Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 120 of 129
Found at i:20309978 original size:10 final size:9
Alignment explanation
Indices: 20309946--20310010 Score: 62
Period size: 10 Copynumber: 6.9 Consensus size: 9
20309936 AACATTGTCA
20309946 TTTTTTATT-
1 TTTTTT-TTG
20309955 TTTATTTTTG
1 TTT-TTTTTG
20309965 TTTTTTTGTG
1 TTTTTTT-TG
20309975 TTTTTTCTTG
1 TTTTTT-TTG
20309985 -TTTTTTTG
1 TTTTTTTTG
*
20309993 TTTTTTTTA
1 TTTTTTTTG
20310002 TATTTTTTT
1 T-TTTTTTT
20310011 TTACCAAAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
8 3 0.06
9 22 0.45
10 23 0.47
11 1 0.02
ACGTcount: A:0.06, C:0.02, G:0.08, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:20310007 original size:18 final size:18
Alignment explanation
Indices: 20309966--20310009 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
20309956 TTATTTTTGT
*
20309966 TTTTTTGTGTTTTTTCTTG
1 TTTTTT-TGTTTTTTCTTA
20309985 TTTTTTTGTTTTTT-TTA
1 TTTTTTTGTTTTTTCTTA
20310002 TATTTTTT
1 T-TTTTTT
20310010 TTTACCAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (18 bp):
TTTTTTTGTTTTTTCTTA
Found at i:20310114 original size:41 final size:41
Alignment explanation
Indices: 20310019--20310478 Score: 651
Period size: 41 Copynumber: 11.1 Consensus size: 41
20310009 TTTTACCAAA
* *
20310019 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATT
* *
20310062 GCTCCTTTAAACAGACGCACCACGACTTTTG-AAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAATAAATT
**
20310103 GCTCCTCTAAACAGAGGCATTACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* *
20310144 GCTCCTCTAAACAGAGGCACCACGACTTTTAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
*
20310185 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* * *
20310226 GCTCCTCTAAACAGAGGCA--ATGGAACTTTGAAAAGTAAACT
1 GCTCCTCTAAACAGAGGCACCA-CG-ACTTTGAAAAATAAATT
* *
20310267 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGAAAAATAAATT
20310308 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
20310349 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* * *
20310390 ACTTCTCTAAATAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAA-TAAATT
*
20310432 GCTCCTCTAATCAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
20310473 GCTCCT
1 GCTCCT
20310479 TGACAATCAT
Statistics
Matches: 379, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.00
40 6 0.02
41 303 0.80
42 40 0.11
43 25 0.07
44 4 0.01
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
Found at i:20311718 original size:11 final size:9
Alignment explanation
Indices: 20311704--20311747 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 9
20311694 CATTTTCTCA
20311704 TTTCTTTCTT
1 TTTCTTT-TT
20311714 CTTTCTTTTT
1 -TTTCTTTTT
20311724 TTTCCTTTTTT
1 TTT-C-TTTTT
20311735 TTTCTTTTT
1 TTTCTTTTT
20311744 TTTC
1 TTTC
20311748 ATCATCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 12 0.39
10 4 0.13
11 15 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:20311723 original size:24 final size:23
Alignment explanation
Indices: 20311691--20311768 Score: 63
Period size: 25 Copynumber: 3.4 Consensus size: 23
20311681 AATCTCCTTT
*
20311691 TTTCATTTTCTCATTTCTTTCTTC
1 TTTCTTTTTCTCATTTCTTT-TTC
* * *
20311715 TTTCTTTTTTTTCCTTTTTTTTTC
1 TTTC-TTTTTCTCATTTCTTTTTC
*
20311739 TTT-TTTTTCATCA--TCTTTTTT
1 TTTCTTTTTC-TCATTTCTTTTTC
20311760 TTTCTTTTT
1 TTTCTTTTT
20311769 TATCATTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
21 9 0.21
22 10 0.23
23 2 0.05
24 10 0.23
25 12 0.28
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTCTTTTTCTCATTTCTTTTTC
Found at i:20311727 original size:20 final size:19
Alignment explanation
Indices: 20311704--20311747 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
20311694 CATTTTCTCA
20311704 TTTCTTTCTTCTTTCTTTTT
1 TTTCTTT-TTCTTTCTTTTT
*
20311724 TTTCCTTTTTTTTTCTTTTT
1 TTT-CTTTTTCTTTCTTTTT
20311744 TTTC
1 TTTC
20311748 ATCATCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTCTTTTTCTTTCTTTTT
Found at i:20311733 original size:10 final size:10
Alignment explanation
Indices: 20311718--20311747 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20311708 TTTCTTCTTT
20311718 CTTTTTTTTC
1 CTTTTTTTTC
*
20311728 CTTTTTTTTT
1 CTTTTTTTTC
20311738 CTTTTTTTTC
1 CTTTTTTTTC
20311748 ATCATCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTTTC
Found at i:20311757 original size:20 final size:20
Alignment explanation
Indices: 20311715--20311762 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
20311705 TTCTTTCTTC
* ** *
20311715 TTTCTTTTTTTTCCTTTTTT
1 TTTCTTTTTTTTCATCATCT
20311735 TTTCTTTTTTTTCATCATCT
1 TTTCTTTTTTTTCATCATCT
20311755 TTT-TTTTT
1 TTTCTTTTT
20311763 CTTTTTTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTTTCATCATCT
Found at i:20311769 original size:24 final size:23
Alignment explanation
Indices: 20311688--20311774 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 23
20311678 TTGAATCTCC
* * *
20311688 TTTTTTCATTTTCTCATTTCTTT
1 TTTTTTCTTTTTTTCATCTCTTT
*
20311711 CTTCTTTCTTTTTTT--TC-CTTT
1 -TTTTTTCTTTTTTTCATCTCTTT
20311732 TTTTTTCTTTTTTTTCATCATCTTT
1 TTTTTTC-TTTTTTTCATC-TCTTT
20311757 TTTTTTCTTTTTTATCAT
1 TTTTTTCTTTTTT-TCAT
20311775 TTTTCATCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 6 0.12
21 11 0.21
22 1 0.02
23 2 0.04
24 17 0.33
25 15 0.29
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTCTTTTTTTCATCTCTTT
Found at i:20315604 original size:12 final size:12
Alignment explanation
Indices: 20315587--20315611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20315577 TTATTTAAAG
20315587 AAAAATCAAAAT
1 AAAAATCAAAAT
20315599 AAAAATCAAAAT
1 AAAAATCAAAAT
20315611 A
1 A
20315612 GAAAGGAAGG
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:20316003 original size:117 final size:117
Alignment explanation
Indices: 20315645--20316055 Score: 535
Period size: 117 Copynumber: 3.5 Consensus size: 117
20315635 TCTTATGTAG
* * *
20315645 GGAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAATCTATTTTTTAGAAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATT
** * *
20315710 GATACTTTCAACTTTT-CCTCAAAAA-ATTTTTTTATGAAACTTTGATTTTCAAA
66 GATACTTTCAACTTTTCCCT-AAAAATAACTTTTTA-AAAATTTTGATTTTC-AA
* * * * *
20315763 GGAAAATTAATACTTTCAACTTTTCCTCAAAAATCCCTTTTTT-AAAATTTATTTCTAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT--ATTTTTTGGAAATTTATTTTTAAGAAAAA
* *
20315827 TTGATACTTTCAACTTTTCCTTAAAAAT--GTTTTTCAAAAATTTTGATTTTCAA
64 TTGATACTTTCAACTTTTCCCTAAAAATAACTTTTT-AAAAATTTTGATTTTCAA
* * *
20315880 GAAAAATTGATACTTTCAACTTTTCCCCAAAGATATTTTTTGGAAATTTATTTTTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATT
*
20315945 GATACTTTCAACTTTTCCCTAAAAATAACTTTTTGAAAATTTTGATTTTCAA
66 GATACTTTCAACTTTTCCCTAAAAATAACTTTTTAAAAATTTTGATTTTCAA
*
20315997 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAA-TTT-ATTTTTA
20316056 TTTAAAGAAA
Statistics
Matches: 256, Mismatches: 26, Indels: 20
0.85 0.09 0.07
Matches are distributed among these distances:
115 6 0.02
116 45 0.18
117 81 0.32
118 65 0.25
119 44 0.17
120 15 0.06
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCTAAAAATAACTTTTTAAAAATTTTGATTTTCAA
Found at i:20316009 original size:176 final size:176
Alignment explanation
Indices: 20315645--20316036 Score: 494
Period size: 176 Copynumber: 2.2 Consensus size: 176
20315635 TCTTATGTAG
* *** **
20315645 GGAAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTGGAAATCTATTTTTTAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCT-TAAAAATATTTTTCAAAAATCTATTTTCAAGAAAAAT
* *
20315709 TGATACTTTCAACTTTTCCTCAAAAAATTTTTTTATGAAACTTTGATTTTCAAAGGAAAATTAAT
65 TGATACTTTCAACTTTTCCCCAAAAAATTTTTTTAGGAAACTTTGATTTTCAAAGGAAAATTAAT
** *
20315774 ACTTTCAACTTTTCCTCAAAAATCCCTTTTTTAAAATTTATTTCTAA
130 ACTTTCAACTTTTCCTCAAAAATAACTTTTTGAAAATTTATTTCTAA
* * *
20315821 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTCAAAAATTTTGATTTTCAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTCAAAAA-TCT-ATTTTCAAGAAAAA
* * *
20315886 TTGATACTTTCAACTTTTCCCC-AAAGATATTTTTT-GGAAA-TTT-ATTTT-TAAGGAAAATTG
64 TTGATACTTTCAACTTTTCCCCAAAAAAT-TTTTTTAGGAAACTTTGATTTTCAAAGGAAAATTA
20315946 ATACTTTCAACTTTTCC-CTAAAAATAACTTTTTGAAAATTTTGATTT-TCAA
128 ATACTTTCAACTTTTCCTC-AAAAATAACTTTTTGAAAA-TTT-ATTTCT-AA
*
20315997 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT
20316037 TTGGAAATTT
Statistics
Matches: 188, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
173 1 0.01
174 43 0.23
175 9 0.05
176 83 0.44
177 13 0.07
178 39 0.21
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (176 bp):
GGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTCAAAAATCTATTTTCAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAAATTTTTTTAGGAAACTTTGATTTTCAAAGGAAAATTAATA
CTTTCAACTTTTCCTCAAAAATAACTTTTTGAAAATTTATTTCTAA
Found at i:20316098 original size:11 final size:11
Alignment explanation
Indices: 20316073--20316125 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
20316063 AAAATAGAAT
20316073 AATAAAAAAATA
1 AATAAAAAAA-A
*
20316085 AAAAATAAAAAA
1 AATAA-AAAAAA
*
20316097 AAGTAAAACAAA
1 AA-TAAAAAAAA
*
20316109 AATAAAAATAA
1 AATAAAAAAAA
20316120 AATAAA
1 AATAAA
20316126 GATAAAAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 13 0.38
12 14 0.41
13 7 0.21
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:20316130 original size:11 final size:11
