Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 18 of 20
Found at i:3101598 original size:2 final size:2
Alignment explanation
Indices: 3101591--3101615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3101581 AAATGAAAAT
3101591 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
3101616 CTAGGACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3102372 original size:18 final size:18
Alignment explanation
Indices: 3102351--3102385 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3102341 TAAAAAATTT
3102351 ATATTATTTAAAATAATA
1 ATATTATTTAAAATAATA
* *
3102369 ATATTTTTTAAATTAAT
1 ATATTATTTAAAATAAT
3102386 TTAACTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATTTAAAATAATA
Found at i:3106716 original size:11 final size:11
Alignment explanation
Indices: 3106700--3106730 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3106690 AAACATTCAG
3106700 TGGCTTAGTGT
1 TGGCTTAGTGT
3106711 TGGCTTAGTGT
1 TGGCTTAGTGT
*
3106722 TAGCTTAGT
1 TGGCTTAGT
3106731 ACAAAGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.32, T:0.45
Consensus pattern (11 bp):
TGGCTTAGTGT
Found at i:3111909 original size:19 final size:17
Alignment explanation
Indices: 3111861--3111909 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3111851 TTTAGATCAA
3111861 TTTAATTTTAAATAATAT
1 TTTAA-TTTAAATAATAT
*
3111879 TTTAATTAAAATAATATAT
1 TTTAATTTAAAT-A-ATAT
*
3111898 TTTTATTTAAAT
1 TTTAATTTAAAT
3111910 TTAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATAATAT
Found at i:3112020 original size:7 final size:6
Alignment explanation
Indices: 3111997--3112026 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3111987 GAGCGAGTAT
3111997 AATTTA AATTTA AATTTAA AATTTA AATTT
1 AATTTA AATTTA AATTT-A AATTTA AATTT
3112027 TTTTAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:3112020 original size:13 final size:12
Alignment explanation
Indices: 3111997--3112026 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
3111987 GAGCGAGTAT
3111997 AATTTAAATTTA
1 AATTTAAATTTA
3112009 AATTTAAAATTTA
1 AATTT-AAATTTA
3112022 AATTT
1 AATTT
3112027 TTTTAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:3112816 original size:22 final size:24
Alignment explanation
Indices: 3112791--3112835 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3112781 GGAAAAAATT
3112791 TAAA-AAA-AATTATTTT-TAAAAG
1 TAAATAAATAATT-TTTTATAAAAG
3112813 TAAATAAATAATTTTTTATAAAA
1 TAAATAAATAATTTTTTATAAAA
3112836 AATATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATAAATAATTTTTTATAAAAG
Found at i:3116556 original size:2 final size:2
Alignment explanation
Indices: 3116549--3116574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3116539 AAGGTACTAA
3116549 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3116575 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3118756 original size:33 final size:34
Alignment explanation
Indices: 3118687--3118771 Score: 136
Period size: 33 Copynumber: 2.5 Consensus size: 34
3118677 TGACATGATC
3118687 AAGCATCAGTTAGTTTTTATTGGACAAAAAAAAAA
1 AAGCATCAGTTAGTTTTTATTGGAC-AAAAAAAAA
*
3118722 AAGCATCAGTTAGTTTTTATTTGAC-AAAAAAAA
1 AAGCATCAGTTAGTTTTTATTGGACAAAAAAAAA
*
3118755 AAGTATCAGTTAGTTTT
1 AAGCATCAGTTAGTTTT
3118772 CGGGCTGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 24 0.50
35 24 0.50
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (34 bp):
AAGCATCAGTTAGTTTTTATTGGACAAAAAAAAA
Found at i:3127400 original size:2 final size:2
Alignment explanation
Indices: 3127393--3127431 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3127383 AATTCTAATT
3127393 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3127432 TCCCTTTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3133756 original size:19 final size:19
Alignment explanation
Indices: 3133732--3133772 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
3133722 TATATATCAC
3133732 AAAACTTAGAGACCGCATT
1 AAAACTTAGAGACCGCATT
*
3133751 AAAACTTAGAGACTGCATT
1 AAAACTTAGAGACCGCATT
3133770 AAA
1 AAA
3133773 GCAAACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (19 bp):
AAAACTTAGAGACCGCATT
Found at i:3135723 original size:2 final size:2
Alignment explanation
Indices: 3135708--3135748 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3135698 TAAATCCAAC
* *
3135708 AT AT AT GT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3135749 ACCTTCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3139744 original size:2 final size:2
Alignment explanation
Indices: 3139739--3139779 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3139729 AAGATTAGCA
3139739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3139780 AAGATTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3142090 original size:21 final size:21
Alignment explanation
Indices: 3142061--3142108 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3142051 ATATTTTTAT
* * *
3142061 TTAATTAAGTAAAATAATATA
1 TTAAATAAGAAAAATAAAATA
3142082 TTAAATAAGAAAAATAAAATA
1 TTAAATAAGAAAAATAAAATA
*
3142103 ATAAAT
1 TTAAAT
3142109 CTTTAAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TTAAATAAGAAAAATAAAATA
Found at i:3142261 original size:16 final size:16
Alignment explanation
Indices: 3142213--3142266 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
3142203 TGAAGTTTTA
3142213 ATATTT-ATAAAATTT
1 ATATTTAATAAAATTT
* *
3142228 TTAATTAAATAAAA-TT
1 AT-ATTTAATAAAATTT
3142244 ATATTTAATAAAATTT
1 ATATTTAATAAAATTT
3142260 AT-TTTAA
1 ATATTTAA
3142267 AATAATACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 16 0.50
16 10 0.31
17 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTAATAAAATTT
Found at i:3143185 original size:23 final size:22
Alignment explanation
Indices: 3143159--3143207 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
3143149 AATATGACAT
*
3143159 AAAAATAATTAAAACATAATATA
1 AAAAATAAATAAAACA-AATATA
* *
3143182 AAAAATAAATGACACAAATATA
1 AAAAATAAATAAAACAAATATA
3143204 AAAA
1 AAAA
3143208 CATATCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAATAAATAAAACAAATATA
Found at i:3144137 original size:16 final size:18
Alignment explanation
Indices: 3144116--3144151 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
3144106 GATAAAAAAT
3144116 AAATTAT-AATACAT-TA
1 AAATTATAAATACATATA
3144132 AAATTATAAATACATATA
1 AAATTATAAATACATATA
3144150 AA
1 AA
3144152 CATATATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTATAAATACATATA
Found at i:3144290 original size:22 final size:21
Alignment explanation
Indices: 3144249--3144305 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
