i:162099 original size:18 final size:17
Alignment explanation
Indices: 162040--162097 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
162030 TTTTTATATG
162040 ATAAAAATTACT-TAATAT
1 ATAAAAATTA-TATAAT-T
*
162058 ATAAAAA-TATAAAATT
1 ATAAAAATTATATAATT
*
162074 AATAAATATTATATAATT
1 -ATAAAAATTATATAATT
162092 ATAAAA
1 ATAAAA
162098 TAAGTGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.06
17 16 0.48
18 15 0.45
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAATTATATAATT
Found at i:162489 original size:2 final size:2
Alignment explanation
Indices: 162482--162509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
162472 GGATTTATCC
162482 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
162510 TTCATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162840 original size:2 final size:2
Alignment explanation
Indices: 162833--162858 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
162823 ATCTTTCTTT
162833 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
162859 GAAGAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:163432 original size:15 final size:15
Alignment explanation
Indices: 163412--163443 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
163402 TACATCACTA
163412 AAGAAAGACCATCGG
1 AAGAAAGACCATCGG
*
163427 AAGAAAGACTATCGG
1 AAGAAAGACCATCGG
163442 AA
1 AA
163444 ATGAATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.25, T:0.09
Consensus pattern (15 bp):
AAGAAAGACCATCGG
Found at i:167685 original size:18 final size:17
Alignment explanation
Indices: 167624--167690 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
167614 TTTAAGATCA
* *
167624 TAATTTATATGTATATC
1 TAATATATATTTATATC
167641 TGAATATATATTTAAATAAT-
1 T-AATATATATTT--AT-ATC
167661 TATATATTATATTTATATC
1 TA-ATA-TATATTTATATC
167680 TAATATATATT
1 TAATATATATT
167691 AAATAAAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
17 7 0.17
18 14 0.34
19 5 0.12
20 6 0.15
21 9 0.22
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TAATATATATTTATATC
Found at i:168006 original size:18 final size:18
Alignment explanation
Indices: 167962--168006 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
167952 AAATTATTAT
*
167962 ATATATCTTATTTTTTAAA
1 ATATAT-TTATTTTTAAAA
167981 AT-TAATTTATTTTTAAAA
1 ATAT-ATTTATTTTTAAAA
167999 ATATATTT
1 ATATATTT
168007 TAAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATATTTATTTTTAAAA
Found at i:168009 original size:13 final size:13
Alignment explanation
Indices: 167991--168015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
167981 ATTAATTTAT
167991 TTTTAAAAATATA
1 TTTTAAAAATATA
168004 TTTTAAAAATAT
1 TTTTAAAAATAT
168016 TAATTATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:175683 original size:16 final size:16
Alignment explanation
Indices: 175658--175755 Score: 65
Period size: 19 Copynumber: 5.6 Consensus size: 16
175648 TGCAATTTCG
175658 TATTTAATATATTTTAT
1 TATTT-ATATATTTTAT
175675 TATTTATATAAATTTTTAT
1 TATTTATAT--A-TTTTAT
*
175694 TATATTA-ATAATTTA-
1 TAT-TTATATATTTTAT
*
175709 TATTATATATATTTAAAAT
1 TATT-TATATATTT--TAT
175728 TATTTATATATTTATAT
1 TATTTATATATTT-TAT
175745 ATATATTATAT
1 -TAT-TTATAT
175756 TAAAGTGCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 1 0.02
15 5 0.08
16 13 0.20
17 9 0.14
18 14 0.21
19 21 0.32
20 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATATATTTTAT
Found at i:175702 original size:37 final size:41
Alignment explanation
Indices: 175661--175757 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 41
175651 AATTTCGTAT
175661 TTAATATATTT-TATTAT-T-TATAT-AAATT-TTTATTATA
1 TTAATATATTTATATTATATATATATAAAATTATTTA-TATA
*
175698 TTAATA-ATTTATATTATATATATTTAAAATTATTTATATA
1 TTAATATATTTATATTATATATATATAAAATTATTTATATA
175738 TTTATATATATATTATATTA
1 -TTA-ATATAT-TTATATTA
175758 AAGTGCAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
36 4 0.08
37 12 0.24
38 1 0.02
39 4 0.08
40 9 0.18
41 7 0.14
42 3 0.06
43 2 0.04
44 8 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (41 bp):
TTAATATATTTATATTATATATATATAAAATTATTTATATA
Found at i:175706 original size:18 final size:20
Alignment explanation
Indices: 175669--175745 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 20
175659 ATTTAATATA
175669 TTTTATTAT-TTATATAAAT
1 TTTTATTATATTATATAAAT
175688 TTTTATTATATTA-AT-AAT
1 TTTTATTATATTATATAAAT
* *
175706 TTATATTATATATATTTAAAAT
1 TTTTATTATAT-TATAT-AAAT
175728 TATTTA-TATATTTATATA
1 T-TTTATTATA-TTATATA
175746 TATATTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
18 13 0.28
19 13 0.28
20 4 0.09
21 1 0.02
22 12 0.26
23 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTATATTATATAAAT
Found at i:175709 original size:13 final size:15
Alignment explanation
Indices: 175664--175756 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 15
175654 TTCGTATTTA
175664 ATATAT-TTTATTATTT
1 ATATATATTTA-TA-TT
* *
175680 ATATAAATTTTTATT
1 ATATATATTTATATT
175695 ATATTAATAATTTATATT
1 ATA-T-AT-ATTTATATT
*
175713 ATATATATTTAAAATT
1 ATATATATTT-ATATT
175729 ATTTATATATTTATATAT
1 A--TATATATTTATAT-T
175747 ATATTATATT
1 ATA-TATATT
175757 AAAGTGCAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
15 9 0.15
16 17 0.27
17 14 0.23
18 22 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATATATTTATATT
Found at i:176041 original size:23 final size:22
Alignment explanation
Indices: 176004--176054 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
175994 AGTAATTTAA
176004 TTTTAATATATTAATAAATATTT
1 TTTTAATATATTAATAAA-ATTT
**
176027 TTTTAATATGA-TAATTTAATTT
1 TTTTAATAT-ATTAATAAAATTT
176049 TTTTAA
1 TTTTAA
176055 AAATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 14 0.56
24 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAATATATTAATAAAATTT
Found at i:177546 original size:23 final size:23
Alignment explanation
Indices: 177502--177546 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
177492 TAAAAGAAAA
* *
177502 TTTATTTTATTAATTATTTTTAT
1 TTTATTTTATAAATGATTTTTAT
177525 TTTATTTT-TAAATGATTATTTA
1 TTTATTTTATAAATGATT-TTTA
177547 AAAGAGTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTATAAATGATTTTTAT
Found at i:178632 original size:20 final size:20
Alignment explanation
Indices: 178609--178648 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
178599 ATTAATTTAA
178609 TTAAAG-TAATTTTAAATATT
1 TTAAAGATAATTTT-AATATT
178629 TTAAAGATAATTTTAATATT
1 TTAAAGATAATTTTAATATT
178649 AAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTAAAGATAATTTTAATATT
Found at i:178658 original size:20 final size:20
Alignment explanation
Indices: 178600--178659 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
178590 GTTAAACTCA
*
178600 TTAAT-TTAATTAAAGTAATT
1 TTAATATTAAATAAA-TAATT
* *
178620 TTAAATATTTTAA-AGATAATT
1 TT-AATA-TTAAATAAATAATT
178641 TTAATATTAAATAAATAAT
1 TTAATATTAAATAAATAAT
178660 ATATAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 10 0.32
22 2 0.06
23 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTAATATTAAATAAATAATT
Found at i:179204 original size:17 final size:16
Alignment explanation
