Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 143 of 313
Found at i:45931896 original size:2 final size:2
Alignment explanation
Indices: 45931889--45931914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45931879 AATTAGACAA
45931889 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
45931915 GCATAAACTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45939507 original size:16 final size:17
Alignment explanation
Indices: 45939481--45939519 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
45939471 GGGAAAAGAA
45939481 CTTTC-CTTTTTC-TTT
1 CTTTCTCTTTTTCATTT
45939496 CTTTCTCTTTTTCATTT
1 CTTTCTCTTTTTCATTT
45939513 C-TTCTCT
1 CTTTCTCT
45939520 ACACTCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTCTCTTTTTCATTT
Found at i:45941411 original size:15 final size:15
Alignment explanation
Indices: 45941391--45941419 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45941381 AAGAACAAAC
45941391 AAAATTCATCTATTA
1 AAAATTCATCTATTA
45941406 AAAATTCATCTATT
1 AAAATTCATCTATT
45941420 TTTACTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTCATCTATTA
Found at i:45942669 original size:30 final size:31
Alignment explanation
Indices: 45942601--45942672 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
45942591 TCATGTAAGC
*
45942601 AATTAATTAATTTTTTAAAATTAAAAAATTAA
1 AATTAATTAATTTTTTAAAA-TAAAAAATAAA
* *
45942633 AA--AATTATTTTTTTAGAA-AAAAAATAAA
1 AATTAATTAATTTTTTAAAATAAAAAATAAA
45942661 AATTAATTAATT
1 AATTAATTAATT
45942673 GCTGATGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 11 0.32
30 21 0.62
32 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
AATTAATTAATTTTTTAAAATAAAAAATAAA
Found at i:45950121 original size:21 final size:21
Alignment explanation
Indices: 45950070--45950113 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
45950060 ATGACATTAA
45950070 TAAGCCTAACTTATCTTAAAC
1 TAAGCCTAACTTATCTTAAAC
45950091 TAAGCCTAACTTATCTTAAAC
1 TAAGCCTAACTTATCTTAAAC
45950112 TA
1 TA
45950114 GTTTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (21 bp):
TAAGCCTAACTTATCTTAAAC
Found at i:45954288 original size:45 final size:45
Alignment explanation
Indices: 45954239--45954412 Score: 249
Period size: 45 Copynumber: 3.9 Consensus size: 45
45954229 TCGGCCATGG
* * * *
45954239 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
45954284 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
45954329 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
45954374 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTG
45954413 TCCACCTCTT
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:45954547 original size:16 final size:16
Alignment explanation
Indices: 45954526--45954557 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45954516 CATTCTGCAT
45954526 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45954542 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45954558 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:45957569 original size:23 final size:23
Alignment explanation
Indices: 45957543--45957640 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
45957533 ATAAGTGCCA
45957543 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
45957566 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
45957589 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
45957611 CACTGAAATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
45957634 CACTGAT
1 CACTGAT
45957641 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:45957608 original size:45 final size:45
Alignment explanation
Indices: 45957550--45957638 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
45957540 CCACACTGAT
* *
45957550 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
*
45957595 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGTTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
45957639 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:45969950 original size:21 final size:22
Alignment explanation
Indices: 45969921--45969981 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
45969911 GTGGACGGTC
45969921 ATATCATATTTATATGT-A-TGTA
1 ATAT-ATATTTATAT-TAACTGTA
*
45969943 ATATATA-TTATGTTAACTGTA
1 ATATATATTTATATTAACTGTA
45969964 ATATATATGTTATATTAA
1 ATATATAT-TTATATTAA
45969982 ACTATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 6 0.18
21 14 0.42
22 4 0.12
23 8 0.24
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (22 bp):
ATATATATTTATATTAACTGTA
Found at i:45972882 original size:29 final size:29
Alignment explanation
Indices: 45972840--45972898 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
45972830 CATGATTTTC
45972840 CATTTGCACCTCTCGTCGCGCATTGCGTA
1 CATTTGCACCTCTCGTCGCGCATTGCGTA
*
45972869 CATTTGCACCTCTCGTCGTGCATTGCGTA
1 CATTTGCACCTCTCGTCGCGCATTGCGTA
45972898 C
1 C
45972899 TTTCCCTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (29 bp):
CATTTGCACCTCTCGTCGCGCATTGCGTA
Found at i:45975101 original size:51 final size:51
Alignment explanation
Indices: 45975025--45975127 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
45975015 TTTCCATGTA
45975025 GATGGTATCTTTAACCTTCCTTCTTATCCAAAGGTCAGCACCGTTGTGAAC
1 GATGGTATCTTTAACCTTCCTTCTTATCCAAAGGTCAGCACCGTTGTGAAC
45975076 GATGGTATCTTTAACCTTCCTTCTTATCCAAAGGTCAGCACCGTTGTGAAC
1 GATGGTATCTTTAACCTTCCTTCTTATCCAAAGGTCAGCACCGTTGTGAAC
45975127 G
1 G
45975128 CAGGAGGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (51 bp):
GATGGTATCTTTAACCTTCCTTCTTATCCAAAGGTCAGCACCGTTGTGAAC
Found at i:45975800 original size:24 final size:26
Alignment explanation
Indices: 45975751--45975801 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
45975741 TTCCACTCTT
*
45975751 AAAACACTAAACCCTAATTACTAATA
1 AAAACACTAAACCCTAATTACAAATA
45975777 AAAAC-CT-AACCCTAAATTA-AAATA
1 AAAACACTAAACCCT-AATTACAAATA
45975801 A
1 A
45975802 TAATAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 11 0.48
25 7 0.30
26 5 0.22
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAACACTAAACCCTAATTACAAATA
Found at i:45982312 original size:20 final size:20
Alignment explanation
Indices: 45982287--45982324 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45982277 AGGTGAACCA
45982287 AATTTTATAAATTTTTAAAT
1 AATTTTATAAATTTTTAAAT
* *
45982307 AATTTTTTTAATTTTTAA
1 AATTTTATAAATTTTTAA
45982325 TTTTAATAAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTATAAATTTTTAAAT
Found at i:45985065 original size:22 final size:22
Alignment explanation
Indices: 45985037--45985082 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
45985027 AAATATGACA
45985037 TTGGTCTCTACTCTTTACAAAT
1 TTGGTCTCTACTCTTTACAAAT
45985059 TTGGTCTCTACTCTTTACAAAT
1 TTGGTCTCTACTCTTTACAAAT
45985081 TT
1 TT
45985083 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (22 bp):
TTGGTCTCTACTCTTTACAAAT
Found at i:45989655 original size:86 final size:87
Alignment explanation
Indices: 45989539--45989704 Score: 289
Period size: 86 Copynumber: 1.9 Consensus size: 87
45989529 ATCGACCCCA
*
45989539 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAGAAGTCGTCACCTTTACATGTCTCTAACAG
1 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
45989604 CAAACTAAATCAACCAAAAAAG
66 CAAACTAAATCAACCAAAAAAG
* * *
45989626 AAAA-TTTCTAGAAATGACTATGCACAGATCATGAAAAGTCGTCACCTTTACATGTGTCTAACAG
1 AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
45989690 CAAACTAAATCAACC
66 CAAACTAAATCAACC
45989705 CAAAGGATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 71 0.95
87 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (87 bp):
AAAATTTTCTAGAAATGACTATCCAAAGATCATGAAAAGTCGTCACCTTTACATGTCTCTAACAG
CAAACTAAATCAACCAAAAAAG
Found at i:46001909 original size:16 final size:16