Alignment explanation
Indices: 20316063--20316132 Score: 58
Period size: 11 Copynumber: 6.4 Consensus size: 11
20316053 TTATTTAAAG
20316063 AAAATAGAATAAT
1 AAAATA-AA-AAT
20316076 AAAA-AAATAA-
1 AAAATAAA-AAT
20316086 AAAATAAAAA-
1 AAAATAAAAAT
*
20316096 AAAGTAAAACA-
1 AAAATAAAA-AT
20316107 AAAATAAAAAT
1 AAAATAAAAAT
*
20316118 AAAATAAAGAT
1 AAAATAAAAAT
20316129 AAAA
1 AAAA
20316133 AGAATATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 15 0.29
11 31 0.61
12 1 0.02
13 4 0.08
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:20316130 original size:17 final size:16
Alignment explanation
Indices: 20316063--20316147 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
20316053 TTATTTAAAG
*
20316063 AAAATAGAATAATAA-A
1 AAAATAAAATAA-AATA
20316079 AAAATAAAAAATAAAA-A
1 AAAAT--AAAATAAAATA
* *
20316096 AAAGTAAAACAAAAATA
1 AAAATAAAA-TAAAATA
20316113 AAAATAAAATAAAGATA
1 AAAATAAAATAAA-ATA
* * *
20316130 AAAAGAATATTAAATA
1 AAAATAAAATAAAATA
20316146 AA
1 AA
20316148 CCTAACCTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
15 4 0.07
16 17 0.30
17 29 0.52
18 6 0.11
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:20316181 original size:17 final size:17
Alignment explanation
Indices: 20316058--20316214 Score: 61
Period size: 16 Copynumber: 8.5 Consensus size: 17
20316048 GATTTTTATT
* * *
20316058 TAAAGAAAATAGAATAA
1 TAAAAAAAATAAAAAAA
20316075 T-AAAAAAAT-AAAAAA
1 TAAAAAAAATAAAAAAA
20316090 TAAAAAAAAGTAAAACAAA
1 TAAAAAAAA-TAAAA-AAA
*
20316109 -AATAAAAATAAAATAAAGA
1 TAAAAAAAAT-AAA-AAA-A
*
20316128 TAAAAAGAATATTAAATAAACC
1 TAAAAA-AA-A-TAAA-AAA-A
*
20316150 TAACCTAATAAATAAAAAAA
1 TAA---AAAAAATAAAAAAA
*
20316170 TAAAAAAAATAAATAAA
1 TAAAAAAAATAAAAAAA
* *
20316187 -CAAAGAAATGAAAAAAA
1 TAAAAAAAAT-AAAAAAA
20316204 TTCAAAAAAAA
1 -T-AAAAAAAA
20316215 ATTAAAATTA
Statistics
Matches: 106, Mismatches: 16, Indels: 33
0.68 0.10 0.21
Matches are distributed among these distances:
15 5 0.05
16 21 0.20
17 21 0.20
18 15 0.14
19 5 0.05
20 13 0.12
21 5 0.05
22 15 0.14
23 2 0.02
24 2 0.02
25 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:20316230 original size:9 final size:8
Alignment explanation
Indices: 20316058--20316204 Score: 55
Period size: 9 Copynumber: 16.1 Consensus size: 8
20316048 GATTTTTATT
20316058 TAAAGAAAA
1 TAAA-AAAA
* *
20316067 TAGAATAA
1 TAAAAAAA
20316075 TAAAAAAA
1 TAAAAAAA
20316083 T-AAAAAA
1 TAAAAAAA
20316090 TAAAAAAAA
1 T-AAAAAAA
20316099 GTAAAACAAA
1 -TAAAA-AAA
20316109 -AATAAAAA
1 TAA-AAAAA
20316117 TAAAATAAAGA
1 T-AAA-AAA-A
20316128 TAAAAAGAA
1 TAAAAA-AA
20316137 TATTAAATAAA
1 TA--AAA-AAA
20316148 CCTAACCTAATAAA
1 --TAA---AA-AAA
20316162 TAAAAAAA
1 TAAAAAAA
20316170 TAAAAAAAA
1 T-AAAAAAA
*
20316179 TAAATAAA
1 TAAAAAAA
* *
20316187 CAAAGAAA
1 TAAAAAAA
20316195 TGAAAAAAA
1 T-AAAAAAA
20316204 T
1 T
20316205 TCAAAAAAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 40
0.69 0.06 0.25
Matches are distributed among these distances:
7 7 0.06
8 31 0.28
9 38 0.35
10 13 0.12
11 8 0.07
12 4 0.04
13 2 0.02
14 6 0.06
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:20317188 original size:17 final size:20
Alignment explanation
Indices: 20317165--20317208 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 20
20317155 CAAGAAAAAA
*
20317165 AAATAAAT-TATAA-TATAT
1 AAATAAATATAGAACTATAT
20317183 -AATAAATATAGAACTATAT
1 AAATAAATATAGAACTATAT
20317202 AAATAAA
1 AAATAAA
20317209 ATACATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 5 0.23
20 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAATAAATATAGAACTATAT
Found at i:20317222 original size:21 final size:21
Alignment explanation
Indices: 20317198--20317292 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
20317188 ATATAGAACT
*
20317198 ATATAAATAAAATACATATAA
1 ATATAAATAAAATAAATATAA
* *
20317219 ATATTAACAAAAT-AA-AT-A
1 ATATAAATAAAATAAATATAA
*
20317237 A-ATAAATAAGTAA-AAATATAC
1 ATATAAATAA--AATAAATATAA
20317258 ATAT-AATAATAATAAATAATAA
1 ATATAAATAA-AATAAAT-ATAA
*
20317280 A-ATACATAAAATA
1 ATATAAATAAAATA
20317293 CAAAAGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 6 0.11
20 6 0.11
21 27 0.47
22 10 0.18
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (21 bp):
ATATAAATAAAATAAATATAA
Found at i:20335270 original size:13 final size:13
Alignment explanation
Indices: 20335252--20335276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20335242 CAGCTCCCTA
20335252 CCTTAATTTGGAT
1 CCTTAATTTGGAT
20335265 CCTTAATTTGGA
1 CCTTAATTTGGA
20335277 GTTTGACCGC
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
CCTTAATTTGGAT
Found at i:20335471 original size:17 final size:16
Alignment explanation
Indices: 20335429--20335471 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
20335419 TCTCATTTTT
*
20335429 ATATTTAAATTTGATA
1 ATATTTATATTTGATA
**
20335445 ATATAAATATTTGTATA
1 ATATTTATATTTG-ATA
20335462 ATATTTATAT
1 ATATTTATAT
20335472 CATATCAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
ATATTTATATTTGATA
Found at i:20350289 original size:5 final size:5
Alignment explanation
Indices: 20350281--20350319 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
20350271 AAGCCGAGAG
20350281 AAAAC AAAAC AAAAC AAAAC AAAAC AGACAA- AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC A-A-AAC AAAAC AAA
20350320 TGAAAATTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 2 0.06
5 25 0.81
6 2 0.06
7 2 0.06
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:20351863 original size:105 final size:105
Alignment explanation
Indices: 20351681--20351995 Score: 533
Period size: 105 Copynumber: 3.0 Consensus size: 105
20351671 CATATGGCGA
* *
20351681 TGTTTTTCATGGAAGGGCTAACACA-TAGCTTTCCTAAATGTAACACCTCATAGAAAAGATTCGG
1 TGTTTTTCATGGAAGGGCTAACACATTA-CTTTCCTCAATGTAACACCTCATAGAAAAGATTCAG
* *
20351745 TGCTAATTTCAGTTATTCACAAACATATAAAAAGCAGTAAG
65 TGCTAATTTCAGTTATTCAGAAATATATAAAAAGCAGTAAG
* *
20351786 TGTTTTTCATGGATGGGCTAACACATTACTTTCCTCAATGTAACACCTCATAGAAAAGCTTCAGT
1 TGTTTTTCATGGAAGGGCTAACACATTACTTTCCTCAATGTAACACCTCATAGAAAAGATTCAGT
*
20351851 GCTAATTTCAGTTATTCAGATATATATAAAAAGCAGTAAG
66 GCTAATTTCAGTTATTCAGAAATATATAAAAAGCAGTAAG
* *
20351891 TGTTTTTCATGGAAGGGCTAACACGTAACTTTCCTCAATGTAACACCTCATAGAAAAGATTCAGT
1 TGTTTTTCATGGAAGGGCTAACACATTACTTTCCTCAATGTAACACCTCATAGAAAAGATTCAGT
20351956 GCTAATTTCAGTTATTCAGAAATATATAAAAAGCAGTAAG
66 GCTAATTTCAGTTATTCAGAAATATATAAAAAGCAGTAAG
20351996 CATACCGGTA
Statistics
Matches: 197, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
105 195 0.99
106 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (105 bp):
TGTTTTTCATGGAAGGGCTAACACATTACTTTCCTCAATGTAACACCTCATAGAAAAGATTCAGT
GCTAATTTCAGTTATTCAGAAATATATAAAAAGCAGTAAG
Found at i:20359098 original size:18 final size:19
Alignment explanation
Indices: 20359070--20359105 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20359060 TTTTTTACAT
20359070 TTATATTTATTATATTATC
1 TTATATTTATTATATTATC
*
20359089 TTAT-TTTATTTTATTAT
1 TTATATTTATTATATTAT
20359106 AATAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATTTATTATATTATC
Found at i:20359371 original size:61 final size:57
Alignment explanation
Indices: 20359295--20359432 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 57
20359285 AAATAATTAT
* *
20359295 AAAATTATTTTTATAATTATAATATA-ATGAGTATTATAATAATTTTGATT-AATTATAATAA
1 AAAAATATTTTTATAATTATAATA-AGA-GA-CATTATAAT--TTTT-ATTCAATTATAATAA
*
20359356 AAAAATATTTTTATAATTATAATAAGAGACATTATAATTTTTATTCAATTATGATAA
1 AAAAATATTTTTATAATTATAATAAGAGACATTATAATTTTTATTCAATTATAATAA
*
20359413 ATAAAATATTTTTTTAATTA
1 A-AAAATATTTTTATAATTA
20359433 AAGAGATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
56 3 0.04
57 15 0.21
58 17 0.24
59 8 0.11
60 3 0.04
61 24 0.34
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (57 bp):
AAAAATATTTTTATAATTATAATAAGAGACATTATAATTTTTATTCAATTATAATAA
Found at i:20359451 original size:57 final size:57
Alignment explanation
Indices: 20359295--20359452 Score: 169
Period size: 57 Copynumber: 2.7 Consensus size: 57
20359285 AAATAATTAT
*
20359295 AAAATTATTTTTATAATTATAATATAATGAGTATTATAATAATTTTGATTAATTATAATAA
1 AAAAATATTTTTATAATTAT-A-ATAA-GA-TATTATAATAATTTTGATTAATTATAATAA
* * * * *
20359356 AAAAATATTTTTATAATTATAATAAGAGA-CATTATAATTTTTATTCAATTATGATAA
1 AAAAATATTTTTATAATTATAATAAGATATTATAATAATTTTGATT-AATTATAATAA
* *
20359413 ATAAAATATTTTTTTAATTA-AA-GAGATATTATAATAATTT
1 A-AAAATATTTTTATAATTATAATAAGATATTATAATAATTT
20359453 CATCATTTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
56 17 0.20
57 23 0.28
58 19 0.23
59 4 0.05
60 1 0.01
61 19 0.23
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (57 bp):
AAAAATATTTTTATAATTATAATAAGATATTATAATAATTTTGATTAATTATAATAA
Found at i:20359507 original size:25 final size:24
Alignment explanation
Indices: 20359442--20359508 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
20359432 AAAGAGATAT
*
20359442 TATAATAATTTCATCATTTATAAAA
1 TATAATATTTTCATCA-TTATAAAA
* **
20359467 GA-AATATTTTGGTCATTATAAAA
1 TATAATATTTTCATCATTATAAAA
20359490 TATATATATTTTCATCATT
1 TATA-ATATTTTCATCATT
20359509 TCAATCACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 9 0.27
24 11 0.33
25 13 0.39
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (24 bp):
TATAATATTTTCATCATTATAAAA
Found at i:20360114 original size:15 final size:14
Alignment explanation
