Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 14 of 138
Found at i:4025233 original size:30 final size:30
Alignment explanation
Indices: 4025197--4025253 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4025187 CGAAATTAAT
* *
4025197 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATATTTA
*
4025227 AAAATATTATTATATAAATATATATAT
1 AAAATATTATTATATAAATATAAATAT
4025254 AAATAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATATTTA
Found at i:4026379 original size:2 final size:2
Alignment explanation
Indices: 4026374--4026399 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4026364 ACACAGATAG
4026374 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
4026400 TGCTAATTGA
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):
AT
Found at i:4029518 original size:31 final size:31
Alignment explanation
Indices: 4029483--4029545 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4029473 AAAGAATTTT
4029483 GGGTGTGGTTGGTAAAGAATTGAATATAGAA
1 GGGTGTGGTTGGTAAAGAATTGAATATAGAA
4029514 GGGTGTGGTTGGTAAAGAATTGAATATAGAA
1 GGGTGTGGTTGGTAAAGAATTGAATATAGAA
4029545 G
1 G
4029546 CTATCTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.29
Consensus pattern (31 bp):
GGGTGTGGTTGGTAAAGAATTGAATATAGAA
Found at i:4030056 original size:17 final size:17
Alignment explanation
Indices: 4029997--4030056 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
4029987 TTATTATTTG
*
4029997 TGTTAATCACATAATAA
1 TGTTAATTACATAATAA
** *
4030014 TGTTAATTATGTTAATCA
1 TGTTAATTA-CATAATAA
* *
4030032 TGCT-ATTACATAATGA
1 TGTTAATTACATAATAA
4030048 TGTTAATTA
1 TGTTAATTA
4030057 TGTTGGTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
16 8 0.25
17 16 0.50
18 8 0.25
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (17 bp):
TGTTAATTACATAATAA
Found at i:4033603 original size:20 final size:21
Alignment explanation
Indices: 4033578--4033623 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4033568 AATTATAAAA
* *
4033578 GGATACCAG-TTTATTGTTTT
1 GGATACAAGTTTTATTGTTTG
4033598 GGATACAAGTTTTATTGTTTG
1 GGATACAAGTTTTATTGTTTG
4033619 GGATA
1 GGATA
4033624 AAGCTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (21 bp):
GGATACAAGTTTTATTGTTTG
Found at i:4033633 original size:21 final size:21
Alignment explanation
Indices: 4033578--4033633 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
4033568 AATTATAAAA
* *
4033578 GGATACCAGT-TTATTGTTTT
1 GGATACAAGTCTTATTGTTTG
*
4033598 GGATACAAGTTTTATTGTTTG
1 GGATACAAGTCTTATTGTTTG
4033619 GGATA-AAGCTCTTAT
1 GGATACAAG-TCTTAT
4033634 GATGCATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (21 bp):
GGATACAAGTCTTATTGTTTG
Found at i:4046513 original size:12 final size:12
Alignment explanation
Indices: 4046496--4046520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4046486 AACCTTAGAG
4046496 ATTAATGTGTGT
1 ATTAATGTGTGT
4046508 ATTAATGTGTGT
1 ATTAATGTGTGT
4046520 A
1 A
4046521 GACATCCTAT
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (12 bp):
ATTAATGTGTGT
Found at i:4048106 original size:25 final size:24
Alignment explanation
Indices: 4048078--4048132 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
4048068 TTGTTTTTGG
* *
4048078 TATTTTCTTTTCTTATTTATTTA-TT
1 TATTTTATTTACTTA-TT-TTTAGTT
4048103 TATTTTATTTACTTATTTTTAGTT
1 TATTTTATTTACTTATTTTTAGTT
4048127 TATTTT
1 TATTTT
4048133 GAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 10 0.37
25 13 0.48
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (24 bp):
TATTTTATTTACTTATTTTTAGTT
Found at i:4048475 original size:17 final size:17
Alignment explanation
Indices: 4048430--4048475 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4048420 TTCCCAAATT
4048430 AAAAATTGAAAATTAAAA
1 AAAAATT-AAAATTAAAA
** *
4048448 AAACCTAAAAATTAAAA
1 AAAAATTAAAATTAAAA
4048465 AAAAATTAAAA
1 AAAAATTAAAA
4048476 ATATAACTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATTAAAATTAAAA
Found at i:4048562 original size:16 final size:18
Alignment explanation
Indices: 4048527--4048566 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4048517 AAGAGACTAA
*
4048527 ATTTTTTTAGTTTAGTTT
1 ATTTTTTTAGTTTAGATT
4048545 ATTTTTTTA-TTTA-ATT
1 ATTTTTTTAGTTTAGATT
4048561 ATTTTT
1 ATTTTT
4048567 ATCATCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (18 bp):
ATTTTTTTAGTTTAGATT
Found at i:4048641 original size:11 final size:11
Alignment explanation
Indices: 4048627--4048656 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4048617 TTTAAAAATT
4048627 TTATAAAATAA
1 TTATAAAATAA
4048638 TTATAAAATAA
1 TTATAAAATAA
*
4048649 TAATAAAA
1 TTATAAAA
4048657 AAGTACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TTATAAAATAA
Found at i:4050865 original size:20 final size:20
Alignment explanation
Indices: 4050840--4050877 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4050830 TAAACACCAG
4050840 TATACCTACAAACCCAAACT
1 TATACCTACAAACCCAAACT
4050860 TATACCTACAAACCCAAA
1 TATACCTACAAACCCAAA
4050878 ATCAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.18
Consensus pattern (20 bp):
TATACCTACAAACCCAAACT
Found at i:4053705 original size:37 final size:39
Alignment explanation
Indices: 4053637--4053721 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 39
4053627 ATTGAATCAT
* *
4053637 TATTTTTAAAATTATATTAAATTAAAATTTTATAAAATA
1 TATTTTTAAAATTATATGAAATTAAAATTTTACAAAATA
* * *
4053676 TATTTTTAAAATT-T-TGAAATTCAAATTTTACAAATTT
1 TATTTTTAAAATTATATGAAATTAAAATTTTACAAAATA
4053713 TATTTTTAA
1 TATTTTTAA
4053722 TTTTATAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 27 0.66
38 1 0.02
39 13 0.32
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (39 bp):
TATTTTTAAAATTATATGAAATTAAAATTTTACAAAATA
Found at i:4055024 original size:8 final size:8
Alignment explanation
Indices: 4055004--4055035 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4054994 AATATAAGTG
4055004 ATTTATAT
1 ATTTATAT
4055012 A--TATAT
1 ATTTATAT
4055018 ATTTATAT
1 ATTTATAT
4055026 ATTTATAT
1 ATTTATAT
4055034 AT
1 AT
4055036 ATACAAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:4058779 original size:15 final size:15
Alignment explanation
Indices: 4058759--4058789 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4058749 ACATCTAGGC
4058759 AAAACTTTAAAGATA
1 AAAACTTTAAAGATA
4058774 AAAACTTTAAAGATA
1 AAAACTTTAAAGATA
4058789 A
1 A
4058790 TTTTTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAACTTTAAAGATA
Found at i:4059557 original size:16 final size:16
Alignment explanation
Indices: 4059452--4059559 Score: 53
Period size: 16 Copynumber: 6.9 Consensus size: 16
4059442 AGTTTTAGGA
* *
4059452 TTTTGAGGTTTT-AGG
1 TTTTAAGGTTTTGAGT
* ** *
4059467 TTTTAGGGTTTCAAGA
1 TTTTAAGGTTTTGAGT
*
4059483 TTTTAAGGTTTTGAAT
1 TTTTAAGGTTTTGAGT
* *
4059499 GTTTATGGTTTTGAAG-
1 TTTTAAGGTTTTG-AGT
* *
4059515 TTTCAAGGTTTCGAGAT
1 TTTTAAGGTTTTGAG-T
* *
4059532 TTATCA--TTTTGAGT
1 TTTTAAGGTTTTGAGT
4059546 TTTTAAGGTTTTGA
1 TTTTAAGGTTTTGA
4059560 AATTTTTTTC
Statistics
Matches: 65, Mismatches: 22, Indels: 11
0.66 0.22 0.11
Matches are distributed among these distances:
14 5 0.08
15 17 0.26
16 39 0.60
17 4 0.06
ACGTcount: A:0.21, C:0.04, G:0.24, T:0.51
Consensus pattern (16 bp):
TTTTAAGGTTTTGAGT
Found at i:4059565 original size:16 final size:16
Alignment explanation
Indices: 4059482--4059565 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
4059472 GGGTTTCAAG
4059482 ATTTTAAGGTTTTG-A
1 ATTTTAAGGTTTTGAA
*
4059497 ATGTTTATGGTTTTGAA
1 AT-TTTAAGGTTTTGAA
* * * *
4059514 GTTTCAAGGTTTCGAG
1 ATTTTAAGGTTTTGAA
* *
4059530 ATTTATCA--TTTTGAG
1 ATTT-TAAGGTTTTGAA
*
4059545 TTTTTAAGGTTTTGAA
1 ATTTTAAGGTTTTGAA
4059561 ATTTT
1 ATTTT
4059566 TTTCTTATGA
Statistics
Matches: 50, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
14 2 0.04
15 11 0.22
16 34 0.68
17 3 0.06
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (16 bp):
ATTTTAAGGTTTTGAA
Found at i:4061114 original size:19 final size:18
Alignment explanation
Indices: 4061087--4061131 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4061077 TTGGTCCGTC
*
4061087 TTCTATGGTCAATTTTTTT
1 TTCTTTGGT-AATTTTTTT
*
4061106 TTCTTTGGTTATTTTTTT
1 TTCTTTGGTAATTTTTTT
*
4061124 TTTTTTGG
1 TTCTTTGG
4061132 GTTCAATCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.71
Consensus pattern (18 bp):
TTCTTTGGTAATTTTTTT
Found at i:4072996 original size:12 final size:12
Alignment explanation
Indices: 4072949--4073000 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
4072939 AGAAGAAGAA
*
4072949 GATGGTGATTTG
1 GATGGTGATATG
*
4072961 GATGGTGATTTG
1 GATGGTGATATG
*
4072973 GACGGTGATATG
1 GATGGTGATATG
*
4072985 GATGGTGCTATG
1 GATGGTGATATG
4072997 GATG
1 GATG
4073001 AGCCTGACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.19, C:0.04, G:0.42, T:0.35
Consensus pattern (12 bp):
GATGGTGATATG
Found at i:4080212 original size:2 final size:2
Alignment explanation
Indices: 4080205--4080232 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4080195 CACAAAATCA
4080205 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
4080233 TTCATGCTTA
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:4083858 original size:39 final size:39
Alignment explanation
Indices: 4083814--4083889 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
4083804 TTCATGTTAG
4083814 AGGATCTAGTTAGATGTTTTGAACT-TGAAAGAGAGTTGA
1 AGGATCTAGTTAGATGTTTTGAA-TGTGAAAGAGAGTTGA
* *
4083853 AGGATCTAGTTTGATGTTTTGGATGTGAAAGAGAGTT
1 AGGATCTAGTTAGATGTTTTGAATGTGAAAGAGAGTT
4083890 TGAGAAGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (39 bp):