Alignment explanation
Indices: 46001888--46001918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46001878 TTTTTTATTT
46001888 TCTTTTTCATTTTCCC
1 TCTTTTTCATTTTCCC
*
46001904 TCTTTTTCTTTTTCC
1 TCTTTTTCATTTTCC
46001919 TATCCTAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTTTCATTTTCCC
Found at i:46002203 original size:40 final size:40
Alignment explanation
Indices: 46002154--46002240 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
46002144 TGATTTCAGT
*
46002154 TTTTTTCAAGCTTAAATTCATA-GCTAATTTTTGGGTTTTC
1 TTTTTTCAAGCTTAAATTCATAGGC-AATTTTTGAGTTTTC
*
46002194 TTTTTTCAAGCTTAAATTCATAGGCAATTTTTTAGTTTTC
1 TTTTTTCAAGCTTAAATTCATAGGCAATTTTTGAGTTTTC
*
46002234 CTTTTTC
1 TTTTTTC
46002241 TTCTTTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.95
41 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (40 bp):
TTTTTTCAAGCTTAAATTCATAGGCAATTTTTGAGTTTTC
Found at i:46005023 original size:2 final size:2
Alignment explanation
Indices: 46005016--46005070 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
46005006 GAAGAAGAAA
46005016 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
46005058 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
46005071 AAAAGCAAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46012479 original size:184 final size:184
Alignment explanation
Indices: 46012136--46012503 Score: 578
Period size: 184 Copynumber: 2.0 Consensus size: 184
46012126 TTTTTAACTG
*
46012136 TAGAAATGGATGAAATTTTTAATAAAAAAGACCAGTTCACTCTTTGATTACTGTACAAGGACAAA
1 TAGAAATGGATGAAATTTTTAATAAAAAAGACCAGTTCACCCTTTGATTACTGTACAAGGACAAA
* * *
46012201 TTTGCCCATTTTTTGTACAAAGGCCTCTATTGTACTTTTACTAAATAAAACATAGGTTTCAGATT
66 TTTGCCCATTTTTTGTACAAAGGCCTCCATGGTAC-TTTA-TAAATAAAACATAGGTTTCAGATA
46012266 GAAAATATTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTCTTTTTTTAA
129 GAAAATATTATTGGACATTTAACATTCTTGAATACTTTCATATGTCT-TTTTTTTAA
* * * *
46012323 TAGAAATGGATGAAATTTTTATTAGAAAGGACTAGTTCACCCTTTGATCTACTGTACAAGGACAA
1 TAGAAATGGATGAAATTTTTAATAAAAAAGACCAGTTCACCCTTTGAT-TACTGTACAAGGACAA
* *
46012388 ATTTGCCCATTTTTTGTACAAGGGCCTCCATGGTAC-TT-TGAATAAAACATAGGTTTCAGATAG
65 ATTTGCCCATTTTTTGTACAAAGGCCTCCATGGTACTTTATAAATAAAACATAGGTTTCAGATAG
* *
46012451 AAAATGTTATTGGACATTTAACATTCTTGAATACTTTCATGTGTCTTTTTTTT
130 AAAATATTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTTTTTTTT
46012504 CTTTTTTCTT
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
183 7 0.04
184 67 0.40
186 2 0.01
187 43 0.26
188 49 0.29
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (184 bp):
TAGAAATGGATGAAATTTTTAATAAAAAAGACCAGTTCACCCTTTGATTACTGTACAAGGACAAA
TTTGCCCATTTTTTGTACAAAGGCCTCCATGGTACTTTATAAATAAAACATAGGTTTCAGATAGA
AAATATTATTGGACATTTAACATTCTTGAATACTTTCATATGTCTTTTTTTTAA
Found at i:46014116 original size:31 final size:31
Alignment explanation
Indices: 46014081--46014148 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
46014071 TTAACAACCT
* *
46014081 AGTGATTTAAATAAAAACTTTTAAATAGTTC
1 AGTGATTTAAATAAAAACTTTCAAAGAGTTC
* * * *
46014112 AGTGACTTAAATGAAAAGTTTCAAGGAGTTC
1 AGTGATTTAAATAAAAACTTTCAAAGAGTTC
46014143 AGTGAT
1 AGTGAT
46014149 CAAATTGTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (31 bp):
AGTGATTTAAATAAAAACTTTCAAAGAGTTC
Found at i:46014661 original size:4 final size:4
Alignment explanation
Indices: 46014652--46014681 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
46014642 AGGCACCATT
*
46014652 TGTA TGTA TGTA TGTA TGTA TATA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
46014682 GTGTTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:46027599 original size:26 final size:26
Alignment explanation
Indices: 46027570--46027621 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
46027560 AGGCAAGTGC
46027570 ACACAAGTCCAGCAAAAGTTAAGGTT
1 ACACAAGTCCAGCAAAAGTTAAGGTT
* *
46027596 ACACAAGTCTAGCAAAAGTTGAGGTT
1 ACACAAGTCCAGCAAAAGTTAAGGTT
46027622 CAAGTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (26 bp):
ACACAAGTCCAGCAAAAGTTAAGGTT
Found at i:46041002 original size:15 final size:17
Alignment explanation
Indices: 46040972--46041004 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46040962 TATAAAAAAC
46040972 AAAAAATATATATAAAT
1 AAAAAATATATATAAAT
46040989 AAAAAATA-AT-TAAAT
1 AAAAAATATATATAAAT
46041004 A
1 A
46041005 GTATCTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATATATATAAAT
Found at i:46051096 original size:19 final size:19
Alignment explanation
Indices: 46051067--46051104 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
46051057 GACATGTAAC
46051067 AAAATATTAAAATATTTATT
1 AAAATATTAAAAT-TTTATT
46051087 AAAA-ATTAAAATTTTATT
1 AAAATATTAAAATTTTATT
46051105 TTTGTCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATTAAAATTTTATT
Found at i:46058778 original size:31 final size:31
Alignment explanation
Indices: 46058740--46058800 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
46058730 AAACTTACAT
* *
46058740 TTCAATAACTTAAATTAAAATTTTTGAATAG
1 TTCAATAACTTAAATGAAAATTTTTAAATAG
*
46058771 TTCAATAACTTGAATGAAAATTTTTAAATA
1 TTCAATAACTTAAATGAAAATTTTTAAATA
46058801 ATTTAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (31 bp):
TTCAATAACTTAAATGAAAATTTTTAAATAG
Found at i:46059448 original size:14 final size:14
Alignment explanation
Indices: 46059431--46059460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
46059421 ATATTCAAAC
46059431 AACAACAAAATAAT
1 AACAACAAAATAAT
*
46059445 AACAATAAAATAAT
1 AACAACAAAATAAT
46059459 AA
1 AA
46059461 AATGATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (14 bp):
AACAACAAAATAAT
Found at i:46059504 original size:33 final size:32
Alignment explanation
Indices: 46059427--46059508 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 32
46059417 TACAATATTC
* * *
46059427 AAACAACAACAAAATAATAACAATAAAATAATA
1 AAACAACAACAAAA-CACAACAATAAAATAAGA
** * *
46059460 AAATGATAACAAAACACAACAATAAAATAGGA
1 AAACAACAACAAAACACAACAATAAAATAAGA
46059492 GAAACAACAACAAAACA
1 -AAACAACAACAAAACA
46059509 GTAAAAATAG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
32 14 0.37
33 24 0.63
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.11
Consensus pattern (32 bp):
AAACAACAACAAAACACAACAATAAAATAAGA
Found at i:46071115 original size:13 final size:14
Alignment explanation
Indices: 46071097--46071127 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
46071087 ACTAAATTCC
46071097 TAGAAATAAAAGT-
1 TAGAAATAAAAGTA
46071110 TAGAAATAAAAGTA
1 TAGAAATAAAAGTA
46071124 TAGA
1 TAGA
46071128 GACTATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (14 bp):
TAGAAATAAAAGTA
Found at i:46076003 original size:17 final size:18
Alignment explanation
Indices: 46075971--46076009 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
46075961 ACGGTAGCTT
* *
46075971 TTTCAACCGCTAAAAAGA
1 TTTCAACAGCTAAAAAAA
46075989 TTTCAACAG-TAAAAAAA
1 TTTCAACAGCTAAAAAAA
46076006 TTTC
1 TTTC
46076010 TTATATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (18 bp):
TTTCAACAGCTAAAAAAA
Found at i:46078204 original size:30 final size:30
Alignment explanation
Indices: 46078168--46078229 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
46078158 CCCTGCACCC
46078168 TTACAACACGAAATTCCCAGGATAAAAAAT
1 TTACAACACGAAATTCCCAGGATAAAAAAT
46078198 TTACAACACGAAATTCCCAGGATAAAAAAT
1 TTACAACACGAAATTCCCAGGATAAAAAAT
46078228 TT
1 TT
46078230 CCCTTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (30 bp):
TTACAACACGAAATTCCCAGGATAAAAAAT
Found at i:46083559 original size:58 final size:58
Alignment explanation
Indices: 46083490--46083628 Score: 181
Period size: 58 Copynumber: 2.4 Consensus size: 58
46083480 GGTCGTCATA
* * * * * *