3144239 AAATTTTTGG
*
3144249 ATAAAGAATAAAGGGAAAATTA
1 ATAAAGAATAAA-GGAAAATGA
*
3144271 ATAAAGAATAAAGGATAAATGG
1 ATAAAGAATAAAGGA-AAATGA
*
3144293 ATAAAGAAAAAAG
1 ATAAAGAATAAAG
3144306 AACAAAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (21 bp):
ATAAAGAATAAAGGAAAATGA
Found at i:3144923 original size:23 final size:24
Alignment explanation
Indices: 3144883--3144932 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3144873 TATAATTAAT
* * *
3144883 ATATTATATTATTTAATTAAATAA
1 ATATAATATTATTAAATTAAAAAA
3144907 ATATAATA-TATTAAATTAAAAAA
1 ATATAATATTATTAAATTAAAAAA
3144930 ATA
1 ATA
3144933 ACATGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAATATTATTAAATTAAAAAA
Found at i:3146604 original size:2 final size:2
Alignment explanation
Indices: 3146592--3146621 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3146582 AGTATCTTAC
*
3146592 AT AT AT GT 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
3146622 GAAGAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3148499 original size:34 final size:33
Alignment explanation
Indices: 3148460--3148547 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 33
3148450 ATTTATATAA
3148460 ATATTATATT-TTTAAGTATTATAT-AAATCTTAAT
1 ATATTATATTATTT-A-TATTATATAAAAT-TTAAT
*
3148494 ATATTA-ATTATTTATATTATATAAAATTTATT
1 ATATTATATTATTTATATTATATAAAATTTAAT
3148526 ATATTTATATCATATTTATATT
1 ATA-TTATAT--TATTTATATT
3148548 TTTATATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
32 15 0.32
33 11 0.23
34 11 0.23
36 10 0.21
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (33 bp):
ATATTATATTATTTATATTATATAAAATTTAAT
Found at i:3148552 original size:25 final size:26
Alignment explanation
Indices: 3148449--3148580 Score: 80
Period size: 26 Copynumber: 5.0 Consensus size: 26
3148439 TTCTGCCTAT
3148449 TATTTATATAA-ATATTATATTT-TTA
1 TATTTATATAATAT-TTATATTTATTA
*
3148474 -AGTATTATATAA-ATCTTA-ATATATTAA
1 TA-T-TTATATAATAT-TTATATTTATT-A
* * *
3148501 TTATTTATATTATA-TAAAATTTATTA
1 -TATTTATATAATATTTATATTTATTA
*
3148527 TATTTATATCATATTTATATTT-TTA
1 TATTTATATAATATTTATATTTATTA
* *
3148552 TATAATATATAATATTATATATTAATTA
1 TAT-TTATATAATATT-TATATTTATTA
3148580 T
1 T
3148581 TTTTTATTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 21
0.72 0.09 0.18
Matches are distributed among these distances:
24 1 0.01
25 22 0.26
26 34 0.40
27 20 0.24
28 6 0.07
29 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (26 bp):
TATTTATATAATATTTATATTTATTA
Found at i:3148573 original size:19 final size:19
Alignment explanation
Indices: 3148492--3148600 Score: 72
Period size: 19 Copynumber: 5.9 Consensus size: 19
3148482 ATAAATCTTA
3148492 ATATATTAAT-TATTTATATT
1 ATATA-TAATATA-TTATATT
* *
3148512 ATATAAAATTTATTATATT
1 ATATATAATATATTATATT
*
3148531 -TATATCATAT-TTATATTT
1 ATATATAATATATTATA-TT
* *
3148549 TTATATAATATATAATATT
1 ATATATAATATATTATATT
3148568 ATATATTAAT-TATT-T-TT
1 ATATA-TAATATATTATATT
3148585 -TAT-TAATTATATTATA
1 ATATATAA-TATATTATA
3148601 AAAATTTCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 7 0.10
17 8 0.11
18 10 0.14
19 28 0.39
20 15 0.21
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATAATATATTATATT
Found at i:3148593 original size:4 final size:5
Alignment explanation
Indices: 3148493--3148600 Score: 63
Period size: 5 Copynumber: 22.8 Consensus size: 5
3148483 TAAATCTTAA
* * *
3148493 TATAT TA-AT TAT-T TATAT TATAT AAAAT T-TAT TATATT TATAT CATATT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATA-T
* * * *
3148542 TATAT T-T-T TATAT AATA- TATAA TAT-T ATATAT TA-AT TATTT TTTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT
3148588 TA-AT TATAT TATA
1 TATAT TATAT TATA
3148601 AAAATTTCAT
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
3 2 0.03
4 24 0.31
5 42 0.54
6 10 0.13
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3150762 original size:2 final size:2
Alignment explanation
Indices: 3150757--3150783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3150747 ACACTCAAAT
3150757 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3150784 TATCCTACCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3150824 original size:2 final size:2
Alignment explanation
Indices: 3150817--3150846 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3150807 AGTTGCTTAA
3150817 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
3150847 TTCTCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3158757 original size:26 final size:26
Alignment explanation
Indices: 3158728--3158779 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3158718 GCTTAATTTT
* *
3158728 TTATATTTTTTTATATATTTAAAATA
1 TTATATTATTATATATATTTAAAATA
* *
3158754 TTATATTATTATATATTTTTTAAATA
1 TTATATTATTATATATATTTAAAATA
3158780 AACGTCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATTATTATATATATTTAAAATA
Found at i:3167187 original size:36 final size:37
Alignment explanation
Indices: 3167146--3167227 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
3167136 CAGTTTAATT
* *
3167146 AATTTAAAGTATTATT-TAATAATAAAATTTTAATAA
1 AATTTAAAGTATAATTATAAAAATAAAATTTTAATAA
* *
3167182 AATTT-AATTATAATTATAAAAATAATATTTTAATAA
1 AATTTAAAGTATAATTATAAAAATAAAATTTTAATAA
3167218 ATATTATAAA
1 A-ATT-TAAA
3167228 TAAAAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
35 8 0.21
36 24 0.63
37 3 0.08
38 1 0.03
39 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (37 bp):
AATTTAAAGTATAATTATAAAAATAAAATTTTAATAA
Found at i:3168295 original size:30 final size:30
Alignment explanation
Indices: 3168238--3168296 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
3168228 CGAAATCAAT
* *
3168238 ATAATAAATATGATATAATATATTATAAAA
1 ATAATAAATATGATACAATATAATATAAAA
* * *
3168268 ATAATTAATATGATACATTTTAATATAAA
1 ATAATAAATATGATACAATATAATATAAA
3168297 TATTACATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (30 bp):
ATAATAAATATGATACAATATAATATAAAA
Found at i:3168457 original size:2 final size:2
Alignment explanation
Indices: 3168452--3168505 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
3168442 TCAATAAAAA
* *
3168452 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3168494 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3168506 TCCTTGGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3169351 original size:27 final size:28
Alignment explanation
Indices: 3169316--3169379 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
3169306 ATTTTAATGT
3169316 TAATAAAATTTTAAAT-AAATATGTTTA
1 TAATAAAATTTTAAATAAAATATGTTTA
*
3169343 TAATAAAA-TTTAAATAAAAATATTTTTA
1 TAATAAAATTTTAAAT-AAAATATGTTTA
*