AGGATCTAGTTAGATGTTTTGAATGTGAAAGAGAGTTGA
Found at i:4094699 original size:7 final size:7
Alignment explanation
Indices: 4094687--4094712 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4094677 CTTTGGGAGC
4094687 GATTAGT
1 GATTAGT
4094694 GATTAGT
1 GATTAGT
4094701 GATTAGT
1 GATTAGT
4094708 GATTA
1 GATTA
4094713 CCGTTTCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
GATTAGT
Found at i:4102753 original size:12 final size:12
Alignment explanation
Indices: 4102736--4102760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4102726 GTAATGGGAT
4102736 TCAATAATTCAA
1 TCAATAATTCAA
4102748 TCAATAATTCAA
1 TCAATAATTCAA
4102760 T
1 T
4102761 GATATACTTA
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:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAATAATTCAA
Found at i:4103639 original size:5 final size:6
Alignment explanation
Indices: 4103612--4103636 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4103602 AAGTTATAAT
4103612 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
4103637 GAAGGGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:4105195 original size:26 final size:26
Alignment explanation
Indices: 4105163--4105214 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4105153 TCAAATAAAA
* *
4105163 ATTTTTAATGAATCATTTAAGTTGAAT
1 ATTTTAAAT-AATCATTTAAATTGAAT
*
4105190 ATTTTAAATAATTATTTAAATTGAA
1 ATTTTAAATAATCATTTAAATTGAA
4105215 ATCAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (26 bp):
ATTTTAAATAATCATTTAAATTGAAT
Found at i:4105243 original size:18 final size:18
Alignment explanation
Indices: 4105222--4105258 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4105212 GAAATCAAAA
*
4105222 TTTATATAATATTTAAAT
1 TTTATATAAAATTTAAAT
4105240 TTTATATAAAATTTAAAT
1 TTTATATAAAATTTAAAT
4105258 T
1 T
4105259 CAAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATATAAAATTTAAAT
Found at i:4105250 original size:29 final size:30
Alignment explanation
Indices: 4105192--4105257 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
4105182 AGTTGAATAT
4105192 TTTAAATAATTATTTAAATTGAAATCAAAA
1 TTTAAATAATTATTTAAATTGAAATCAAAA
* * *
4105222 TTTATATAA-TATTTAAATTTTATAT-AAAA
1 TTTAAATAATTATTTAAA-TTGAAATCAAAA
4105251 TTTAAAT
1 TTTAAAT
4105258 TCAAATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTAAATAATTATTTAAATTGAAATCAAAA
Found at i:4105859 original size:17 final size:18
Alignment explanation
Indices: 4105839--4105879 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
4105829 ATATTCTTTA
*
4105839 TTTTATTTTATTATA-TT
1 TTTTATTTTATTAAATTT
4105856 TTTTA--TTATTAAATTT
1 TTTTATTTTATTAAATTT
4105872 TTTTATTT
1 TTTTATTT
4105880 ACAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 7 0.35
16 7 0.35
17 5 0.25
18 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTAAATTT
Found at i:4105982 original size:18 final size:19
Alignment explanation
Indices: 4105950--4105987 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4105940 TAATTATGTT
4105950 AAAAATAATTAAAAATAAA
1 AAAAATAATTAAAAATAAA
*
4105969 AAAAAT-ATTTAAAATAAA
1 AAAAATAATTAAAAATAAA
4105987 A
1 A
4105988 TTTTAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATAATTAAAAATAAA
Found at i:4106340 original size:21 final size:21
Alignment explanation
Indices: 4106311--4106357 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4106301 TTAACAAATA
* * * *
4106311 AATTGAAGAAAATATTTTTTT
1 AATTAAAGAAAAAAATTTTAT
4106332 AATTAAAGAAAAAAATTTTAT
1 AATTAAAGAAAAAAATTTTAT
4106353 AATTA
1 AATTA
4106358 TTGAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
AATTAAAGAAAAAAATTTTAT
Found at i:4106363 original size:21 final size:23
Alignment explanation
Indices: 4106312--4106364 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
4106302 TAACAAATAA
*
4106312 ATTGAAGAAAATATTTTTTTAATT
1 ATTGAA-AAAATATTTTTATAATT
**
4106336 AAAGAAAAAA-A-TTTTATAATT
1 ATTGAAAAAATATTTTTATAATT
4106357 ATTGAAAA
1 ATTGAAAA
4106365 TTTATAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 4 0.17
24 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTGAAAAAATATTTTTATAATT
Found at i:4111294 original size:18 final size:18
Alignment explanation
Indices: 4111223--4111359 Score: 95
Period size: 18 Copynumber: 7.4 Consensus size: 18
4111213 AATTTTTCTT
4111223 ATAAATAATATTATATT-
1 ATAAATAATATTATATTA
*
4111240 AT-AAT-ATATTA-ATAA
1 ATAAATAATATTATATTA
* *
4111255 ATAATATTATAATATATTA
1 ATAA-ATAATATTATATTA
*
4111274 ATAAATAATATTATTTTA
1 ATAAATAATATTATATTA
4111292 ATAAATAATATAATAAATATTATTA
1 ATAAAT-A-AT-AT---TA-TATTA
4111317 ATAAATAATA-TATTATTA
1 ATAAATAATATTA-TATTA
* * *
4111335 ATAAATAATATAAAAATA
1 ATAAATAATATTATATTA
4111353 ATAAATA
1 ATAAATA
4111360 GTTTTATTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
14 2 0.02
15 8 0.08
16 4 0.04
17 4 0.04
18 50 0.52
19 9 0.09
20 2 0.02
21 2 0.02
22 1 0.01
23 2 0.02
24 3 0.03
25 10 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:4111325 original size:43 final size:42
Alignment explanation
Indices: 4111246--4111352 Score: 166
Period size: 43 Copynumber: 2.6 Consensus size: 42
4111236 TATTATAATA
*
4111246 TATTAATAAATAATATTAT-AATATATTAATAAATAATATTAT
1 TATTAATAAATAATATAATAAATATATTAATAAATAATA-TAT
4111288 T-TTAATAAATAATATAATAAATATTATTAATAAATAATATAT
1 TATTAATAAATAATATAATAAATA-TATTAATAAATAATATAT
4111330 TATTAATAAATAATATAA-AAATA
1 TATTAATAAATAATATAATAAATA
4111353 ATAAATAGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
41 16 0.26
42 14 0.23
43 31 0.51
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (42 bp):
TATTAATAAATAATATAATAAATATATTAATAAATAATATAT
Found at i:4111341 original size:15 final size:15
Alignment explanation
Indices: 4111223--4111341 Score: 68
Period size: 15 Copynumber: 7.5 Consensus size: 15
4111213 AATTTTTCTT
4111223 ATAAATAATATTA-TA
1 ATAAAT-ATATTATTA
* *
4111238 TTATAATATATTAATAA
1 ATA-AATATATT-ATTA
4111255 ATAATATTATAATATATTA
1 ATAA-A-TAT-AT-TATTA
4111274 ATAAATAATATTATTTTA
1 ATAAAT-ATATTA--TTA
4111292 ATAAATA-A-TA-TA
1 ATAAATATATTATTA
*
4111304 ATAAATATTATTAATA
1 ATAAATA-TATTATTA
4111320 A-ATAATATATTATTA
1 ATA-AATATATTATTA
4111335 ATAAATA
1 ATAAATA
4111342 ATATAAAAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 32
0.69 0.04 0.27
Matches are distributed among these distances:
12 9 0.11
14 1 0.01
15 24 0.29
16 16 0.19
17 8 0.10
18 15 0.18
19 9 0.11
20 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATATATTATTA
Found at i:4111356 original size:9 final size:10
Alignment explanation
Indices: 4111223--4111359 Score: 56
Period size: 10 Copynumber: 13.7 Consensus size: 10
4111213 AATTTTTCTT
4111223 ATAAATAATA
1 ATAAATAATA
* * *
4111233 TTATATTATA
1 ATAAATAATA
*
4111243 AT--ATATTA
1 ATAAATAATA
4111251 ATAAATAATA
1 ATAAATAATA
*
4111261 TTATAATATATTA
1 --ATAA-ATAATA
4111274 ATAAATAAT-
1 ATAAATAATA
* **
4111283 AT-TATTTTA
1 ATAAATAATA
4111292 ATAAATAATATA
1 ATAAAT-A-ATA
4111304 ATAAATATTATTA
1 ATAAATA--A-TA
4111317 ATAAATAAT-
1 ATAAATAATA
* *
4111326 AT-ATTATTA
1 ATAAATAATA
4111335 ATAAATAAT-
1 ATAAATAATA
4111344 ATAAA-AATA
1 ATAAATAATA
4111353 ATAAATA
1 ATAAATA
4111360 GTTTTATTTT
Statistics
Matches: 93, Mismatches: 19, Indels: 30
0.65 0.13 0.21
Matches are distributed among these distances:
8 16 0.17
9 18 0.19
10 25 0.27
11 6 0.06
12 14 0.15
13 14 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAAATAATA
Found at i:4115064 original size:36 final size:36
Alignment explanation
Indices: 4114994--4115065 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
4114984 GCAGGAAGAC
*
4114994 TAGATTAATTTGATATTCCATTAAATGGTTATTTAT
1 TAGATTAATTTGATATTCCATTAAATGGTCATTTAT
* **
4115030 TAGATTAATTTGATATTCTATTAGGTGGTCATTTAT
1 TAGATTAATTTGATATTCCATTAAATGGTCATTTAT
4115066 ACAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (36 bp):
TAGATTAATTTGATATTCCATTAAATGGTCATTTAT
Found at i:4116682 original size:19 final size:18
Alignment explanation
Indices: 4116655--4116690 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4116645 CAAAATTTAT
4116655 TATTAAAATAATAAAAATA
1 TATTAAAAT-ATAAAAATA
*
4116674 TATTTAAATATAAAAAT
1 TATTAAAATATAAAAAT
4116691 TTGATTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAAATATAAAAATA
Found at i:4117578 original size:15 final size:15
Alignment explanation
Indices: 4117558--4117625 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
4117548 CAAAATATTA
4117558 TTTAATATTAATAAT
1 TTTAATATTAATAAT
4117573 TTTAAT-TTAATATAT
1 TTTAATATTAATA-AT
**
4117588 AATAAAATATTAA-AATT
1 --TTTAATATTAATAA-T
4117605 TTTAATATTAAT--T
1 TTTAATATTAATAAT
4117618 TTTAATAT
1 TTTAATAT
4117626 AAATGTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
13 9 0.21
14 6 0.14
15 17 0.40
16 1 0.02
17 6 0.14
18 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATATTAATAAT
Found at i:4117638 original size:15 final size:13
Alignment explanation
Indices: 4117600--4117634 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4117590 TAAAATATTA
4117600 AAATTTTTAATAT
1 AAATTTTTAATAT
*
4117613 TAATTTTTAATAT
1 AAATTTTTAATAT
4117626 AAATGTTTT
1 AAAT-TTTT
4117635 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AAATTTTTAATAT
Found at i:4117645 original size:16 final size:15
Alignment explanation
Indices: 4117603--4117643 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
4117593 AATATTAAAA
*
4117603 TTTTTAATATTAA--
1 TTTTTAATATAAATG
4117616 TTTTTAATATAAATG
1 TTTTTAATATAAATG
*
4117631 TTTTTAATTTAAA
1 TTTTTAATATAAA
4117644 ATATTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTTAATATAAATG
Found at i:4117689 original size:28 final size:28
Alignment explanation
Indices: 4117633--4117685 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4117623 TATAAATGTT
* *
4117633 TTTAATTTAAAATATTATTTATATTATA
1 TTTAATATAAAATATTATTTATATAATA
4117661 TTTAATATAAAATATTATTT-TATAA
1 TTTAATATAAAATATTATTTATATAA
4117686 ATATAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTAATATAAAATATTATTTATATAATA
Found at i:4120187 original size:13 final size:14
Alignment explanation
Indices: 4120162--4120188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4120152 CGTTCGCGTG
4120162 AAAAATAATTTTTA
1 AAAAATAATTTTTA
4120176 AAAAATAATTTTT
1 AAAAATAATTTTT
4120189 GTATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:4120377 original size:18 final size:16
Alignment explanation
Indices: 4120354--4120643 Score: 104
Period size: 15 Copynumber: 18.2 Consensus size: 16
4120344 AATTTTACTT
4120354 ATAAATAATATTATATGA
1 ATAAATAATA-TATAT-A
4120372 ATAAATAATATACTAT-
1 ATAAATAATATA-TATA
4120388 -TAATATAATATAT-TA
1 ATAA-ATAATATATATA
*
4120403 ATAAATAATATTATATTC
1 ATAAATAATA-TATA-TA
* *
4120421 ATAAAT-ATTTTTATAA
1 ATAAATAATATATAT-A
*
4120437 ATAAATATTATA-ATA
1 ATAAATAATATATATA
*
4120452 ATATATTAGCAT-TA-ATAA
1 ATA-AATA--ATATATAT-A
4120470 ATAATATTGCAATATAT-TA
1 ATAA-A-T--AATATATATA
4120489 ATAAATAATATAT-T-
1 ATAAATAATATATATA
*
4120503 ATTAATAA-ATAATATA
1 ATAAATAATAT-ATATA
4120519 ATAAAT-AT-TAT-TA
1 ATAAATAATATATATA
* * *
4120532 ATTTAATTAATAAATATT
1 A--TAAATAATATATATA
*
4120550 AT-AATAATATAT-TT
1 ATAAATAATATATATA
*
4120564 ATAAATAATATATTATTC
1 ATAAATAATATA-TA-TA
4120582 ATAAATAATATACTAT-
1 ATAAATAATATA-TATA
4120598 -TAATATAATATAT-TA
1 ATAA-ATAATATATATA
*
4120613 ATAAAT-GT-TAT-TA
1 ATAAATAATATATATA
*
4120626 ATAAACAATAT-TATA
1 ATAAATAATATATATA
4120641 ATA
1 ATA
4120644 TGTTAACAAA
Statistics
Matches: 212, Mismatches: 22, Indels: 79
0.68 0.07 0.25
Matches are distributed among these distances:
13 15 0.07
14 20 0.09
15 59 0.28
16 48 0.23
17 15 0.07
18 43 0.20
19 8 0.04
20 3 0.01
21 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
ATAAATAATATATATA
Found at i:4120396 original size:34 final size:32
Alignment explanation
Indices: 4120358--4120618 Score: 122
Period size: 31 Copynumber: 8.6 Consensus size: 32
4120348 TTACTTATAA
4120358 ATAATATTATATGAATAAATAATATACTATTAAT
1 ATAATATTATAT-AATAAATAATATA-TATTAAT
*
4120392 ATAATA-TAT-TAATAAATAATATTATATTCAT
1 ATAATATTATATAATAAATAATA-TATATTAAT
* *
4120423 A-AATATT-T-TTATAAATAAATATTATAATAAT
1 ATAATATTATATAATAAAT-AATA-TATATTAAT
* ** **
4120454 ATATTAGCAT-TAATAAATAATAT-T-GCAAT
1 ATAATATTATATAATAAATAATATATATTAAT
*
4120483 AT-AT-TAATA-AAT-AAT-ATAT-TATTAAT
1 ATAATATTATATAATAAATAATATATATTAAT
*
4120509 A-AATA--ATATAATAAATATTAT-TAATTTAAT
1 ATAATATTATATAATAAATAATATAT-A-TTAAT
* * *
4120539 -TAATA-AATATTAT-AATAATATAT-TTATAA
1 ATAATATTATATAATAAATAATATATATTA-AT
*
4120568 ATAATA-TATTATTCATAAATAATATACTATTAAT
1 ATAATATTA-TA-TAATAAATAATATA-TATTAAT
4120602 ATAATA-TAT-TAATAAAT
1 ATAATATTATATAATAAAT
4120619 GTTATTAATA
Statistics
Matches: 180, Mismatches: 23, Indels: 51
0.71 0.09 0.20
Matches are distributed among these distances:
25 8 0.04
26 12 0.07
27 8 0.04
28 8 0.04
29 7 0.04
30 35 0.19
31 49 0.27
32 13 0.07
33 21 0.12
34 16 0.09
35 3 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (32 bp):
ATAATATTATATAATAAATAATATATATTAAT
Found at i:4120629 original size:13 final size:12
Alignment explanation
Indices: 4120492--4120630 Score: 64
Period size: 13 Copynumber: 11.5 Consensus size: 12
4120482 TATATTAATA
4120492 AATAATATATTATT
1 AATAA-ATA-TATT
4120506 AATAAATA-ATAT
1 AATAAATATAT-T
4120518 AATAAATATTATT
1 AATAAATA-TATT
*
4120531 AAT--TTA-ATT
1 AATAAATATATT
4120540 AATAAATAT-TAT
1 AATAAATATAT-T
4120552 AAT-AATATATT
1 AATAAATATATT
*
4120563 TATAAATA-A-T
1 AATAAATATATT
* *
4120573 -AT-ATTATTCATA
1 AATAAATA-T-ATT
4120585 AATAATATACTATT
1 AATAA-ATA-TATT
4120599 AATATAATATATT
1 AATA-AATATATT
*
4120612 AATAAATGTTATT
1 AATAAAT-ATATT
4120625 AATAAA
1 AATAAA
4120631 CAATATTATA
Statistics
Matches: 98, Mismatches: 9, Indels: 37
0.68 0.06 0.26
Matches are distributed among these distances:
8 3 0.03
9 8 0.08
10 1 0.01
11 17 0.17
12 21 0.21
13 27 0.28
14 17 0.17
15 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (12 bp):
AATAAATATATT
Found at i:4120675 original size:119 final size:115
Alignment explanation
Indices: 4120433--4120676 Score: 246
Period size: 119 Copynumber: 2.1 Consensus size: 115
4120423 AAATATTTTT
* *
4120433 ATAAATAA-ATATTATAATAATATATTAGCATTAATAAATAATATTGCAATATATTAATAAATAA
1 ATAAATAATATATTATAATAATATATTAGCATAAATAAATAATATT-CAATATAATAATAAATAA
* ** *
4120497 TATATTATTAATAAATAATATAATAAATATTATTAATTTAATTAATAAATA
65 TATATTATTAATAAACAATATAATAAATATTAACAATATAATTAATAAATA
* * * *
4120548 TTATAATAATATATTTATAAATAATATATTATTCATAAATAATATACTATT-AATATAATATATT
1 ATA-AATAATATA-TTAT-AATAATATATTA-GCATAAATAA-ATAATATTCAATATAATA-ATA
* * *
4120612 AATAA-ATGTTATTAATAAACAATATTATAATATGTTAACAA-ATAATATAA-AGAATA
60 AATAATATATTATTAATAAACAATATAATAA-ATATTAACAATATAAT-TAATA-AATA
4120668 ATAAATAAT
1 ATAAATAAT
4120677 TTTATTTTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
115 2 0.02
116 5 0.05
117 3 0.03
118 4 0.04
119 53 0.50
120 31 0.30
121 7 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (115 bp):
ATAAATAATATATTATAATAATATATTAGCATAAATAAATAATATTCAATATAATAATAAATAAT
ATATTATTAATAAACAATATAATAAATATTAACAATATAATTAATAAATA
Found at i:4120718 original size:19 final size:18
Alignment explanation
Indices: 4120691--4120784 Score: 60
Period size: 19 Copynumber: 5.6 Consensus size: 18
4120681 TTTTAAGTAT
*
4120691 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
4120710 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
*
4120728 TTATTAA-A--ATATAAT-
1 TT-TTAATATTAAATAATA
* *
4120743 TATTCAT-TT-AAT-ATA
1 TTTTAATATTAAATAATA
*
4120758 TTTTAATAATAAATAAT-
1 TTTTAATATTAAATAATA
4120775 TTTTAATATT
1 TTTTAATATT
4120785 TTAATAGTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 18
0.66 0.13 0.21
Matches are distributed among these distances:
14 5 0.09
15 8 0.14
16 6 0.11
17 12 0.21
18 10 0.18
19 15 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:4120931 original size:14 final size:14
Alignment explanation
Indices: 4120906--4120939 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4120896 AAAATATAAA
4120906 TATTTTTCAAAAAT
1 TATTTTTCAAAAAT
4120920 TAGTTTTT-AAAAAT
1 TA-TTTTTCAAAAAT
4120934 TATTTT
1 TATTTT
4120940 CTGCAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 10 0.53
15 5 0.26
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTTTTCAAAAAT
Found at i:4124340 original size:22 final size:24
Alignment explanation
Indices: 4124289--4124340 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
4124279 TTGAATAATG
*
4124289 ATATCAAATTTAAATAAATATTAA
1 ATATTAAATTTAAATAAATATTAA
*
4124313 A-A-TAAATTTAAAT-ATTA-TAA
1 ATATTAAATTTAAATAAATATTAA
4124333 ATATTAAA
1 ATATTAAA
4124341 CGAATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 14 0.58
23 1 0.04
24 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTAAATTTAAATAAATATTAA
Found at i:4127663 original size:2 final size:2
Alignment explanation
Indices: 4127656--4127680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4127646 ATCAGATGTA
4127656 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
4127681 AATCAATCAA
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:4127984 original size:95 final size:98
Alignment explanation
Indices: 4127809--4128000 Score: 309
Period size: 96 Copynumber: 2.0 Consensus size: 98
4127799 GTCCAATACT
4127809 GAGCCTTATTTTGAATAATCATGTTTTTTTTTAACCACTGAATAGACATTTTTTTGGTGATCTCT
1 GAGCCTTATTTTGAATAATCATGTTTTTTTTTAACCACTGAATAGACATTTTTTTGGTGATCTCT
* *
4127874 ACACTTGAGTGAT-AAACTGTAACTACATAGAC
66 ACACTTGAGTCATAAAACTGGAACTACATAGAC
* * * *
4127906 GAGCCTTATTTTGAATAATCATG-TTTTTTTTAATCATTGAGTAGGCA-TTTTTTGGTGATCTCT
1 GAGCCTTATTTTGAATAATCATGTTTTTTTTTAACCACTGAATAGACATTTTTTTGGTGATCTCT
4127969 ACACTTGAGTCATAAAACTGGAACTACATAGA
66 ACACTTGAGTCATAAAACTGGAACTACATAGA
4128001 TCTATGGAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
95 28 0.32
96 37 0.42
97 23 0.26
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (98 bp):
GAGCCTTATTTTGAATAATCATGTTTTTTTTTAACCACTGAATAGACATTTTTTTGGTGATCTCT
ACACTTGAGTCATAAAACTGGAACTACATAGAC
Found at i:4128623 original size:105 final size:105
Alignment explanation
Indices: 4128439--4128636 Score: 308
Period size: 105 Copynumber: 1.9 Consensus size: 105
4128429 TGAGCTCTAC
* *
4128439 ATTTATTGTTGATCTAGGTTGTCATTTTTGTTCTTGTAGCTTAAACCGTATGTATCTTATGTGGA
1 ATTTATTGTTGATCTAGGTTGTCATTTTTGTTCTTGCAGCTCAAACCGTATGTATCTTATGTGGA
*
4128504 AAATAGTGATTCAAATCTCATATGTGATAAAACATTTTTT
66 AAATAGTGACTCAAATCTCATATGTGATAAAACATTTTTT
* * * *
4128544 ATTTATTGTTGATTTAGGTTGTTC-TTTTTGTTTTTGCAGCTCAAACTGTATGTATCTTATGTTG
1 ATTTATTGTTGATCTAGGTTG-TCATTTTTGTTCTTGCAGCTCAAACCGTATGTATCTTATGTGG
*
4128608 AGAATAGTGACTCAAATCTCATATGTGAT
65 AAAATAGTGACTCAAATCTCATATGTGAT
4128637 TTATTTGAGA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 82 0.98
106 2 0.02
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTATTGTTGATCTAGGTTGTCATTTTTGTTCTTGCAGCTCAAACCGTATGTATCTTATGTGGA
AAATAGTGACTCAAATCTCATATGTGATAAAACATTTTTT
Found at i:4129873 original size:553 final size:552
Alignment explanation
Indices: 4128823--4129938 Score: 1803
Period size: 553 Copynumber: 2.0 Consensus size: 552
4128813 ATAGGAGTAC
*