46083490 ACGTCTTTCATCTATAGTCTTACACCGTATACCTTAT-TCATTATACCTTACTGCCATG
1 ACGTCTTTCATCCATGGTCTTACACCATATACATTATACCATT-TACCTTACTACCATG
* *
46083548 ACGTCTTTCATCCATGGTCTTACACCATATACATTATACCATTTACCTTGCTACTATG
1 ACGTCTTTCATCCATGGTCTTACACCATATACATTATACCATTTACCTTACTACCATG
*
46083606 ACATCTTTCATCCATGGTCTTAC
1 ACGTCTTTCATCCATGGTCTTAC
46083629 GTGTAACACC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 67 0.94
59 4 0.06
ACGTcount: A:0.24, C:0.28, G:0.09, T:0.39
Consensus pattern (58 bp):
ACGTCTTTCATCCATGGTCTTACACCATATACATTATACCATTTACCTTACTACCATG
Found at i:46084635 original size:20 final size:20
Alignment explanation
Indices: 46084610--46084649 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
46084600 CATTTCATTT
46084610 ATGCAATTGCTTTATCCATA
1 ATGCAATTGCTTTATCCATA
*
46084630 ATGCAATTGCTTTTTCCATA
1 ATGCAATTGCTTTATCCATA
46084650 CCATATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGCAATTGCTTTATCCATA
Found at i:46085072 original size:11 final size:11
Alignment explanation
Indices: 46085056--46085080 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46085046 TTCAATTCAA
46085056 ATAATCAATAT
1 ATAATCAATAT
46085067 ATAATCAATAT
1 ATAATCAATAT
46085078 ATA
1 ATA
46085081 TACCAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:46085818 original size:15 final size:14
Alignment explanation
Indices: 46085780--46085822 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
46085770 AAAACCCTAA
46085780 TTTCTTCTTTCTTTT
1 TTTCTT-TTTCTTTT
46085795 TTTCCCTTTTTCTTTT
1 TTT--CTTTTTCTTTT
46085811 CTTTCTTTTTCT
1 -TTTCTTTTTCT
46085823 CCCTATTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
16 8 0.32
17 6 0.24
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:46085842 original size:26 final size:25
Alignment explanation
Indices: 46085784--46085871 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
46085774 CCCTAATTTC
* * *
46085784 TTCTTTCTTTTTTTCCCTTTTTCTT
1 TTCTTTCTTTTTCTCCCTATTTCGT
46085809 TTCTTTCTTTTTCTCCCTATTTCGT
1 TTCTTTCTTTTTCTCCCTATTTCGT
* ** *
46085834 TTCTATTCTGTTTCTTTCTATTTCTTT
1 TTCT-TTCTTTTTCTCCCTATTTC-GT
*
46085861 TTGTTTCTTTT
1 TTCTTTCTTTT
46085872 ATTTATTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 26 0.50
26 22 0.42
27 4 0.08
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (25 bp):
TTCTTTCTTTTTCTCCCTATTTCGT
Found at i:46085847 original size:16 final size:16
Alignment explanation
Indices: 46085828--46085868 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
46085818 TTTCTCCCTA
46085828 TTTCGTTTCTA-TTCT
1 TTTCGTTTCTATTTCT
46085843 GTTTC-TTTCTATTTCT
1 -TTTCGTTTCTATTTCT
*
46085859 TTTTGTTTCT
1 TTTCGTTTCT
46085869 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (16 bp):
TTTCGTTTCTATTTCT
Found at i:46085851 original size:20 final size:20
Alignment explanation
Indices: 46085833--46085875 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
46085823 CCCTATTTCG
46085833 TTTCTATTCTGTTTCTTTCTA
1 TTTCT-TTCTGTTTCTTTCTA
*
46085854 TTTCTTTTTGTTTCTTT-TA
1 TTTCTTTCTGTTTCTTTCTA
46085873 TTT
1 TTT
46085876 ATTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTCTTTCTGTTTCTTTCTA
Found at i:46090796 original size:17 final size:17
Alignment explanation
Indices: 46090761--46090802 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
46090751 GGTTAATTTT
**
46090761 TTTTTATAATTTTTGTA
1 TTTTTATAATTTTAATA
*
46090778 TTTTTGTAATTTTAATA
1 TTTTTATAATTTTAATA
46090795 -TTTTATAA
1 TTTTTATAA
46090803 ACTTTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTTATAATTTTAATA
Found at i:46090825 original size:17 final size:18
Alignment explanation
Indices: 46090794--46090827 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46090784 TAATTTTAAT
46090794 ATTTTATAAACTTTTTTA
1 ATTTTATAAACTTTTTTA
*
46090812 ATTTT-TAAAGTTTTTT
1 ATTTTATAAACTTTTTT
46090828 TAAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTATAAACTTTTTTA
Found at i:46091643 original size:15 final size:15
Alignment explanation
Indices: 46091623--46091657 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46091613 TAGTCCCTAA
* *
46091623 GTTTTTTGGTTTAGG
1 GTTTTTAGGGTTAGG
46091638 GTTTTTAGGGTTAGG
1 GTTTTTAGGGTTAGG
46091653 GTTTT
1 GTTTT
46091658 GTTAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.34, T:0.57
Consensus pattern (15 bp):
GTTTTTAGGGTTAGG
Found at i:46091780 original size:33 final size:34
Alignment explanation
Indices: 46091727--46091816 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
46091717 GTTCTTTTTA
* *
46091727 AAAATTAATTAAA-TT-AGTTTAG-AGTTTTAA-
1 AAAATTAAATAAATTTGGGTTTAGTAGTTTTAAG
**
46091757 ATAAATTAAATAAATTTGGGTTTAGTTTTTTTAAG
1 A-AAATTAAATAAATTTGGGTTTAGTAGTTTTAAG
*
46091792 AAAATTAATTAAATTTGGGTTTAGT
1 AAAATTAAATAAATTTGGGTTTAGT
46091817 TCTTTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 11 0.22
32 2 0.04
33 6 0.12
34 29 0.58
35 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
AAAATTAAATAAATTTGGGTTTAGTAGTTTTAAG
Found at i:46091797 original size:34 final size:35
Alignment explanation
Indices: 46091751--46091826 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
46091741 TAGTTTAGAG
46091751 TTTTAAATAAATTAAATAAATTTGGGTTTAGTT-T
1 TTTTAAATAAATTAAATAAATTTGGGTTTAGTTCT
*
46091785 TTTTAAGA-AAATTAATTAAATTTGGGTTTAGTTCT
1 TTTTAA-ATAAATTAAATAAATTTGGGTTTAGTTCT
46091820 TTTTAAA
1 TTTTAAA
46091827 ATAATATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 31 0.79
35 8 0.21
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (35 bp):
TTTTAAATAAATTAAATAAATTTGGGTTTAGTTCT
Found at i:46092119 original size:125 final size:125
Alignment explanation
Indices: 46091888--46092154 Score: 383
Period size: 125 Copynumber: 2.1 Consensus size: 125
46091878 GATTTTGGTT
* * * * *
46091888 TTTTTTTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTTAATAAATTGTGTCCAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTAAAGAAATAGTGTCAAAA
*
46091953 ACGCTTCAAGCAGGATGCACTATCAGCAAAAAACTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAAAACTGAAAAAAGCTCCCACGTAGACGCTC
* * * *
46092013 TTTTTCTATAGTAGTTCCTTAAAAACTAATTTTGAGAATACGGTTCTAAAGAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTAAAGAAATAGTGTCAAAA
* * * *
46092078 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACGTAGACTCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAA--AACTGAAAAAAGCTCCCACGTAGACGCTC
46092139 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
46092155 ATCTTCTGAA
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
125 86 0.69
126 38 0.30
127 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTAAAGAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTATCAGCAAAAAACTGAAAAAAGCTCCCACGTAGACGCTC
Found at i:46092305 original size:186 final size:186
Alignment explanation
Indices: 46091987--46092340 Score: 532
Period size: 186 Copynumber: 1.9 Consensus size: 186
46091977 AGCAAAAAAC
* * * *
46091987 TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTCCTTAAAAACTAATTTTGAGAAT
1 TGAAAAAAGCTCACACGTGGACGCTCTTTTTCTACAGTAGTTCCTTAAAAAATAATTTTGAGAAG
*
46092052 ACGGTTCTAAAGAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAA
66 ACGGTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAA
* *
46092117 AAAAGCTCCTACGTAGACTCTCTTTTTCTACAGTAGTTATCTTCTGAACAAATTGA
131 AAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTTATCTTCTGAACAAATTGA
* * * *
46092173 TGAAAAAATCTCACACGTGGACGTTTTTTTTCTACAGTA-TTTCTTGAAAAAATAATTTTGAGAA
1 TGAAAAAAGCTCACACGTGGACGCTCTTTTTCTACAGTAGTTCCTT-AAAAAATAATTTTGAGAA
* * * *
46092237 GACGTTTCTGAACAAGTAGTGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTG
65 GACGGTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TG
*