3169371 TAATTAAAT
1 TAATAAAAT
3169380 AATAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.22
27 8 0.25
28 17 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATAAAATTTTAAATAAAATATGTTTA
Found at i:3169361 original size:11 final size:12
Alignment explanation
Indices: 3169317--3169361 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3169307 TTTTAATGTT
3169317 AATAAAATTTTA
1 AATAAAATTTTA
3169329 AATAAATATGTTTA
1 AATAAA-AT-TTTA
3169343 TAATAAAA-TTTA
1 -AATAAAATTTTA
3169355 AATAAAA
1 AATAAAA
3169362 ATATTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.23
12 10 0.33
13 2 0.07
14 5 0.17
15 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
AATAAAATTTTA
Found at i:3169373 original size:14 final size:15
Alignment explanation
Indices: 3169316--3169380 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 15
3169306 ATTTTAATGT
3169316 TAATAAA-A-TTTTA
1 TAATAAATATTTTTA
*
3169329 -AATAAATATGTTTA
1 TAATAAATATTTTTA
**
3169343 TAATAAA-ATTTAAA
1 TAATAAATATTTTTA
3169357 TAA-AAATATTTTTA
1 TAATAAATATTTTTA
3169371 TAATTAAATA
1 TAA-TAAATA
3169381 ATAAATTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 19 0.47
15 6 0.15
16 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATAAATATTTTTA
Found at i:3169409 original size:17 final size:18
Alignment explanation
Indices: 3169389--3169423 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3169379 TAATAAATTT
*
3169389 AATTTAA-TTTAATTTAA
1 AATTTAAGTTAAATTTAA
3169406 AATTTAAGTTAAATTTAA
1 AATTTAAGTTAAATTTAA
3169424 TAAACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTTAAGTTAAATTTAA
Found at i:3169421 original size:11 final size:10
Alignment explanation
Indices: 3169371--3169424 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
3169361 AATATTTTTA
3169371 TAATTAAA--
1 TAATTAAATT
3169379 TAA-TAAATT
1 TAATTAAATT
*
3169388 TAATTTAATT
1 TAATTAAATT
3169398 TAATTTAAAATT
1 TAA-TT-AAATT
3169410 TAAGTTAAATT
1 TAA-TTAAATT
3169421 TAAT
1 TAAT
3169425 AAACTAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 4 0.11
8 3 0.08
9 3 0.08
10 9 0.24
11 10 0.26
12 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TAATTAAATT
Found at i:3169733 original size:23 final size:23
Alignment explanation
Indices: 3169722--3169802 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 23
3169712 TTTTATCAAG
3169722 TTTAAA-TATTAATATTATTTAAA
1 TTTAAATTATTAA-ATTATTTAAA
*
3169745 TTTAAATTATTAAATTAATT-AA
1 TTTAAATTATTAAATTATTTAAA
* *
3169767 TTGAATAATTTATTAATTTATTTTAAA
1 TT---TAAATTATTAAATTA-TTTAAA
3169794 TTTAAATTA
1 TTTAAATTA
3169803 AGTTTAAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 12 0.26
25 13 0.28
26 2 0.04
27 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
TTTAAATTATTAAATTATTTAAA
Found at i:3169808 original size:17 final size:16
Alignment explanation
Indices: 3169700--3169819 Score: 72
Period size: 17 Copynumber: 7.3 Consensus size: 16
3169690 TAAATGGATG
3169700 AATTAATTTAAATTT-
1 AATTAATTTAAATTTA
* *
3169715 TATCAAGTTTAAATATTA
1 AATTAA-TTTAAAT-TTA
3169733 ATATT-ATTTAAATTTA
1 A-ATTAATTTAAATTTA
3169749 AATT-A-TTAAA-TT-
1 AATTAATTTAAATTTA
*
3169761 AATTAATTGAATAATTTA
1 AATTAATT-TA-AATTTA
*
3169779 TTAATTTATTTTAAATTTA
1 --AA-TTAATTTAAATTTA
*
3169798 AATTAAGTTTAAGTTTA
1 AATTAA-TTTAAATTTA
3169815 AATTA
1 AATTA
3169820 TTATTTTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
12 4 0.05
13 3 0.04
14 6 0.07
15 9 0.11
16 16 0.20
17 27 0.33
18 1 0.01
19 8 0.10
20 3 0.04
21 5 0.06
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTAATTTAAATTTA
Found at i:3172985 original size:33 final size:33
Alignment explanation
Indices: 3172939--3173006 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
3172929 GTAGCATTAG
3172939 AAAATCTAATCAATGTCTCTGCATCTTGCTCCT
1 AAAATCTAATCAATGTCTCTGCATCTTGCTCCT
* * *
3172972 AAAATCTACTCAATGTCTTTGCATCTTGTTCCT
1 AAAATCTAATCAATGTCTCTGCATCTTGCTCCT
3173005 AA
1 AA
3173007 GTACAGACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (33 bp):
AAAATCTAATCAATGTCTCTGCATCTTGCTCCT
Found at i:3175816 original size:2 final size:2
Alignment explanation
Indices: 3175811--3175840 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3175801 ATAACATGTC
*
3175811 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3175841 TTGGTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:3178564 original size:5 final size:5
Alignment explanation
Indices: 3178548--3178577 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3178538 CCACTCGAAT
3178548 ATTAA ATT-A ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
3178578 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:3183546 original size:5 final size:5
Alignment explanation
Indices: 3183536--3183562 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3183526 AAATTATTTG
3183536 TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TA
3183563 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:3183760 original size:2 final size:2
Alignment explanation
Indices: 3183753--3183783 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3183743 CTAATATACA
3183753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3183784 GCTGAAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3183919 original size:1 final size:1
Alignment explanation
Indices: 3183913--3183942 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
3183903 TTTGGAGCTC
*
3183913 TTTTTTTTTTTTTTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3183943 CCTTTAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:3184758 original size:14 final size:15
Alignment explanation
Indices: 3184733--3184777 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3184723 CAAATTGAAT
3184733 TTTAT-TTA-AAAAA
1 TTTATATTATAAAAA
3184746 TTTA-ATTATAAAAA
1 TTTATATTATAAAAA
* *
3184760 TTTATATTTTAATAA
1 TTTATATTATAAAAA
3184775 TTT
1 TTT
3184778 TAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 9 0.33
15 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATATTATAAAAA
Found at i:3184776 original size:15 final size:15
Alignment explanation
Indices: 3184730--3184777 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
3184720 ATTCAAATTG
*
3184730 AATTT-TATTTAAAA
1 AATTTATATTTTAAA
*
3184744 AATTTA-ATTATAAA
1 AATTTATATTTTAAA
*
3184758 AATTTATATTTTAAT
1 AATTTATATTTTAAA
3184773 AATTT
1 AATTT
3184778 TAAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTATATTTTAAA
Found at i:3187440 original size:44 final size:44
Alignment explanation
Indices: 3187386--3187472 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
3187376 TAATATACAC