Indices: 179184--179299 Score: 70
Period size: 18 Copynumber: 6.6 Consensus size: 16
179174 TATATTCAAG
179184 TTATATTAGTATTATTT
1 TTATATTA-TATTATTT
*
179201 TTATATTATAATATTAT
1 TTATATTATATTATT-T
* *
179218 TTAAAATATATTATATT
1 TTATATTATATTAT-TT
* * *
179235 TATAAATTTTAATATTTT
1 T-TATATTATATTA-TTT
*
179253 TATATATTTTTATTATTTT
1 T-TATA-TTATATTA-TTT
*
179272 TTATATTTTAATTATTTT
1 TTATATTAT-ATTA-TTT
179290 TTATATTATA
1 TTATATTATA
179300 AAATTATGTT
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
16 6 0.07
17 27 0.33
18 37 0.45
19 13 0.16
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (16 bp):
TTATATTATATTATTT
Found at i:179261 original size:10 final size:10
Alignment explanation
Indices: 179241--179296 Score: 68
Period size: 9 Copynumber: 6.1 Consensus size: 10
179231 TATTTATAAA
179241 TTTTA-ATAT
1 TTTTATATAT
179250 TTTTATATAT
1 TTTTATATAT
179260 TTTTAT-TAT
1 TTTTATATAT
179269 TTTT-TATAT
1 TTTTATATAT
*
179278 TTTAAT-TAT
1 TTTTATATAT
179287 TTTT-TATAT
1 TTTTATATAT
179296 T
1 T
179297 ATAAAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 2 0.05
9 28 0.68
10 11 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATATAT
Found at i:179291 original size:18 final size:18
Alignment explanation
Indices: 179240--179296 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
179230 ATATTTATAA
179240 ATTTTAA-TATTTTTATAT
1 ATTTTAATTATTTTT-TAT
*
179258 ATTTTTATTATTTTTTAT
1 ATTTTAATTATTTTTTAT
179276 ATTTTAATTATTTTTTAT
1 ATTTTAATTATTTTTTAT
179294 ATT
1 ATT
179297 ATAAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 29 0.81
19 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTAATTATTTTTTAT
Found at i:179304 original size:20 final size:18
Alignment explanation
Indices: 179247--179306 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
179237 TAAATTTTAA
**
179247 TATTTTTATATATTTTTAT
1 TATTTTT-TATATTTAAAT
*
179266 TATTTTTTATATTTTAAT
1 TATTTTTTATATTTAAAT
179284 TATTTTTTATATTATAAAAT
1 TATTTTTTATATT-T-AAAT
179304 TAT
1 TAT
179307 GTTACATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 23 0.62
19 8 0.22
20 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTTATATTTAAAT
Found at i:180002 original size:9 final size:9
Alignment explanation
Indices: 179988--180030 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
179978 ATTATATACG
179988 TATATTATA
1 TATATTATA
179997 TATATTATA
1 TATATTATA
*
180006 TACATTATA
1 TATATTATA
180015 TATA-TATA
1 TATATTATA
*
180023 TATTTTAT
1 TATATTAT
180031 GAGGAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATTATA
Found at i:180006 original size:22 final size:24
Alignment explanation
Indices: 179978--180026 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
179968 CATTTAAAAC
179978 ATTATATAC-GTATAT-TATATAT
1 ATTATATACAGTATATATATATAT
*
180000 ATTATATACATTATATATATATAT
1 ATTATATACAGTATATATATATAT
180024 ATT
1 ATT
180027 TTATGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 5 0.21
24 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTATATACAGTATATATATATAT
Found at i:181755 original size:29 final size:30
Alignment explanation
Indices: 181698--181766 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 30
181688 TAATTAATAA
*
181698 AAATAATAAATATTTTTATATTTTATAA-TT
1 AAAT-ATAAATATTTTTATATTATATAATTT
181728 AAATATAAATAATTTTT-TAATTAT-TAATTT
1 AAATATAAAT-ATTTTTAT-ATTATATAATTT
181758 AAAT-TAAAT
1 AAATATAAAT
181767 TATATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATAAATATTTTTATATTATATAATTT
Found at i:182053 original size:25 final size:26
Alignment explanation
Indices: 182025--182082 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
182015 TAATTTTATG
* * *
182025 AAAATTTTA-AATTTGAATTTAATTT
1 AAAATTTTATAATTTAAAATTAAATT
182050 AAAA-TTTATAATTTAAAATTAAATT
1 AAAATTTTATAATTTAAAATTAAATT
*
182075 AAGATTTT
1 AAAATTTT
182083 TTCTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
AAAATTTTATAATTTAAAATTAAATT
Found at i:190867 original size:2 final size:2
Alignment explanation
Indices: 190862--190888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
190852 ACACACACAC
190862 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
190889 AATTCTGAAA
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:191148 original size:2 final size:2
Alignment explanation
Indices: 191135--191174 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
191125 TAACGACTTT
* *
191135 TA TA TT TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191175 CAAGCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:191358 original size:20 final size:21
Alignment explanation
Indices: 191335--191444 Score: 73
Period size: 21 Copynumber: 5.2 Consensus size: 21
191325 GAATTAATAG
*
191335 ATTTATTTAA-AATTAAAATT
1 ATTTATTTAATAATTAAAAAT
*
191355 ATTTATTTAATATTTAAAAAT
1 ATTTATTTAATAATTAAAAAT
* * * * **
191376 ATTTAAATAAAAAAATATTAA-
1 ATTT-ATTTAATAATTAAAAAT
* *
191397 ACTTATTGAATGAA-TAAAAATT
1 ATTTATTTAAT-AATTAAAAA-T
*
191419 ATTTATTTAATATTTAAAAAT
1 ATTTATTTAATAATTAAAAAT
191440 ATTTA
1 ATTTA
191445 AATAAAAAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
20 18 0.27
21 24 0.36
22 24 0.36
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTATTTAATAATTAAAAAT
Found at i:191418 original size:64 final size:64
Alignment explanation
Indices: 191349--191480 Score: 255
Period size: 64 Copynumber: 2.1 Consensus size: 64
191339 ATTTAAAATT
*
191349 AAAATTATTTATTTAATATTTAAAAATATTTAAATAAAAAAATATTAAACTTATTGAATGAATA
1 AAAATTATTTATTTAATATTTAAAAATATTTAAATAAAAAAATATTAAACTTATTGAACGAATA
191413 AAAATTATTTATTTAATATTTAAAAATATTTAAATAAAAAAATATTAAACTTATTGAACGAATA
1 AAAATTATTTATTTAATATTTAAAAATATTTAAATAAAAAAATATTAAACTTATTGAACGAATA
191477 AAAA
1 AAAA
191481 ACTTCGATAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (64 bp):
AAAATTATTTATTTAATATTTAAAAATATTTAAATAAAAAAATATTAAACTTATTGAACGAATA
Found at i:192308 original size:20 final size:20
Alignment explanation
Indices: 192283--192340 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
192273 AATCGAAAGG
192283 TATTAACTATAAATATTAAT
1 TATTAACTATAAATATTAAT
* * *
192303 TATTAACTACAAAAATTATT
1 TATTAACTATAAATATTAAT
192323 TCATTAA-T-T-AATATTAAT
1 T-ATTAACTATAAATATTAAT
192341 GAAATCAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 7 0.23
20 19 0.61
21 5 0.16
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAACTATAAATATTAAT
Found at i:192985 original size:22 final size:22
Alignment explanation
Indices: 192957--193004 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
192947 AATTTTTTAA
*
192957 AAAATTTTATATTAAGATATTT
1 AAAATTTTATATTAAAATATTT
192979 AAAA-TTTATATTAAAATATTT
1 AAAATTTTATATTAAAATATTT
193000 AAAAT
1 AAAAT
193005 CTTGTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATTTTATATTAAAATATTT
Found at i:193263 original size:15 final size:16
Alignment explanation
Indices: 193243--193273 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
193233 ATCAGCTTAG
193243 TTGAATTAAA-ATTAA
1 TTGAATTAAATATTAA
193258 TTGAATTAAATATTAA
1 TTGAATTAAATATTAA
193274 ATTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TTGAATTAAATATTAA