Indices: 20360086--20360125 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
20360076 TATATTTTAG
20360086 ATTATAAT-TAATT
1 ATTATAATATAATT
20360099 ATTTATAATATAATT
1 A-TTATAATATAATT
20360114 ATTATAA-ATAAT
1 ATTATAATATAAT
20360126 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATAATATAATT
Found at i:20360136 original size:15 final size:18
Alignment explanation
Indices: 20360088--20360130 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20360078 TATTTTAGAT
**
20360088 TATAATTAATTATTTATAA
1 TATAATT-ATTATAAATAA
20360107 TATAATTATTATAAATAA
1 TATAATTATTATAAATAA
20360125 TA-AATT
1 TATAATT
20360131 TTTAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATTATTATAAATAA
Found at i:20362231 original size:16 final size:16
Alignment explanation
Indices: 20362200--20362230 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20362190 AATTCCGAAT
20362200 TAAAAAAAGATTAAAA
1 TAAAAAAAGATTAAAA
20362216 TAAAAAAA-ATTAAAA
1 TAAAAAAAGATTAAAA
20362231 ACATGCTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
TAAAAAAAGATTAAAA
Found at i:20363681 original size:28 final size:28
Alignment explanation
Indices: 20363627--20363681 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
20363617 CATAAAAATA
* *
20363627 ATTTTTTAATATATAAAATATATATTAT
1 ATTTTTTAATATAGAAAAAATATATTAT
*
20363655 ATTTTTTATTATGAGAAAAAATA-ATTA
1 ATTTTTTAATAT-AGAAAAAATATATTA
20363682 ACTAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
ATTTTTTAATATAGAAAAAATATATTAT
Found at i:20363806 original size:147 final size:148
Alignment explanation
Indices: 20363635--20363936 Score: 597
Period size: 147 Copynumber: 2.0 Consensus size: 148
20363625 TAATTTTTTA
20363635 ATATATAAAATATATATTATATTTTTTATTATGAGAAAAAATAATTAACTAAAAGAAAATTTTAA
1 ATATATAAAATATATATTATATTTTTTATTATGAGAAAAAATAATTAACTAAAAGAAAATTTTAA
20363700 TATGTAAAAATAATTGGTTAAAAACTTATAATTAGTTAGAAAATATAAATATATAAAATATATTT
66 TATGTAAAAATAATTGGTTAAAAACTTATAATTAGTTAGAAAATATAAATATATAAAATATATTT
20363765 TT-TCATATATTATAATT
131 TTGTCATATATTATAATT
20363782 ATATATAAAATATATATTATATTTTTTATTATGAGAAAAAATAATTAACTAAAAGAAAATTTTAA
1 ATATATAAAATATATATTATATTTTTTATTATGAGAAAAAATAATTAACTAAAAGAAAATTTTAA
20363847 TATGTAAAAATAATTGGTTAAAAACTTATAATTAGTTAGAAAATATAAATATATAAAATATATTT
66 TATGTAAAAATAATTGGTTAAAAACTTATAATTAGTTAGAAAATATAAATATATAAAATATATTT
20363912 TTGTCATATATTATAATT
131 TTGTCATATATTATAATT
20363930 ATATATA
1 ATATATA
20363937 TATTCATTTA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 132 0.86
148 22 0.14
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (148 bp):
ATATATAAAATATATATTATATTTTTTATTATGAGAAAAAATAATTAACTAAAAGAAAATTTTAA
TATGTAAAAATAATTGGTTAAAAACTTATAATTAGTTAGAAAATATAAATATATAAAATATATTT
TTGTCATATATTATAATT
Found at i:20367362 original size:39 final size:39
Alignment explanation
Indices: 20367319--20367421 Score: 179
Period size: 39 Copynumber: 2.6 Consensus size: 39
20367309 GACAGTTTGA
* *
20367319 TAGGTGTAGTGTAATAAATCTTGAATAAAAATTGATGGG
1 TAGGTGAAATGTAATAAATCTTGAATAAAAATTGATGGG
20367358 TAGGTGAAATGTAATAAATCTTGAATAAAAATTGATGGG
1 TAGGTGAAATGTAATAAATCTTGAATAAAAATTGATGGG
*
20367397 CAGGTGAAATGTAATAAATCTTGAA
1 TAGGTGAAATGTAATAAATCTTGAA
20367422 AGATAGGTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (39 bp):
TAGGTGAAATGTAATAAATCTTGAATAAAAATTGATGGG
Found at i:20367570 original size:14 final size:14
Alignment explanation
Indices: 20367551--20367580 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20367541 ATTTATGGCC
20367551 TTGGCCTTGGTCAA
1 TTGGCCTTGGTCAA
20367565 TTGGCCTTGGTCAA
1 TTGGCCTTGGTCAA
20367579 TT
1 TT
20367581 AACTAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (14 bp):
TTGGCCTTGGTCAA
Found at i:20373246 original size:22 final size:22
Alignment explanation
Indices: 20373219--20373278 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
20373209 AATTCAGCAG
20373219 CAGAAAATGAGAAGATAAGAGTA
1 CAGAAAATGAGAAGATAAGAG-A
20373242 -AGAAAA-GAAAGAGAGATAAGAGA
1 CAGAAAATG--AGA-AGATAAGAGA
20373265 CAGAAAATGGAGAA
1 CAGAAAAT-GAGAA
20373279 CAAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 5 0.16
24 18 0.58
26 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.28, T:0.08
Consensus pattern (22 bp):
CAGAAAATGAGAAGATAAGAGA
Found at i:20381327 original size:29 final size:29
Alignment explanation
Indices: 20381257--20381327 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 29
20381247 TTATAGTTCA
20381257 TGAATTTTAATAAAATATTTAATATAATATT
1 TGAA-TTTAA-AAAATATTTAATATAATATT
* *
20381288 TAAATGTTAAAAAAT-TTTAATATTATATT
1 TGAAT-TTAAAAAATATTTAATATAATATT
20381317 TGAATTATAAA
1 TGAATT-TAAA
20381328 TTTATTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 21 0.60
30 6 0.17
31 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (29 bp):
TGAATTTAAAAAATATTTAATATAATATT
Found at i:20389955 original size:9 final size:8
Alignment explanation
Indices: 20389926--20389958 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
20389916 TCACATTCGA
20389926 TTAAA-TT
1 TTAAATTT
20389933 TTAAATTT
1 TTAAATTT
20389941 TTAAATTT
1 TTAAATTT
20389949 TTAAAATTT
1 TT-AAATTT
20389958 T
1 T
20389959 GTATTCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 5 0.21
8 12 0.50
9 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTAAATTT
Found at i:20391302 original size:3 final size:3
Alignment explanation
Indices: 20391294--20391341 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
20391284 TTGTTTGTGT
* * *
20391294 ATA ATA ATA ATA ACA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20391342 TAACGATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:20391794 original size:16 final size:16
Alignment explanation
Indices: 20391775--20391813 Score: 57
Period size: 13 Copynumber: 2.6 Consensus size: 16
20391765 AATTTTTTTT
20391775 ACTATGAAAATAAACA
1 ACTATGAAAATAAACA
20391791 ACTATG---ATAAACA
1 ACTATGAAAATAAACA
20391804 ACTATGAAAA
1 ACTATGAAAA
20391814 GATAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 13 0.65
16 7 0.35
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (16 bp):
ACTATGAAAATAAACA
Found at i:20395435 original size:20 final size:20
Alignment explanation
Indices: 20395398--20395435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20395388 TTGTAATATA
* *
20395398 AAAATAATATTTATATTAAT
1 AAAATAATAATTAAATTAAT
20395418 AAAATAATAATTAAATTA
1 AAAATAATAATTAAATTA
20395436 GACTTTGGAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAATAATTAAATTAAT
Found at i:20396588 original size:38 final size:38
Alignment explanation
Indices: 20396541--20396647 Score: 196
Period size: 38 Copynumber: 2.8 Consensus size: 38
20396531 GATTCAAAAA
*
20396541 TTAATATAAAAAACCTTTAAATTGATAATTTGAATTTTT
1 TTAA-ATAAAAAACCTTTAATTTGATAATTTGAATTTTT
20396580 TTAAATAAAAAACCTTTAATTTGATAATTTGAATTTTT
1 TTAAATAAAAAACCTTTAATTTGATAATTTGAATTTTT
20396618 TTAAATAAAAAACCTTTAATTTGATAATTT
1 TTAAATAAAAAACCTTTAATTTGATAATTT
20396648 TATGATAGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 63 0.94
39 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (38 bp):
TTAAATAAAAAACCTTTAATTTGATAATTTGAATTTTT
Found at i:20396737 original size:14 final size:15
Alignment explanation
Indices: 20396711--20396742 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
20396701 TGACAACATA
20396711 TAATAACTGTAAATC
1 TAATAACTGTAAATC
20396726 TAATAA-TGTAAATC
1 TAATAACTGTAAATC
20396740 TAA
1 TAA
20396743 ACATATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (15 bp):
TAATAACTGTAAATC
Found at i:20397831 original size:15 final size:15
Alignment explanation
Indices: 20397813--20397842 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20397803 AACTTTTAAA
*
20397813 TAATCGATTATAATT
1 TAATCGATTAAAATT
20397828 TAATCGATTAAAATT
1 TAATCGATTAAAATT
20397843 AATTTGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TAATCGATTAAAATT
Found at i:20397943 original size:16 final size:17
Alignment explanation
Indices: 20397916--20397962 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
20397906 ATTTAATTAT
20397916 AAATTT-AATTC-AATA
1 AAATTTAAATTCAAATA
20397931 AAATTTAAATTCAAATA
1 AAATTTAAATTCAAATA
**
20397948 TTATTTAAATT-AAAT
1 AAATTTAAATTCAAAT
20397963 CATTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTAAATTCAAATA
Found at i:20397953 original size:17 final size:17
Alignment explanation
Indices: 20397933--20397967 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20397923 ATTCAATAAA
20397933 ATTTAAATTCAAAT-ATT
1 ATTTAAATT-AAATCATT
20397950 ATTTAAATTAAATCATT
1 ATTTAAATTAAATCATT
20397967 A
1 A
20397968 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATTAAATCATT
Found at i:20398798 original size:2 final size:2
Alignment explanation
Indices: 20398791--20398815 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20398781 TAATTGAGGG
20398791 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 T
20398816 TAATTTTGGT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20413038 original size:12 final size:12
Alignment explanation
Indices: 20413021--20413056 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
20413011 TAATTTAATT
20413021 AATTAATTATTA
1 AATTAATTATTA
20413033 AATTAATT-TT-
1 AATTAATTATTA
20413043 AATTAATTATTA
1 AATTAATTATTA
20413055 AA
1 AA
20413057 AATAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.36
11 4 0.18