* *
3187386 AAAATAAAAAATCGATATCTTTCCATTAAAAAGCCTAATTGTGA
1 AAAAAAAAAAATCGATATCTTTCCATTAAAAAGCCTAACTGTGA
*
3187430 AAAAAAAAAAATCGATTTCTTTCCATTAAAAAGCCTAACTGTG
1 AAAAAAAAAAATCGATATCTTTCCATTAAAAAGCCTAACTGTG
3187473 TGACATCTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (44 bp):
AAAAAAAAAAATCGATATCTTTCCATTAAAAAGCCTAACTGTGA
Found at i:3192217 original size:15 final size:15
Alignment explanation
Indices: 3192197--3192230 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3192187 TTGACCATTT
3192197 CATGCCTTTAACTTG
1 CATGCCTTTAACTTG
3192212 CATGCCTTTAACTTG
1 CATGCCTTTAACTTG
3192227 CATG
1 CATG
3192231 ATAATCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (15 bp):
CATGCCTTTAACTTG
Found at i:3198590 original size:20 final size:19
Alignment explanation
Indices: 3198567--3198615 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 19
3198557 TATAATTTTA
3198567 AAAATAATAATATTTTATTT
1 AAAATAAT-ATATTTTATTT
3198587 --AA-AATAT-TTTTATTT
1 AAAATAATATATTTTATTT
3198602 AAAATAATATATTT
1 AAAATAATATATTT
3198616 ATATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 8 0.32
16 2 0.08
17 5 0.20
18 7 0.28
19 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATAATATATTTTATTT
Found at i:3198624 original size:29 final size:29
Alignment explanation
Indices: 3198592--3198710 Score: 72
Period size: 29 Copynumber: 4.2 Consensus size: 29
3198582 TATTTAAAAT
3198592 ATTTTTATTTAAAATAATATATTTATATA
1 ATTTTTATTTAAAATAATATATTTATATA
* * *
3198621 ATTTTAAGTTTACGAATAAT-T-TTTAT-TT
1 ATTTTTA-TTTA-AAATAATATATTTATATA
* * * *
3198649 GTGTTTA--TATAAT-GTATATTTATTATA
1 ATTTTTATTTAAAATAATATATTTA-TATA
* *
3198676 ATTATAATTT-AAATAATATATTTATATA
1 ATTTTTATTTAAAATAATATATTTATATA
*
3198704 AATTTTA
1 ATTTTTA
3198711 ATATATTAAT
Statistics
Matches: 63, Mismatches: 18, Indels: 19
0.63 0.18 0.19
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 6 0.10
26 1 0.02
27 4 0.06
28 16 0.25
29 20 0.32
30 5 0.08
31 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (29 bp):
ATTTTTATTTAAAATAATATATTTATATA
Found at i:3198677 original size:16 final size:15
Alignment explanation
Indices: 3198652--3198704 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
3198642 TTTATTTGTG
3198652 TTTATATAATGTAT-A
1 TTTATATAAT-TATAA
3198667 TTTATTATAATTATAA
1 TTTA-TATAATTATAA
*
3198683 TTTAAATAA-TAT-A
1 TTTATATAATTATAA
3198696 TTTATATAA
1 TTTATATAA
3198705 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
15 11 0.32
16 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTATATAATTATAA
Found at i:3198712 original size:29 final size:31
Alignment explanation
Indices: 3198663--3198737 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
3198653 TTATATAATG
*
3198663 TATATTTAT-TATAATTATAAT-T-TAAATAA
1 TATATTTATATA-AATTTTAATATATAAATAA
*
3198692 TATATTTATATAAATTTTAATATATTAATAA
1 TATATTTATATAAATTTTAATATATAAATAA
*
3198723 T-T-TTTATATATATTT
1 TATATTTATATAAATTT
3198738 ATATAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 29 0.73
30 4 0.10
31 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATATTTATATAAATTTTAATATATAAATAA
Found at i:3198724 original size:17 final size:19
Alignment explanation
Indices: 3198689--3198754 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 19
3198679 ATAATTTAAA
3198689 TAATATATTTATATAAATTT
1 TAATATA-TTATATAAATTT
*
3198709 TAATATATTA-ATAATTTT
1 TAATATATTATATAAATTT
3198727 TATATATATTTATATAATATTT
1 TA-ATATA-TTATATAA-ATTT
3198749 TAATAT
1 TAATAT
3198755 TTTTTAATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.22
19 8 0.20
20 10 0.25
21 8 0.20
22 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATATATTATATAAATTT
Found at i:3199403 original size:2 final size:2
Alignment explanation
Indices: 3199384--3199418 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3199374 CCGTCGGATC
* *
3199384 AT AT AT AG AT AT AG AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3199419 ATTTTGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3202873 original size:9 final size:8
Alignment explanation
Indices: 3202861--3202917 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 8
3202851 TTTTTTTTTT
3202861 AATATTACA
1 AATATTA-A
3202870 AATATT-A
1 AATATTAA
3202877 AATATTAA
1 AATATTAA
3202885 AAT-TTAA
1 AATATTAA
*
3202892 ATTAATT-A
1 AAT-ATTAA
*
3202900 AATATTAT
1 AATATTAA
3202908 AAT-TTAA
1 AATATTAA
3202915 AAT
1 AAT
3202918 CATGTGACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
7 22 0.55
8 10 0.25
9 8 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATTAA
Found at i:3202893 original size:14 final size:16
Alignment explanation
Indices: 3202861--3202893 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3202851 TTTTTTTTTT
3202861 AATATTACAAATATTA
1 AATATTACAAATATTA
3202877 AATATTA-AAAT-TTA
1 AATATTACAAATATTA
3202891 AAT
1 AAT
3202894 TAATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATTACAAATATTA
Found at i:3209055 original size:14 final size:15
Alignment explanation
Indices: 3209030--3209058 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3209020 TTATAAATCA
3209030 TAAAATTTTAAATTT
1 TAAAATTTTAAATTT
3209045 TAAAA-TTTAAATTT
1 TAAAATTTTAAATTT
3209059 AATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAATTTTAAATTT
Found at i:3209209 original size:8 final size:8
Alignment explanation
Indices: 3209191--3209262 Score: 51
Period size: 8 Copynumber: 9.0 Consensus size: 8
3209181 TAATAAAAAT
3209191 TATAT-AA
1 TATATAAA
3209198 TATATAAA
1 TATATAAA
3209206 TATATAAA
1 TATATAAA
*
3209214 TATTTTATAA
1 TA-TATA-AA
* *
3209224 TTTATATA
1 TATATAAA
3209232 TA-ATAAA
1 TATATAAA
* *
3209239 -ATTTTAA
1 TATATAAA
3209246 TATATAAA
1 TATATAAA
3209254 TATAATAAA
1 TAT-ATAAA
3209263 ATAAACAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
6 1 0.02
7 12 0.24
8 22 0.45
9 11 0.22
10 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TATATAAA
Found at i:3209214 original size:24 final size:24
Alignment explanation
Indices: 3209186--3209264 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 24
3209176 TTTTTTAATA
3209186 AAAATTATATAATATATAAATATAT
1 AAAATT-TATAATATATAAATATAT
* *
3209211 AAATATTTTATAATTTATATATA-AT
1 AAA-A-TTTATAATATATAAATATAT
3209236 AAAATTT-TAATATATAAATATAAT
1 AAAATTTATAATATATAAATAT-AT
3209260 AAAAT
1 AAAAT
3209265 AAACAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
22 11 0.24
23 3 0.07
24 8 0.17
25 8 0.17
26 14 0.30
27 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTTATAATATATAAATATAT
Found at i:3209775 original size:14 final size:15
Alignment explanation