Found at i:193454 original size:3 final size:3
Alignment explanation
Indices: 193440--193469 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
193430 TTTTAAAAAT
*
193440 ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
193470 TTTATCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:193812 original size:17 final size:19
Alignment explanation
Indices: 193781--193824 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
193771 CTTTAATTAG
193781 TTTTAAAAGATAAAAAA-A
1 TTTTAAAAGATAAAAAATA
193799 TTTTAAAA-ATAAAAAATA
1 TTTTAAAAGATAAAAAATA
193817 TTTTAAAA
1 TTTTAAAA
193825 TAATATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
TTTTAAAAGATAAAAAATA
Found at i:193877 original size:29 final size:29
Alignment explanation
Indices: 193844--193901 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
193834 TCTCTAACAA
193844 TATTAAATTAGA-GATAATATTTATTTTTT
1 TATTAAATTA-ACGATAATATTTATTTTTT
193873 TATTAAATTAACGATAATATTTATTTTTT
1 TATTAAATTAACGATAATATTTATTTTTT
193902 ATCATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (29 bp):
TATTAAATTAACGATAATATTTATTTTTT
Found at i:195823 original size:11 final size:11
Alignment explanation
Indices: 195807--195872 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
195797 ATATAATTAT
195807 TTAAAATAATA
1 TTAAAATAATA
*
195818 TTAAAATATTA
1 TTAAAATAATA
* *
195829 -AAAAATAATT
1 TTAAAATAATA
*
195839 TTATAATAATA
1 TTAAAATAATA
*
195850 TTAATATATTATA
1 TTAA-A-ATAATA
*
195863 TAAAAATAAT
1 TTAAAATAAT
195873 TGTTTATTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 7 0.17
11 24 0.59
12 2 0.05
13 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAATAATA
Found at i:195864 original size:21 final size:20
Alignment explanation
Indices: 195832--195870 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
195822 AATATTAAAA
* *
195832 AATAATTTTATAATAATATT
1 AATAATTATATAAAAATATT
195852 AATATATTATATAAAAATA
1 AATA-ATTATATAAAAATA
195871 ATTGTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAATTATATAAAAATATT
Found at i:195900 original size:17 final size:18
Alignment explanation
Indices: 195857--195902 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
195847 ATATTAATAT
195857 ATTAT-ATAAAAATAATTG
1 ATTATAATAAAAAT-ATTG
*
195875 TTTATTAATAAAAAT-TTG
1 ATTA-TAATAAAAATATTG
195893 ATTATAATAA
1 ATTATAATAA
195903 CTTAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 1 0.04
20 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTATAATAAAAATATTG
Found at i:196106 original size:32 final size:32
Alignment explanation
Indices: 196040--196107 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
196030 TTACATAGTA
* * *
196040 ATATAAATTTTAATATATTGATGATTTGTGTT
1 ATATAAATTTTAATATATTCATGATTCGTATT
196072 ATATAAATTTTAATA-ATTCATGTATTCGTATT
1 ATATAAATTTTAATATATTCATG-ATTCGTATT
196104 ATAT
1 ATAT
196108 TTGTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (32 bp):
ATATAAATTTTAATATATTCATGATTCGTATT
Found at i:198693 original size:14 final size:14
Alignment explanation
Indices: 198675--198707 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
198665 TAATTTTTAA
198675 TTATTTTAT-ATTT
1 TTATTTTATAATTT
198688 TATATTTTATAATTT
1 T-TATTTTATAATTT
198703 TTATT
1 TTATT
198708 AAATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 12 0.67
15 5 0.28
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTTATAATTT
Found at i:199032 original size:18 final size:19
Alignment explanation
Indices: 199002--199044 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
198992 TTAACATATT
199002 AAATT-TTATATATAATAA
1 AAATTATTATATATAATAA
*
199020 AAATTATTA-ATATATTAA
1 AAATTATTATATATAATAA
*
199038 AATTTAT
1 AAATTAT
199045 AAAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTATTATATATAATAA
Found at i:199041 original size:17 final size:17
Alignment explanation
Indices: 198990--199041 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
198980 TATAATACGA
*
198990 TATTAACATATT-AAAT
1 TATTAATATATTAAAAT
*
199006 T-TTATATATAATAAAAAT
1 TATTA-ATAT-ATTAAAAT
199024 TATTAATATATTAAAAT
1 TATTAATATATTAAAAT
199041 T
1 T
199042 TATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.10
16 4 0.14
17 10 0.34
18 9 0.31
19 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAATATATTAAAAT
Found at i:199051 original size:20 final size:20
Alignment explanation
Indices: 199028--199086 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 20
199018 AAAAATTATT
199028 AATATATTAAAATTTATAAA
1 AATATATTAAAATTTATAAA
*
199048 AATATA-TAATATTT-TAAA
1 AATATATTAAAATTTATAAA
* *
199066 TATA-ATTATAA--TATAAA
1 AATATATTAAAATTTATAAA
199083 AATA
1 AATA
199087 ATATAAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 1 0.03
17 8 0.25
18 10 0.31
19 7 0.22
20 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATATTAAAATTTATAAA
Found at i:199427 original size:5 final size:5
Alignment explanation
Indices: 199412--199518 Score: 66
Period size: 5 Copynumber: 22.2 Consensus size: 5
199402 AAATACAATA
* * * *
199412 TATAT TA-AT TATAT TAT-T TATTTT TAAAA TATAT TATAT CATAT T-TAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
* * * *
199460 TATAT TATTTT TATAT T-TAT TA-AA TATAT TATTT TGATAT CATAT T-T-T
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT
199508 TATAT TATAT T
1 TATAT TATAT T
199519 TAAAATTTTC
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
3 2 0.03
4 20 0.26
5 45 0.58
6 10 0.13
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:199473 original size:11 final size:11
Alignment explanation
Indices: 199453--199520 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
199443 TATTATATCA
199453 TATTTATTATAT
1 TATTT-TTATAT
199465 TATTTTTATATT
1 TATTTTTATA-T
**
199477 TATTAAATATAT
1 TATT-TTTATAT
*
199489 TATTTTGATAT
1 TATTTTTATAT
199500 CATATTTTTATAT
1 --TATTTTTATAT
*
199513 TATATTTA
1 TATTTTTA
199521 AAATTTTCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 16 0.36
12 15 0.33
13 14 0.31
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:199511 original size:24 final size:23
Alignment explanation
Indices: 199430--199520 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 23
199420 TTATATTATT
* * *
199430 TATTTTTAAAATATATTATATCA
1 TATTTTTATATTATTTTATATCA
*
199453 TATTTATTATATTATTTTTATAT-T
1 TATTT-TTATATTA-TTTTATATCA
**
199477 TATTAAATATATTATTTTGATATCA
1 TATT-TTTATATTATTTT-ATATCA
199502 TATTTTTATATTATATTTA
1 TATTTTTATATTAT-TTTA
199521 AAATTTTCGA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
23 9 0.17
24 30 0.57
25 14 0.26
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (23 bp):
TATTTTTATATTATTTTATATCA
Found at i:201708 original size:2 final size:2
Alignment explanation
Indices: 201658--201696 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
201648 TTTGATAAGA
201658 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
201697 GTAGGGATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:201810 original size:5 final size:5
Alignment explanation
Indices: 201800--201912 Score: 77
Period size: 5 Copynumber: 22.6 Consensus size: 5