12 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAATTATTA
Found at i:20413049 original size:30 final size:29
Alignment explanation
Indices: 20413009--20413088 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 29
20412999 GTCAAATTGA
* * *
20413009 TTTAATTTAATTAATTAATTATTAAATTAAT
1 TTTAA-TTAATTAATTAAATAATAAA-AAAT
20413040 TTTAATTAATT-ATTAAAAATAATAAAAAAT
1 TTTAATTAATTAATT--AAATAATAAAAAAT
20413070 TTTAATTAATTCAATTAAA
1 TTTAATTAATT-AATTAAA
20413089 ATATTATGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
29 3 0.07
30 23 0.55
31 13 0.31
32 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAATTAATTAATTAAATAATAAAAAAT
Found at i:20413210 original size:7 final size:8
Alignment explanation
Indices: 20413191--20413218 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
20413181 TCATGTATGA
20413191 AAAAAATT
1 AAAAAATT
20413199 AAAAAATT
1 AAAAAATT
20413207 AAAAAATT
1 AAAAAATT
20413215 AAAA
1 AAAA
20413219 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:20414948 original size:347 final size:346
Alignment explanation
Indices: 20413957--20414994 Score: 2003
Period size: 342 Copynumber: 3.0 Consensus size: 346
20413947 TTCAAGTAAA
*
20413957 TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATTCCTCTAATTAATTATTAGA
1 TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
20414022 CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
66 CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
*
20414087 GAACGAAGTAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTAGACATGTGAAACAC
131 GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTAGACATGTGAAACAC
20414152 ATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCTT
196 ATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCTT
20414217 CGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCAC-GACCAGCACCCTGCTG
261 CGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCTG
20414281 CACGCCAGGCCGGCTAGATCC
326 CACGCCAGGCCGGCTAGATCC
20414302 TTGTGTCGGTGAAGTCATACACAAG-AAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
1 TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
*
20414366 CAAGTAATAGACATTTAGGTGTTAT-TTATTCTAAATT-GATATCAGGAAGCATCAACGGTTCAG
66 CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
20414429 GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTAGACATGTGAAACAC
131 GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTAGACATGTGAAACAC
20414494 ATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCTT
196 ATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCTT
20414559 CGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCTG
261 CGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCTG
20414624 CACGCCAGGCCGGCTAGATCC
326 CACGCCAGGCCGGCTAGATCC
20414645 TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
1 TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
20414710 CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
66 CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
*
20414775 GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTTAGACAAGTGAAACA
131 GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGG-TAGACATGTGAAACA
20414840 CATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCT
195 CATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCT
20414905 TCGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCT
260 TCGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCT
20414970 GCACGCCAGGCCGGCTAGATCC
325 GCACGCCAGGCCGGCTAGATCC
20414992 TTG
1 TTG
20414995 ATGGCGCTAG
Statistics
Matches: 683, Mismatches: 5, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
342 202 0.30
343 74 0.11
344 127 0.19
345 37 0.05
346 74 0.11
347 169 0.25
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (346 bp):
TTGTGTCGGTGAAGTCATACACAAGAAAAAGGAAAAACAGCTCATGCCTCTAATTAATTATTAGA
CAAGTAATAGACATTTAGGTGTTATCTTATTCTAAATTGGATATCAGGAGGCATCAACGGTTCAG
GAACGAAGAAACTTGATTCATCAAATCCACAGCCTTCTGACAAGATGGGTAGACATGTGAAACAC
ATGACCCTCTCCTGGAGTCTCGAAAATGTCTATCACCCCTTCCCACCCACTCTTTCGTACTGCTT
CGTAGTAAGATATGGCCCTGTCCCTCAAGAAATCTTTCTCTGAAGCACAGACCAGCACCCTGCTG
CACGCCAGGCCGGCTAGATCC
Found at i:20424296 original size:25 final size:27
Alignment explanation
Indices: 20424239--20424296 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
20424229 AAGATGAGAG
*
20424239 AAGAATGAGAAGGAGCAAGAAAAAAAA
1 AAGAAAGAGAAGGAGCAAGAAAAAAAA
*
20424266 AAGAAAGAGAAGG-G-AAGGAAAAAAA
1 AAGAAAGAGAAGGAGCAAGAAAAAAAA
*
20424291 ATGAAA
1 AAGAAA
20424297 AAAAATGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 15 0.54
26 1 0.04
27 12 0.43
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.03
Consensus pattern (27 bp):
AAGAAAGAGAAGGAGCAAGAAAAAAAA
Found at i:20424349 original size:13 final size:13
Alignment explanation
Indices: 20424331--20424355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20424321 ATTAGCATTT
20424331 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
20424344 AAAAGAAAAAAA
1 AAAAGAAAAAAA
20424356 TTCAACAAGA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:20427092 original size:23 final size:23
Alignment explanation
Indices: 20427066--20427111 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20427056 ATTTACTCAT
20427066 TTTTAATAAAAAAATTTCATGAA
1 TTTTAATAAAAAAATTTCATGAA
* * * *
20427089 TTTTACTTATAAAATTTTATGAA
1 TTTTAATAAAAAAATTTCATGAA
20427112 AATTTTGTCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTAATAAAAAAATTTCATGAA
Found at i:20428172 original size:13 final size:13
Alignment explanation
Indices: 20428150--20428188 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20428140 TTAATTTTTA
*
20428150 ATTTTTATATATT
1 ATTTTAATATATT
**
20428163 ATTTTAATATAAA
1 ATTTTAATATATT
20428176 ATTTTAATATATT
1 ATTTTAATATATT
20428189 TAAATAGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:20431838 original size:13 final size:13
Alignment explanation
Indices: 20431822--20431847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20431812 ACACATCTAA
20431822 AACTTTCAACTCT
1 AACTTTCAACTCT
20431835 AACTTTCAACTCT
1 AACTTTCAACTCT
20431848 TCTATAATGT
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:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
AACTTTCAACTCT
Found at i:20432151 original size:13 final size:13
Alignment explanation
Indices: 20432133--20432158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20432123 ATTGCTTGAG
20432133 GTTCAAGAATTCT
1 GTTCAAGAATTCT
20432146 GTTCAAGAATTCT
1 GTTCAAGAATTCT
20432159 TAAAGACACT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTTCAAGAATTCT
Found at i:20432423 original size:10 final size:11
Alignment explanation
Indices: 20432399--20432453 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
20432389 AATATATAAA
*
20432399 TTTAAAAATATT
1 TTTAATAATA-T
20432411 TTTAATAA-AT
1 TTTAATAATAT
20432421 TTTAATATATATT
1 TTTAATA-ATA-T
20432434 TTTAAATAATAT
1 TTT-AATAATAT
20432446 TTTAATAA
1 TTTAATAA
20432454 AAATATTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 8 0.21
11 7 0.18
12 12 0.32
13 7 0.18
14 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:20432436 original size:13 final size:12
Alignment explanation
Indices: 20432408--20432473 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
20432398 ATTTAAAAAT
20432408 ATTTTTAATA-A
1 ATTTTTAATATA
20432419 A-TTTTAATATA
1 ATTTTTAATATA
20432430 TATTTTTAA-ATA
1 -ATTTTTAATATA
*
20432442 ATATTTTAATAAA
1 AT-TTTTAATATA
* * *
20432455 AATATTAATAAA
1 ATTTTTAATATA
20432467 ATTTTTA
1 ATTTTTA
20432474 TTATTGAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
10 8 0.18
11 4 0.09
12 24 0.53
13 9 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTTAATATA
Found at i:20432458 original size:14 final size:12
Alignment explanation
Indices: 20432399--20432460 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
20432389 AATATATAAA
20432399 TTTAAAAATATT
1 TTTAAAAATATT
*
20432411 TTTAATAA-A-T
1 TTTAAAAATATT
*
20432421 TTTAATATATATT
1 TTTAA-AAATATT
20432434 TTTAAATAATATT
1 TTTAAA-AATATT
20432447 TTAATAAAAATATT
1 TT--TAAAAATATT
20432461 AATAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 6 0.15
11 2 0.05
12 9 0.22
13 13 0.32
14 6 0.15
15 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAAATATT
Found at i:20432470 original size:23 final size:24
Alignment explanation
Indices: 20432412--20432471 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
20432402 AAAAATATTT
* * *
20432412 TTAAT-AAATTTTAATATATATTT
1 TTAATAAAATTTTAATATAAAATA
*
20432435 TTAAATAATATTTTAATA-AAAATA
1 TT-AATAAAATTTTAATATAAAATA
20432459 TTAATAAAATTTT
1 TTAATAAAATTTT
20432472 TATTATTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAATAAAATTTTAATATAAAATA
Found at i:20432595 original size:12 final size:14
Alignment explanation
Indices: 20432580--20432611 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
20432570 TGATTTAAAT
20432580 TTTTTATTA-A-TA
1 TTTTTATTAGATTA
20432592 TTTTTATTAGATTA
1 TTTTTATTAGATTA
20432606 TTTTTA
1 TTTTTA
20432612 AGAAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTTATTAGATTA
Found at i:20432656 original size:24 final size:23
Alignment explanation
Indices: 20432621--20432670 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
20432611 AAGAAGAAAT
*
20432621 TTTATAAATTTTATCTAAAAAAA
1 TTTATAAATTTTATCGAAAAAAA