Indices: 3209750--3209778 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3209740 TGCATTAACA
3209750 AATTATTAATTAATT
1 AATTATTAATTAATT
3209765 AATTA-TAATTAATT
1 AATTATTAATTAATT
3209779 TGAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATTAATTAATT
Found at i:3209939 original size:22 final size:22
Alignment explanation
Indices: 3209888--3209941 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
3209878 TTTCAATTCA
*
3209888 AAATAAAAGATTAATTTAAGTT
1 AAATAAAAAATTAATTTAAGTT
3209910 AAATTAAAAAATT-ATTT-AGATAT
1 AAA-TAAAAAATTAATTTAAG-T-T
3209933 AAATAAAAA
1 AAATAAAAA
3209942 TATAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 14 0.50
23 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATAAAAAATTAATTTAAGTT
Found at i:3209948 original size:30 final size:30
Alignment explanation
Indices: 3209910--3210002 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
3209900 AATTTAAGTT
*
3209910 AAAT-TAAAAAATTATTTAGATATAAATAA
1 AAATATAAAAATTTATTTAGATATAAATAA
*
3209939 AAATATAAAAATTTATTTACATATAAATTAA
1 AAATATAAAAATTTATTTAGATATAAA-TAA
* *
3209970 AAGTA-AAAAATTTATTT-GAGTAT-GATAA
1 AAATATAAAAATTTATTTAGA-TATAAATAA
3209998 AAATA
1 AAATA
3210003 ATTTTTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.13
29 6 0.11
30 35 0.64
31 7 0.13
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATATAAAAATTTATTTAGATATAAATAA
Found at i:3210138 original size:13 final size:14
Alignment explanation
Indices: 3210117--3210149 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3210107 GGCCTCGTTC
*
3210117 TTTTCTCCTTTTT-
1 TTTTTTCCTTTTTA
3210130 TTTTTTCCTTTTTA
1 TTTTTTCCTTTTTA
3210144 TTTTTT
1 TTTTTT
3210150 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTCCTTTTTA
Found at i:3210154 original size:2 final size:2
Alignment explanation
Indices: 3210149--3210184 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3210139 TTTTATTTTT
3210149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3210185 GTACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3210768 original size:2 final size:2
Alignment explanation
Indices: 3210761--3210791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3210751 TATATCCGTG
3210761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3210792 TTATTATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3210914 original size:3 final size:3
Alignment explanation
Indices: 3210906--3210949 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3210896 CTACGAGGAG
3210906 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3210950 TAAACACCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3211807 original size:2 final size:2
Alignment explanation
Indices: 3211800--3211824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3211790 CTTTTAATTA
3211800 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3211825 ATCAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3212686 original size:2 final size:2
Alignment explanation
Indices: 3212679--3212704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3212669 TGGGTTTTTG
3212679 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
3212705 CATAAGGTAA
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:3213674 original size:2 final size:2
Alignment explanation
Indices: 3213667--3213695 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3213657 ATTATAGTTT
3213667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3213696 GTCATTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3214300 original size:17 final size:17
Alignment explanation
Indices: 3214278--3214325 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
3214268 TTTAATAAAT
3214278 AATTAATTATT-ATTTTA
1 AATTAATT-TTAATTTTA
3214295 AATTAATTTTAATTTT-
1 AATTAATTTTAATTTTA
*
3214311 ATTTAATATTTAATT
1 AATTAAT-TTTAATT
3214326 AATTTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTAATTTTAATTTTA
Found at i:3218500 original size:2 final size:2
Alignment explanation
Indices: 3218493--3218524 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3218483 AACTCCAAAG
3218493 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
3218525 TTCTTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3219452 original size:21 final size:21
Alignment explanation
Indices: 3219415--3219461 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3219405 AATATAATAT
*
3219415 TAAAAAATAATTAAAATA-AGA
1 TAAAAAATAACTAAAATATA-A
*
3219436 TAAAAAATAACTGAAATATAA
1 TAAAAAATAACTAAAATATAA
3219457 TAAAA
1 TAAAA
3219462 CGTAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (21 bp):
TAAAAAATAACTAAAATATAA
Found at i:3219551 original size:18 final size:18
Alignment explanation
Indices: 3219498--3219553 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
3219488 AAATGCAAAA
*
3219498 ATATTTTAAAATTTATAT
1 ATATATTAAAATTTATAT
*
3219516 A-A-AGT-AAA-TTAT-T
1 ATATATTAAAATTTATAT
3219529 AATATATTAAAATTTATAT
1 -ATATATTAAAATTTATAT
3219548 ATATAT
1 ATATAT
3219554 AACATCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 4 0.14
16 3 0.10
17 4 0.14
18 11 0.38
19 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATATTAAAATTTATAT
Found at i:3219564 original size:18 final size:16
Alignment explanation
Indices: 3219498--3219551 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3219488 AAATGCAAAA
*
3219498 ATATTTTAAAATTTAT
1 ATATATTAAAATTTAT
* * *
3219514 ATAAAGTAAATTATTA-
1 ATATATTAAAAT-TTAT
3219530 ATATATTAAAATTTAT
1 ATATATTAAAATTTAT
3219546 ATATAT
1 ATATAT
3219552 ATAACATCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATTAAAATTTAT
Found at i:3222084 original size:25 final size:26
Alignment explanation
Indices: 3222056--3222127 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 26
3222046 AATTTATTTA
*
3222056 TTTATATTATTTTTATATATTTTATTT
1 TTTATATTATTTTTAAATATTTTA-TT
*
3222083 TATTATAATTATATTTAAAATATTTTATT
1 T-TTAT-ATTAT-TTTTAAATATTTTATT
*
3222112 TTTATATTAATTTTAA
1 TTTATATTATTTTTAA
3222128 TTTATTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.13
27 5 0.13
28 8 0.21
29 8 0.21
30 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATATTATTTTTAAATATTTTATT
Found at i:3222092 original size:43 final size:46
Alignment explanation
Indices: 3222041--3222149 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
3222031 GAAATTAAAT
* *
3222041 TTAATAATTTATTTATTTATATTATTTTTATA-T-ATTTTATTTTA
1 TTAATAATTTATTTATATATATTATTTTTATATTAATTTTAATTTA
* *
3222085 TT-ATAATTATATTTAAAATATTTTATTTTTATATTAATTTTAATTTA
1 TTAATAATT-TATTT-ATATATATTATTTTTATATTAATTTTAATTTA
3222132 TTAATAATTTATATTATA
1 TTAATAATTTAT-TTATA