4128823 TAGAGATTTACATCTTATAGGTATATATTTAAATATTTGTAAGTGGACTAAAAAAGAGTGAGATG
1 TAGAGATTTACATCTTATAGGTATATATTTAAATATTTGTAAGTGGACTAAAAAAGAGTGAAATG
*
4128888 ATCCAAATAGATATGGTACATGGATACACATAGATATATGTTTGCTTAGGTTGAAAATACTTTGT
66 ATCCAAATAGATATGGTACATGGATACACATAGATATATGTTTGCTTAGGTTGAAAATACTTTAT
* *
4128953 AAGGACTACAAAAATTAAAAGGTCTATGGGTATTGATTGTTAAGTGATTGATTGATTTGATTTGA
131 AAGGACTACAAAAATTAAAAGGTCTAAGGGTATTGATTGTT-A-TGAGTGATTGATTTGATTTGA
*
4129018 TATATATTTGTAATTCTATACAACTAATGGATCTTTTTTATTATCCATGAATATAGGTTGATTGG
194 TATATATTTATAATTCTATACAACTAATGGATCTTTTTTATTATCCATGAATATAGGTTGATTGG
*
4129083 ATCGAACCATATTAAATTGATGTTTTTTGTGTAATTGATTGATTATTTGATTATGCTTCCATTGG
259 ATCGAACCATATTAAATTGATATTTTTTGTGTAATTGATTGATTATTTGATTATGCTTCCATTGG
*
4129148 TATGATTAAATTAAGGCTTTTAGCCTAACAAATGATATCAGAGTTGAAGGTTCAAGACGTGGAAT
324 TATGATTAAATTAAGGCTTTTAGCCTAACAAATGATATCAGAGCTGAAGGTTCAAGACGTGGAAT
* * *
4129213 AGTTGAAGGTTTGAGGCATGAAAAGAGGCAAATCTAGAAGAGCTCGAATCAAGAAAGAAGTTTAA
389 AGTTGAAGGATTGAGGCATGAAAAGAAGCAAATCTAGAAGAGCTCGAATCAAGAAAGAAGTTCAA
* *
4129278 GTTCGTGTTTTGAAGATTGATTTGCATAAAGCGTGAAGACACACAAAAGAAGATTGTGAGACTTT
454 GTTCGTGTTTTGAAGATTGATTTGCATAAAGCGTGAAGACACA-AAAA-AAAATTGTAAGAC-TT
* * *
4129343 CTATTACAGATGGAGCCAAGCATGTCTAGCATGAAAA
516 CCATTACAGATGAAGCCAAGCATGTCTAGCATAAAAA
*
4129380 TAGAGATTTACATCTTATAGGTATATATTTAAATATTTGTAAGTGGACTAAAAGAGAGTGAAATG
1 TAGAGATTTACATCTTATAGGTATATATTTAAATATTTGTAAGTGGACTAAAAAAGAGTGAAATG
* * * *
4129445 GTCCAAATAGATATGGTACATGGATACATATAGATATATGTTTGTTTAGGTTGAGAATACTTTAT
66 ATCCAAATAGATATGGTACATGGATACACATAGATATATGTTTGCTTAGGTTGAAAATACTTTAT
* * *
4129510 -AGGATTACAAAAAATTGAGAGGGTCTAAGGGTATTGATTG-T-TGAGTGATTGATTTGATTTGA
131 AAGGACTAC-AAAAATT-AAAAGGTCTAAGGGTATTGATTGTTATGAGTGATTGATTTGATTTGA
* * *
4129572 TGTATGTTTATAATTCTATACAACTAATGGAT-TTTTTTATTATCCATGAATGTAGGTTGATTGG
194 TATATATTTATAATTCTATACAACTAATGGATCTTTTTTATTATCCATGAATATAGGTTGATTGG
4129636 ATCGAA-CATATTAAATT-ATTATTTTTTGTGTAATTGATTGATTATTTGATTATGCTTCCATTG
259 ATCGAACCATATTAAATTGA-TATTTTTTGTGTAATTGATTGATTATTTGATTATGCTTCCATTG
* * *
4129699 GTATGATTAAATTAGGGCTTTTAGCCTAACAAGTGATATCAGAGCTGAAGGTTCAAGATGTGGGA
323 GTATGATTAAATTAAGGCTTTTAGCCTAACAAATGATATCAGAGCTGAAGGTTCAAGACGT-GGA
*
4129764 ATAGTTGAAGGATTGAGGCATGAAAAGAAGCAAATCTAGAAGAGCTCGACTCAAGAAAGAAGTTC
387 ATAGTTGAAGGATTGAGGCATGAAAAGAAGCAAATCTAGAAGAGCTCGAATCAAGAAAGAAGTTC
*
4129829 AAGTTCGTGTTTTGAAGATTGATTTGCATAAAGTGTGAAGACACAAAAAAAAATTGTAAGACTTC
452 AAGTTCGTGTTTTGAAGATTGATTTGCATAAAGCGTGAAGACACAAAAAAAAATTGTAAGACTTC
* *
4129894 CATTGCAGATGAAGCTAAGCATGTCTAGCATAAAAA
517 CATTACAGATGAAGCCAAGCATGTCTAGCATAAAAA
*
4129930 TAGATATTT
1 TAGAGATTT
4129939 GATAGAATTT
Statistics
Matches: 521, Mismatches: 34, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
550 42 0.08
551 12 0.02
552 115 0.22
553 145 0.28
554 49 0.09
556 7 0.01
557 131 0.25
558 20 0.04
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (552 bp):
TAGAGATTTACATCTTATAGGTATATATTTAAATATTTGTAAGTGGACTAAAAAAGAGTGAAATG
ATCCAAATAGATATGGTACATGGATACACATAGATATATGTTTGCTTAGGTTGAAAATACTTTAT
AAGGACTACAAAAATTAAAAGGTCTAAGGGTATTGATTGTTATGAGTGATTGATTTGATTTGATA
TATATTTATAATTCTATACAACTAATGGATCTTTTTTATTATCCATGAATATAGGTTGATTGGAT
CGAACCATATTAAATTGATATTTTTTGTGTAATTGATTGATTATTTGATTATGCTTCCATTGGTA
TGATTAAATTAAGGCTTTTAGCCTAACAAATGATATCAGAGCTGAAGGTTCAAGACGTGGAATAG
TTGAAGGATTGAGGCATGAAAAGAAGCAAATCTAGAAGAGCTCGAATCAAGAAAGAAGTTCAAGT
TCGTGTTTTGAAGATTGATTTGCATAAAGCGTGAAGACACAAAAAAAAATTGTAAGACTTCCATT
ACAGATGAAGCCAAGCATGTCTAGCATAAAAA
Found at i:4132117 original size:21 final size:21
Alignment explanation
Indices: 4132079--4132125 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4132069 AAAAAGATGT
*
4132079 TTTAAGTCTTCAAATTTTAAA
1 TTTAAGTCTCCAAATTTTAAA
** *
4132100 TTTAAGTCTCCAGGTTTTAAT
1 TTTAAGTCTCCAAATTTTAAA
4132121 TTTAA
1 TTTAA
4132126 TTTATTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTAAGTCTCCAAATTTTAAA
Found at i:4134595 original size:6 final size:7
Alignment explanation
Indices: 4134578--4134602 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4134568 AAGTATAGCA
4134578 AAAAAAT
1 AAAAAAT
4134585 AAAAAAT
1 AAAAAAT
4134592 AAAAAAT
1 AAAAAAT
4134599 AAAA
1 AAAA
4134603 GTGAGATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:4136470 original size:13 final size:14
Alignment explanation
Indices: 4136445--4136475 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4136435 GAATATCTCT
4136445 TAAATTATAATTTA
1 TAAATTATAATTTA
4136459 TAAATT-TAATTTA
1 TAAATTATAATTTA
4136472 TAAA
1 TAAA
4136476 ACATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATTATAATTTA
Found at i:4136792 original size:13 final size:14
Alignment explanation
Indices: 4136776--4136837 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
4136766 ATTTAACATA
4136776 ATAAAATAT-AAAT
1 ATAAAATATAAAAT
4136789 AT--AATATAAAA-
1 ATAAAATATAAAAT
*
4136800 ATAAAATATGAAAT
1 ATAAAATATAAAAT
* *
4136814 GATATAATTTAAAATT
1 -ATAAAATATAAAA-T
4136830 ATAAAATA
1 ATAAAATA
4136838 ATTATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
11 7 0.19
12 3 0.08
13 10 0.27
15 16 0.43
16 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
ATAAAATATAAAAT
Found at i:4137284 original size:28 final size:29
Alignment explanation
Indices: 4137244--4137307 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
4137234 ATTTTTTAAA
*
4137244 TTAAAATAAAATATATTAT-ATTTA-ATAAT
1 TTAAAATAAAATA-ATTATAAATTATAT-AT
4137273 TTAAAAT-AAATAATTATAAATTATATAT
1 TTAAAATAAAATAATTATAAATTATATAT
4137301 TTAAAAT
1 TTAAAAT
4137308 GATCTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.16
28 18 0.56
29 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAAAATAAAATAATTATAAATTATATAT
Found at i:4139953 original size:29 final size:29
Alignment explanation
Indices: 4139917--4139974 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4139907 ACTATGTATT
4139917 TCTACATGCAGCATTGTCTCAAATATGTA
1 TCTACATGCAGCATTGTCTCAAATATGTA
4139946 TCTACATGCAGCATTGTCTCAAATATGTA
1 TCTACATGCAGCATTGTCTCAAATATGTA
4139975 AACTATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (29 bp):
TCTACATGCAGCATTGTCTCAAATATGTA
Found at i:4144091 original size:26 final size:26
Alignment explanation
Indices: 4144062--4144120 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4144052 GTTTGGATTG
* *
4144062 AAAAAATATTTTTTATTT-TCATTTTT
1 AAAAAATAGTTTTCATTTAT-ATTTTT
* *
4144088 AAAAAAAAGTTTTCATTTATTTTTTT
1 AAAAAATAGTTTTCATTTATATTTTT
4144114 AAAAAAT
1 AAAAAAT
4144121 GTATTTGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (26 bp):
AAAAAATAGTTTTCATTTATATTTTT
Found at i:4152095 original size:19 final size:19
Alignment explanation
Indices: 4152073--4152110 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4152063 TCATTTAAAA
* *
4152073 TTAATTTAATAATTTTAAT
1 TTAATATAATAATTATAAT
4152092 TTAATATAATAATTATAAT
1 TTAATATAATAATTATAAT
4152111 ATATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATATAATAATTATAAT
Found at i:4152123 original size:23 final size:23
Alignment explanation
Indices: 4152096--4152165 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
4152086 TTTAATTTAA
4152096 TATAATAATTATAATATATTATT
1 TATAATAATTATAATATATTATT
* * *
4152119 TATAAT-ATTAATTATATCTTAAT
1 TATAATAATT-ATAATATATTATT
* *
4152142 TATATATAAATATAATATTTTATT
1 TATA-ATAATTATAATATATTATT
4152166 AAATTAATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 3 0.08
23 20 0.54
24 12 0.32
25 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TATAATAATTATAATATATTATT
Found at i:4152128 original size:12 final size:12
Alignment explanation
Indices: 4152081--4152160 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 12
4152071 AATTAATTTA
*
4152081 ATAATTTTAATT
1 ATAATATTAATT
4152093 -TAATATAATAATT
1 ATAATAT--TAATT
*
4152106 ATAATATATTATTT
1 AT-A-ATATTAATT
4152120 ATAATATTAATT
1 ATAATATTAATT
*
4152132 AT-ATCTTAATT
1 ATAATATTAATT
*
4152143 AT-ATA-TAAAT
1 ATAATATTAATT
4152153 ATAATATT
1 ATAATATT
4152161 TTATTAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 6 0.11
11 20 0.36
12 11 0.20
13 6 0.11
14 7 0.13
15 1 0.02
16 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:4152186 original size:18 final size:17
Alignment explanation
Indices: 4152148--4152179 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4152138 TAATTATATA
4152148 TAAATATAATATTTTAT
1 TAAATATAATATTTTAT
4152165 TAAAT-TAATATTTTA
1 TAAATATAATATTTTA
4152180 AATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATATAATATTTTAT
Found at i:4152218 original size:24 final size:23
Alignment explanation
Indices: 4152181--4152225 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4152171 AATATTTTAA
*
4152181 ATTAAAATATTATATAATAATTTT
1 ATTAAAATAATATAT-ATAATTTT
*
4152205 ATTAATATAATATATATAATT
1 ATTAAAATAATATATATAATT
4152226 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAAAATAATATATATAATTTT
Found at i:4157141 original size:16 final size:17
Alignment explanation
Indices: 4157109--4157141 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4157099 GAAGCTTTTG
*
4157109 AAAAAAAAAAGTAAAAA
1 AAAAAAAAAACTAAAAA
4157126 AAAAAAAAAACTAAAA
1 AAAAAAAAAACTAAAA
4157142 CTATTAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.03, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAACTAAAAA
Found at i:4157284 original size:24 final size:24
Alignment explanation
Indices: 4157257--4157302 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4157247 TTCTATCTAG
4157257 TTGTTGGACAAGTGATGTGGGCGC
1 TTGTTGGACAAGTGATGTGGGCGC
*
4157281 TTGTTGGACGAGTGATGTGGGC