201790 TTTTCCATAC
* * ** **
201800 ATAAT ATAAT ATACT ATAAT ATAAT ATTAT ATAAT ATAAT ATTTT ATTTT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * * * * *
201850 ATAAT ATAAT A-GA- ATAAT ATAAC ACAAT TTAATAT ATAAC ACAAT TTAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT
201900 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
201913 TGGGTAAAAA
Statistics
Matches: 82, Mismatches: 22, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 74 0.90
6 2 0.02
7 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:201888 original size:17 final size:17
Alignment explanation
Indices: 201866--201902 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
201856 TAATAGAATA
201866 ATATAACACAATTTAAT
1 ATATAACACAATTTAAT
201883 ATATAACACAATTTAAT
1 ATATAACACAATTTAAT
201900 ATA
1 ATA
201903 ATATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAACACAATTTAAT
Found at i:202706 original size:6 final size:6
Alignment explanation
Indices: 202697--202739 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
202687 TTAATTATAA
*
202697 AATATT AATATT AATATT AATATAAT AATATT -ATTTT AATATT
1 AATATT AATATT AATATT AATAT--T AATATT AATATT AATATT
202740 TTAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
8 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATATT
Found at i:202737 original size:19 final size:19
Alignment explanation
Indices: 202702--202757 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
202692 TATAAAATAT
*
202702 TAATATTAATATTAATATAA
1 TAATATT-ATTTTAATATAA
**
202722 TAATATTATTTTAATATTT
1 TAATATTATTTTAATATAA
202741 TAATA-TATTTTAA-ATAA
1 TAATATTATTTTAATATAA
202758 AAATTTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 2 0.06
18 8 0.26
19 14 0.45
20 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATTATTTTAATATAA
Found at i:204035 original size:20 final size:22
Alignment explanation
Indices: 204010--204049 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
204000 AAAATATTAT
204010 AAAAT-ATAATT-TATTTAATA
1 AAAATAATAATTATATTTAATA
204030 AAAATAATAATTATATTTAA
1 AAAATAATAATTATATTTAA
204050 ATATGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATAATAATTATATTTAATA
Found at i:204075 original size:37 final size:35
Alignment explanation
Indices: 203969--204082 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 35
203959 AATTGCGCTC
*
203969 ATTTAAATATGATAAATTTAAATATAATATAA-AAAT
1 ATTTAAATATGATTAATTT-AATA-AATATAATAAAT
* * *
204005 ATTATAAAATATAATTTATTTAATAAAAATAATAATTAT
1 ATT-T-AAATATGATTAATTTAATAAATATAATAA--AT
* *
204044 ATTTAAATATGATTAATATAATAAATTTAATATAAT
1 ATTTAAATATGATTAATTTAATAAATATAATA-AAT
204080 ATT
1 ATT
204083 ATATATTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
36 14 0.22
37 30 0.48
38 14 0.22
39 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (35 bp):
ATTTAAATATGATTAATTTAATAAATATAATAAAT
Found at i:204413 original size:32 final size:33
Alignment explanation
Indices: 204357--204446 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 33
204347 GATAATTATG
*
204357 TTTAAAATATTAT-ATA-T-AT-TTATATAAAT
1 TTTAATATATTATAATATTAATATTATATAAAT
*
204386 TTTTATATATTAATAAT-TTAA-ATTATATAAAT
1 TTTAATATATT-ATAATATTAATATTATATAAAT
*
204418 TTTAATATATTTTAATATTAATATTATAT
1 TTTAATATATTATAATATTAATATTATAT
204447 TTGTGTTATG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 9 0.18
30 2 0.04
31 7 0.14
32 25 0.50
33 7 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTAATATATTATAATATTAATATTATATAAAT
Found at i:204925 original size:17 final size:18
Alignment explanation
Indices: 204897--204957 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
204887 ATATTAATAT
204897 TTAAATTTTAAAATCAAA
1 TTAAATTTTAAAATCAAA
* *
204915 TTAAA-TTTAAATTTAAA
1 TTAAATTTTAAAATCAAA
*
204932 TAAAATTTTAAAA--AAA
1 TTAAATTTTAAAATCAAA
*
204948 TTATATTTTA
1 TTAAATTTTA
204958 CTTGATTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 11 0.31
17 14 0.39
18 11 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATTTTAAAATCAAA
Found at i:205545 original size:27 final size:26
Alignment explanation
Indices: 205505--205570 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
205495 ATCCTTATTA
* *
205505 AATATTTTAAATTT-ATCTTTAAT-TC
1 AATATATTATATTTAAT-TTTAATATC
*
205530 AATTATATATATATTTAATTTTAATATT
1 AA-TATAT-TATATTTAATTTTAATATC
205558 AATATATTATATT
1 AATATATTATATT
205571 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 2 0.06
26 10 0.29
27 17 0.50
28 5 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
AATATATTATATTTAATTTTAATATC
Found at i:205654 original size:16 final size:17
Alignment explanation
Indices: 205628--205663 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
205618 AGAAATTGGT
205628 TAAACATAAAATAAAAA
1 TAAACATAAAATAAAAA
205645 TAAACA-AAAATAAAAA
1 TAAACATAAAATAAAAA
205661 TAA
1 TAA
205664 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAACATAAAATAAAAA
Found at i:205957 original size:16 final size:17
Alignment explanation
Indices: 205938--205970 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
205928 TTTAACATAC
205938 ATTTAAATTAA-AATAA
1 ATTTAAATTAATAATAA
*
205954 ATTTAACTTAATAATAA
1 ATTTAAATTAATAATAA
205971 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAAATTAATAATAA
Found at i:212667 original size:20 final size:20
Alignment explanation
Indices: 212642--212680 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
212632 TAATTATATA
*
212642 TTTTTT-ATTCTTTTTCTTTT
1 TTTTTTCATT-TTTTCCTTTT
212662 TTTTTTCATTTTTTCCTTT
1 TTTTTTCATTTTTTCCTTT
212681 AACCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCATTTTTTCCTTTT
Found at i:213069 original size:27 final size:27
Alignment explanation
Indices: 212982--213076 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 27
212972 AGAAATTAGT
* *
212982 ATATTTTTTACCAAACTTTAAAGATAA
1 ATATTTTTTACTAAACTTAAAAGATAA
* *
213009 ATAAATATTTT--TAAACTATAAAAAATAA
1 AT--ATTTTTTACTAAACT-TAAAAGATAA
*
213037 GTATATTTTTTACTAAACTTGAAAGATAA
1 --ATATTTTTTACTAAACTTAAAAGATAA
213066 ATATCTTTTTA
1 ATAT-TTTTTA
213077 TTTTTTATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
27 11 0.21
28 20 0.38
29 14 0.26
30 8 0.15
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (27 bp):
ATATTTTTTACTAAACTTAAAAGATAA
Found at i:216992 original size:16 final size:16
Alignment explanation
Indices: 216963--216996 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
216953 AAGGGGCTAG
*
216963 TTTTTCTTCCCTTTTT
1 TTTTTCTTCACTTTTT
*
216979 TTTTTTTTCACTTTTT
1 TTTTTCTTCACTTTTT
216995 TT
1 TT
216997 GTTTGGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTTCACTTTTT
Found at i:219731 original size:14 final size:14
Alignment explanation
Indices: 219714--219765 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
219704 TATTTATGCA
219714 AAAATACCTGTGCC
1 AAAATACCTGTGCC
* *
219728 AAAAGTACTTGTGTC
1 AAAA-TACCTGTGCC
* * *
219743 AAATTACCTCTACC
1 AAAATACCTGTGCC
219757 AAAATACCT
1 AAAATACCT
219766 TTTTCAAAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (14 bp):
AAAATACCTGTGCC
Found at i:219811 original size:43 final size:44