46092301 AAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
129 AAAAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTT
46092341 CATGTTTGGC
Statistics
Matches: 150, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
185 6 0.04
186 144 0.96
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (186 bp):
TGAAAAAAGCTCACACGTGGACGCTCTTTTTCTACAGTAGTTCCTTAAAAAATAATTTTGAGAAG
ACGGTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAA
AAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTTATCTTCTGAACAAATTGA
Found at i:46095271 original size:11 final size:11
Alignment explanation
Indices: 46095255--46095279 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46095245 CACTTTTTAC
46095255 AATATAAAAAT
1 AATATAAAAAT
46095266 AATATAAAAAT
1 AATATAAAAAT
46095277 AAT
1 AAT
46095280 TTATTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:46095666 original size:20 final size:18
Alignment explanation
Indices: 46095625--46095660 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46095615 AAAAAGAAAT
* *
46095625 ATATAAGGGTTAGGATAC
1 ATATAAGGGCTACGATAC
46095643 ATATAAGGGCTACGATAC
1 ATATAAGGGCTACGATAC
46095661 GCATATGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (18 bp):
ATATAAGGGCTACGATAC
Found at i:46097160 original size:43 final size:42
Alignment explanation
Indices: 46097091--46097244 Score: 159
Period size: 43 Copynumber: 3.6 Consensus size: 42
46097081 CTGATAAGTG
* * *
46097091 TTTTCGTGAAGACCACGT-TTGAGACATTGACATCGACTTGTA
1 TTTTCGTGTAGACCACGTCTAG-GACATTGGCATCGACTTGTA
46097133 TTTTCGTGTAGTACCACGTCTAGGACATTGGCATCGACTTGTA
1 TTTTCGTGTAG-ACCACGTCTAGGACATTGGCATCGACTTGTA
** * *
46097176 TTTTCGTGTAAGACCTTGTCTAGGACAGTGGCATCGATTTGTGA
1 TTTTCGTGT-AGACCACGTCTAGGACATTGGCATCGACTTGT-A
* * *
46097220 -TTACATGTAAGACCACGTCTGGGAC
1 TTTTCGTGT-AGACCACGTCTAGGAC
46097245 GTTGACGTTG
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
42 10 0.10
43 81 0.84
44 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (42 bp):
TTTTCGTGTAGACCACGTCTAGGACATTGGCATCGACTTGTA
Found at i:46101229 original size:41 final size:41
Alignment explanation
Indices: 46101184--46101265 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
46101174 TGCGACTAAG
46101184 TCTCTAGCTAACCGTTTAATGTTGAAACAACGTCTATTTAC
1 TCTCTAGCTAACCGTTTAATGTTGAAACAACGTCTATTTAC
46101225 TCTCTAGCTAACCGTTTAATGTTGAAACAACGTCTATTTAC
1 TCTCTAGCTAACCGTTTAATGTTGAAACAACGTCTATTTAC
46101266 GTTTCGCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (41 bp):
TCTCTAGCTAACCGTTTAATGTTGAAACAACGTCTATTTAC
Found at i:46105253 original size:30 final size:30
Alignment explanation
Indices: 46105219--46105282 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
46105209 TTAATTAAAG
46105219 AGAGCTTTGAGAAATTTAAGGAGAAATTTA
1 AGAGCTTTGAGAAATTTAAGGAGAAATTTA
* *
46105249 AGAGCTTTGAGAAATTTAGGGAGAAATTTG
1 AGAGCTTTGAGAAATTTAAGGAGAAATTTA
46105279 AGAG
1 AGAG
46105283 TTTTTTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (30 bp):
AGAGCTTTGAGAAATTTAAGGAGAAATTTA
Found at i:46106389 original size:29 final size:29
Alignment explanation
Indices: 46106336--46106391 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
46106326 GTAGTGACTT
** *
46106336 AATTATGAAAAGTTATTAAATGATCACGC
1 AATTATGAAAAGTTACAAAACGATCACGC
46106365 AATTATGAAAAGTTACAAAACGATCAC
1 AATTATGAAAAGTTACAAAACGATCAC
46106392 CTAACAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
AATTATGAAAAGTTACAAAACGATCACGC
Found at i:46109315 original size:37 final size:38
Alignment explanation
Indices: 46109256--46109355 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
46109246 CAAAAATAAT
*
46109256 ATTATTTTAATAGTTTAATATTAAATTAAAT-TTAA-TG
1 ATTATCTTAATAGTTTAATATT-AATTAAATATTAAGTG
* * *
46109293 CTTATCTTAATAGTATT-TTATTAATTTAATATTAAGGTG
1 ATTATCTTAATAGT-TTAATATTAATTAAATATTAA-GTG
*
46109332 ATTATCTTAATA-TTAAAT-TTAATT
1 ATTATCTTAATAGTTTAATATTAATT
46109356 TAATGTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
36 7 0.14
37 27 0.53
38 4 0.08
39 13 0.25
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (38 bp):
ATTATCTTAATAGTTTAATATTAATTAAATATTAAGTG
Found at i:46116206 original size:37 final size:37
Alignment explanation
Indices: 46116136--46116253 Score: 121
Period size: 37 Copynumber: 3.5 Consensus size: 37
46116126 AACTATAAAG
46116136 GCCGAATGC--ACATAT-T-CACTTATACCCACCTAT
1 GCCGAATGCATACATATATACACTTATACCCACCTAT
* * *
46116169 GCCGAATGCATACATATATACACTTATATCTATCTAT
1 GCCGAATGCATACATATATACACTTATACCCACCTAT
*
46116206 GCCGAATGCATACA-A-AT--A--TATATCCACCTAT
1 GCCGAATGCATACATATATACACTTATACCCACCTAT
*
46116237 GCCGAATGCCTACATAT
1 GCCGAATGCATACATAT
46116254 GCACACATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
31 24 0.33
32 1 0.01
33 10 0.14
35 8 0.11
36 2 0.03
37 28 0.38
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (37 bp):
GCCGAATGCATACATATATACACTTATACCCACCTAT
Found at i:46116613 original size:41 final size:41
Alignment explanation
Indices: 46116438--46116606 Score: 284
Period size: 41 Copynumber: 4.1 Consensus size: 41
46116428 AATTCATCAT
* *
46116438 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
46116479 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
46116520 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
46116561 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
46116602 ATTCA
1 ATTCA
46116607 ATTCACCAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 119 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:46116613 original size:82 final size:82
Alignment explanation
Indices: 46116444--46116606 Score: 326
Period size: 82 Copynumber: 2.0 Consensus size: 82
46116434 TCATATTCGG
46116444 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
46116509 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
46116526 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
46116591 TTTATAACCTGATTCA
66 TTTATAACCTGATTCA
46116607 ATTCACCAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:46116872 original size:15 final size:17
Alignment explanation
Indices: 46116834--46116874 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
46116824 ATCCACATAT
46116834 ATATATATATTACACAC
1 ATATATATATTACACAC
*
46116851 ATATATATATT-CGCAC
1 ATATATATATTACACAC
46116867 AT-TATATA
1 ATATATATA
46116875 AACACAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 6 0.26
17 11 0.48
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATATATATTACACAC
Found at i:46116873 original size:19 final size:18
Alignment explanation
Indices: 46116827--46116874 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
46116817 TTGTTCGATC
46116827 CACATATATATATATATTA
1 CACAT-TATATATATATTA
* *
46116846 CACA-CATATATATATTCG
1 CACATTATATATATATT-A
46116864 CACATTATATA
1 CACATTATATA
46116875 AACACAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 11 0.46
18 4 0.17
19 9 0.38
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (18 bp):
CACATTATATATATATTA
Found at i:46123731 original size:41 final size:41
Alignment explanation
Indices: 46123638--46123724 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
46123628 AATTCATCAT
* *
46123638 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
46123679 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
46123720 ATTCA
1 ATTCA
46123725 ATTCACCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:46123986 original size:15 final size:17
Alignment explanation
Indices: 46123945--46123988 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
46123935 TTGTTCGATC
46123945 CACATATATATATTACA
1 CACATATATATATTACA
*
46123962 CACATATATATATT-CG
1 CACATATATATATTACA
46123978 CACAT-TATATA
1 CACATATATATA
46123989 AACACAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 14 0.54