1 TTGTTGGACAAGTGATGTGGGC
4157303 CTAGCACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.11, G:0.43, T:0.30
Consensus pattern (24 bp):
TTGTTGGACAAGTGATGTGGGCGC
Found at i:4157880 original size:26 final size:26
Alignment explanation
Indices: 4157850--4157900 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4157840 CAAATAAATT
*
4157850 TTTTTAATAAATTATTTAAATTGAATA
1 TTTTGAAT-AATTATTTAAATTGAATA
* *
4157877 TTTTGGATAATTTTTTAAATTGAA
1 TTTTGAATAATTATTTAAATTGAA
4157901 ATCAAAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (26 bp):
TTTTGAATAATTATTTAAATTGAATA
Found at i:4166272 original size:16 final size:16
Alignment explanation
Indices: 4166251--4166282 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4166241 TCTTAAAAAT
4166251 TATTTTTATAAATATA
1 TATTTTTATAAATATA
*
4166267 TATTTTTATAATTATA
1 TATTTTTATAAATATA
4166283 ACTTATTTTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTATAAATATA
Found at i:4177252 original size:42 final size:42
Alignment explanation
Indices: 4177205--4177306 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
4177195 CAGTTCCTAT
* * * *
4177205 CCTTTCATTCTCTACTGCCTCACTTACATGTTGATTTTCTAC
1 CCTTTCATTCCCTACTACATCAATTACATGTTGATTTTCTAC
*
4177247 CCTTTCATTCCCTACTACATCAATTACATGTTGATTTTTTAC
1 CCTTTCATTCCCTACTACATCAATTACATGTTGATTTTCTAC
*
4177289 CATTTCATTCCCTACTAC
1 CCTTTCATTCCCTACTAC
4177307 CGTAGCTACA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.21, C:0.30, G:0.05, T:0.44
Consensus pattern (42 bp):
CCTTTCATTCCCTACTACATCAATTACATGTTGATTTTCTAC
Found at i:4177891 original size:32 final size:32
Alignment explanation
Indices: 4177841--4177918 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
4177831 TACATGTCCC
* **
4177841 TTACATTGTTATTTAATTTCTT-TTATAA-TCTT
1 TTACTTTGTTATAAAATTT-TTGTTATAAGT-TT
*
4177873 TTACTTTTTTATAAAATTTTTGTTATAAGTTT
1 TTACTTTGTTATAAAATTTTTGTTATAAGTTT
4177905 TTACTTTGTTATAA
1 TTACTTTGTTATAA
4177919 CCAAGGGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 36 0.92
33 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (32 bp):
TTACTTTGTTATAAAATTTTTGTTATAAGTTT
Found at i:4178484 original size:42 final size:42
Alignment explanation
Indices: 4178438--4178535 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
4178428 AATATATCTA
* * **
4178438 AACAGTAAAAAACTCTAATTACAAATTCAAGTAATTAAGAAC
1 AACAGTAAAAAACCCTAACTACAAATTCAAACAATTAAGAAC
* * ** * *
4178480 AACAGTAGAAGACCCTAACTATTATTTGAAACAATTAAGAAC
1 AACAGTAAAAAACCCTAACTACAAATTCAAACAATTAAGAAC
4178522 AACAGTAAAAAACC
1 AACAGTAAAAAACC
4178536 TCAAATATAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.21
Consensus pattern (42 bp):
AACAGTAAAAAACCCTAACTACAAATTCAAACAATTAAGAAC
Found at i:4178702 original size:42 final size:42
Alignment explanation
Indices: 4178606--4178703 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
4178596 AATTAAAAAC
* * *
4178606 AACAACAGAAAACCATAAATCATAATATGCCTAAGAATGAAA
1 AACAACAGAAAACCATAAACCAGAATATGCCTAACAATGAAA
* * * ** *
4178648 AACTATAGAAAACCTTAAACCAGAATATGCCTAACTTTGAAG
1 AACAACAGAAAACCATAAACCAGAATATGCCTAACAATGAAA
*
4178690 AACAACAAAAAACC
1 AACAACAGAAAACC
4178704 CTCAATCACA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.54, C:0.19, G:0.09, T:0.17
Consensus pattern (42 bp):
AACAACAGAAAACCATAAACCAGAATATGCCTAACAATGAAA
Found at i:4185682 original size:25 final size:25
Alignment explanation
Indices: 4185652--4185702 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4185642 CCGACGGATC
4185652 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
4185677 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
4185702 G
1 G
4185703 TTGGAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (25 bp):
GACCTCAGGCAGTGGTGGGCGACTG
Found at i:4185771 original size:79 final size:79
Alignment explanation
Indices: 4185677--4185886 Score: 357
Period size: 79 Copynumber: 2.6 Consensus size: 79
4185667 TGGGCGACTG
* *
4185677 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAATAGATTTGGGCGTATCCAGTTCTGGGCGTAGTC
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
4185742 CCTTCCGACAGATC
66 CCTTCCGACAGATC
* *
4185756 GACCTCAAGCAGTGGTGGGCGACTGGTTGGAACAGATTTAGGCGCATCCAGTTCTGGGCGTAGTC
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
*
4185821 CCTTCCGACGGATC
66 CCTTCCGACAGATC
*
4185835 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAG
4185887 ACTGAGGGTC
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 105 0.86
80 17 0.14
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (79 bp):
GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
CCTTCCGACAGATC
Found at i:4185945 original size:118 final size:118
Alignment explanation
Indices: 4185781--4186004 Score: 405
Period size: 118 Copynumber: 1.9 Consensus size: 118
4185771 TGGGCGACTG
*
4185781 GTTGGAACAGATTTAGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACAGATTCAGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
4185846 GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
66 GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
*
4185899 GTTGGAACCAGATTCGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAA-CAGATTCAGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
*
4185963 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAG
65 AGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
4186005 TTCTGGGCGT
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 81 0.79
119 21 0.21
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.22
Consensus pattern (118 bp):
GTTGGAACAGATTCAGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
Found at i:4186043 original size:198 final size:196
Alignment explanation
Indices: 4185702--4186448 Score: 801
Period size: 198 Copynumber: 3.8 Consensus size: 196
4185692 TGGGCGACTG
* * *
4185702 GTTGGAA-TAGATTTGGGCGTATCCAGTTCTGGGCGTAGTCCCTTCCGACAGATCGACCTCAAGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACAGATCGACCTCAAGC
*
4185766 AGTGGTGGGCGACTGGTTGGAA-CAGATTTAGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGAC
66 AG-GGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGAC
4185830 GGATCGACCTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGAGGG
130 GGATCGACCTCAGGCA-TGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTG-GGG
4185895 TCTT
193 TCTT
* *
4185899 GTTGGAACCAGATTCGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACAGATCGACCTCAAGC
*
4185963 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGAC
66 AG-GGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGAC
* * * *
4186028 GGATCAACTTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGG
130 GGATCGACCTCAGGCA-TGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG-ACTGGGG
4186092 -C--
193 TCTT
* *** * * * ** * ** *
4186093 GTAGTCCCTTCTGA--CGGGTCAACTTCAAGCAGTGGTGGGCG-ACT-GGTT-GGAACCAGATTC
1 GTTGGAAC--CAGATTCGGG-C-GCATC---CAGTTCTGGGCGTAGTCCCTTCCG-A-CAGA-TC
** * ** ** * * * *
4186153 GGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTT-GGCGCATCCAGTTCTGGGCGTAATC
56 GACCTCAAGCAGGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
4186217 CCTTCCGACGGATCGACCTCAGGCA-GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
121 CCTTCCGACGGATCGACCTCAGGCATGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
4186281 ACTGGGGGTCTT
186 ACT-GGGGTCTT
* * * *
4186293 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGACGTAGTCCCTTCTGAC-GAATCGACTTCAAG
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACAG-ATCGACCTCAAG
* * * *
4186357 CA-GGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAATTCTGAGG-ATAGTCCCTTCCGA
65 CAGGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTG-GGCGTAGTCCCTTCCGA
*
4186420 CTGATCGACCTCAGGCAT-GTGGGCGACTG
129 CGGATCGACCTCAGGCATGGTGGGCGACTG
4186449 TGTGTTTGTG
Statistics
Matches: 449, Mismatches: 73, Indels: 58
0.77 0.13 0.10
Matches are distributed among these distances:
194 28 0.06
195 74 0.16
196 51 0.11
197 70 0.16
198 171 0.38
199 35 0.08
200 20 0.04
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.24
Consensus pattern (196 bp):
GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACAGATCGACCTCAAGC
AGGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACG
GATCGACCTCAGGCATGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGTCT
T
Found at i:4186046 original size:80 final size:80
Alignment explanation
Indices: 4185899--4186164 Score: 462
Period size: 80 Copynumber: 3.3 Consensus size: 80
4185889 TGAGGGTCTT
* * *
4185899 GTTGGAACCAGATTCGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAGGC
4185963 AGTGGTGGGCGACTG
66 AGTGGTGGGCGACTG
*
4185978 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAGGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAGGC
4186043 AGTGGTGGGCGACTG
66 AGTGGTGGGCGACTG
* * *
4186058 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGGTCAACTTCAAGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAGGC
4186123 AGTGGTGGGCGACTG
66 AGTGGTGGGCGACTG
4186138 GTTGGAACCAGATTCGGGCGCATCCAG
1 GTTGGAACCAGATTCGGGCGCATCCAG
4186165 ACTGGGGGTC
Statistics
Matches: 179, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
79 30 0.17
80 149 0.83
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (80 bp):
GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAGGC
AGTGGTGGGCGACTG
Found at i:4186394 original size:117 final size:117
Alignment explanation
Indices: 4186058--4186396 Score: 572
Period size: 117 Copynumber: 2.9 Consensus size: 117
4186048 TGGGCGACTG
* *