* * *
20432644 TTTATTAAGTTTTCTCGAAAAAGA
1 TTTA-TAAATTTTATCGAAAAAAA
20432668 TTT
1 TTT
20432671 GCGTGACCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTATAAATTTTATCGAAAAAAA
Found at i:20433252 original size:41 final size:42
Alignment explanation
Indices: 20433176--20433270 Score: 99
Period size: 41 Copynumber: 2.3 Consensus size: 42
20433166 ATTGATTAAA
* * *
20433176 AATTATTTTAATAAAATTTTTTTAAAATTTAAATTTATTTAT
1 AATTATTTTAATAAAATTATCTCAAAATTTAAATTTATTTAT
*
20433218 AATTA-TTTATTAAAATTATCTCAAATATTT-AATTTATAATTAT
1 AATTATTTTAATAAAATTATCTCAAA-ATTTAAATTTAT--TTAT
20433261 --TTATTTTAAT
1 AATTATTTTAAT
20433271 TTATCGATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
41 26 0.59
42 14 0.32
43 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
AATTATTTTAATAAAATTATCTCAAAATTTAAATTTATTTAT
Found at i:20434289 original size:11 final size:12
Alignment explanation
Indices: 20434262--20434290 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20434252 TCATTAATTA
20434262 AATTTAAATATT
1 AATTTAAATATT
20434274 AATTTAAATA-T
1 AATTTAAATATT
20434285 AATTTA
1 AATTTA
20434291 TTTAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTTAAATATT
Found at i:20434295 original size:15 final size:15
Alignment explanation
Indices: 20434275--20434317 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20434265 TTAAATATTA
20434275 ATTTAAATATAATTT
1 ATTTAAATATAATTT
20434290 ATTT-AATATAATTT
1 ATTTAAATATAATTT
*
20434304 -TTGTAATTATAATT
1 ATT-TAAATATAATT
20434318 ATAATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTAAATATAATTT
Found at i:20434299 original size:14 final size:14
Alignment explanation
Indices: 20434263--20434317 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
20434253 CATTAATTAA
*
20434263 ATTTAA-AT-ATTA
1 ATTTAATATAATTT
20434275 ATTTAAATATAATTT
1 ATTT-AATATAATTT
20434290 ATTTAATATAATTT
1 ATTTAATATAATTT
20434304 -TTGTAATTATAATT
1 ATT-TAA-TATAATT
20434318 ATAATAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
14 15 0.41
15 14 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTAATATAATTT
Found at i:20437007 original size:188 final size:188
Alignment explanation
Indices: 20436690--20437069 Score: 688
Period size: 188 Copynumber: 2.0 Consensus size: 188
20436680 CCAAGAAAGC
*
20436690 ATCTGGATATCAGCAACAGTATTCTTCACAAGGTATCTTAGTGTTTTGTCCTTCCCAAATTAGTC
1 ATCTGGATATCAGCAACAGTATTCTTCACAAGGTATCTTAGTATTTTGTCCTTCCCAAATTAGTC
* *
20436755 TAGTTGTTTCCCCTTGAATTAAATTGTGAAGTGTCAAACGTAGGGGCCCTTTTTTGGGTTCTGTA
66 TAGTTGTTTCCCCTTAAATTAAATTGTGAAGGGTCAAACGTAGGGGCCCTTTTTTGGGTTCTGTA
* * *
20436820 TGATTTCTGCCATAAGGGTGAGGGGAAGTGATTAATACTTGGGTGGCCTTCCATGTAA
131 TGATTTCTGCCATAAGGGTGAGGAGAAATGATTAATACTTGGGTGGCCTTCCACGTAA
*
20436878 ATCTGGATATCAGCAACAGTATTCTTCACACGGTATCTTAGTATTTTGTCCTTCCCAAATTAGTC
1 ATCTGGATATCAGCAACAGTATTCTTCACAAGGTATCTTAGTATTTTGTCCTTCCCAAATTAGTC
*
20436943 TAGTTGTTTCCCCTTAAATTAAATTGTGAAGGGTCAAATGTAGGGGCCCTTTTTTGGGTTCTGTA
66 TAGTTGTTTCCCCTTAAATTAAATTGTGAAGGGTCAAACGTAGGGGCCCTTTTTTGGGTTCTGTA
20437008 TGATTTCTGCCATAAGGGTGAGGAGAAATGATTAATACTTGGGTGGCCTTCCACGTAA
131 TGATTTCTGCCATAAGGGTGAGGAGAAATGATTAATACTTGGGTGGCCTTCCACGTAA
20437066 ATCT
1 ATCT
20437070 TCCTCTGTTC
Statistics
Matches: 184, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
188 184 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (188 bp):
ATCTGGATATCAGCAACAGTATTCTTCACAAGGTATCTTAGTATTTTGTCCTTCCCAAATTAGTC
TAGTTGTTTCCCCTTAAATTAAATTGTGAAGGGTCAAACGTAGGGGCCCTTTTTTGGGTTCTGTA
TGATTTCTGCCATAAGGGTGAGGAGAAATGATTAATACTTGGGTGGCCTTCCACGTAA
Found at i:20439243 original size:20 final size:20
Alignment explanation
Indices: 20439185--20439238 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
20439175 TATATATATA
**
20439185 TATATAATTTTTTAATTATT
1 TATATAATTTAATAATTATT
*
20439205 TATTTAATTTAATAATTATT
1 TATATAATTTAATAATTATT
20439225 TATATATATTTAAT
1 TATATA-ATTTAAT
20439239 TTTATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATAATTTAATAATTATT
Found at i:20439246 original size:12 final size:13
Alignment explanation
Indices: 20439195--20439253 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
20439185 TATATAATTT
20439195 TTTAATTATT-TA
1 TTTAATTATTATA
*
20439207 TTTAATT-TAATA
1 TTTAATTATTATA
* *
20439219 ATTATTTATATATA
1 TTTAATTAT-TATA
20439233 TTTAATT-TTATA
1 TTTAATTATTATA
20439245 TTTATATTA
1 TTTA-ATTA
20439254 AAAATAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 1 0.03
12 22 0.61
13 5 0.14
14 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATTATTATA
Found at i:20439250 original size:20 final size:20
Alignment explanation
Indices: 20439175--20439251 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 20
20439165 TTTTGATATA
* *
20439175 TATATATATATATATAATTT
1 TATATTTATATATTTAATTT
* * *
20439195 TTTAATTATTTATTTAATTT
1 TATATTTATATATTTAATTT
20439215 AATAATTATTTATATATATTTAATTT
1 --T-A-TA-TT-TATATATTTAATTT
20439241 TATATTTATAT
1 TATATTTATAT
20439252 TAAAAATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 20 0.47
21 2 0.05
22 3 0.07
23 1 0.02
24 3 0.07
25 1 0.02
26 13 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTATATATTTAATTT
Found at i:20446899 original size:2 final size:2
Alignment explanation
Indices: 20446892--20446917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20446882 TCGCCTCTGA
20446892 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
20446918 CTCACACTAA
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:20448378 original size:89 final size:89
Alignment explanation
Indices: 20448218--20448396 Score: 229
Period size: 89 Copynumber: 2.0 Consensus size: 89
20448208 GCACCCTTTC
* * * * * *
20448218 AACATAATCAAACACATACCAATATGCTTCCATATACCATACTTATATAGACTCTTTCAGTCTCC
1 AACATAACCAAACACATACCAATATGCTCCCATACACCATACCTATATAGAATCTCTCAGTCTCC
*
20448283 TTTAGTTCACTCACAAATAAACAT
66 TCTAGTTCACTCACAAATAAACAT
*
20448307 AACATAACCAAACACATATCC-ATATGCTCCCATACATCATACCTATAT-GAATCCTCTCAG-CT
1 AACATAACCAAACACATA-CCAATATGCTCCCATACACCATACCTATATAGAAT-CTCTCAGTC-
*
20448369 TTCTCTAGTTCACTCACAAATAAACAT
63 TCCTCTAGTTCACTCACAAATAAACAT
20448396 A
1 A
20448397 CACCCATAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
88 4 0.05
89 72 0.92
90 2 0.03
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (89 bp):
AACATAACCAAACACATACCAATATGCTCCCATACACCATACCTATATAGAATCTCTCAGTCTCC
TCTAGTTCACTCACAAATAAACAT
Found at i:20448942 original size:25 final size:24
Alignment explanation
Indices: 20448910--20448978 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
20448900 CATCTTAAAC
20448910 CTTT-AGCTTTTCTCACATCTCGAA
1 CTTTCAGCTTTTC-CACATCTCGAA
* *
20448934 CTTTCAGCTCTTCCACGTCTCGAA
1 CTTTCAGCTTTTCCACATCTCGAA
* *
20448958 CCTTCGGCTATTTCCACATCT
1 CTTTCAGCT-TTTCCACATCT
20448979 TAAATCTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 21 0.57
25 16 0.43
ACGTcount: A:0.17, C:0.35, G:0.10, T:0.38
Consensus pattern (24 bp):
CTTTCAGCTTTTCCACATCTCGAA
Found at i:20448954 original size:24 final size:24
Alignment explanation
Indices: 20448893--20448958 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
20448883 AAACTATGCA
**
20448893 CTTCTCACATCTTAAACCTTTAGCT
1 CTTCTCACATCTCGAA-CTTTAGCT
*
20448918 TTTCTCACATCTCGAACTTTCAGCT
1 CTTCTCACATCTCGAACTTT-AGCT
*
20448943 CTTC-CACGTCTCGAAC
1 CTTCTCACATCTCGAAC
20448959 CTTCGGCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (24 bp):
CTTCTCACATCTCGAACTTTAGCT
Found at i:20449650 original size:52 final size:51
Alignment explanation
Indices: 20449509--20449651 Score: 164
Period size: 52 Copynumber: 2.7 Consensus size: 51
20449499 AAATTTACCC
* * *
20449509 ATTAAGAATCT-TTCTCATCTTAGAATTCTTCTCCTGTAAGTCAAATTTACTT
1 ATTAAGAATCTCTT-TC-TCTTAGAATTCTTCTCTTGCAAGTCAAACTTACTT
* *
20449561 ATTAAGAATCTCTTTCCTTTTAGAATTTTTCTCTTGCAAGTCAAACTTAGC-T
1 ATTAAGAATCTCTTT-CTCTTAGAATTCTTCTCTTGCAAGTCAAACTTA-CTT
* *
20449613 ATTAAGAATCCTCTTTCTCTTAGGATTCTTCTTTTGCAA
1 ATTAAGAAT-CTCTTTCTCTTAGAATTCTTCTCTTGCAA
20449652 ATTTTTTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
52 68 0.87
53 10 0.13
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (51 bp):
ATTAAGAATCTCTTTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACTT
Found at i:20449695 original size:11 final size:11
Alignment explanation
Indices: 20449679--20449720 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
20449669 ACAATAGCTG
20449679 ACAAATCTCAA
1 ACAAATCTCAA
*
20449690 ACAAATCTCTA
1 ACAAATCTCAA
*
20449701 ACAATTCTCAA
1 ACAAATCTCAA
20449712 ACAAATCTC
1 ACAAATCTC
20449721 TTATGAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:20449709 original size:22 final size:22
Alignment explanation
Indices: 20449679--20449721 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20449669 ACAATAGCTG
20449679 ACAAATCTCAAACAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
*
20449701 ACAATTCTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
20449722 TATGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:20457857 original size:173 final size:174
Alignment explanation
Indices: 20457522--20457871 Score: 657
Period size: 173 Copynumber: 2.0 Consensus size: 174
20457512 ATTTCTTTTC
*
20457522 TATTATTTCTATTAATTATCTATTTTTCTAACAAAAAGTTTGGTGAAAGGCTGCACTAACAAGCT
1 TATTATTTCTATTAATTATCTATTTTTCTAACAAAAAGTTCGGTGAAAGGCTGCACTAACAAGCT
*