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.36
Consensus pattern (17 bp):
CACATATATATATTACA
Found at i:46125571 original size:28 final size:28
Alignment explanation
Indices: 46125539--46125592 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
46125529 ATTTTGGACT
*
46125539 AAATTGAGAA-GAATGATAAATTGTGGTA
1 AAATTGAGAATGAATGA-AAAATGTGGTA
*
46125567 AAATTGTGAATGAATGAAAAATGTGG
1 AAATTGAGAATGAATGAAAAATGTGG
46125593 GTCGTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (28 bp):
AAATTGAGAATGAATGAAAAATGTGGTA
Found at i:46126095 original size:42 final size:42
Alignment explanation
Indices: 46126035--46126140 Score: 185
Period size: 42 Copynumber: 2.5 Consensus size: 42
46126025 GGATACTGAG
*
46126035 ATGAGATTACGTGTAAGACCATGTCTGGGGCATTGGCATCGAT
1 ATGAGATT-CGTGTAAGACCATGTCTGGGACATTGGCATCGAT
46126078 ATGAGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
1 ATGAGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
*
46126120 ACGAGATTCGTGTAAGACCAT
1 ATGAGATTCGTGTAAGACCAT
46126141 AGCTGGCTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 53 0.87
43 8 0.13
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (42 bp):
ATGAGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:46128689 original size:25 final size:27
Alignment explanation
Indices: 46128632--46128690 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
46128622 TATTCATACC
*
46128632 TTATTTCACTATCTCAATTCCATTAGA
1 TTATTTCACTATCTCAATTCCAATAGA
46128659 TT-TTTCAC-ATCTC-ATTCCAATAG-
1 TTATTTCACTATCTCAATTCCAATAGA
46128682 TTGATTTCA
1 TT-ATTTCA
46128691 ATTCATATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 9 0.31
25 10 0.34
26 6 0.21
27 2 0.07
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (27 bp):
TTATTTCACTATCTCAATTCCAATAGA
Found at i:46129649 original size:17 final size:17
Alignment explanation
Indices: 46129619--46129662 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
46129609 CCGGCCTGAT
* * *
46129619 ATATATTTATTTTTTAA
1 ATATTTTTAATTTTAAA
*
46129636 ATTTTTTTAATTTTAAA
1 ATATTTTTAATTTTAAA
46129653 ATATTTTTAA
1 ATATTTTTAA
46129663 AATACTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTTAATTTTAAA
Found at i:46129660 original size:11 final size:11
Alignment explanation
Indices: 46129646--46129766 Score: 62
Period size: 11 Copynumber: 11.4 Consensus size: 11
46129636 ATTTTTTTAA
46129646 TTTTAAAATAT
1 TTTTAAAATAT
46129657 TTTTAAAATACTTT
1 TTTTAAAATA---T
** *
46129671 TTTTTTATTAT
1 TTTTAAAATAT
*
46129682 TTTT-TAA--T
1 TTTTAAAATAT
46129690 TT-TAAAATAT
1 TTTTAAAATAT
46129700 TTTTAAAATACT
1 TTTTAAAATA-T
46129712 TTTTAAAAT-T
1 TTTTAAAATAT
*
46129722 TTTT----TAA
1 TTTTAAAATAT
46129729 TTTTAAAATAT
1 TTTTAAAATAT
*
46129740 TTTAAAAATAT
1 TTTTAAAATAT
**
46129751 TTAAAAAATACT
1 TTTTAAAATA-T
46129763 TTTT
1 TTTT
46129767 TAATTTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
6 1 0.01
7 5 0.06
8 5 0.06
10 10 0.12
11 43 0.51
12 13 0.15
14 8 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:46129716 original size:12 final size:11
Alignment explanation
Indices: 46129689--46129766 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 11
46129679 TATTTTTTAA
46129689 TTTTAAAATAT
1 TTTTAAAATAT
46129700 TTTTAAAATACT
1 TTTTAAAATA-T
46129712 TTTTAAAAT-T
1 TTTTAAAATAT
*
46129722 TTTT----TAA
1 TTTTAAAATAT
46129729 TTTTAAAATAT
1 TTTTAAAATAT
*
46129740 TTTAAAAATAT
1 TTTTAAAATAT
**
46129751 TTAAAAAATACT
1 TTTTAAAATA-T
46129763 TTTT
1 TTTT
46129767 TAATTTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
10 5 0.09
11 31 0.57
12 13 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:46131783 original size:21 final size:20
Alignment explanation
Indices: 46131757--46131796 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
46131747 AAGGGACTTT
*
46131757 ATGATGATGTTTGACTATGAG
1 ATGATGATGTATGAC-ATGAG
46131778 ATGATGATGTATGACATGA
1 ATGATGATGTATGACATGA
46131797 TTGTGAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (20 bp):
ATGATGATGTATGACATGAG
Found at i:46133956 original size:9 final size:9
Alignment explanation
Indices: 46133944--46133968 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46133934 TTAAAAATGT
46133944 TTAAAATTA
1 TTAAAATTA
46133953 TTAAAATTA
1 TTAAAATTA
46133962 TTAAAAT
1 TTAAAAT
46133969 AAAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:46134105 original size:16 final size:17
Alignment explanation
Indices: 46134069--46134105 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
46134059 AATTTTATTT
46134069 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
46134086 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
46134101 TAATA
1 TAATA
46134106 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:46134623 original size:19 final size:19
Alignment explanation
Indices: 46134589--46134629 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
46134579 TAAAAATCAG
*
46134589 AAAATAATAATTTTTCTAA
1 AAAATAATAATTTTTCCAA
46134608 AAAATAAATAA-TTTTCCAA
1 AAAAT-AATAATTTTTCCAA
46134627 AAA
1 AAA
46134630 TTATTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATAATTTTTCCAA
Found at i:46134629 original size:20 final size:19
Alignment explanation
Indices: 46134589--46134629 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
46134579 TAAAAATCAG
* *
46134589 AAAATAATAATTTTTCTAA
1 AAAATAATAATTTTCCAAA
46134608 AAAATAAATAATTTTCCAAA
1 AAAAT-AATAATTTTCCAAA
46134628 AA
1 AA
46134630 TTATTTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATAATTTTCCAAA
Found at i:46142589 original size:13 final size:12
Alignment explanation
Indices: 46142571--46142644 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 12
46142561 ACCCTAATTT
46142571 TTTCTCCTTTTTC
1 TTTCT-CTTTTTC
46142584 TTTCTCTTTTTC
1 TTTCTCTTTTTC
*
46142596 -TTCTCTATTTC
1 TTTCTCTTTTTC
*
46142607 GTTCTACTTTGTTC
1 TTTCT-CTTT-TTC
46142621 --T-TCTTTTTC
1 TTTCTCTTTTTC
*
46142630 TAT-TCTTTTTC
1 TTTCTCTTTTTC
46142641 TTTC
1 TTTC
46142645 ATTTATTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
11 22 0.42
12 12 0.23
13 8 0.15
14 3 0.06
ACGTcount: A:0.04, C:0.24, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:46149788 original size:93 final size:92
Alignment explanation
Indices: 46149656--46149850 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
46149646 TTGATTTTAG
* *
46149656 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
46149720 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
46149748 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
46149813 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
46149841 CAAATTCATA
1 TAAATTCATA
46149851 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:46149898 original size:48 final size:52
Alignment explanation
Indices: 46149828--46149926 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
46149818 AATAATTATT
46149828 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
46149876 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
46149927 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:46149908 original size:17 final size:17
Alignment explanation
Indices: 46149883--46149916 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46149873 ATAATTTTAA
*
46149883 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
46149900 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
46149917 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:46149933 original size:17 final size:16
Alignment explanation
Indices: 46149888--46149935 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
46149878 TTTAAATTTT
46149888 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