3222150 AAATTTTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
43 6 0.11
44 7 0.13
45 15 0.28
46 1 0.02
47 17 0.31
48 8 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (46 bp):
TTAATAATTTATTTATATATATTATTTTTATATTAATTTTAATTTA
Found at i:3222094 original size:23 final size:24
Alignment explanation
Indices: 3222052--3222096 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3222042 TAATAATTTA
**
3222052 TTTATTTATATTATTTTTATATAT
1 TTTATTTATATTATAATTATATAT
3222076 TTTATTT-TATTATAATTATAT
1 TTTATTTATATTATAATTATAT
3222097 TTAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTATTTATATTATAATTATATAT
Found at i:3222117 original size:45 final size:50
Alignment explanation
Indices: 3222062--3222153 Score: 140
Period size: 47 Copynumber: 1.9 Consensus size: 50
3222052 TTTATTTATA
*
3222062 TTATTTTTATA-T-ATTTTATTTTATT-ATAA-TTATATT-TAAAATATT
1 TTATTTTTATATTAATTTTAATTTATTAATAATTTATATTATAAAATATT
3222107 TTATTTTTATATTAATTTTAATTTATTAATAATTTATATTATAAAAT
1 TTATTTTTATATTAATTTTAATTTATTAATAATTTATATTATAAAAT
3222154 TTTAATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 11 0.27
46 1 0.02
47 12 0.29
48 4 0.10
49 7 0.17
50 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (50 bp):
TTATTTTTATATTAATTTTAATTTATTAATAATTTATATTATAAAATATT
Found at i:3222187 original size:31 final size:30
Alignment explanation
Indices: 3222057--3222188 Score: 91
Period size: 31 Copynumber: 4.4 Consensus size: 30
3222047 ATTTATTTAT
* *
3222057 TTATATTATTTT--TATATATTTTATTTTA
1 TTATATTATTTTAATATATATTTTAATATA
*
3222085 TTATAATTATATTTAA-A-ATATTTT-AT-TT
1 TTAT-ATTAT-TTTAATATATATTTTAATATA
*
3222113 TTATATTAATTTTAAT-T-TATTAATAATTTATA
1 TTATATT-ATTTTAATATATATT-TTAA--TATA
**
3222145 TTATAAAATTTTAATATATATTTTTAATATA
1 TTATATTATTTTAATATATA-TTTTAATATA
3222176 TTATATTATTTTA
1 TTATATTATTTTA
3222189 TATTTAAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
27 12 0.15
28 12 0.15
29 7 0.09
30 10 0.12
31 25 0.31
32 7 0.09
33 5 0.06
34 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATATTATTTTAATATATATTTTAATATA
Found at i:3222190 original size:15 final size:15
Alignment explanation
Indices: 3222052--3222192 Score: 61
Period size: 15 Copynumber: 9.5 Consensus size: 15
3222042 TAATAATTTA
3222052 TTTAT-TTATATTAT
1 TTTATATTATATTAT
3222066 TTT-TA-TATATT-T
1 TTTATATTATATTAT
*
3222078 TATTTTATTATAATTAT
1 T-TTATATTAT-ATTAT
* * *
3222095 ATTTAAAATATTTTATT
1 -TTTATATTATATTA-T
3222112 TTTATATTA-ATT-T
1 TTTATATTATATTAT
*
3222125 TAATT-TATTA-A-TAA
1 T--TTATATTATATTAT
**
3222139 TTTATATTATAAAAT
1 TTTATATTATATTAT
3222154 TTTA-ATATATATT-T
1 TTTATAT-TATATTAT
3222168 TTAATATATTATATTAT
1 TT--TATATTATATTAT
3222185 TTTATATT
1 TTTATATT
3222193 TAAAATTATC
Statistics
Matches: 96, Mismatches: 12, Indels: 37
0.66 0.08 0.26
Matches are distributed among these distances:
12 4 0.04
13 17 0.18
14 18 0.19
15 22 0.23
16 21 0.22
17 13 0.14
18 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTATATTAT
Found at i:3222472 original size:17 final size:18
Alignment explanation
Indices: 3222450--3222486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3222440 GTTGAAAGTT
3222450 ATAATT-TAAAAATTAAA
1 ATAATTATAAAAATTAAA
*
3222467 ATAATTATAAATATTAAA
1 ATAATTATAAAAATTAAA
3222485 AT
1 AT
3222487 TAAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTATAAAAATTAAA
Found at i:3223011 original size:2 final size:2
Alignment explanation
Indices: 3223004--3223038 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3222994 ATTATTATTT
3223004 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3223039 GATTTGGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3224849 original size:2 final size:2
Alignment explanation
Indices: 3224842--3224874 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3224832 TTTTGAAGTT
3224842 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3224875 GGAGTACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3225985 original size:24 final size:24
Alignment explanation
Indices: 3225938--3225987 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
3225928 TTATAATTTT
3225938 TTTAAAAAAATTAATATAATTAAA
1 TTTAAAAAAATTAATATAATTAAA
*
3225962 TTTAAAATAAA-TATATATAATAAAA
1 TTTAAAA-AAATTA-ATATAATTAAA
3225987 T
1 T
3225988 AATATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTAAAAAAATTAATATAATTAAA
Found at i:3235754 original size:16 final size:16
Alignment explanation
Indices: 3235733--3235764 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3235723 TTGTTTCCAG
3235733 GCAGAAAAAAAAAAAC
1 GCAGAAAAAAAAAAAC
*
3235749 GCAGAAAGAAAAAAAC
1 GCAGAAAAAAAAAAAC
3235765 CAGGCTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (16 bp):
GCAGAAAAAAAAAAAC
Found at i:3237916 original size:8 final size:8
Alignment explanation
Indices: 3237905--3237935 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3237895 TTTAAAAGGG
3237905 GAAAAGAA
1 GAAAAGAA
*
3237913 GAAAAGAC
1 GAAAAGAA
3237921 GAAAAGAA
1 GAAAAGAA
3237929 GAAAAGA
1 GAAAAGA
3237936 CAAGACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (8 bp):
GAAAAGAA
Found at i:3237924 original size:16 final size:16
Alignment explanation
Indices: 3237905--3237936 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3237895 TTTAAAAGGG
3237905 GAAAAGAAGAAAAGAC
1 GAAAAGAAGAAAAGAC
3237921 GAAAAGAAGAAAAGAC
1 GAAAAGAAGAAAAGAC
3237937 AAGACAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.25, T:0.00
Consensus pattern (16 bp):
GAAAAGAAGAAAAGAC
Found at i:3238658 original size:33 final size:33
Alignment explanation
Indices: 3238616--3238683 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3238606 ACAAAAGTCT
3238616 CTATTGTCAACATAAAACTATCAGAAACTTTCA
1 CTATTGTCAACATAAAACTATCAGAAACTTTCA
3238649 CTATTGTCAACATAAAACTATCAGAAACTTTCA
1 CTATTGTCAACATAAAACTATCAGAAACTTTCA
3238682 CT
1 CT
3238684 TACTTCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (33 bp):
CTATTGTCAACATAAAACTATCAGAAACTTTCA
Found at i:3239799 original size:21 final size:22
Alignment explanation
Indices: 3239775--3239832 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3239765 AAATAAAATA
*
3239775 TATGATATAATTA-ATTTTATT
1 TATGAAATAATTATATTTTATT
**
3239796 TATGAAATTTTTATATTTTATT
1 TATGAAATAATTATATTTTATT
3239818 TA--ATAATAATTATAT
1 TATGA-AATAATTATAT
3239833 GTATTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 19 0.63
22 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
TATGAAATAATTATATTTTATT
Found at i:3239962 original size:16 final size:16
Alignment explanation
Indices: 3239931--3239965 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3239921 GAATTAATAA