20457587 CACCTTCCCACCCCCCCCCCCTCCCCTTGTTTATAAACCAACTCAAAGTTATTTCATTAATTTAG
66 CACCTTCCCACCCCCCCCCCCTCCCCTTGTTTATAAACCAACTCAAAGTTATTCCATTAATTTAG
20457652 AGTAGCTGTTATGGTAGAGCAAGGTACTCATTCAGAACTGGTGG
131 AGTAGCTGTTATGGTAGAGCAAGGTACTCATTCAGAACTGGTGG
20457696 TATTATTTCTATTAATTATCTATTTTTCTAACAAAAAGTTCGGTGAAAGGCTGCACTAACAAGCT
1 TATTATTTCTATTAATTATCTATTTTTCTAACAAAAAGTTCGGTGAAAGGCTGCACTAACAAGCT
*
20457761 CACCTTCCCA-CCCCCCCCCCTCCCCTTGTTTATACACCAACTCAAAGTTATTCCATTAATTTAG
66 CACCTTCCCACCCCCCCCCCCTCCCCTTGTTTATAAACCAACTCAAAGTTATTCCATTAATTTAG
*
20457825 AGTAGCTGTTATGGTAGAGCAAGTTACTCATTCAGAACTGGTGG
131 AGTAGCTGTTATGGTAGAGCAAGGTACTCATTCAGAACTGGTGG
20457869 TAT
1 TAT
20457872 GACACTTCAG
Statistics
Matches: 172, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
173 98 0.57
174 74 0.43
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (174 bp):
TATTATTTCTATTAATTATCTATTTTTCTAACAAAAAGTTCGGTGAAAGGCTGCACTAACAAGCT
CACCTTCCCACCCCCCCCCCCTCCCCTTGTTTATAAACCAACTCAAAGTTATTCCATTAATTTAG
AGTAGCTGTTATGGTAGAGCAAGGTACTCATTCAGAACTGGTGG
Found at i:20461796 original size:2 final size:2
Alignment explanation
Indices: 20461789--20461821 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20461779 TATGCTATGA
20461789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20461822 CATGCGTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20462671 original size:25 final size:25
Alignment explanation
Indices: 20462642--20462691 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
20462632 ATGTAAAGAT
20462642 GTCAATAGT-AGAAGTTAGGTGACTA
1 GTCAATAGTCA-AAGTTAGGTGACTA
20462667 GTCAATAGTCAAAGTTAGGTGACTA
1 GTCAATAGTCAAAGTTAGGTGACTA
20462692 AGTGTGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (25 bp):
GTCAATAGTCAAAGTTAGGTGACTA
Found at i:20463933 original size:8 final size:8
Alignment explanation
Indices: 20463920--20463965 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
20463910 TTATAAAAAG
20463920 TTTTAAAT
1 TTTTAAAT
20463928 TTTTAAAT
1 TTTTAAAT
* *
20463936 ATATAAAT
1 TTTTAAAT
20463944 TTTTAAATT
1 TTTTAAA-T
20463953 TTTTAAAAT
1 TTTT-AAAT
20463962 TTTT
1 TTTT
20463966 GCATATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 19 0.59
9 10 0.31
10 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTTAAAT
Found at i:20464032 original size:4 final size:4
Alignment explanation
Indices: 20464023--20464048 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20464013 AGGCTTGAAG
20464023 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
20464049 CTCCATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:20469406 original size:145 final size:145
Alignment explanation
Indices: 20469138--20469409 Score: 332
Period size: 145 Copynumber: 1.9 Consensus size: 145
20469128 AAGCTCCAAG
* * * * * *
20469138 TATGGTTTATCTCCCCAACAAGTGATATCGGAACCAAGGTTACGACGAGTTCGAGTTTCAGTGGT
1 TATGGTTTATCTCCCCAACAAGTGATATCAGAACCAAAGATACGACGAGTTCGAATCTCAGTAGT
* * * * * *
20469203 GTTGCTGAGGGAGAGATTACTCCATGTATTCTAACGTCAGTATTAAAATATTCAACTTGGATGCA
66 GTTGCTGAGGGAAAGACTACTCCATGTACTCGAACGCCAGTATTAAAAGATTCAACTTGGATGCA
20469268 GCAAGTCTATGATAA
131 GCAAGTCTATGATAA
* * *
20469283 TATGGTTTATCTCCCCAACAAGTGATATCAGAGCTAAAGATACGACG-GATTTGAATCTCAGTAG
1 TATGGTTTATCTCCCCAACAAGTGATATCAGAACCAAAGATACGACGAG-TTCGAATCTCAGTAG
* * * * *
20469347 TGTTGTTG-GGGAAAAGACTACTCCATGTGCTCGAATGCCGGTATTAAAAGATTCGACTTGGAT
65 TGTTGCTGAGGG-AAAGACTACTCCATGTACTCGAACGCCAGTATTAAAAGATTCAACTTGGAT
20469410 CAGAGCCAAC
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
144 4 0.04
145 101 0.96
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (145 bp):
TATGGTTTATCTCCCCAACAAGTGATATCAGAACCAAAGATACGACGAGTTCGAATCTCAGTAGT
GTTGCTGAGGGAAAGACTACTCCATGTACTCGAACGCCAGTATTAAAAGATTCAACTTGGATGCA
GCAAGTCTATGATAA
Found at i:20469761 original size:148 final size:148
Alignment explanation
Indices: 20469574--20469862 Score: 382
Period size: 148 Copynumber: 2.0 Consensus size: 148
20469564 GATATTACGA
* * * **
20469574 GTTTGAGTCCCAGTAGTGTTACTGGAGGGAGATTGCTCCATGTGCTTAAATGTCGATATTAAAAG
1 GTTTGAGTCCCAGTAGTATTACTGGAGGGAGATTACTCCATGTGCTCAAACATCGATATTAAAAG
* * ** *
20469639 GTTTGACTTAGATTTAACGAGTCTATGATAATATGCAGAAGCAAATATCAATATTAAAAGGTTCG
66 ATTCGACTTAGATACAACGAGTCTATGATAATATGCAGAAACAAATATCAATATTAAAAGGTTCG
20469704 ACTTGGATGCAACGACGG
131 ACTTGGATGCAACGACGG
* *
20469722 GTTTGAGTCTCAGTAGTATTGCTGG-GAGGAGATTACTCCATGTGCTCAAACATCGATATTAAAA
1 GTTTGAGTCCCAGTAGTATTACTGGAG-GGAGATTACTCCATGTGCTCAAACATCGATATTAAAA
* ** * * * **
20469786 GATTCGACTTGGATACAGTGAGTCTATGATAGTATGTAGAAACGAATATCGGTATTAAAAGGTTC
65 GATTCGACTTAGATACAACGAGTCTATGATAATATGCAGAAACAAATATCAATATTAAAAGGTTC
20469851 GACTTGGATGCA
130 GACTTGGATGCA
20469863 GCGAGTCTAT
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
147 1 0.01
148 119 0.99
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (148 bp):
GTTTGAGTCCCAGTAGTATTACTGGAGGGAGATTACTCCATGTGCTCAAACATCGATATTAAAAG
ATTCGACTTAGATACAACGAGTCTATGATAATATGCAGAAACAAATATCAATATTAAAAGGTTCG
ACTTGGATGCAACGACGG
Found at i:20469871 original size:60 final size:60
Alignment explanation
Indices: 20469773--20469886 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
20469763 GTGCTCAAAC
* * *
20469773 ATCGATATTAAAAGATTCGACTTGGATACAGTGAGTCTATGATAGTATGTAGAAACGAAT
1 ATCGATATTAAAAGATTCGACTTGGATACAGCGAGTCTATGATAATATGCAGAAACGAAT
* * *
20469833 ATCGGTATTAAAAGGTTCGACTTGGATGCAGCGAGTCTATGATAATATGCAGAA
1 ATCGATATTAAAAGATTCGACTTGGATACAGCGAGTCTATGATAATATGCAGAA
20469887 GCCGAACACG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (60 bp):
ATCGATATTAAAAGATTCGACTTGGATACAGCGAGTCTATGATAATATGCAGAAACGAAT
Found at i:20471196 original size:2 final size:2
Alignment explanation
Indices: 20471189--20471226 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
20471179 CTTTTGTATT
* *
20471189 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20471227 CAAAAATTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20472657 original size:30 final size:29
Alignment explanation
Indices: 20472612--20472672 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
20472602 TTTTTAATTT
*
20472612 ATTTAAATTATTAAATGTAATTCACATTA
1 ATTTAAATCATTAAATGTAATTCACATTA
* *
20472641 ATTTAAGATCATTAAATGTAATTTATATTA
1 ATTTAA-ATCATTAAATGTAATTCACATTA
20472671 AT
1 AT
20472673 CTACGTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (29 bp):
ATTTAAATCATTAAATGTAATTCACATTA
Found at i:20472940 original size:46 final size:47
Alignment explanation
Indices: 20472873--20472965 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 47
20472863 ACAGATAAAA
20472873 AACTAACTCTTAACGTTTCTTAACTATACTTTTCTATTACAAATCAT
1 AACTAACTCTTAACGTTTCTTAACTATACTTTTCTATTACAAATCAT
20472920 AACTAACTC-TAACGTTTCTTAACTATACTTTTCTATTACAAATCAT
1 AACTAACTCTTAACGTTTCTTAACTATACTTTTCTATTACAAATCAT
20472966 TTCCAACGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 37 0.80
47 9 0.20
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (47 bp):
AACTAACTCTTAACGTTTCTTAACTATACTTTTCTATTACAAATCAT
Found at i:20476597 original size:14 final size:15
Alignment explanation
Indices: 20476578--20476607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20476568 AATCAAATTG
20476578 ATAATT-TTTTAAAT
1 ATAATTATTTTAAAT
20476592 ATAATTATTTTAAAT
1 ATAATTATTTTAAAT
20476607 A
1 A
20476608 CATAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTATTTTAAAT
Found at i:20477349 original size:8 final size:8
Alignment explanation
Indices: 20477336--20477373 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
20477326 ACGTGTGCGC
20477336 ATGTATAT
1 ATGTATAT
20477344 ATGTATAT
1 ATGTATAT
20477352 ATGTATAT
1 ATGTATAT
*
20477360 ATATATAT
1 ATGTATAT
*
20477368 GTGTAT
1 ATGTAT
20477374 TTATTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (8 bp):
ATGTATAT
Found at i:20488903 original size:16 final size:16
Alignment explanation
Indices: 20488877--20489000 Score: 56
Period size: 16 Copynumber: 7.4 Consensus size: 16
20488867 TAATTATTAA
20488877 AATATTTAAAATTATTT
1 AATA-TTAAAATTATTT
* *
20488894 ATTATTAAAATTA-TG
1 AATATTAAAATTATTT
*
20488909 AATATTACAAA-TAATT
1 AATATTA-AAATTATTT
*
20488925 ATATTTTAATAATAATATTT
1 A-ATATTAA-AAT--TATTT
*
20488945 AATATTAAAATATTCTGTT
1 AATATT-AAA-ATTAT-TT
* *
20488964 AATATAAAAATTACTT
1 AATATTAAAATTATTT
* *
20488980 AA-AATAAAACTATTT
1 AATATTAAAATTATTT
*
20488995 ATTATT
1 AATATT
20489001 CTTTATATTA
Statistics
Matches: 79, Mismatches: 17, Indels: 23
0.66 0.14 0.19
Matches are distributed among these distances:
15 19 0.24
16 21 0.27
17 13 0.16
18 5 0.06
19 12 0.15
20 9 0.11
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (16 bp):
AATATTAAAATTATTT
Found at i:20489016 original size:23 final size:23
Alignment explanation
Indices: 20489005--20489069 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 23
20488995 ATTATTCTTT
20489005 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
20489028 ATATTATTTATTAATAATATTTATTA
1 ATATTATTTATTAAT-ATA-TTA-TA
20489054 ATA-TATTATATTAATA
1 ATATTATT-TATTAATA
20489070 GTATATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
23 15 0.39
24 3 0.08
25 8 0.21
26 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:20489045 original size:26 final size:27
Alignment explanation
Indices: 20489005--20489127 Score: 87
Period size: 31 Copynumber: 4.4 Consensus size: 27
20488995 ATTATTCTTT