4186058 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGGTCAACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACTTCAAGC
4186123 AGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
66 A--GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
* * * *
4186177 GTTGGAACCAGATTT-GGCGCATCCAGTTCTGGGCGTAATCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACTTCAAGC
4186241 AGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
66 AGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
* *
4186293 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGACGTAGTCCCTTCTGACGAATCGACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACTTCAAGC
*
4186358 AGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCA
66 AGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCA
4186397 ATTCTGAGGA
Statistics
Matches: 206, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
116 66 0.32
117 81 0.39
118 44 0.21
119 15 0.07
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (117 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACTTCAAGC
AGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
Found at i:4186427 original size:78 final size:78
Alignment explanation
Indices: 4186297--4186448 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 78
4186287 GGTCTTGTTG
* * * *
4186297 GAACCAGATTTGGGCGCATCCAGTTCTGGACGTAGTCCCTTCTGACGAATCGACTTCAAGCAGGT
1 GAACCAGATTCGGGCGCATCCAATTCTGGACGTAGTCCCTTCCGACGAATCGACCTCAAGCAGGT
4186362 GGGCGACTGGTTA
66 GGGCGACTGGTTA
* * *
4186375 GAACCAGATTCGGGCGCATCCAATTCT-GAGGATAGTCCCTTCCGACTG-ATCGACCTCAGGCAT
1 GAACCAGATTCGGGCGCATCCAATTCTGGACG-TAGTCCCTTCCGAC-GAATCGACCTCAAGCAG
4186438 GTGGGCGACTG
64 GTGGGCGACTG
4186449 TGTGTTTGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 61 0.94
79 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (78 bp):
GAACCAGATTCGGGCGCATCCAATTCTGGACGTAGTCCCTTCCGACGAATCGACCTCAAGCAGGT
GGGCGACTGGTTA
Found at i:4189399 original size:16 final size:13
Alignment explanation
Indices: 4189368--4189421 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 13
4189358 GGTAAATAAT
4189368 ATTATT-TTTTTA
1 ATTATTATTTTTA
4189380 ATTAATTCATTTTTA
1 ATT-ATT-ATTTTTA
4189395 TATTATTATTTTTAA
1 -ATTATTATTTTT-A
4189410 ATATATTATTTT
1 AT-TATTATTTT
4189422 ATGAGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 8 0.22
15 19 0.53
16 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATTATTTTTA
Found at i:4189423 original size:28 final size:28
Alignment explanation
Indices: 4189366--4189421 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
4189356 TTGGTAAATA
*
4189366 ATATTATTTTTTTAATTAATTCATTTTT
1 ATATTATTTTTTTAAATAATTCATTTTT
4189394 ATATTATTATTTTTAAATATATT-ATTTT
1 ATATTATT-TTTTTAAATA-ATTCATTTT
4189422 ATGAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 14 0.56
30 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
ATATTATTTTTTTAAATAATTCATTTTT
Found at i:4190457 original size:30 final size:29
Alignment explanation
Indices: 4190423--4190493 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
4190413 TATTTTTTAT
* *
4190423 TTTTTATTTATATATATTTATATAATAATA
1 TTTTTATTTAT-TATATTTAAAAAATAATA
4190453 TTTTTAAATTT-TTATATTTAAAAAATAATA
1 TTTTT--ATTTATTATATTTAAAAAATAATA
4190483 TTTTATATTTA
1 TTTT-TATTTA
4190494 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
29 4 0.11
30 25 0.71
31 2 0.06
32 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTATTTATTATATTTAAAAAATAATA
Found at i:4190488 original size:21 final size:22
Alignment explanation
Indices: 4190462--4190510 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
4190452 ATTTTTAAAT
4190462 TTTTATATTT-AAAAAATAATA
1 TTTTATATTTAAAAAAATAATA
4190483 TTTTATATTTAAAAAAATAATA
1 TTTTATATTTAAAAAAATAATA
4190505 TTTTAT
1 TTTTAT
4190511 TAATTTCGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTATATTTAAAAAAATAATA
Found at i:4190794 original size:24 final size:24
Alignment explanation
Indices: 4190731--4190798 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
4190721 TTTGCTTTTT
*
4190731 TTATCAATT-TATAATT-TTTAAA
1 TTATCATTTATATAATTATTTAAA
*
4190753 TTA--ATTTATTATAATTATTTAAC
1 TTATCATTTA-TATAATTATTTAAA
4190776 TTATCATTTATATAATTATTTAA
1 TTATCATTTATATAATTATTTAA
4190799 TAAATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 3 0.08
22 10 0.26
23 8 0.21
24 13 0.33
25 5 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATCATTTATATAATTATTTAAA
Found at i:4194361 original size:24 final size:25
Alignment explanation
Indices: 4194334--4194383 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4194324 ATTTATTTAA
4194334 TTTTATATTTA-TAAATATTATATT
1 TTTTATATTTACTAAATATTATATT
* *
4194358 TTTTATATTTACTTAATTTTATATT
1 TTTTATATTTACTAAATATTATATT
4194383 T
1 T
4194384 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTATATTTACTAAATATTATATT
Found at i:4195164 original size:12 final size:11
Alignment explanation
Indices: 4195135--4195172 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
4195125 TTTAATTTTA
4195135 ATTTTT-ATAT
1 ATTTTTAATAT
4195145 ATTATTTAATAT
1 ATT-TTTAATAT
4195157 GATTTTTAATAT
1 -ATTTTTAATAT
4195169 ATTT
1 ATTT
4195173 AAATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.12
11 7 0.28
12 12 0.48
13 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:4195469 original size:24 final size:24
Alignment explanation
Indices: 4195442--4195488 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4195432 TCATTAAATT
*
4195442 TTTTTTAATTATAATTGTAATAAC
1 TTTTTTAATTATAATTATAATAAC
4195466 TTTTTTAATTATAATTATAATAA
1 TTTTTTAATTATAATTATAATAA
4195489 TAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTTTAATTATAATTATAATAAC
Found at i:4199527 original size:1 final size:1
Alignment explanation
Indices: 4199521--4199551 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
4199511 AAGTTGAAAG
4199521 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4199552 CCCCAATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4206656 original size:26 final size:26
Alignment explanation
Indices: 4206600--4206656 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4206590 TTTGGTCAAA
*
4206600 AATTTTTAAAATAAGAGAAATTATTC
1 AATTTTTAAAATAAAAGAAATTATTC
* * *
4206626 TATTTTTAAAATTAAAATAAA-TCTTC
1 AATTTTTAAAA-TAAAAGAAATTATTC
4206652 AATTT
1 AATTT
4206657 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTTTTAAAATAAAAGAAATTATTC
Found at i:4213136 original size:22 final size:22
Alignment explanation
Indices: 4213108--4213154 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4213098 ACTTTTTCGA
4213108 CATCTCAGATCAGTCTTCCTGT
1 CATCTCAGATCAGTCTTCCTGT
* *
4213130 CATCTCATATCAGTCTTCTTGT
1 CATCTCAGATCAGTCTTCCTGT
4213152 CAT
1 CAT
4213155 GGTCCTGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.40
Consensus pattern (22 bp):
CATCTCAGATCAGTCTTCCTGT
Found at i:4213166 original size:33 final size:33
Alignment explanation
Indices: 4213124--4213188 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4213114 AGATCAGTCT
*
4213124 TCCTGTCATCTCATATCAGTC-TTCTTGTCATGG
1 TCCTGTCATCTCAGATCAGTCTTTC-TGTCATGG
4213157 TCCTGTCATCTCAGATCAGTCTTTCTGTCATG
1 TCCTGTCATCTCAGATCAGTCTTTCTGTCATG
4213189 ATTCACATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (33 bp):
TCCTGTCATCTCAGATCAGTCTTTCTGTCATGG
Found at i:4215919 original size:29 final size:30
Alignment explanation
Indices: 4215887--4215956 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
4215877 TAATTGACTC
** *
4215887 AAAATACTTTAATT-TTGAAATAAAATTTA
1 AAAATACTTTAATTAAAGAAATAAAATTAA
*
4215916 AAAATA-TTCTTATTAAAGAAATAAAATTAA
1 AAAATACTT-TAATTAAAGAAATAAAATTAA
4215946 AAAATAACTTT
1 AAAAT-ACTTT
4215957 TACTTTGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.06
29 10 0.30
30 17 0.52
31 2 0.06
32 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATACTTTAATTAAAGAAATAAAATTAA
Found at i:4222938 original size:27 final size:27
Alignment explanation
Indices: 4222882--4222940 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
4222872 CAAACTAATT
* * * *
4222882 TAATTTTTTATATATATTATTTTAATA
1 TAATTTTTAATATATATTAGTATAAAA
4222909 TAATTTTTAATATAT-TTAAGTATAAAA
1 TAATTTTTAATATATATT-AGTATAAAA
4222936 TAATT
1 TAATT
4222941 ATTTTTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TAATTTTTAATATATATTAGTATAAAA
Found at i:4229648 original size:31 final size:31
Alignment explanation
Indices: 4229580--4229654 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
4229570 TTTTTATTTT
* *
4229580 ATATTTTTATGT-AAATATAAATTATAATAC
1 ATATTTTTATATAAAATATAAATTATAATAA
4229610 ATAATTTTTATATAAAATAT-AA-TATAAATATA
1 AT-ATTTTTATATAAAATATAAATTAT-AATA-A
4229642 ATA-TTTTATATAA
1 ATATTTTTATATAA
4229655 TACAATAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 15 0.38
31 16 0.41
32 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
ATATTTTTATATAAAATATAAATTATAATAA
Found at i:4233528 original size:19 final size:18
Alignment explanation
Indices: 4233506--4233544 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4233496 TGATTTGCAA
4233506 TTTTGTATATAATTTTATG
1 TTTTGTATAT-ATTTTATG
* *
4233525 TTTTGTGTATGTTTTATG
1 TTTTGTATATATTTTATG
4233543 TT
1 TT
4233545 GGATTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (18 bp):
TTTTGTATATATTTTATG
Found at i:4233630 original size:21 final size:21
Alignment explanation
Indices: 4233574--4233631 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
4233564 AATTTTAATG
*
4233574 AAAATTTT-T-ATGATATTTT
1 AAAATTTTATAATAATATTTT
*
4233593 --AATTTTATATTGAAATATTTT
1 AAAATTTTATAAT--AATATTTT
4233614 AAAATTTTATAATAATAT