3239931 ATAATTAGTTATTTAT
1 ATAATTAGTTATTTAT
3239947 ATAATATAGTTA-TTAT
1 ATAAT-TAGTTATTTAT
3239963 ATA
1 ATA
3239966 TTTAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
ATAATTAGTTATTTAT
Found at i:3240412 original size:2 final size:2
Alignment explanation
Indices: 3240405--3240440 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3240395 AGTTTTGTAC
3240405 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
3240441 CACTTGCATG
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:3251555 original size:21 final size:21
Alignment explanation
Indices: 3251529--3251579 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3251519 TATAAAACTT
3251529 TGCAGACATGCACTGAACAAG
1 TGCAGACATGCACTGAACAAG
3251550 TGCAGACATGCACTGAACAAG
1 TGCAGACATGCACTGAACAAG
*
3251571 TACAGACAT
1 TGCAGACAT
3251580 TCAATCATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (21 bp):
TGCAGACATGCACTGAACAAG
Found at i:3255627 original size:16 final size:19
Alignment explanation
Indices: 3255606--3255644 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3255596 TATAATTATT
3255606 TAAT-AAAA-TTAATA-TA
1 TAATAAAAATTTAATACTA
3255622 TAATAAAAATTTAATACTA
1 TAATAAAAATTTAATACTA
3255641 TAAT
1 TAAT
3255645 TTGATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 6 0.30
19 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAAAAATTTAATACTA
Found at i:3261499 original size:28 final size:28
Alignment explanation
Indices: 3261453--3261526 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
3261443 TGAATTAATT
3261453 TTTTAATTAAATT-TA-ATTAAAAAATAA
1 TTTTAATT-AATTATATATTAAAAAATAA
* * *
3261480 TTTT-ATTATTTATCATATTAAAATATCA
1 TTTTAATTAATTAT-ATATTAAAAAATAA
3261508 TTTTAATTAATTATATATT
1 TTTTAATTAATTATATATT
3261527 TTCTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.08
26 4 0.10
27 5 0.13
28 19 0.49
29 8 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTAATTAATTATATATTAAAAAATAA
Found at i:3263267 original size:17 final size:17
Alignment explanation
Indices: 3263245--3263279 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3263235 GGACACGAAT
3263245 ATATATATGATAGGGTC
1 ATATATATGATAGGGTC
3263262 ATATATATGATAGGGTC
1 ATATATATGATAGGGTC
3263279 A
1 A
3263280 ATTTAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (17 bp):
ATATATATGATAGGGTC
Found at i:3264670 original size:4 final size:4
Alignment explanation
Indices: 3264661--3264691 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
3264651 AAACGGAGTA
3264661 TATG TATG TATG TATG TATG TATG TAATG TA
1 TATG TATG TATG TATG TATG TATG T-ATG TA
3264692 CCAGCAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:3266055 original size:16 final size:16
Alignment explanation
Indices: 3266034--3266066 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3266024 TTTTTTATAT
3266034 ATTTTTA-ATGATTAAA
1 ATTTTTATAT-ATTAAA
3266050 ATTTTTATATATTAAA
1 ATTTTTATATATTAAA
3266066 A
1 A
3266067 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTTTATATATTAAA
Found at i:3268641 original size:18 final size:19
Alignment explanation
Indices: 3268615--3268663 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
3268605 TTTATTTAAA
3268615 ATAT-TATTTTTTATATATT
1 ATATATATTTTTT-TATATT
*
3268634 A-ATA-ATTTATTTTATTTT
1 ATATATATTT-TTTTATATT
3268652 ATATATATTTTT
1 ATATATATTTTT
3268664 ATAAGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 12 0.48
19 9 0.36
20 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATATATTTTTTTATATT
Found at i:3268660 original size:11 final size:11
Alignment explanation
Indices: 3268646--3268731 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
3268636 TAATTTATTT
3268646 TATTTTATATA
1 TATTTTATATA
3268657 TATTTT-TATA
1 TATTTTATATA
* * *
3268667 -AGTATATGTA
1 TATTTTATATA
*
3268677 TATTATGTACATA
1 TATT-T-TATATA
3268690 TCATTTTTATATTA
1 T-A-TTTTATA-TA
*
3268704 TATTTTAAATA
1 TATTTTATATA
* *
3268715 TTTTTTATAAA
1 TATTTTATATA
3268726 TATTTT
1 TATTTT
3268732 GTTTATTTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
9 3 0.05
10 7 0.13
11 23 0.42
12 6 0.11
13 9 0.16
14 5 0.09
15 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (11 bp):
TATTTTATATA
Found at i:3270214 original size:27 final size:29
Alignment explanation
Indices: 3270184--3270248 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 29
3270174 TATATTCAAG
3270184 TTATATTTAT-ATTATTTTT-ATATCATA
1 TTATATTTATAATTATTTTTCATATCATA
*
3270211 TTATATTT-TAATTATTTTTCATATTATA
1 TTATATTTATAATTATTTTTCATATCATA
3270239 TT-TATGTTAT
1 TTATAT-TTAT
3270249 GTCTTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.03
27 20 0.61
28 11 0.33
29 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (29 bp):
TTATATTTATAATTATTTTTCATATCATA
Found at i:3270358 original size:16 final size:16
Alignment explanation
Indices: 3270331--3270371 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3270321 ATTTTAAAAT
3270331 AAATTTTA-TTAATTA
1 AAATTTTATTTAATTA
*
3270346 TAATTTTATTTAATTA
1 AAATTTTATTTAATTA
3270362 AATATTTTAT
1 AA-ATTTTAT
3270372 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTTTATTTAATTA
Found at i:3270518 original size:16 final size:16
Alignment explanation
Indices: 3270507--3270574 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 16
3270497 AAAAAAGTAG
3270507 AAAGG-AAGAAAAGAA
1 AAAGGAAAGAAAAGAA
3270522 AAAGGAAAGAAAGAGAA
1 AAAGGAAAGAAA-AGAA
*
3270539 GAAAAGAAA-ACAAAGGAA
1 -AAAGGAAAGA-AAA-GAA
**
3270557 AAAGG-GGGAAAAGAA
1 AAAGGAAAGAAAAGAA
3270572 AAA
1 AAA
3270575 AAAAAGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.26
16 9 0.21
17 11 0.26
18 12 0.28
ACGTcount: A:0.71, C:0.01, G:0.28, T:0.00
Consensus pattern (16 bp):
AAAGGAAAGAAAAGAA
Found at i:3270527 original size:15 final size:15
Alignment explanation
Indices: 3270507--3270574 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 15
3270497 AAAAAAGTAG
3270507 AAAGGAAGAAAAGAA
1 AAAGGAAGAAAAGAA
3270522 AAAGGAAAGAAAGAGAA
1 AAAGG-AAGAAA-AGAA
* *
3270539 GAAAAGAAAACAAAGGAA
1 -AAAGGAAGA-AAA-GAA
**
3270557 AAAGGGGGAAAAGAA
1 AAAGGAAGAAAAGAA
3270572 AAA
1 AAA
3270575 AAAAAGAGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
15 11 0.26
16 9 0.21
17 13 0.31
18 9 0.21
ACGTcount: A:0.71, C:0.01, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGGAAGAAAAGAA
Found at i:3270529 original size:20 final size:20
Alignment explanation
Indices: 3270506--3270543 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3270496 AAAAAAAGTA
*
3270506 GAAAGGAAGAAAAGAAAAAG
1 GAAAGAAAGAAAAGAAAAAG
*
3270526 GAAAGAAAGAGAAGAAAA
1 GAAAGAAAGAAAAGAAAA