20489005 ATATTATTTA-T--TAATATATTA-TA
1 ATATTATTTATTAATAATATATTATTA
20489028 ATATTATTTATTAATAATAT-TTATTA
1 ATATTATTTATTAATAATATATTATTA
*
20489054 ATA-TATTATATTAATAGTATATTTTTATTA
1 ATATTATT-TATTAATA--ATA-TATTATTA
* *
20489084 ATAGTATATTATTTATTAATATATTTTATTA
1 ATATTAT-TTA-TTAATAATATA--TTATTA
*
20489115 ATAGTATATTATT
1 ATATTAT-TTATT
20489128 TATTTATAAG
Statistics
Matches: 84, Mismatches: 2, Indels: 21
0.79 0.02 0.20
Matches are distributed among these distances:
23 10 0.12
24 1 0.01
25 7 0.08
26 19 0.23
28 3 0.04
29 2 0.02
30 14 0.17
31 22 0.26
32 6 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
ATATTATTTATTAATAATATATTATTA
Found at i:20489048 original size:13 final size:13
Alignment explanation
Indices: 20489009--20489127 Score: 80
Period size: 13 Copynumber: 9.6 Consensus size: 13
20488999 TTCTTTATAT
20489009 TATTTATTAAT-A
1 TATTTATTAATAA
*
20489021 TA-TTA-TAATAT
1 TATTTATTAATAA
20489032 TATTTATTAATAA
1 TATTTATTAATAA
20489045 TATTTATTAAT-A
1 TATTTATTAATAA
20489057 TATTATATTAATAGTA
1 TATT-TATTAATA--A
*
20489073 TATTT-TTATTAA
1 TATTTATTAATAA
*
20489085 TA-GTA-T-AT--
1 TATTTATTAATAA
20489093 TATTTATTAAT-A
1 TATTTATTAATAA
*
20489105 TATTTTATTAATAG
1 TA-TTTATTAATAA
20489119 TATATTATT
1 TAT-TTATT
20489128 TATTTATAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
8 2 0.02
9 2 0.02
10 6 0.07
11 9 0.11
12 15 0.18
13 33 0.39
14 12 0.14
15 1 0.01
16 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TATTTATTAATAA
Found at i:20489114 original size:31 final size:31
Alignment explanation
Indices: 20489028--20489131 Score: 135
Period size: 31 Copynumber: 3.4 Consensus size: 31
20489018 ATATATTATA
20489028 ATATTATTTATTAATA-ATATTTATT-A-A-T
1 ATATTATTTATTAATATAT-TTTATTAATAGT
* *
20489056 ATATTATATTAATAGTATATTTTTATTAATAGT
1 ATATTAT-TTATTAATATA-TTTTATTAATAGT
20489089 ATATTATTTATTAATATATTTTATTAATAGT
1 ATATTATTTATTAATATATTTTATTAATAGT
20489120 ATATTATTTATT
1 ATATTATTTATT
20489132 TATAAGTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.11
29 7 0.11
30 7 0.11
31 27 0.41
32 10 0.15
33 8 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
ATATTATTTATTAATATATTTTATTAATAGT
Found at i:20489135 original size:13 final size:13
Alignment explanation
Indices: 20489002--20489135 Score: 59
Period size: 13 Copynumber: 10.5 Consensus size: 13
20488992 TTTATTATTC
20489002 TTTATATTATTTA
1 TTTATATTATTTA
*
20489015 TTAATA-TA-TTA
1 TTTATATTATTTA
*
20489026 -TAATATTATTTA
1 TTTATATTATTTA
* *
20489038 TTAATAATATTTA
1 TTTATATTATTTA
20489051 TTAATATATTATATTAA
1 TT--TATATTAT-TT-A
*
20489068 TAGTATATT-TTTA
1 T-TTATATTATTTA
* *
20489081 TTAATAGTATATTA
1 TTTATATTAT-TTA
* *
20489095 TTTAT-TAATATA
1 TTTATATTATTTA
*
20489107 TTT-TATTA-ATA
1 TTTATATTATTTA
*
20489118 -GTATATTATTTA
1 TTTATATTATTTA
20489130 TTTATA
1 TTTATA
20489136 AGTAAAATTA
Statistics
Matches: 91, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
10 6 0.07
11 14 0.15
12 18 0.20
13 27 0.30
14 9 0.10
15 7 0.08
16 8 0.09
17 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTATATTATTTA
Found at i:20489793 original size:41 final size:43
Alignment explanation
Indices: 20489737--20489820 Score: 145
Period size: 41 Copynumber: 2.0 Consensus size: 43
20489727 ATCAATTAAG
*
20489737 ATAAGTGTTAAATTTTTTTATTTTTATTATTTA-GCAATAAAA
1 ATAAGTATTAAATTTTTTTATTTTTATTATTTAGGCAATAAAA
20489779 ATAAGTATT-AATTTTTTTATTTTTATTATTTAGGCAATAAAA
1 ATAAGTATTAAATTTTTTTATTTTTATTATTTAGGCAATAAAA
20489821 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 23 0.57
42 17 0.43
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (43 bp):
ATAAGTATTAAATTTTTTTATTTTTATTATTTAGGCAATAAAA
Found at i:20491386 original size:11 final size:11
Alignment explanation
Indices: 20491357--20491390 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
20491347 TGATGGACAT
*
20491357 AATAATTTAAA
1 AATAATATAAA
20491368 ATATAATATAAA
1 A-ATAATATAAA
20491380 AATAATATAAA
1 AATAATATAAA
20491391 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAA
Found at i:20491392 original size:29 final size:28
Alignment explanation
Indices: 20491360--20491420 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
20491350 TGGACATAAT
20491360 AATTTAAAA-TATAATATAAAAATAATATA
1 AATTTAAAATTATAATA-AAAAA-AATATA
*
20491389 AA-TTAAAATTTTAATAAAAAAAATATA
1 AATTTAAAATTATAATAAAAAAAATATA
20491416 AATTT
1 AATTT
20491421 GATAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.28
28 13 0.45
29 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTTAAAATTATAATAAAAAAAATATA
Found at i:20491441 original size:21 final size:21
Alignment explanation
Indices: 20491392--20491442 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
20491382 TAATATAAAT
20491392 TAAAAT-TTTAATAAAAAAAA
1 TAAAATATTTAATAAAAAAAA
* *
20491412 TATAA-ATTTGATAAAAATAAA
1 TAAAATATTTAATAAAAA-AAA
20491433 -AAAATATTTA
1 TAAAATATTTA
20491443 TTTTATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAATATTTAATAAAAAAAA
Found at i:20492120 original size:23 final size:23
Alignment explanation
Indices: 20492072--20492117 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
20492062 ATTAAGATAT
* * *
20492072 TATAAATATTAAACATATTCGAA
1 TATAAATATTAAAAATAATAGAA
20492095 TATAAATATTTAAAAATAATAGA
1 TATAAATA-TTAAAAATAATAGA
20492118 TATCTACCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
TATAAATATTAAAAATAATAGAA
Found at i:20493439 original size:14 final size:13
Alignment explanation
Indices: 20493389--20493426 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20493379 TTTTTTATTG
20493389 AAAATAATT-AAAT
1 AAAA-AATTAAAAT
20493402 -AAAAATTAAAAT
1 AAAAAATTAAAAT
20493414 AAAAAATTAAAAT
1 AAAAAATTAAAAT
20493427 TGATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 7 0.30
13 12 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:20493506 original size:14 final size:14
Alignment explanation
Indices: 20493489--20493534 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
20493479 ATTTTAATAA
*
20493489 ATTTTTATATATAT
1 ATTTTTATATAAAT
*
20493503 ATTTTTATGTAAAT
1 ATTTTTATATAAAT
*
20493517 ATTTTTAATAAAAAT
1 ATTTTT-ATATAAAT
20493532 ATT
1 ATT
20493535 GATAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTTTATATAAAT
Found at i:20501223 original size:32 final size:32
Alignment explanation
Indices: 20501182--20501245 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20501172 GTAATCATTC
*
20501182 TTTTGATGTTTATCGCAGCTATAAACATGAAA
1 TTTTGATGTTCATCGCAGCTATAAACATGAAA
20501214 TTTTGATGTTCATCGCAGCTATAAACATGAAA
1 TTTTGATGTTCATCGCAGCTATAAACATGAAA
20501246 AATAATCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TTTTGATGTTCATCGCAGCTATAAACATGAAA
Found at i:20501801 original size:63 final size:62
Alignment explanation
Indices: 20501698--20501844 Score: 147
Period size: 63 Copynumber: 2.4 Consensus size: 62
20501688 AGGGTTAATA
* *** * * * *
20501698 TTTTATAAAATGATTATTTAAGGTGTTTTTATATATAAAACAT-CTTAAATAAT-TATTTTTTAT
1 TTTTATAAAAAGATTATTTAAGACATTTTTATACAAAAAAC-TCCATAAAT-ATCT-TTTTATAT
*
20501761 TTTTATAAAAAGATTATTTAAGACATTTTTGTACAAAAAACTCCATAAATATCTTTTTATAT
1 TTTTATAAAAAGATTATTTAAGACATTTTTATACAAAAAACTCCATAAATATCTTTTTATAT
*
20501823 TTTTACAAATAA-ATTATTTAAG
1 TTTTATAAA-AAGATTATTTAAG
20501845 GAGTATAGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
62 28 0.39
63 43 0.61
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (62 bp):
TTTTATAAAAAGATTATTTAAGACATTTTTATACAAAAAACTCCATAAATATCTTTTTATAT
Found at i:20502156 original size:63 final size:61
Alignment explanation
Indices: 20502063--20502272 Score: 181
Period size: 62 Copynumber: 3.4 Consensus size: 61
20502053 AATACCACAT
* * * * * *
20502063 ATTTTTTAAAAGG-CATTATTTAAGCCATTTTTGGTTCAAAATTGCTTTAAATAATCTCTTG
1 ATTTTTTTAAAGGACATTATTTAAGCCATTTTT-ATCCAAAAATACCTTAAATAATCTCTTG
* * ** * *
20502124 ATATTTTTTAACGGAGATTATTTAAGGTATTTTTATCCAAAAATACCTTAAATAATTTCTTT
1 AT-TTTTTTAAAGGACATTATTTAAGCCATTTTTATCCAAAAATACCTTAAATAATCTCTTG
* * ** * * *
20502186 ATTTTTTTAAAGGTCATTATTTAAAG-CATTTCTAGACAAAAATTACCTTAAATAATATCATA
1 ATTTTTTTAAAGGACATTATTT-AAGCCATTTTTATCCAAAAA-TACCTTAAATAATCTCTTG
* *
20502248 AATTTTTTAAAGGATATTATTTAAG
1 ATTTTTTTAAAGGACATTATTTAAG
20502273 GCTTTTTTTT
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
61 34 0.28
62 70 0.58
63 16 0.13
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (61 bp):
ATTTTTTTAAAGGACATTATTTAAGCCATTTTTATCCAAAAATACCTTAAATAATCTCTTG
Found at i:20503647 original size:20 final size:20
Alignment explanation
Indices: 20503600--20503648 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20503590 ATTCAAATTC
*
20503600 GATTGAGTTTTATTTTTTTA
1 GATTGAGCTTTATTTTTTTA
*
20503620 GATCGAGCTTTATTTTTTTA
1 GATTGAGCTTTATTTTTTTA
20503640 -ACTTGAGCT
1 GA-TTGAGCT
20503649 CGTTCGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.55
Consensus pattern (20 bp):
GATTGAGCTTTATTTTTTTA
Found at i:20504826 original size:37 final size:36
Alignment explanation
Indices: 20504740--20504847 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 36
20504730 TATATTCTTA
*
20504740 TAATATAAAATATTAAAA---ATATAT-ATTTATA-
1 TAATATTAAATATTAAAATTTATATATAATTTATAT
** *
20504771 TAATATTTTATATAAAAATTTATATCATAATTTATAT
1 TAATATTAAATATTAAAATTTATAT-ATAATTTATAT
*
20504808 TAATATTAAATATTAAAATTTATTATTTTAATTT-TAT
1 TAATATTAAATATTAAAATTTA-TA-TATAATTTATAT
20504845 TAA
1 TAA