1 AAAATTTTATAATAATAT
4233632 ATAAATCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 1 0.03
21 12 0.40
23 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
AAAATTTTATAATAATATTTT
Found at i:4236015 original size:21 final size:20
Alignment explanation
Indices: 4235991--4236033 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
4235981 TTCTTTTCAG
*
4235991 TATAATAACAATAATAATTTT
1 TATAATAACAATAA-AATATT
*
4236012 TATAATAATAATAAAATATT
1 TATAATAACAATAAAATATT
4236032 TA
1 TA
4236034 AAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATAACAATAAAATATT
Found at i:4237583 original size:30 final size:30
Alignment explanation
Indices: 4237520--4237586 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
4237510 CCTCAAATTT
* *
4237520 TAAAACCAAAATCCTAAAATCTTCAAACTC
1 TAAAATCAAAATCCTAAAATCTTCAAACCC
* *
4237550 TAAAATCAAAATCCT-AAACCTTTCATACCC
1 TAAAATCAAAATCCTAAAATC-TTCAAACCC
4237580 TAAAATC
1 TAAAATC
4237587 CAAGCCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (30 bp):
TAAAATCAAAATCCTAAAATCTTCAAACCC
Found at i:4248175 original size:213 final size:214
Alignment explanation
Indices: 4247820--4248238 Score: 606
Period size: 213 Copynumber: 2.0 Consensus size: 214
4247810 CCGTTACACA
* * * *
4247820 TCTTGGCATCACTATGACCTTTCTCCATATGAAGAATGGATGTGATCGGACCCATAACCCCAAAA
1 TCTTGGCACCACCATGACCTTTCTCCATATGAAGAATAGATGTGATCCGACCCATAACCCCAAAA
* *
4247885 GCTTTAAACAGGCATCAATTTATCTTTGTGATAATCGATTACTTTACAAAATGGATAGAAACAGC
66 GCTTCAAACAGGCATCAATTTATCTTTGTGATAATCGAATACTTTACAAAATGGATAGAAACAGC
* * * * * **
4247950 TTTATATGCTAGTATTATGTGATCAGTGGTGTGTAGATTTAT-AGAAAAAGAGATAATATGTCGG
131 TTCATATGCTAGTATTACGCGATCAGTGGTGTGTAAATTTATAAAAAAAAGAGATAATATACCGG
4248014 TATGGGCTCCCGTTGCATG
196 TATGGGCTCCCGTTGCATG
* * * ** **
4248033 TCTTGGCACCACCATGGCCTTTTTCCATGTGGGGAATAGATGTGATCCGACCCATAACCTTAAAA
1 TCTTGGCACCACCATGACCTTTCTCCATATGAAGAATAGATGTGATCCGACCCATAACCCCAAAA
* * *
4248098 GCTTCAAATAGGCATCGATTTATCTTTGTGATAATCGAATACTTTACAAAATGGATAGAAATAGC
66 GCTTCAAACAGGCATCAATTTATCTTTGTGATAATCGAATACTTTACAAAATGGATAGAAACAGC
* *
4248163 TTCGTATGCTAGTATTACGCGATCAGTGGTGTGTAAATTTATAAAAAAAAGAGATAATATACCTG
131 TTCATATGCTAGTATTACGCGATCAGTGGTGTGTAAATTTATAAAAAAAAGAGATAATATACCGG
4248228 TATGGGCTCCC
196 TATGGGCTCCC
4248239 AAAAAAGATT
Statistics
Matches: 180, Mismatches: 25, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
213 151 0.84
214 29 0.16
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (214 bp):
TCTTGGCACCACCATGACCTTTCTCCATATGAAGAATAGATGTGATCCGACCCATAACCCCAAAA
GCTTCAAACAGGCATCAATTTATCTTTGTGATAATCGAATACTTTACAAAATGGATAGAAACAGC
TTCATATGCTAGTATTACGCGATCAGTGGTGTGTAAATTTATAAAAAAAAGAGATAATATACCGG
TATGGGCTCCCGTTGCATG
Found at i:4250426 original size:171 final size:170
Alignment explanation
Indices: 4250201--4251220 Score: 1192
Period size: 171 Copynumber: 6.0 Consensus size: 170
4250191 TCGCTTTTAT
* ** * * * *
4250201 TTTTTTGACTCGCGATTTAATCTTAATTTTTTTATTC-TCTGATTCGTAGTTCAATCTCGATCTC
1 TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTC-GATTCGTGGTTCAATCTCAATCTC
* *
4250265 TTTAATTCAAAATCATAGTTTAATCTCGGTTGTTATTATCCCCTGACTCGTGGTTTAATCCCAGT
65 TTTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATCCC-GT
* * *
4250330 CTTCTTATTTTTTGACTTATGATTCAATCAAAGTTAATATCA
129 CTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
*
4250372 TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTCGATTCGTGGTTCAATCCCAATCTCT
1 TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTCAATCTCT
* * * *
4250437 TTAATTCAAAATCGTAGTTTAATCTC-AGTTGTTATTATCCCCTGACTCGTAGTTTAATCTCGAT
66 TTAATTCAAAATCATAGTTTAATCTCGA-TTGTTGTTATCCCCTGACTCGTGGTTTAATCCCG-T
* *
4250501 CTTCTTATTTTTTGACTTGTGATTTAATACAAGTTAACATCA
129 CTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
* * * ** * *
4250543 TTTTTTAACTCACGGTTTAATCCCGATCTCTTTATTC-TCTGATTTATGGTTAAATCTCAATCTT
1 TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTC-GATTCGTGGTTCAATCTCAATCTC
* * * *
4250607 TTTAATTCAAAATTACAGTTTAATCTCGGTTGTTGTTATCCCCTAACTCGTGGTTTAATCCCGGT
65 TTTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATCCC-GT
4250672 CTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
129 CTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
* * * * * * * * *
4250714 TTTTCTGACTCGC-AGTTTAATCT-TAGTCTCTTTATTATCCGATTC-TCAGTTTAATCCCAATA
1 TTTTTTGACTCACGA-TTTAATCTCGA-TCTCTTTATTCTTCGATTCGT-GGTTCAATCTCAATC
* * * * *
4250776 TCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATCCCCTGACTTGTGATTTAATCTCG
63 TCTTTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATC-CC
* *
4250841 GTCTTCTTATTTTCTGACTTGTGATTCAATCCAAGTTAACATTA
127 GTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
* * * *** * *
4250885 TTTTTTGACTCACGATTTAATCTCGGTCTCTTTATTTTTTGATTTACGATTCAATC-CTGATCTC
1 TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTC-AATCTC
* * * * *
4250949 TTTAATTCAAAATCACAATTTAATCTCGATTGTTGTTATCTCCTGACTCGTGATTTAATCTCGAT
65 TTTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATCCCG-T
* * *
4251014 CTTCTTATTTTTTTTACTTGTGATACAATCCAAGTTAACGTCA
129 CTTCTTA-TTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
* * * * * *
4251057 TTTTTTAACTTAC-AGTTTAATCTTGATCTCTTTATTCTTCGATTCGCGGTTCAATTTCGATCTC
1 TTTTTTGACTCACGA-TTTAATCTCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTCAATCTC
* * * *
4251121 TTTAATTCAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTATTCCCAGT
65 TTTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATCCC-GT
*
4251186 CTCCTTATTTTTTGACTTGTGATTCAATCCAAGTT
129 CTTCTTATTTTTTGACTTGTGATTCAATCCAAGTT
4251221 CAATCCTGAT
Statistics
Matches: 720, Mismatches: 109, Indels: 40
0.83 0.13 0.05
Matches are distributed among these distances:
170 7 0.01
171 565 0.78
172 146 0.20
173 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (170 bp):
TTTTTTGACTCACGATTTAATCTCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTCAATCTCT
TTAATTCAAAATCATAGTTTAATCTCGATTGTTGTTATCCCCTGACTCGTGGTTTAATCCCGTCT
TCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCA
Found at i:4250848 original size:342 final size:342
Alignment explanation
Indices: 4250231--4251220 Score: 1326
Period size: 342 Copynumber: 2.9 Consensus size: 342
4250221 TCTTAATTTT
** * *
4250231 TTTATTCTCTGATTCGTAGTTCAATCTCGATCTCTTTAATTCAAAATCATAGTTTAATCTCGGTT
1 TTTATTCTCTGATTTATGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGGTT
* * * *
4250296 GTTATTATCCCCTGACTCGTGGTTTAATCCCAGTCTTCTTATTTTTTGACTTATGATTCAATCAA
66 GTTGTTATCCCCTGACTCGTGGTTTAATCCCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCA
* *
4250361 AGTTAATATCATTTTTTGACTCAC-GATTTAATCTCGATCTCTTTATTCTTCGATTCGT-GGTTC
131 AGTTAACATCATTTTTTGACTCACAG-TTTAATCTTGATCTCTTTATTCTTCGATTC-TCGGTTC
* *
4250424 AATCCCAATCTCTTTAATTCAAAATCGTAGTTTAATC-TCAGTTGTTATTATCCCCTGACTCGT-
194 AATCCCAATCTCTTTAATTCAAAATCGTAGTTTAATCTTGA-TTGTTGTTATCCCCTGACTCGTG
* * *
4250487 AGTTTAATCTCGATCTTCTTATTTTTTGACTTGTGATTTAATACAAGTTAACATCATTTTTTAAC
258 A-TTTAATCTCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCATTTTTTAAC
*
4250552 TCACGGTTTAATCCCGATCTC
322 TCACGATTTAATCCCGATCTC
* * * *
4250573 TTTATTCTCTGATTTATGGTTAAATCTCAATCTTTTTAATTCAAAATTACAGTTTAATCTCGGTT
1 TTTATTCTCTGATTTATGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGGTT
*
4250638 GTTGTTATCCCCTAACTCGTGGTTTAATCCCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCA
66 GTTGTTATCCCCTGACTCGTGGTTTAATCCCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCA
* * * * * *
4250703 AGTTAACATCATTTTCTGACTCGCAGTTTAATCTT-AGTCTCTTTATTATCCGATTCTCAGTTTA
131 AGTTAACATCATTTTTTGACTCACAGTTTAATCTTGA-TCTCTTTATTCTTCGATTCTCGGTTCA
* *
4250767 ATCCCAATATCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATCCCCTGACTTGTGAT
195 ATCCCAATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATCCCCTGACTCGTGAT
* * *
4250832 TTAATCTCGGTCTTCTTATTTTCTGACTTGTGATTCAATCCAAGTTAACATTATTTTTTGACTCA
260 TTAATCTCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCATTTTTTAACTCA
* *
4250897 CGATTTAATCTCGGTCTC
325 CGATTTAATCCCGATCTC
* * * * * *
4250915 TTTATTTTTTGATTTACGATTCAATC-CTGATCTCTTTAATTCAAAATCACAATTTAATCTCGAT
1 TTTATTCTCTGATTTATGGTTCAATCTC-GATCTCTTTAATTCAAAATCACAGTTTAATCTCGGT
* * * * * *
4250979 TGTTGTTATCTCCTGACTCGTGATTTAATCTCGATCTTCTTATTTTTTTTACTTGTGATACAATC
65 TGTTGTTATCCCCTGACTCGTGGTTTAATCCCGGTCTTCTTA-TTTTTTGACTTGTGATTCAATC
* * * *
4251044 CAAGTTAACGTCATTTTTTAACTTACAGTTTAATCTTGATCTCTTTATTCTTCGATTCGCGGTTC
129 CAAGTTAACATCATTTTTTGACTCACAGTTTAATCTTGATCTCTTTATTCTTCGATTCTCGGTTC
** * * * * *
4251109 AATTTCGATCTCTTTAATTCAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGG
194 AATCCCAATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATCCCCTGACTCGTGA
* * * *
4251174 TTTATTCCCAGTCTCCTTATTTTTTGACTTGTGATTCAATCCAAGTT
259 TTTAATCTCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTT
4251221 CAATCCTGAT
Statistics
Matches: 565, Mismatches: 75, Indels: 15
0.86 0.11 0.02
Matches are distributed among these distances:
341 3 0.01
342 386 0.68
343 175 0.31
344 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (342 bp):
TTTATTCTCTGATTTATGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGGTT
GTTGTTATCCCCTGACTCGTGGTTTAATCCCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCA
AGTTAACATCATTTTTTGACTCACAGTTTAATCTTGATCTCTTTATTCTTCGATTCTCGGTTCAA
TCCCAATCTCTTTAATTCAAAATCGTAGTTTAATCTTGATTGTTGTTATCCCCTGACTCGTGATT
TAATCTCGGTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACATCATTTTTTAACTCAC
GATTTAATCCCGATCTC
Found at i:4250949 original size:34 final size:34