Alignment explanation
Indices: 219714--219817 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 44
219704 TATTTATGCA
* * *
219714 AAAATACC-TGTGCCAAAAGTACTTGTGTCAAATTACCTCTACC
1 AAAATACCTTTTGTCAAAAGTACGTGTGTCAAATTACCTCTACC
*
219757 AAAATACCTTTT-TCAAAAGTACGTGTGT-TAATGTACCTCTACCC
1 AAAATACCTTTTGTCAAAAGTACGTGTGTCAAAT-TACCTCTA-CC
*
219801 AAAGTA-CTTTTGTCAAA
1 AAAATACCTTTTGTCAAA
219818 GTATCTTTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 3 0.06
43 35 0.67
44 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (44 bp):
AAAATACCTTTTGTCAAAAGTACGTGTGTCAAATTACCTCTACC
Found at i:219880 original size:14 final size:14
Alignment explanation
Indices: 219861--219915 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
219851 AAAGTGCTAA
219861 TGCCAAAGTACTTT
1 TGCCAAAGTACTTT
* * *
219875 TACCAAAGTTCTTG
1 TGCCAAAGTACTTT
* *
219889 TGCTAAAGTATTTT
1 TGCCAAAGTACTTT
219903 TGCCAAAGTACTT
1 TGCCAAAGTACTT
219916 ATGCTAAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (14 bp):
TGCCAAAGTACTTT
Found at i:219920 original size:28 final size:28
Alignment explanation
Indices: 219846--219923 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
219836 AAAGTACCCA
* * *
219846 TGCCAAAAGTGCTAATGCCAAAGTACTTT
1 TGCC-AAAGTACTTATGCTAAAGTACTTT
* * * *
219875 TACCAAAGTTCTTGTGCTAAAGTATTTT
1 TGCCAAAGTACTTATGCTAAAGTACTTT
219903 TGCCAAAGTACTTATGCTAAA
1 TGCCAAAGTACTTATGCTAAA
219924 ATATCTCTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 37 0.93
29 3 0.08
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (28 bp):
TGCCAAAGTACTTATGCTAAAGTACTTT
Found at i:222222 original size:28 final size:28
Alignment explanation
Indices: 222191--222282 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
222181 TACTTGTGTT
222191 AAAGTA-ATACTGCCAAGTACCTGTGCCA
1 AAAGTACATA-TGCCAAGTACCTGTGCCA
* * * * *
222219 AAAGTACTTATTCAAAGTACCTCTGCTA
1 AAAGTACATATGCCAAGTACCTGTGCCA
*
222247 AAAGTATC-TATGGCCAAAGTATCTGTGCCA
1 AAAGTA-CATAT-GCC-AAGTACCTGTGCCA
222277 AAAGTA
1 AAAGTA
222283 TTTATGCTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 29 0.58
29 4 0.08
30 17 0.34
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGTACATATGCCAAGTACCTGTGCCA
Found at i:222225 original size:15 final size:15
Alignment explanation
Indices: 222205--222282 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
222195 TAATACTGCC
*
222205 AAGTACCTGTGCCAA
1 AAGTACCTATGCCAA
* *
222220 AAGTACTTAT-TC-A
1 AAGTACCTATGCCAA
* *
222233 AAGTACCTCTGCTAA
1 AAGTACCTATGCCAA
*
222248 AAGTATCTATGGCC-A
1 AAGTACCTAT-GCCAA
* *
222263 AAGTATCTGTGCCAA
1 AAGTACCTATGCCAA
222278 AAGTA
1 AAGTA
222283 TTTATGCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
13 9 0.19
14 4 0.08
15 33 0.69
16 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (15 bp):
AAGTACCTATGCCAA
Found at i:222283 original size:15 final size:15
Alignment explanation
Indices: 222232--222289 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
222222 GTACTTATTC
* * *
222232 AAAGTACCTCTGCTA
1 AAAGTATCTATGCCA
222247 AAAGTATCTATGGCC-
1 AAAGTATCTAT-GCCA
*
222262 AAAGTATCTGTGCCA
1 AAAGTATCTATGCCA
*
222277 AAAGTATTTATGC
1 AAAGTATCTATGC
222290 TAAACAAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 3 0.09
15 30 0.86
16 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (15 bp):
AAAGTATCTATGCCA
Found at i:223111 original size:13 final size:13
Alignment explanation
Indices: 223093--223120 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
223083 CAATGGTTGC
223093 AAAAATTATAGAG
1 AAAAATTATAGAG
223106 AAAAATTATAGAG
1 AAAAATTATAGAG
223119 AA
1 AA
223121 TTCTTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAAATTATAGAG
Found at i:223763 original size:58 final size:56
Alignment explanation
Indices: 223632--223763 Score: 138
Period size: 58 Copynumber: 2.3 Consensus size: 56
223622 TCTCTGAAGT
* * * * *
223632 ACTTCTGTCAAAATACCTTTGTCAGAATACTTGTGCTAAATCCCTCTACTAAAAGT
1 ACTTCTGTCAAAATACCTGTGCCAGAATACTTATGCTAAATACCTCTACTAAAAGC
* * * * *
223688 ACTTCTATCAAAGTACCTGTGCCAAGAATATTTATGCTAAAGTACCTTTATTAAAAGC
1 ACTTCTGTCAAAATACCTGTGCC-AGAATACTTATGCTAAA-TACCTCTACTAAAAGC
* *
223746 ATTTTTGTCAAAATACCT
1 ACTTCTGTCAAAATACCT
223764 TTGCTAAAAG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
56 19 0.32
57 15 0.25
58 26 0.43
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (56 bp):
ACTTCTGTCAAAATACCTGTGCCAGAATACTTATGCTAAATACCTCTACTAAAAGC
Found at i:223815 original size:14 final size:14
Alignment explanation
Indices: 223780--223827 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
223770 AAAGTACTTG
* *
223780 TACTAAAGTACCTA
1 TACTAAAGTATCTC
*
223794 TACCAAAGTATCTC
1 TACTAAAGTATCTC
*
223808 TACTAAAGAATCTC
1 TACTAAAGTATCTC
*
223822 TGCTAA
1 TACTAA
223828 TGAGTATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (14 bp):
TACTAAAGTATCTC
Found at i:224181 original size:15 final size:15
Alignment explanation
Indices: 224163--224196 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
224153 AGAAAATTAG
*
224163 AAAAATCAAAATCAT
1 AAAAATAAAAATCAT
*
224178 AAAATTAAAAATCAT
1 AAAAATAAAAATCAT
224193 AAAA
1 AAAA
224197 TTATGATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAATCAT
Found at i:224197 original size:15 final size:15
Alignment explanation
Indices: 224170--224199 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
224160 TAGAAAAATC
224170 AAAATCATAAAATTA
1 AAAATCATAAAATTA
224185 AAAATCATAAAATTA
1 AAAATCATAAAATTA
224200 TGATCTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATCATAAAATTA
Found at i:235189 original size:21 final size:21
Alignment explanation
Indices: 235163--235218 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
235153 CATAAGTAAA
235163 TGTATCGATACATTTACT-ATT
1 TGTATCGATACATTTACTCA-T
* *
235184 TGTATCAATACA-TTATTCAT
1 TGTATCGATACATTTACTCAT
*
235204 TATATCGATACATTT
1 TGTATCGATACATTT
235219 TGGGTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATTTACTCAT
Found at i:242200 original size:51 final size:51
Alignment explanation
Indices: 242141--242239 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 51
242131 ATAACAGGGT
*
242141 TGGAGTATC-CCTGATTATAGAAAATCGGTATTTT-GAAAATAAAATCGGAGG
1 TGGAGTATCTCC-GATTATAAAAAATCGGTATTTTAG-AAATAAAATCGGAGG
* *
242192 TGGAGTATCTCCGATTGTAAAAAATTGGTATTTTAGAAATAAAATCGG
1 TGGAGTATCTCCGATTATAAAAAATCGGTATTTTAGAAATAAAATCGG
242240 GGTTGGGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 40 0.93
52 3 0.07
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.31
Consensus pattern (51 bp):
TGGAGTATCTCCGATTATAAAAAATCGGTATTTTAGAAATAAAATCGGAGG
Found at i:242381 original size:28 final size:28
Alignment explanation
Indices: 242349--242416 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 28
242339 AGAAAGCCGA
242349 GGTTGGAGTATCCCCTTG-GAAATAACGG
1 GGTTGGAGTATCCCC-TGAGAAATAACGG
242377 GGTTGGAGTAT-CCCTGATGAAATAACGG
1 GGTTGGAGTATCCCCTGA-GAAATAACGG
242405 GGTTGGAGTATC
1 GGTTGGAGTATC
242417 TCCAATTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 32 0.86
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTGAGAAATAACGG
Found at i:244861 original size:20 final size:20
Alignment explanation
Indices: 244818--244994 Score: 138
Period size: 20 Copynumber: 8.8 Consensus size: 20
244808 AAAATGCTTG
* *
244818 AATGTATCGACACATTGTAA-
1 AATGTATCGATACAATG-AAC
*
244838 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAC
244858 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAAC
244874 -A--TATCGATACAAT-AAGC
1 AATGTATCGATACAATGAA-C
*
244891 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAC
*
244911 AATGTATCGATACATCAGGGTAAACCC
1 AATGTATCGATACA--A---TGAA--C
244938 AAAATGTATCGATACAATGAAC
1 --AATGTATCGATACAATGAAC
244960 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
244980 AAAGTATCGATACAA
1 AATGTATCGATACAA
244995 ATTGAGAAAA
Statistics
Matches: 131, Mismatches: 8, Indels: 36
0.75 0.05 0.21
Matches are distributed among these distances:
13 12 0.09
15 1 0.01
18 1 0.01
19 1 0.01
20 91 0.69
21 2 0.02
22 2 0.02
24 3 0.02
25 3 0.02
27 1 0.01
29 14 0.11
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:244884 original size:33 final size:33
Alignment explanation
Indices: 244842--244906 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
244832 TTGTAAAATG
*
244842 TATCGATACAATGAGCAATGTATCGATACAATA
1 TATCGATACAATAAGCAATGTATCGATACAATA
244875 TATCGATACAATAAGCAATGTATCGATACAAT
1 TATCGATACAATAAGCAATGTATCGATACAAT
244907 GAAAAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
TATCGATACAATAAGCAATGTATCGATACAATA
Found at i:244906 original size:13 final size:13
Alignment explanation
Indices: 244857--244887 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
244847 ATACAATGAG
*
244857 CAATGTATCGATA
1 CAATATATCGATA
244870 CAATATATCGATA
1 CAATATATCGATA
244883 CAATA
1 CAATA
244888 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (13 bp):
CAATATATCGATA
Found at i:245731 original size:34 final size:34
Alignment explanation
Indices: 245687--245764 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 34
245677 TCAAGGATAA
* *
245687 AGGAAAAAAGAAAATGAAA-TG-GTCCTGCTCTTTG
1 AGGACAAAAG-AAAT-AAAGTGCGTCCTACTCTTTG
245721 AGGACAAAAG-AATAAAGTGCGTCCTACTCTTTG
1 AGGACAAAAGAAATAAAGTGCGTCCTACTCTTTG
245754 AGGACAAAAGA
1 AGGACAAAAGA
245765 GAAAAGAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 3 0.08
32 5 0.13
33 22 0.56
34 9 0.23
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (34 bp):
AGGACAAAAGAAATAAAGTGCGTCCTACTCTTTG
Found at i:245817 original size:45 final size:45
Alignment explanation
Indices: 245729--245823 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
245719 TGAGGACAAA
*
245729 AGAATAAAGTGCGTCCTACTCTTTGAGGACAAAAGAGAAAAGAAG
1 AGAATAAAGTGCGTACTACTCTTTGAGGACAAAAGAGAAAAGAAG
* *
245774 AGAATGAAGTGCGTACTGCTCTTTGAGGAC-AAAG-G-AAAGAAG
1 AGAATAAAGTGCGTACTACTCTTTGAGGACAAAAGAGAAAAGAAG
*
245816 AAAATAAA
1 AGAATAAA
245824 CTGCATCCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 13 0.29
43 1 0.02
44 4 0.09
45 27 0.60
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18
Consensus pattern (45 bp):
AGAATAAAGTGCGTACTACTCTTTGAGGACAAAAGAGAAAAGAAG
Found at i:245837 original size:42 final size:45
Alignment explanation
Indices: 245747--245850 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 45
245737 GTGCGTCCTA
* * * * *
245747 CTCTTTGAGGACAAAAGAGAAAAGAAGAGAATGAAGTGCGTACTG
1 CTCTTTGAGGACAAAAGAGAAAAGAAGAAAATAAACTGCATACCG
*
245792 CTCTTTGAGGAC-AAAG-G-AAAGAAGAAAATAAACTGCATCCCG
1 CTCTTTGAGGACAAAAGAGAAAAGAAGAAAATAAACTGCATACCG
*
245834 CTCTTTGGGGACTAAAA
1 CTCTTTGAGGAC-AAAA
245851 AGTATCACCA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 30 0.60
43 1 0.02
44 7 0.14
45 12 0.24
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (45 bp):
CTCTTTGAGGACAAAAGAGAAAAGAAGAAAATAAACTGCATACCG
Found at i:245921 original size:61 final size:62
Alignment explanation
Indices: 245856--246124 Score: 327
Period size: 61 Copynumber: 4.4 Consensus size: 62
245846 TAAAAAGTAT
* *
245856 CACCAACTCGTGTGGGCTTTGAAAAAG-AAAGGCATCCTGCTCTTTGAGGACTAGAAGATGC
1 CACCAACTTGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGATGC
* * *
245917 CACCAACTTGTGTGGGCTTTG-CAAAGAGAAA-GCATCCTACTCTTTGAGGACTAAGAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAAAGA-AAAGGCGTCCTGCTCTTTGAGGACT-AGAAGATGC
* * *
245978 CACCAACTTGTGTGGGCTTTG-AAAGGAAAATGCGTCCTGCTCTTTGAGGACTAGAAAATGC
1 CACCAACTTGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGATGC
* * * * * * *
246039 AACTAACTTGTGTAGGCTTTG-AAAGGAAAAGGCGTTCTACTCTTTGAGGACTAGAAAAGTGC
1 CACCAACTTGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGA-TGC
246101 CACCAACTTGTGTGGGCTTT-AAAA
1 CACCAACTTGTGTGGGCTTTGAAAA
246125 GGGAAAAGAA
Statistics
Matches: 185, Mismatches: 16, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
60 11 0.06
61 144 0.78
62 30 0.16
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (62 bp):
CACCAACTTGTGTGGGCTTTGAAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGATGC
Found at i:246047 original size:122 final size:123
Alignment explanation
Indices: 245834--246132 Score: 385
Period size: 122 Copynumber: 2.4 Consensus size: 123
245824 CTGCATCCCG
* ** * *
245834 CTCTTTGGGGACTAA-AAAGTATCACCAACTCGTGTGGGCTTTGAAA-AAGAAAGGCATCCTGCT
1 CTCTTTGAGGACTAAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAAGGCATCCTGCT
* * *
245897 CTTTGAGGACTAGAAGATGCCACCAACTTGTGTGGGCTTTGCAAA-GAGAAA-GCATCCTA
65 CTTTGAGGACTAGAAAATGCAACCAACTTGTGTAGGCTTTG-AAAGGA-AAAGGCATCCTA
* *
245956 CTCTTTGAGGACTAAGAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAATGCGTCCTGCTC
1 CTCTTTGAGGACTAAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTC
* * *
246020 TTTGAGGACTAGAAAATGCAACTAACTTGTGTAGGCTTTGAAAGGAAAAGGCGTTCTA
66 TTTGAGGACTAGAAAATGCAACCAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCCTA
*
246078 CTCTTTGAGGACT-AGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAAG
1 CTCTTTGAGGACTAAG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAA-GGAAAAG
246133 AAGAAAATGA
Statistics
Matches: 155, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
121 8 0.05
122 111 0.72
123 30 0.19
124 6 0.04
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (123 bp):
CTCTTTGAGGACTAAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTGCTC
TTTGAGGACTAGAAAATGCAACCAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCCTA
Found at i:246283 original size:60 final size:61
Alignment explanation
Indices: 246176--246605 Score: 517
Period size: 60 Copynumber: 6.9 Consensus size: 61
246166 AAGGGGGAAT
* * * *
246176 AAAGTGCGTCCTT-CTCTTTGAGGACTAGGAGGTGCCACCAACTTGTGTCGGCTTTGAAAG-GA
1 AAAG-GCGT-CTTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAA
* * * * *
246238 AAAGGCATCTTGCTCTTTCAAGACTAAAGATGCCACCAATTTGTGTGGGCTTTAAAAAGAAA
1 AAAGGCGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAA
* * * * *
246300 AAAAGCGTCATACTCTTTGAGGACTGGAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAA
1 AAAGGCGTCTTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--AAA
* *
246365 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAAGAAAA
1 AAAGGCGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAA
* * * *
246428 AAAGGCATCTTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTTGAAAG-GA
1 AAAGGCGTCTTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAA
* * *
246489 AAATGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AGA
1 AAAGGCGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAA
*
246549 AAAGGCGTCTTGCTTTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAGGCGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
246606 AGTGTTTTGT
Statistics
Matches: 319, Mismatches: 41, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
60 111 0.35
61 43 0.13
62 24 0.08
63 61 0.19
64 55 0.17
65 25 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (61 bp):
AAAGGCGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAA
Found at i:246673 original size:121 final size:120
Alignment explanation
Indices: 246192--246699 Score: 492
Period size: 127 Copynumber: 4.1 Consensus size: 120
246182 CGTCCTTCTC
* * * * * * *
246192 TTTGAGGACTAGGAGGTGCCACCAACTTGTGTCGGCTTTGAAAGGAAAAGGCATCTTGCTCTTTC
1 TTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTT--AA-GAAAATGCGTCCTGCTCTTTG
* * * * * * *
246257 AAGACTAAAGATGCCACCAATTTGTGTGGGCTTTAAAAAGAAAAAAA-GCGTCATACTC
62 AGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCTTGCTT
* * * *
246315 TTTGAGGACTGGAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAAGGCGTCCTGCTC
1 TTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTT---AAG----AAAATGCGTCCTGCTC
* *
246380 TTTGAGGACTAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAAAAGGCATCTTGCTC
58 TTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCTTGCTT
246443 TTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAATGCGTCCTGCTCTTTG
1 TTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTT--AA-GAAAATGCGTCCTGCTCTTTG
*
246508 AGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG---AAAAGGCGTCTTGCTT
62 AGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCTTGCTT
* * ** *
246564 TTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-A-AAAA-GTGTTTTGTTCTTTGAGGA
1 TTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAAAATGCGTCCTGCTCTTTGAGGA
* * * * *
246626 CTAGAAAAGTGCTACCAACTTATGTGGGCTTAAAAAAGAAAAAAAAAGGCATCCTG-TT
66 CT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG--AAAAAAAGGCATCTTGCTT
246684 CTTTGAGGACTAAAGG
1 -TTTGAGGACTAAAGG
246700 GCGAAATGAG
Statistics
Matches: 334, Mismatches: 34, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
114 17 0.05
115 4 0.01
116 30 0.09
117 1 0.00
120 28 0.08
121 51 0.15
123 35 0.10
124 61 0.18
127 63 0.19
128 44 0.13
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (120 bp):
TTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAAAATGCGTCCTGCTCTTTGAGGA
CTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCATCTTGCTT
Found at i:246802 original size:55 final size:55
Alignment explanation
Indices: 246713--246993 Score: 332
Period size: 55 Copynumber: 5.0 Consensus size: 55
246703 AAATGAGAGA
* ***
246713 GCGTTCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
* *
246768 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
*
246823 GCGTCCTGCTCTTTGAGGACTAAAAAAAAG-GCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACT---AAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * **
246880 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGAATGGGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT------AAAAG
* * * *
246941 GCGTTCTGCTTTTTGAGGA-TTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
246994 AGAAAAAATG
Statistics
Matches: 199, Mismatches: 17, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
54 8 0.04
55 90 0.45
57 48 0.24
58 5 0.03
60 27 0.14
61 21 0.11
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:249129 original size:19 final size:19
Alignment explanation
Indices: 249105--249154 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
249095 AGACAGAACA
*
249105 TGTATCGATACATGAGTGT
1 TGTATCGATACATAAGTGT
*
249124 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
249143 TGTATCGATACA
1 TGTATCGATACA
249155 ATGTTTCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:253826 original size:31 final size:29
Alignment explanation
Indices: 253788--253866 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 29
253778 CTTCTCTTTT
253788 AAAAAAAAAAAGAAAAAAAAAACAAAAGCAA
1 AAAAAAAAAAAGAAAAAAAAAACAAAA--AA
* *
253819 AAAAAAAACAACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAGAAAAAAAAAACAAAAAA
253848 AAAACAAAACAAAGAAAAA
1 AAAA-AAAA-AAAGAAAAA
253867 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.14
30 4 0.10
31 32 0.76
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAGAAAAAAAAAACAAAAAA
Found at i:253834 original size:25 final size:25
Alignment explanation
Indices: 253789--253866 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
253779 TTCTCTTTTA
*
253789 AAAAAAAAAAGAAAAAAAAAACAAAAGC
1 AAAAAAAAAA-CAAAAAAAAA-AAAA-C
*
253817 AAAAAAAAAACAACAAAAAAAAAAC
1 AAAAAAAAAACAAAAAAAAAAAAAC
*
253842 AAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAACAAAA-AAAAAAAAA
253867 GAGAGAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.33
26 12 0.27
27 8 0.18
28 10 0.22
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAACAAAAAAAAAAAAAC
Found at i:253881 original size:1 final size:1
Alignment explanation
Indices: 253788--253866 Score: 68
Period size: 1 Copynumber: 79.0 Consensus size: 1
253778 CTTCTCTTTT
* * ** * * * *
253788 AAAAAAAAAAAGAAAAAAAAAACAAAAGCAAAAAAAAAACAACAAAAAAAAAACAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
253853 AAAACAAAGAAAAA
1 AAAAAAAAAAAAAA
253867 GAGAGAAAAG
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:253881 original size:42 final size:41
Alignment explanation
Indices: 253788--253866 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 41
253778 CTTCTCTTTT
*
253788 AAAAAAAAAAAGAAAAAAAAAACAAAAGCAAAAAAAAAACA
1 AAAAAAAAAAACAAAAAAAAAACAAAAGCAAAAAAAAAACA
*
253829 ACAAAAAAAAAACAAAAAAAAAACAAAA-CAAAGAAAAA
1 A-AAAAAAAAAACAAAAAAAAAACAAAAGCAAAAAAAAA
253867 GAGAGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (41 bp):
AAAAAAAAAAACAAAAAAAAAACAAAAGCAAAAAAAAAACA
Found at i:255021 original size:55 final size:55
Alignment explanation
Indices: 254937--255188 Score: 308
Period size: 55 Copynumber: 4.5 Consensus size: 55
254927 CCTCCTTTTG
* * *
254937 CCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
254992 CCTTTTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTAAAGCTCACACAAGTTGATGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCC---T--TTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
255052 -CTTCCTAGTCCTCAAAAAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTT-TTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
255107 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCTACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
255162 CATTCTAGTCCTCAAAGAGCAGGACGC
1 CCTTTTAGTCCTCAAAGAGCAGGACGC
255189 TCTCTCTTTT
Statistics
Matches: 166, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