46149905 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
46149919 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
46149936 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:46150010 original size:16 final size:16
Alignment explanation
Indices: 46149989--46150030 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46149979 TTATTAAATT
*
46149989 ATATATTTTAATTATA
1 ATATATTTTAATAATA
46150005 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
46150020 AT-TATGTTTAA
1 ATATAT-TTTAA
46150031 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:46150015 original size:15 final size:15
Alignment explanation
Indices: 46149980--46150021 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46149970 TTAAGAATTT
*
46149980 TATTAAATTAT-ATA
1 TATTTAATTATAATA
46149994 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
46150008 TATTTAATAATAAT
1 TATTTAATTATAAT
46150022 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:46150133 original size:154 final size:156
Alignment explanation
Indices: 46149964--46150277 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 156
46149954 ATAAGAATAT
*
46149964 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
46150029 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAAT
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAAT
*
46150092 AATAATTTACCAAAACAGATTTATGC
131 AATAATTTACCAAAACAAATTTATGC
46150118 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
46150183 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAA
* *
46150248 TAATCATTTACCAAAACAAATTTCTGC
130 TAATAATTTACCAAAACAAATTTATGC
46150275 TAA
1 TAA
46150278 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
154 92 0.60
155 2 0.01
157 59 0.39
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAAT
AATAATTTACCAAAACAAATTTATGC
Found at i:46150158 original size:18 final size:17
Alignment explanation
Indices: 46150130--46150164 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46150120 ATTATTAAGA
*
46150130 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
46150147 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
46150165 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:46150418 original size:16 final size:16
Alignment explanation
Indices: 46150397--46150435 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46150387 TTGATTTGCT
*
46150397 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
46150413 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
46150429 ATTACAC
1 ATTACAC
46150436 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:46150436 original size:16 final size:16
Alignment explanation
Indices: 46150410--46150466 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
46150400 ACACAGCTTT
* *
46150410 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
46150426 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
46150442 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
46150458 TCCAATACA
1 TCCAATACA
46150467 GCGAATCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:46151027 original size:18 final size:19
Alignment explanation
Indices: 46150989--46151032 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
46150979 TGGTGTAATG
*
46150989 TAATTTTATATATAAATTT
1 TAATTTTATATATAAACTT
*
46151008 TAATTTTGTAT-TAAACTT
1 TAATTTTATATATAAACTT
46151026 TAATTTT
1 TAATTTT
46151033 TGTTCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTTATATATAAACTT
Found at i:46152320 original size:31 final size:30
Alignment explanation
Indices: 46152284--46152371 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
46152274 AATGTGTATG
46152284 ATTGAACCATAATCAAAGTTTCATGTATACA
1 ATTGAACCA-AATCAAAGTTTCATGTATACA
* * * *
46152315 TTTGAACCACAACCAAAGTTTCATGTGTATA
1 ATTGAACCA-AATCAAAGTTTCATGTATACA
*
46152346 ATTGCACCAAATCAAA-TTTCATGTAT
1 ATTGAACCAAATCAAAGTTTCATGTAT
46152372 CAGACTACAC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 9 0.19
30 6 0.12
31 33 0.69
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (30 bp):
ATTGAACCAAATCAAAGTTTCATGTATACA
Found at i:46154313 original size:32 final size:32
Alignment explanation
Indices: 46154270--46154335 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
46154260 TGTGACTCAG
*
46154270 TGAGACGGCTTTGAATGCACTATAAATAATAA
1 TGAGACAGCTTTGAATGCACTATAAATAATAA
46154302 TGAGACAGCTTTGAATGCACTATAAATAATAA
1 TGAGACAGCTTTGAATGCACTATAAATAATAA
46154334 TG
1 TG
46154336 GAATTATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (32 bp):
TGAGACAGCTTTGAATGCACTATAAATAATAA
Found at i:46157732 original size:23 final size:23
Alignment explanation
Indices: 46157687--46157733 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
46157677 ATGATTAAAC
* *
46157687 ATTTTAATATTTTGATTAGTTTA
1 ATTTTAATAATTTGATCAGTTTA
46157710 ATTTATAATAATTTGATCA-TTTA
1 ATTT-TAATAATTTGATCAGTTTA
46157733 A
1 A
46157734 ACACTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTTAATAATTTGATCAGTTTA
Found at i:46166445 original size:30 final size:31
Alignment explanation
Indices: 46166384--46166447 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
46166374 TACAAAATTA
46166384 TCACTAAACTATTCAAAAGATTATATTTAAG
1 TCACTAAACTATTCAAAAGATTATATTTAAG
* * *
46166415 TCACTTAACTATTCAAAAGCTT-TTTTTAAG
1 TCACTAAACTATTCAAAAGATTATATTTAAG
46166445 TCA
1 TCA
46166448 ACTGGGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGATTATATTTAAG
Found at i:46172416 original size:17 final size:17
Alignment explanation
Indices: 46172396--46172431 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
46172386 TTTTTTTAAA
46172396 AATTTTA-AATTTTGATT
1 AATTTTATAA-TTTGATT
46172413 AATTTTATAATTTGATT
1 AATTTTATAATTTGATT
46172430 AA
1 AA
46172432 ATGGTAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AATTTTATAATTTGATT
Found at i:46177845 original size:25 final size:25
Alignment explanation
Indices: 46177816--46177891 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
46177806 CCTGAAAGAG
46177816 CAGAGTTCTGGCTTGATAATACCAT
1 CAGAGTTCTGGCTTGATAATACCAT
* * *
46177841 TAGAGTGT-TGG-ATG--AAT--TAT
1 CAGAGT-TCTGGCTTGATAATACCAT
46177861 CAGAGTTCTGGCTTGATAATACCAT
1 CAGAGTTCTGGCTTGATAATACCAT
46177886 CAGAGT
1 CAGAGT
46177892 GTTGGATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 2 0.05
22 3 0.08
23 3 0.08
24 2 0.05
25 16 0.42
26 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (25 bp):
CAGAGTTCTGGCTTGATAATACCAT
Found at i:46177880 original size:45 final size:45
Alignment explanation
Indices: 46177816--46177906 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
46177806 CCTGAAAGAG
*
46177816 CAGAGTTCTGGCTTGATAATACCATTAGAGTGTTGGATGAATTAT
1 CAGAGTTCTGGCTTGATAATACCATCAGAGTGTTGGATGAATTAT
46177861 CAGAGTTCTGGCTTGATAATACCATCAGAGTGTTGGATGAATTAT
1 CAGAGTTCTGGCTTGATAATACCATCAGAGTGTTGGATGAATTAT
46177906 C
1 C
46177907 TTGTACTCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (45 bp):
CAGAGTTCTGGCTTGATAATACCATCAGAGTGTTGGATGAATTAT
Found at i:46178728 original size:12 final size:12
Alignment explanation
Indices: 46178711--46178745 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
46178701 TAAGATCTGA
46178711 AGCGAGAGCTTC
1 AGCGAGAGCTTC
*
46178723 AGCGAGAGCTCC
1 AGCGAGAGCTTC
46178735 AGCGAGAGCTT
1 AGCGAGAGCTT
46178746 ATGCCATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (12 bp):
AGCGAGAGCTTC
Found at i:46185264 original size:18 final size:17
Alignment explanation
Indices: 46185231--46185269 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
46185221 TTTTATAAAT
46185231 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
46185249 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
46185266 TGTG
1 TGTG