20504848 ATATAGATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 14 0.23
34 4 0.07
35 2 0.03
36 7 0.11
37 25 0.41
38 8 0.13
39 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (36 bp):
TAATATTAAATATTAAAATTTATATATAATTTATAT
Found at i:20504834 original size:13 final size:12
Alignment explanation
Indices: 20504764--20504848 Score: 57
Period size: 12 Copynumber: 7.0 Consensus size: 12
20504754 AAAAATATAT
20504764 ATTTATA-TAATA
1 ATTTATATTAA-A
* *
20504776 TTTTATATAAAA
1 ATTTATATTAAA
* *
20504788 ATTTATATCATA
1 ATTTATATTAAA
*
20504800 ATTTATATTAAT
1 ATTTATATTAAA
*
20504812 ATTAAATATTAAA
1 ATT-TATATTAAA
**
20504825 ATTTATTATTTTA
1 ATTTA-TATTAAA
20504838 ATTT-TATTAAA
1 ATTTATATTAAA
20504849 TATAGATATA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
11 5 0.09
12 29 0.53
13 21 0.38
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTATATTAAA
Found at i:20504906 original size:24 final size:24
Alignment explanation
Indices: 20504878--20504946 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
20504868 AAAATTAAAA
* *
20504878 ATTATATTATTTTTATATTTTA-T
1 ATTATATCATTTTTATATTATATT
*
20504901 ATTTATATCATATTTATATTATATT
1 A-TTATATCATTTTTATATTATATT
20504926 ATTATATCATATTTTATATTA
1 ATTATATCAT-TTTTATATTA
20504947 AAATATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 27 0.69
25 11 0.28
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATATCATTTTTATATTATATT
Found at i:20512795 original size:23 final size:23
Alignment explanation
Indices: 20512765--20512809 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20512755 GACTAAGAAA
20512765 GTCCACATAAGTATGATGTATGT
1 GTCCACATAAGTATGATGTATGT
*
20512788 GTCCACATAGGTATGATGTATG
1 GTCCACATAAGTATGATGTATG
20512810 AGTGCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (23 bp):
GTCCACATAAGTATGATGTATGT
Found at i:20512824 original size:23 final size:23
Alignment explanation
Indices: 20512764--20512825 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
20512754 AGACTAAGAA
20512764 AGTCCACATAA-GTATGATGTATG
1 AGTCCACA-AACGTATGATGTATG
* * *
20512787 TGTCCACATAGGTATGATGTATG
1 AGTCCACAAACGTATGATGTATG
* *
20512810 AGTGCATAAACGTATG
1 AGTCCACAAACGTATG
20512826 TGTTTGGTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (23 bp):
AGTCCACAAACGTATGATGTATG
Found at i:20514849 original size:2 final size:2
Alignment explanation
Indices: 20514844--20514882 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20514834 CAAAAAAAGC
20514844 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20514883 TGTGATTAAA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20529191 original size:63 final size:62
Alignment explanation
Indices: 20529124--20529505 Score: 237
Period size: 63 Copynumber: 6.1 Consensus size: 62
20529114 GGATTGTACC
* * * * * * *
20529124 GGTGGTGGTGGTGAGTATACTGGTGGAGGTGGGGATTGTACCGGTGGTGGTGGTGAGTATACT
1 GGTGGTGGTGGTGAATAGACTGGTGGTGG-GGGGAGTGAACTGGTGGTGGTGGTGAGTAGACT
* * * * * * *
20529187 GGTGGAGGTGGAGAGTGGACGGGTGGTGGAGGGGAGTAAACTGGT-GT--TGGTG-GT-G-GT
1 GGTGGTGGTGGTGAATAGACTGGTGGTGG-GGGGAGTGAACTGGTGGTGGTGGTGAGTAGACT
* * *
20529244 GGT-GTGGTGGTGAAT-GAACAGGTGGTGGCGGGGAGT-AGACTGGTGGTGGTGGCGAGTAGACA
1 GGTGGTGGTGGTGAATAG-ACTGGTGGTGG-GGGGAGTGA-ACTGGTGGTGGTGGTGAGTAGACT
* * * * *
20529306 GGAGGTGGTGGTGAGTGGACTGGTGG-GGGTGGTGAGT-AAATAGGTGAAGGTGGTGGTGGAGAA
1 GGTGGTGGTGGTGAATAGACTGGTGGTGGG-GG-GAGTGAACT-GGT---GGTGGTGGT-GAG-T
20529369 AGGACT
58 A-GACT
* * * * *
20529375 GGTGGTGGTGGTGAATATACTGGTGGTGGGGGTGAGTGGACGGGTGGGGGTGGAGAGTAGACT
1 GGTGGTGGTGGTGAATAGACTGGTGGTGGGGG-GAGTGAACTGGTGGTGGTGGTGAGTAGACT
* * * * * * *
20529438 GGTGGTGGTGGGGAATGGACTGGTGGAGGGGGAGATTGAACTGGTGGTGGTGGGGAATGGACT
1 GGTGGTGGTGGTGAATAGACTGGTGGTGGGGG-GAGTGAACTGGTGGTGGTGGTGAGTAGACT
20529501 GGTGG
1 GGTGG
20529506 AGGGGGAGAT
Statistics
Matches: 248, Mismatches: 50, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
55 2 0.01
56 32 0.13
57 6 0.02
59 6 0.02
60 7 0.03
61 2 0.01
62 10 0.04
63 120 0.48
64 2 0.01
65 3 0.01
66 15 0.06
67 3 0.01
68 1 0.00
69 35 0.14
70 4 0.02
ACGTcount: A:0.17, C:0.05, G:0.54, T:0.24
Consensus pattern (62 bp):
GGTGGTGGTGGTGAATAGACTGGTGGTGGGGGGAGTGAACTGGTGGTGGTGGTGAGTAGACT
Found at i:20529277 original size:119 final size:119
Alignment explanation
Indices: 20529128--20529364 Score: 264
Period size: 119 Copynumber: 2.0 Consensus size: 119
20529118 TGTACCGGTG
* * * * * * * *
20529128 GTGGTGGTGAGTATACTGGTGGAGGTGGGGA-TTGTACCGGTGGTGGTGGTGAGTATACTGGTGG
1 GTGGTGGTGAATATACAGGTGGAGGCGGGGAGTAG-ACCGGTGGTGGTGGCGAGTAGACAGGAGG
* **
20529192 AGGTGGAGAGTGGACGGGTGGTGGAGGGGAGTAAACT-GGTGTTGGTGGTGGTGGT
65 AGGTGGAGAGTGGACGGGTGGGGGAGGGGAGTAAA-TAGGTGAAGGTGGTGGTGGT
* *
20529247 GTGGTGGTGAATGA-ACAGGTGGTGGCGGGGAGTAGACTGGTGGTGGTGGCGAGTAGACAGGAGG
1 GTGGTGGTGAAT-ATACAGGTGGAGGCGGGGAGTAGACCGGTGGTGGTGGCGAGTAGACAGGAGG
* * * * *
20529311 TGGTGGTGAGTGGACTGGTGGGGGTGGTGAGTAAATAGGTGAAGGTGGTGGTGG
65 AGGTGGAGAGTGGACGGGTGGGGGAGGGGAGTAAATAGGTGAAGGTGGTGGTGG
20529365 AGAAAGGACT
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
118 1 0.01
119 93 0.96
120 3 0.03
ACGTcount: A:0.17, C:0.05, G:0.54, T:0.24
Consensus pattern (119 bp):
GTGGTGGTGAATATACAGGTGGAGGCGGGGAGTAGACCGGTGGTGGTGGCGAGTAGACAGGAGGA
GGTGGAGAGTGGACGGGTGGGGGAGGGGAGTAAATAGGTGAAGGTGGTGGTGGT
Found at i:20529501 original size:21 final size:21
Alignment explanation
Indices: 20529081--20529529 Score: 211
Period size: 21 Copynumber: 21.4 Consensus size: 21
20529071 GAGCTCGTGG
* *
20529081 TGGTGGTGGTGGTGAG-GAAAC
1 TGGTGGTGGTGGGGAGTG-GAC
* * * *
20529102 CGGTGGAGGTGGGGATTGTAC
1 TGGTGGTGGTGGGGAGTGGAC
* * **
20529123 CGGTGGTGGTGGTGAGTATAC
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529144 TGGTGGAGGTGGGGATTGTAC
1 TGGTGGTGGTGGGGAGTGGAC
* * **
20529165 CGGTGGTGGTGGTGAGTATAC
1 TGGTGGTGGTGGGGAGTGGAC
* *
20529186 TGGTGGAGGTGGAGAGTGGAC
1 TGGTGGTGGTGGGGAGTGGAC
* * **
20529207 GGGTGGTGGAGGGGAGTAAAC
1 TGGTGGTGGTGGGGAGTGGAC
*
20529228 TGGT-GT--TGGTG-GTGG--
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529243 TGGT-GTGGTGGTGAATGAAC
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529263 AGGTGGTGGCGGGGAGTAGAC
1 TGGTGGTGGTGGGGAGTGGAC
* *
20529284 TGGTGGTGGTGGCGAGTAGAC
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529305 AGGAGGTGGTGGTGAGTGGAC
1 TGGTGGTGGTGGGGAGTGGAC
* * * *
20529326 TGGTGGGGGTGGTGAGT-AAA
1 TGGTGGTGGTGGGGAGTGGAC
*
20529346 TAGGTGAAGGTGGTGGTGGAGAAAGGAC
1 T-GGT---GGTGGTGG-GGAG--TGGAC
* * **
20529374 TGGTGGTGGTGGTGAATATAC
1 TGGTGGTGGTGGGGAGTGGAC
20529395 TGGTGGTGG-GGGTGAGTGGAC
1 TGGTGGTGGTGGG-GAGTGGAC
* * * *
20529416 GGGTGGGGGTGGAGAGTAGAC
1 TGGTGGTGGTGGGGAGTGGAC
*
20529437 TGGTGGTGGTGGGGAATGGAC
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529458 TGGTGGAGG-GGGAGATTGAAC
1 TGGTGGTGGTGGG-GAGTGGAC
*
20529479 TGGTGGTGGTGGGGAATGGAC
1 TGGTGGTGGTGGGGAGTGGAC
* * *
20529500 TGGTGGAGG-GGGAGATTGAAC
1 TGGTGGTGGTGGG-GAGTGGAC
20529521 TGGTGGTGG
1 TGGTGGTGG
20529530 AGGCATTGGT
Statistics
Matches: 320, Mismatches: 88, Indels: 40
0.71 0.20 0.09
Matches are distributed among these distances:
15 6 0.02
17 7 0.02
18 5 0.02
20 15 0.05
21 256 0.80
22 6 0.02
23 2 0.01
24 15 0.05
25 3 0.01
27 3 0.01
28 2 0.01
ACGTcount: A:0.17, C:0.05, G:0.54, T:0.23
Consensus pattern (21 bp):
TGGTGGTGGTGGGGAGTGGAC
Found at i:20529531 original size:24 final size:24
Alignment explanation
Indices: 20529458--20529532 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
20529448 GGGAATGGAC
20529458 TGGTGGAGGGGGAGATTGAACTGG
1 TGGTGGAGGGGGAGATTGAACTGG
* *
20529482 TGGTGG-TGGGGA-A-TGGAC---
1 TGGTGGAGGGGGAGATTGAACTGG
20529500 TGGTGGAGGGGGAGATTGAACTGG
1 TGGTGGAGGGGGAGATTGAACTGG
20529524 TGGTGGAGG
1 TGGTGGAGG
20529533 CATTGGTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 6 0.15
19 5 0.12
20 1 0.02
21 8 0.20
22 1 0.02
23 5 0.12
24 15 0.37
ACGTcount: A:0.19, C:0.04, G:0.56, T:0.21
Consensus pattern (24 bp):
TGGTGGAGGGGGAGATTGAACTGG
Found at i:20529829 original size:42 final size:42
Alignment explanation
Indices: 20529782--20529875 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
20529772 TTGATGGTTT
*
20529782 TGGCTTTGGCGTTGGAGGAGCAGTAACTGGAGGTTTTGGATG
1 TGGCTTTGGCGTTGGAGGACCAGTAACTGGAGGTTTTGGATG
* * * * *
20529824 TGGCTTTGGCGTTGGAGGCCCTGTGACTGGTGGTTTTGGCTG
1 TGGCTTTGGCGTTGGAGGACCAGTAACTGGAGGTTTTGGATG
*
20529866 TGGCTCTGGC
1 TGGCTTTGGC
20529876 TCTGATGGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.10, C:0.15, G:0.43, T:0.33
Consensus pattern (42 bp):
TGGCTTTGGCGTTGGAGGACCAGTAACTGGAGGTTTTGGATG
Found at i:20531812 original size:15 final size:17
Alignment explanation
Indices: 20531771--20531816 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
20531761 TCATTTTTTT
20531771 ATTATAAATAATT-ATTTA
1 ATTATAAAT--TTAATTTA
20531789 ATTATAAATTTAATTTA
1 ATTATAAATTTAATTTA
20531806 A-TA-AAATTTAA
1 ATTATAAATTTAA
20531817 ATTCAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.30
16 4 0.15
17 6 0.22
18 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATAAATTTAATTTA
Found at i:20541358 original size:2 final size:2
Alignment explanation
Indices: 20541353--20541379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20541343 TGTGTGTGTG
20541353 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 T
20541380 GTATTTTCCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.