3270544 GAAAACAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAAGAAAAAG
Found at i:3270805 original size:75 final size:74
Alignment explanation
Indices: 3270726--3270863 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 74
3270716 GTTTATGTTG
* * * * *
3270726 TATTTGAATTCATCATATTTTTTATATAATTTGTTAT-TATG-TTTCAATTTAGAAAAATTTATA
1 TATTTCAATTCATAATATATTTTACATAATTTGTTATAT-TGATTT-AATTTA-AAAAAATTATA
3270789 TGTTCATACTTA
63 TGTTCATACTTA
* *
3270801 TATTTCAATTTATAATATATTTTACATGATTTGTTATATTGATTTAATTTAAAAAAATTATAT
1 TATTTCAATTCATAATATATTTTACATAATTTGTTATATTGATTTAATTTAAAAAAATTATAT
3270864 TCGTGTTCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
74 11 0.20
75 39 0.72
76 4 0.07
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (74 bp):
TATTTCAATTCATAATATATTTTACATAATTTGTTATATTGATTTAATTTAAAAAAATTATATGT
TCATACTTA
Found at i:3271385 original size:13 final size:13
Alignment explanation
Indices: 3271367--3271392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3271357 TAAAATAAAA
3271367 TTAAATAAATTAT
1 TTAAATAAATTAT
3271380 TTAAATAAATTAT
1 TTAAATAAATTAT
3271393 AATTATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATAAATTAT
Found at i:3272447 original size:2 final size:2
Alignment explanation
Indices: 3272440--3272467 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3272430 AAACTGTTGA
3272440 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
3272468 GGAAGAAAGA
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:3277725 original size:2 final size:2
Alignment explanation
Indices: 3277718--3277742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3277708 CTGAACCAAA
3277718 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3277743 AAATTTCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3278899 original size:28 final size:28
Alignment explanation
Indices: 3278863--3278918 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3278853 TTATTTTTAA
3278863 AAATAAATATAAATAAATTCTTTAAATTT
1 AAATAAATATAAATAAATT-TTTAAATTT
* *
3278892 AAAT-AATATATATATATTTTTAAATTT
1 AAATAAATATAAATAAATTTTTAAATTT
3278919 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATAAATATAAATAAATTTTTAAATTT
Found at i:3279085 original size:11 final size:11
Alignment explanation
Indices: 3279034--3279097 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 11
3279024 TAAAATTAAA
3279034 TTTTAAATTTAT
1 TTTTAAA-TTAT
3279046 TATTCTAAA-TAT
1 T-TT-TAAATTAT
*
3279058 ATTTAAATTA-
1 TTTTAAATTAT
*
3279068 ATTTAAATTAT
1 TTTTAAATTAT
3279079 TTTTAAA-TAT
1 TTTTAAATTAT
3279089 TTATTAAAT
1 TT-TTAAAT
3279098 AAATTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 19 0.43
11 15 0.34
12 4 0.09
13 2 0.05
14 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAATTAT
Found at i:3283372 original size:17 final size:18
Alignment explanation
Indices: 3283339--3283372 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3283329 ATTTAATTCA
*
3283339 AAAATTAATTAATTAATT
1 AAAATAAATTAATTAATT
3283357 AAAATAAATT-ATTAAT
1 AAAATAAATTAATTAAT
3283373 ATTTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAAATTAATTAATT
Found at i:3283480 original size:18 final size:19
Alignment explanation
Indices: 3283444--3283482 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3283434 TAATACAATA
3283444 AAAATATAAAAATATTTTT
1 AAAATATAAAAATATTTTT
3283463 AAAATA-AAATAA-ATTTTT
1 AAAATATAAA-AATATTTTT
3283481 AA
1 AA
3283483 TATTTTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATAAAAATATTTTT
Found at i:3291174 original size:3 final size:3
Alignment explanation
Indices: 3291166--3291194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3291156 TAACTTCCAA
3291166 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3291195 AGAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3295136 original size:2 final size:2
Alignment explanation
Indices: 3295129--3295170 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3295119 TTCAAATGCA
3295129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3295171 TAGCTTCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3302036 original size:6 final size:6
Alignment explanation
Indices: 3302025--3302050 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3302015 TAGAAACTTC
3302025 CCCAAT CCCAAT CCCAAT CCCAAT CC
1 CCCAAT CCCAAT CCCAAT CCCAAT CC
3302051 TTGTAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCAAT
Found at i:3303978 original size:13 final size:14
Alignment explanation
Indices: 3303962--3303991 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3303952 TTTCAATAAC
3303962 AAAAAAAAAAA-AG
1 AAAAAAAAAAAGAG
3303975 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
3303989 AAA
1 AAA
3303992 TTGATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:3303980 original size:12 final size:12
Alignment explanation
Indices: 3303963--3303987 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3303953 TTCAATAACA
3303963 AAAAAAAAAAAG
1 AAAAAAAAAAAG
3303975 AAAAAAAAAAAG
1 AAAAAAAAAAAG
3303987 A
1 A
3303988 GAAATTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:3303981 original size:14 final size:14
Alignment explanation
Indices: 3303962--3303991 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3303952 TTTCAATAAC
3303962 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
3303976 AAAAAAAAAAGAGA
1 AAAAAAAAAAAAGA
3303990 AA
1 AA
3303992 TTGATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:3306049 original size:2 final size:2
Alignment explanation
Indices: 3306042--3306072 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3306032 ATACTTTAAG
3306042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3306073 TTGCAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3311544 original size:12 final size:12
Alignment explanation
Indices: 3311527--3311551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3311517 ATATATATAT
3311527 TTTATAATTAAA
1 TTTATAATTAAA
3311539 TTTATAATTAAA
1 TTTATAATTAAA
3311551 T
1 T
3311552 ATTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTATAATTAAA
Found at i:3311560 original size:14 final size:14
Alignment explanation
Indices: 3311508--3311561 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
3311498 ATTAAAAAAT
*
3311508 ATATTTTTAATATAT
1 ATATTTTTAAT-TAA
3311523 ATATTTTATAATT-A
1 ATATTTT-TAATTAA
*
3311537 A-ATTTATAATTAA
1 ATATTTTTAATTAA
3311550 ATATTTTTAATT
1 ATATTTTTAATT
3311562 TATTTCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 6 0.18
14 10 0.30
15 8 0.24
16 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTTTTAATTAA
Done.