46185270 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:46185521 original size:23 final size:23
Alignment explanation
Indices: 46185495--46185564 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
46185485 AGTGTTATTG
46185495 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46185518 ATCAGTGGTAGCTTCTGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
46185541 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46185564 A
1 A
46185565 ACGTCAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:46190432 original size:41 final size:39
Alignment explanation
Indices: 46190333--46190440 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 39
46190323 CAGATAATTT
* ** *
46190333 GAAGTAGTAAATTGACACCCAGTGTCTCATCGGCTAAACT
1 GAAGTAAT-AATTGACACCCAGTGTCTCATCGAATAAACC
* * *
46190373 GAAGT-A-AATTGGCACCCAGTGCCTCATCGAATATATCC
1 GAAGTAATAATTGACACCCAGTGTCTCATCGAATA-AACC
46190411 GAAGTAATAACTTGACACCCAGTGTCTCAT
1 GAAGTAATAA-TTGACACCCAGTGTCTCAT
46190441 TGACTCAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 23 0.42
38 7 0.13
39 1 0.02
40 7 0.13
41 17 0.31
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (39 bp):
GAAGTAATAATTGACACCCAGTGTCTCATCGAATAAACC
Found at i:46191431 original size:18 final size:18
Alignment explanation
Indices: 46191408--46191445 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46191398 TTATTTGTTT
46191408 TATTATAATA-ATATAATA
1 TATTATAATATA-ATAATA
*
46191426 TATTATTATATAATAATA
1 TATTATAATATAATAATA
46191444 TA
1 TA
46191446 ATCTTATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATAATATAATAATA
Found at i:46198385 original size:13 final size:13
Alignment explanation
Indices: 46198369--46198407 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
46198359 TTTGTTTTAT
46198369 TATAATAATATAA
1 TATAATAATATAA
46198382 TATAAT-AT-T-A
1 TATAATAATATAA
46198392 TATAATAATATAA
1 TATAATAATATAA
46198405 TAT
1 TAT
46198408 TTTTACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 3 0.13
13 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:46199777 original size:12 final size:12
Alignment explanation
Indices: 46199760--46199784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46199750 AAATTGCTTT
46199760 TAGAAGAAGCGC
1 TAGAAGAAGCGC
46199772 TAGAAGAAGCGC
1 TAGAAGAAGCGC
46199784 T
1 T
46199785 CTTAAAAAGT
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:0.40, C:0.16, G:0.32, T:0.12
Consensus pattern (12 bp):
TAGAAGAAGCGC
Found at i:46200000 original size:16 final size:16
Alignment explanation
Indices: 46199981--46200019 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
46199971 ATAATATATA
46199981 AAATATTTTAAAAAAT
1 AAATATTTTAAAAAAT
**
46199997 AAATATAATAAAAAAT
1 AAATATTTTAAAAAAT
46200013 -AATATTT
1 AAATATTT
46200020 AAATAACTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:46209809 original size:21 final size:21
Alignment explanation
Indices: 46209783--46209826 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
46209773 AAAGAACGGA
46209783 TCTCGACACCATCCTGCATGT
1 TCTCGACACCATCCTGCATGT
46209804 TCTCGACACCATCCTGCATGT
1 TCTCGACACCATCCTGCATGT
46209825 TC
1 TC
46209827 CTTTCAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.14, T:0.30
Consensus pattern (21 bp):
TCTCGACACCATCCTGCATGT
Found at i:46212670 original size:16 final size:16
Alignment explanation
Indices: 46212649--46212684 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
46212639 TTTGATTCGC
46212649 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGA
*
46212665 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGA
46212681 TGTA
1 TGTA
46212685 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGA
Found at i:46212731 original size:45 final size:44
Alignment explanation
Indices: 46212664--46212755 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
46212654 TGGATTAGAG
* * *
46212664 ATGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGA
1 ATGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGA
* ***
46212709 ATGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGA
1 ATGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGA
46212753 ATG
1 ATG
46212756 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.36
Consensus pattern (44 bp):
ATGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGA
Found at i:46213091 original size:156 final size:157
Alignment explanation
Indices: 46212807--46213122 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 157
46212797 TAGAATACCC
*
46212807 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
46212872 TTATCAATAATAAATATTTTAGTCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
46212937 TATATAATTTAAT-AAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
46212963 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
46213028 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
46213093 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
46213120 TTA
1 TTA
46213123 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 137 0.90
157 16 0.10
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:46213093 original size:16 final size:16
Alignment explanation
Indices: 46213056--46213097 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46213046 TTAATCATAT
*
46213056 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
46213072 TT-AAATATATTATAA
1 TTAAAATATATTATAA
46213087 TTAAAATATAT
1 TTAAAATATAT
46213098 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:46213104 original size:14 final size:15
Alignment explanation
Indices: 46213065--46213106 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46213055 TTTAAACATA
*
46213065 ATTATTATTAAATAT
1 ATTATAATTAAATAT
46213080 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
46213094 A-TATAATTTAATA
1 ATTATAATTAAATA
46213107 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:46213237 original size:17 final size:18
Alignment explanation
Indices: 46213196--46213230 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46213186 TTATTATTAA
*
46213196 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
46213214 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
46213231 TATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:46223754 original size:30 final size:31
Alignment explanation
Indices: 46223699--46223758 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
46223689 CGGTCCAGTG
*
46223699 ACTTAAATAAAAACTTTTGAATAGTTTAGTA
1 ACTTAAATAAAAACTTTTAAATAGTTTAGTA
**
46223730 ACTTAAAT-AAATTTTTTAAATAGTTTAGT
1 ACTTAAATAAAAACTTTTAAATAGTTTAGT
46223759 CACTATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTAAATAGTTTAGTA
Found at i:46241956 original size:3 final size:3
Alignment explanation
Indices: 46241948--46241979 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
46241938 GATTTAGTCC
46241948 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46241980 CCTATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:46243981 original size:30 final size:31
Alignment explanation
Indices: 46243947--46244004 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
46243937 TTAAAATAAA
*
46243947 AAAAAGAATATATTTAAT-CATTA-AAAAGAT
1 AAAAAGAATA-AATTAATACATTATAAAAGAT
*
46243977 AAAAATAATAAATTAATACATTATAAAA
1 AAAAAGAATAAATTAATACATTATAAAA
46244005 TTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 14 0.58
31 4 0.17
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAAAGAATAAATTAATACATTATAAAAGAT
Found at i:46244878 original size:17 final size:17
Alignment explanation
Indices: 46244837--46244871 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46244827 AATTTGATAA
46244837 ACAAAAAATAATTAAGT
1 ACAAAAAATAATTAAGT
46244854 ACAGAAAAA-AATTAAGT