Alignment explanation
Indices: 4250882--4250952 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
4250872 CAAGTTAACA
* *
4250882 TTATTTTTTGACTCACGATTTAATCTCGGTCTCT
1 TTATTTTTTGACTCACGATTCAATCTCGATCTCT
* *
4250916 TTATTTTTTGATTTACGATTCAATC-CTGATCTCT
1 TTATTTTTTGACTCACGATTCAATCTC-GATCTCT
4250950 TTA
1 TTA
4250953 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.52
Consensus pattern (34 bp):
TTATTTTTTGACTCACGATTCAATCTCGATCTCT
Found at i:4252443 original size:21 final size:22
Alignment explanation
Indices: 4252400--4252448 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4252390 CCAAACCAGA
4252400 TCGAACCGCTCCCTAGATCGGC
1 TCGAACCGCTCCCTAGATCGGC
*
4252422 TCGAACTGCT-CCTCAG-TCGGC
1 TCGAACCGCTCCCT-AGATCGGC
4252443 TC-AACC
1 TCGAACC
4252449 AAACCACACG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 10 0.42
22 11 0.46
ACGTcount: A:0.18, C:0.41, G:0.20, T:0.20
Consensus pattern (22 bp):
TCGAACCGCTCCCTAGATCGGC
Found at i:4252690 original size:3 final size:3
Alignment explanation
Indices: 4252682--4252725 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
4252672 AAATGCTTTA
*
4252682 AAT AAT AAT AAT AAT AAT AAT AAT CTAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
4252726 TTTTATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4253055 original size:20 final size:20
Alignment explanation
Indices: 4253021--4253111 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 20
4253011 CAAAATCCCT
4253021 AAAATCCAAACCCTTAAATC
1 AAAATCCAAACCCTTAAATC
*
4253041 AAAACTCCAAA-CCTTAAATTTT
1 AAAA-TCCAAACCCTTAAA--TC
* *
4253063 AAAATCAAAACCCTAAAATC
1 AAAATCCAAACCCTTAAATC
* *
4253083 ----TCCAAACTCTAAAATC
1 AAAATCCAAACCCTTAAATC
4253099 AAAATCCTAAACC
1 AAAATCC-AAACC
4253112 TTTCACACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
16 14 0.25
20 15 0.27
21 15 0.27
22 11 0.20
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATCCAAACCCTTAAATC
Found at i:4253081 original size:14 final size:14
Alignment explanation
Indices: 4253062--4253109 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4253052 CCTTAAATTT
4253062 TAAAATCAAAACCC
1 TAAAATCAAAACCC
* *
4253076 TAAAATCTCCAAACTC
1 TAAAA--TCAAAACCC
*
4253092 TAAAATCAAAATCC
1 TAAAATCAAAACCC
4253106 TAAA
1 TAAA
4253110 CCTTTCACAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAATCAAAACCC
Found at i:4253165 original size:13 final size:13
Alignment explanation
Indices: 4253147--4253172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4253137 AAGATCCTAT
4253147 AAACCTTAAAACC
1 AAACCTTAAAACC
4253160 AAACCTTAAAACC
1 AAACCTTAAAACC
4253173 CTCAAAACTC
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:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
AAACCTTAAAACC
Found at i:4257846 original size:30 final size:30
Alignment explanation
Indices: 4257812--4257875 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4257802 ATCTAACTGG
4257812 ACCGGAATCGAACCGCCCAGACCGAACCGA
1 ACCGGAATCGAACCGCCCAGACCGAACCGA
* * * *
4257842 ACCGGTATTGAACCGCCCAGACTGAGCCGA
1 ACCGGAATCGAACCGCCCAGACCGAACCGA
4257872 ACCG
1 ACCG
4257876 CCCGTTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.25, T:0.08
Consensus pattern (30 bp):
ACCGGAATCGAACCGCCCAGACCGAACCGA
Found at i:4258263 original size:21 final size:21
Alignment explanation
Indices: 4258216--4258280 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
4258206 TGGAGTATTT
*
4258216 ATAAAAAAAAA-TTTTCAATA
1 ATAAAAAAAAATTTTTTAATA
4258236 CAGTAAAAAAAAATTTTTTAATA
1 -A-TAAAAAAAAATTTTTTAATA
* **
4258259 ATAAATAAAAATTGATTAATA
1 ATAAAAAAAAATTTTTTAATA
4258280 A
1 A
4258281 ATTAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 19 0.50
22 11 0.29
23 8 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
ATAAAAAAAAATTTTTTAATA
Found at i:4258268 original size:22 final size:21
Alignment explanation
Indices: 4258216--4258271 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
4258206 TGGAGTATTT
4258216 ATAAAAAAAAATTTTCAATAC
1 ATAAAAAAAAATTTTCAATAC
*
4258237 AGTAAAAAAAAATTTTTTAATA-
1 A-TAAAAAAAAA-TTTTCAATAC
*
4258259 ATAAATAAAAATT
1 ATAAAAAAAAATT
4258272 GATTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 10 0.32
22 11 0.35
23 8 0.26
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAAAAAAATTTTCAATAC
Found at i:4258493 original size:208 final size:205
Alignment explanation
Indices: 4258047--4258442 Score: 473
Period size: 207 Copynumber: 1.9 Consensus size: 205
4258037 AAACTTTAAA
* **
4258047 AATAATAATATAAAAATAAATTTAAT-AA-TAATATTA-AAGTAATAAAAAATGAAAGAAAAAAG
1 AATAATAA-ATAAAAATTAA-TTAATAAATTAATAAAACAAGTAAT-AAAAAT-AAAGAAAAAAG
* * * * *
4258109 AAATTTTTATCCGACGATGAGATTCAAAGGTATTCCGAGTAGTGATGCCTACGAAATCTCTAGGT
62 AAATTTTAATCCAACGATGAGATTCAAAAGTATTCCGAGTAGAGATGCCTAAGAAATCTCTAGGT
* * *
4258174 GAGAAGATTTTTTTAAAATACTGCCAGCGTATTGGAGTATTTATAAAAAAAAATTTTCAATACAG
127 GAGAAGATTTTTTTAAAATACTACCAGCGTATTGGAATATTTAT--AAAAAAATCTTCAATACAG
4258239 TAAAAAAAAATTTTTT
190 TAAAAAAAAATTTTTT
* *
4258255 AATAATAAATAAAAATTGATTAATAAATTAA-AAATATAAGTAATAAAAAT-AAGAAGAAAAGAA
1 AATAATAAATAAAAATTAATTAATAAATTAATAAA-ACAAGTAATAAAAATAAAGAA-AAAAGAA
* * *
4258318 A-TTTAATCCAATGATGGGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTAGGT
64 ATTTTAATCCAACGATGAGATTC-AAAAGTATTCCGAGTAGAGATGC-CTAAGAAATCTCTAGGT
* *
4258382 GAGAAGATTTTTTTGTAAAATATTACCAGCGTATTGGAATATTTAT-AGAAAATCTTCAATA
127 GAGAAGA-TTTTTT-TAAAATACTACCAGCGTATTGGAATATTTATAAAAAAATCTTCAATA
4258443 TGATTAAATT
Statistics
Matches: 162, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
206 27 0.17
207 54 0.33
208 40 0.25
209 13 0.08
210 28 0.17
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (205 bp):
AATAATAAATAAAAATTAATTAATAAATTAATAAAACAAGTAATAAAAATAAAGAAAAAAGAAAT
TTTAATCCAACGATGAGATTCAAAAGTATTCCGAGTAGAGATGCCTAAGAAATCTCTAGGTGAGA
AGATTTTTTTAAAATACTACCAGCGTATTGGAATATTTATAAAAAAATCTTCAATACAGTAAAAA
AAAATTTTTT
Found at i:4268439 original size:13 final size:13
Alignment explanation
Indices: 4268421--4268445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4268411 AGAATTTGTT
4268421 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
4268434 AGAAAAAGAAAA
1 AGAAAAAGAAAA
4268446 GAAAAGAAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:4270551 original size:3 final size:3
Alignment explanation
Indices: 4270545--4270593 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
4270535 TTATTACCAG
* * *
4270545 TAA TAA T-A TAA -AA TAA CAA TAA TAG TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4270591 TAA
1 TAA
4270594 CATCATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:4270621 original size:19 final size:18
Alignment explanation
Indices: 4270597--4270650 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
4270587 ACAATAACAT
4270597 CATAAAAATAAAAAAATAA
1 CATAAAAATAAAAAAA-AA
*
4270616 CATAAAAAATCAAAATCAAAA
1 CAT-AAAAAT-AAAA-AAAAA
4270637 CA-AAAAATAAAAAA
1 CATAAAAATAAAAAA
4270651 TAAAAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 9 0.30
20 6 0.20
21 8 0.27
22 2 0.07
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (18 bp):
CATAAAAATAAAAAAAAA
Found at i:4270630 original size:26 final size:24
Alignment explanation
Indices: 4270601--4270660 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 24
4270591 TAACATCATA
4270601 AAAATAAAA-AAATAACATAAAAAAT
1 AAAATAAAACAAA-AA-ATAAAAAAT
4270626 CAAAATCAAAACAAAAAATAAAAAAT
1 -AAAAT-AAAACAAAAAATAAAAAAT
4270652 AAAA-AAAAC
1 AAAATAAAAC
4270661 CTACGAAGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 5 0.16
25 4 0.12
26 14 0.44
27 6 0.19
28 3 0.09
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (24 bp):
AAAATAAAACAAAAAATAAAAAAT
Found at i:4270649 original size:13 final size:12
Alignment explanation
Indices: 4270600--4270656 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
4270590 ATAACATCAT
4270600 AAAAATAAAAAA
1 AAAAATAAAAAA
*
4270612 ATAACATAAAAAA
1 A-AAAATAAAAAA
* *
4270625 TCAAAATCAAAACA
1 -AAAAAT-AAAAAA
4270639 AAAAATAAAAAA
1 AAAAATAAAAAA
4270651 TAAAAA
1 -AAAAA
4270657 AAACCTACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
12 6 0.17
13 24 0.69
14 5 0.14
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:4270658 original size:8 final size:7
Alignment explanation
Indices: 4270600--4270657 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
4270590 ATAACATCAT
4270600 AAAAATA
1 AAAAATA
4270607 AAAAA-A
1 AAAAATA
* *
4270613 TAACATA
1 AAAAATA
4270620 AAAAAT-
1 AAAAATA
*
4270626 CAAAAT-
1 AAAAATA
* *
4270632 CAAAACA
1 AAAAATA
4270639 AAAAATA
1 AAAAATA
4270646 AAAAATA
1 AAAAATA
4270653 AAAAA
1 AAAAA
4270658 AACCTACGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 14 0.34
7 27 0.66
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:4271447 original size:16 final size:17
Alignment explanation
Indices: 4271422--4271454 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4271412 TGAAATCAAA
4271422 TACTTCTTTTT-TTTTT
1 TACTTCTTTTTCTTTTT
*
4271438 TACTTTTTTTTCTTTTT
1 TACTTCTTTTTCTTTTT
4271455 GTTTTAAAGA
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:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TACTTCTTTTTCTTTTT
Found at i:4274906 original size:17 final size:17
Alignment explanation
Indices: 4274881--4274920 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4274871 ATTTTATAAA
*
4274881 AATTT-AAAATATATAT
1 AATTTAAAAAAATATAT
4274897 AATTTAAAAAAATATAT
1 AATTTAAAAAAATATAT
4274914 AATTTAA
1 AATTTAA
4274921 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAAAAATATAT
Done.