55 115 0.69
56 3 0.02
57 1 0.01
58 1 0.01
59 3 0.02
60 43 0.26
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:255274 original size:94 final size:95
Alignment explanation
Indices: 255107--255280 Score: 278
Period size: 94 Copynumber: 1.8 Consensus size: 95
255097 GTTGGTGGCA
* * * * *
255107 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCTACACAAGTTGGTGGCACATTCTAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACACTCCAATC
255172 CTCAAAGAGCAGGACGCTCTCTCTTTTCAC
66 CTCAAAGAGCAGGACGCTCTCTCTTTTCAC
* *
255202 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCCAATC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACACTCCAATC
255266 CTCAAAGAGCAGGAC
66 CTCAAAGAGCAGGAC
255281 ACCTTTTTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 67 0.93
95 5 0.07
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.22
Consensus pattern (95 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACACTCCAATC
CTCAAAGAGCAGGACGCTCTCTCTTTTCAC
Found at i:255424 original size:43 final size:43
Alignment explanation
Indices: 255325--255504 Score: 174
Period size: 42 Copynumber: 4.1 Consensus size: 43
255315 GCACTTTGTA
*
255325 GTCCTCAAAGAGCAGGACTCACTTT-ATTTTCCTCTTTCT--TTT
1 GTCCTCAAAGAGCAGGACACA-TTTCATTTTCCT-TTTCTCCTTT
* *
255367 GTCCTCAAAGAGCAGGGCACATTTCGTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTCTCCTTT
* *
255410 GTCCTCAAAGAGCAGGACGTTC-TTT-A-TTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGAC--ACATTTCATTTTCCTT-TTCT-CCTT-T
* *
255455 AGTCCTCAAAGAGCATGACACATTTCATTTTCCTTTTCTCTTTT
1 -GTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTCTCCTTT
*
255499 TTCCTC
1 GTCCTC
255505 GAAAAATGGG
Statistics
Matches: 114, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
41 8 0.07
42 33 0.29
43 28 0.25
44 9 0.08
45 8 0.07
46 21 0.18
47 7 0.06
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTCTCCTTT
Found at i:255490 original size:89 final size:85
Alignment explanation
Indices: 255325--255504 Score: 229
Period size: 89 Copynumber: 2.1 Consensus size: 85
255315 GCACTTTGTA
* *
255325 GTCCTCAAAGAGCAGGACTCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGGCACATT
1 GTCCTCAAAGAGCAGGACTCACTTTATTTTCCTCTTTCTTTAGTCCTCAAAGAGCAGGACACATT
*
255390 TCGTTTTCCTTTTCTCCTTT
66 TCATTTTCCTTTTCTCCTTT
* *
255410 GTCCTCAAAGAGCAGGACGT-TCTTTA-TTTCCTTCTTTTCCCTTCTAGTCCTCAAAGAGCATGA
1 GTCCTCAAAGAGCAGGAC-TCACTTTATTTTCC-TC-TTT--CTT-TAGTCCTCAAAGAGCAGGA
*
255473 CACATTTCATTTTCCTTTTCTCTTTT
60 CACATTTCATTTTCCTTTTCTCCTTT
*
255499 TTCCTC
1 GTCCTC
255505 GAAAAATGGG
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
84 5 0.06
85 25 0.30
86 4 0.05
88 3 0.04
89 45 0.55
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (85 bp):
GTCCTCAAAGAGCAGGACTCACTTTATTTTCCTCTTTCTTTAGTCCTCAAAGAGCAGGACACATT
TCATTTTCCTTTTCTCCTTT
Found at i:256314 original size:19 final size:19
Alignment explanation
Indices: 256290--256336 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
256280 GTATCGATAC
*
256290 ATCGATACATGAGTGTTGT
1 ATCGATACATAAGTGTTGT
*
256309 ATCGATACATAAGTTTTGT
1 ATCGATACATAAGTGTTGT
256328 ATCGATACA
1 ATCGATACA
256337 ATGTTTCGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (19 bp):
ATCGATACATAAGTGTTGT
Found at i:256409 original size:13 final size:14
Alignment explanation
Indices: 256390--256451 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 14
256380 TTAAGGAAAT
*
256390 ATATCGATATATTG
1 ATATCGATATATCG
256404 -TATCGATATATCG
1 ATATCGATATATCG
*
256417 ATAT--ATTGTATCG
1 ATATCGA-TATATCG
*
256430 ATATCGATATATTG
1 ATATCGATATATCG
256444 -TATCGATA
1 ATATCGATA
256452 CATCAATCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.03
13 30 0.75
14 8 0.20
15 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (14 bp):
ATATCGATATATCG
Found at i:256412 original size:21 final size:21
Alignment explanation
Indices: 256388--256471 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
256378 CATTAAGGAA
256388 ATATATCGATATATTGTATCG
1 ATATATCGATATATTGTATCG
256409 ATATATCGATATATTGTATCG
1 ATATATCGATATATTGTATCG
256430 --ATATCGATATATTGTATCG
1 ATATATCGATATATTGTATCG
* * *
256449 ATACATCAATCT-TTGTATCG
1 ATATATCGATATATTGTATCG
256469 ATA
1 ATA
256472 CATCTAGGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
19 19 0.33
20 11 0.19
21 28 0.48
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATATCGATATATTGTATCG
Found at i:256445 original size:40 final size:39
Alignment explanation
Indices: 256390--256471 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
256380 TTAAGGAAAT
* *
256390 ATATCGATATATTGTATCGATATATCGATATATTGTATCG
1 ATATCGATATATTGTATCGATACATCAATAT-TTGTATCG
*
256430 ATATCGATATATTGTATCGATACATCAATCTTTGTATCG
1 ATATCGATATATTGTATCGATACATCAATATTTGTATCG
256469 ATA
1 ATA
256472 CATCTAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 11 0.28
40 28 0.72
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATATCGATATATTGTATCGATACATCAATATTTGTATCG
Found at i:259971 original size:34 final size:35
Alignment explanation
Indices: 259933--259999 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
259923 CCTTACAACA
259933 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
259967 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
260000 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:262031 original size:13 final size:13
Alignment explanation
Indices: 262013--262037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262003 ACTGAAGCAA
262013 TGTATCGATACAT
1 TGTATCGATACAT
262026 TGTATCGATACA
1 TGTATCGATACA
262038 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262403 original size:20 final size:21
Alignment explanation
Indices: 262378--262418 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
262368 AATCAAGATT
* *
262378 AATCAATATTTGAA-AAAAAA
1 AATCAAAAATTGAATAAAAAA
262398 AATCAAAAATTGAATAAAAAA
1 AATCAAAAATTGAATAAAAAA
262419 TCATTTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (21 bp):
AATCAAAAATTGAATAAAAAA
Found at i:262670 original size:23 final size:24
Alignment explanation
Indices: 262625--262671 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
262615 CAAAGAATTG
*
262625 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
262649 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
262672 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:264129 original size:21 final size:21
Alignment explanation
Indices: 264105--264146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
264095 ATCCATTTCT
* *
264105 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
264126 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
264147 ACGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:265277 original size:34 final size:35
Alignment explanation
Indices: 265239--265305 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
265229 CCTTACAACA
265239 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
265273 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
265306 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Done.