1 ACA-AAAAATAATTAAGT
46244871 A
1 A
46244872 TTAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.20
Consensus pattern (17 bp):
ACAAAAAATAATTAAGT
Found at i:46248925 original size:30 final size:28
Alignment explanation
Indices: 46248870--46248925 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
46248860 GGAAGAAAGA
* *
46248870 CCTAAAATGTGAATTGTCACTTTTTAAC
1 CCTAAAATGCGAATTGTCACCTTTTAAC
46248898 CCTAAAATGCGAATTGAGTCACCTTTTA
1 CCTAAAATGCGAATT--GTCACCTTTTA
46248926 CCTTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
30 10 0.42
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (28 bp):
CCTAAAATGCGAATTGTCACCTTTTAAC
Found at i:46250372 original size:38 final size:38
Alignment explanation
Indices: 46250324--46250402 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
46250314 ATGTTTTGGT
46250324 GTTGATTTGTGGCATATTGGATTGGTTGAATTGAATTG
1 GTTGATTTGTGGCATATTGGATTGGTTGAATTGAATTG
46250362 GTTGATTTGTGGCATATTGGATTGGTTGAATTGAATTG
1 GTTGATTTGTGGCATATTGGATTGGTTGAATTGAATTG
46250400 GTT
1 GTT
46250403 AAAATGCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.20, C:0.03, G:0.32, T:0.46
Consensus pattern (38 bp):
GTTGATTTGTGGCATATTGGATTGGTTGAATTGAATTG
Found at i:46255523 original size:41 final size:42
Alignment explanation
Indices: 46255451--46255576 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
46255441 CGAAGGCTGC
* * * *
46255451 ACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGA
1 ACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAA
* *
46255493 ACAGAAGCTCGTAAG-GCTGAACGGAAACCCATAAGGGTTAA
1 ACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAA
* * *
46255534 ACTGAAGCTCAAAAGAGCTGAACAGAAACCCATTAGGGTTAA
1 ACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAA
46255576 A
1 A
46255577 TGGAAACTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 35 0.48
42 38 0.52
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (42 bp):
ACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAA
Found at i:46255527 original size:20 final size:20
Alignment explanation
Indices: 46255443--46255566 Score: 77
Period size: 21 Copynumber: 6.0 Consensus size: 20
46255433 CAGAAGCCCG
* * *
46255443 AAGGCTGCACAGAAGCACAT
1 AAGGCTGAACAGAAACCCAT
*
46255463 AAGTGCTAAACAGAAACCCAT
1 AAG-GCTGAACAGAAACCCAT
* * * *
46255484 AAGGGTTGAACAGAAGCTCGT
1 AA-GGCTGAACAGAAACCCAT
*
46255505 AAGGCTGAACGGAAACCCAT
1 AAGGCTGAACAGAAACCCAT
* * * * * *
46255525 AAGGGTTAAACTGAAGCTCAA
1 AA-GGCTGAACAGAAACCCAT
46255546 AAGAGCTGAACAGAAACCCAT
1 AAG-GCTGAACAGAAACCCAT
46255567 TAGGGTTAAA
Statistics
Matches: 74, Mismatches: 26, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
20 19 0.26
21 54 0.73
22 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
AAGGCTGAACAGAAACCCAT
Found at i:46259738 original size:6 final size:6
Alignment explanation
Indices: 46259727--46259801 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
46259717 AAAGTATAAG
* * *
46259727 AAAATA AAAATA AAACA-A AACAACTA AAAATA GAAATA AACATA AACATA
1 AAAATA AAAATA AAA-ATA AA-AA-TA AAAATA AAAATA AAAATA AAAATA
46259777 AAAA-A TAAAAT- AAAAT- AAAATA AAA
1 AAAATA -AAAATA AAAATA AAAATA AAA
46259802 CAAATAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
5 11 0.19
6 40 0.69
7 4 0.07
8 3 0.05
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:46259741 original size:5 final size:5
Alignment explanation
Indices: 46259727--46259811 Score: 57
Period size: 5 Copynumber: 16.0 Consensus size: 5
46259717 AAAGTATAAG
* * *
46259727 AAAAT AAAAAT AAAAC AAAA- CAACT AAAAAT AGAAAT AAACAT AAACAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT A-AAAT A-AAAT AAA-AT AAA-AT
*
46259776 AAAAAAT AAAAT AAAAT AAAAT AAAA- CAAAT AAAAT
1 --AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
46259812 CAATTATCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
4 5 0.08
5 33 0.51
6 22 0.34
7 2 0.03
8 3 0.05
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:46265590 original size:13 final size:13
Alignment explanation
Indices: 46265574--46265598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46265564 AAATTAAGCT
46265574 AAAAAAACAAAAA
1 AAAAAAACAAAAA
46265587 AAAAAAACAAAA
1 AAAAAAACAAAA
46265599 TGCAATAAAA
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:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:46278843 original size:127 final size:126
Alignment explanation
Indices: 46278609--46278848 Score: 310
Period size: 127 Copynumber: 1.9 Consensus size: 126
46278599 ATTCAAAAAG
* *
46278609 AAAATTTTAAAATAAGGCAATATCTCGCATTTTAGGAAATTCGAAGAATCGTACCCTAACTTACT
1 AAAATTTAAAAATAAGGCAATATCTCGCATTTTAGAAAATTCGAAGAATCGTACCCTAACTTACT
* *
46278674 GGGTCTCGATTTTCTCGTTAAACCTGAATAGCAAAATATCCTTTTAAATTTCCAAACGTAT
66 GGGTCTCGATTTTCTCGTTAAACCTAAATAACAAAATATCCTTTTAAATTTCCAAACGTAT
* *
46278735 AAAATTTCAAAAATAAAGGCAATAT-TC-TATATTTAGAAAATTCG-AGAAATCGTGCCCTAACT
1 AAAATTT-AAAAAT-AAGGCAATATCTCGCAT-TTTAGAAAATTCGAAG-AATCGTACCCTAACT
* **
46278797 TACTGGG-CTTCGATTTTTCTCGTT-GACCTAAATAACCGAATATCCTTTTAAA
62 TACTGGGTC-TCGA-TTTTCTCGTTAAACCTAAATAACAAAATATCCTTTTAAA
46278849 ATTAAAATAA
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
126 12 0.12
127 67 0.68
128 20 0.20
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (126 bp):
AAAATTTAAAAATAAGGCAATATCTCGCATTTTAGAAAATTCGAAGAATCGTACCCTAACTTACT
GGGTCTCGATTTTCTCGTTAAACCTAAATAACAAAATATCCTTTTAAATTTCCAAACGTAT
Found at i:46279468 original size:15 final size:14
Alignment explanation
Indices: 46279449--46279483 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
46279439 CGTCTTGATT
46279449 TTGGTAGTTTAAGC
1 TTGGTAGTTTAAGC
46279463 TGTGGTAGTTTAAGC
1 T-TGGTAGTTTAAGC
46279478 TTGGTA
1 TTGGTA
46279484 TACTGCTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (14 bp):
TTGGTAGTTTAAGC
Found at i:46280472 original size:62 final size:63
Alignment explanation
Indices: 46280404--46280524 Score: 217
Period size: 62 Copynumber: 1.9 Consensus size: 63
46280394 ATTTTTTTTC
*
46280404 CATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAA-TACGCATT
1 CATGCATCAACATTACACTTCATTGCATACAATAAATTTCCTAAAATCCAAAAAGTACGCATT
*
46280466 CATGCATCAACATTACACTTCATTGCATACAATAAATTTCCTAAAATCTAAAAAGTACG
1 CATGCATCAACATTACACTTCATTGCATACAATAAATTTCCTAAAATCCAAAAAGTACG
46280525 TTGAGTTTAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 52 0.93
63 4 0.07
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (63 bp):
CATGCATCAACATTACACTTCATTGCATACAATAAATTTCCTAAAATCCAAAAAGTACGCATT
Found at i:46282333 original size:13 final size:13
Alignment explanation
Indices: 46282315--46282390 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
46282305 CTTCACTTGA
*
46282315 AAAAAAAGAAGAG
1 AAAAAAAGAAAAG
*
46282328 AAAAAATGAAAAG
1 AAAAAAAGAAAAG
46282341 AAAAAAAATGAAAAAG
1 -AAAAAAA-G-AAAAG
46282357 AAAAGAAA-AAAAG
1 AAAA-AAAGAAAAG
* *
46282370 AAAGAATGAAAA-
1 AAAAAAAGAAAAG
46282382 AAGAAAAAG
1 AA-AAAAAG
46282391 GAGAGGCCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
12 4 0.08
13 27 0.54
14 6 0.12
15 5 0.10
16 8 0.16
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:46282341 original size:15 final size:14
Alignment explanation
Indices: 46282326--46282389 Score: 69
Period size: 15 Copynumber: 4.5 Consensus size: 14
46282316 AAAAAAGAAG
46282326 AGAAAAAATGAAAA
1 AGAAAAAATGAAAA
*
46282340 GAAAAAAAATGAAAA
1 -AGAAAAAATGAAAA
46282355 AGAAAAGAA--AAAA
1 AGAAAA-AATGAAAA
*
46282368 AGAAAGAATGAAAAA
1 AGAAAAAATG-AAAA
46282383 AGAAAAA
1 AGAAAAA
46282390 GGAGAGGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 9 0.22
14 5 0.12
15 25 0.61
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (14 bp):
AGAAAAAATGAAAA
Done.