Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 178 of 195
Found at i:30037700 original size:36 final size:36
Alignment explanation
Indices: 30037653--30037721 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
30037643 TTATGGCTAA
* *
30037653 TAAATAATGGTCCTATTTTCCTCATGCTTCAAAACG
1 TAAATAATGGTCCAATTTTCCCCATGCTTCAAAACG
*
30037689 TAAATAGTGGTCCAATTTTCCCCATGCTTCAAA
1 TAAATAATGGTCCAATTTTCCCCATGCTTCAAA
30037722 CCGAGGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (36 bp):
TAAATAATGGTCCAATTTTCCCCATGCTTCAAAACG
Found at i:30041367 original size:38 final size:36
Alignment explanation
Indices: 30041295--30041367 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
30041285 CATAATGCCT
* * *
30041295 TTGTAGTTTGGTTACCAGAAAATGAAAGCTATTAAA
1 TTGTAGTTTCGTTACCAGAAAAAGAAAGCAATTAAA
30041331 TTGTAGTTTCGTTAACCAGAAAGAAGAAAGCAATTAA
1 TTGTAGTTTCGTT-ACCAGAAA-AAGAAAGCAATTAA
30041368 TTCAGACCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 12 0.38
37 8 0.25
38 12 0.38
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (36 bp):
TTGTAGTTTCGTTACCAGAAAAAGAAAGCAATTAAA
Found at i:30051661 original size:21 final size:21
Alignment explanation
Indices: 30051613--30051654 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30051603 AAGTGGTTAG
* *
30051613 AATTTAAATTATAATTTTTAA
1 AATTAAAATTATAATATTTAA
*
30051634 AATTAAAATTTTAATATTTAA
1 AATTAAAATTATAATATTTAA
30051655 TAATAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAAAATTATAATATTTAA
Found at i:30051811 original size:27 final size:27
Alignment explanation
Indices: 30051773--30051826 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
30051763 GTCTGGGTCA
30051773 GGGTCAGGTCTGGCTATTGGCCAACAC
1 GGGTCAGGTCTGGCTATTGGCCAACAC
30051800 GGGTCAGGTCTGGCTATTGGCCAACAC
1 GGGTCAGGTCTGGCTATTGGCCAACAC
30051827 TGAAATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (27 bp):
GGGTCAGGTCTGGCTATTGGCCAACAC
Found at i:30053196 original size:15 final size:16
Alignment explanation
Indices: 30053163--30053199 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
30053153 ATTTAAAAAA
30053163 AAAATTAAATATAAAT
1 AAAATTAAATATAAAT
30053179 AAAATT-AATA-AAATT
1 AAAATTAAATATAAA-T
30053194 AAAATT
1 AAAATT
30053200 TTATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 11 0.55
16 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATTAAATATAAAT
Found at i:30054939 original size:30 final size:31
Alignment explanation
Indices: 30054859--30054949 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
30054849 TAATTTATGC
* *
30054859 TAAAAATTTATTTAAATACAAATTAAAATTT
1 TAAAAATTTATTTAAATATAAATTAAAATCT
**
30054890 TAAAAATTTATTTTGATATAAATTAAAA-CT
1 TAAAAATTTATTTAAATATAAATTAAAATCT
* *
30054920 TGAAGATTTATTTAAATAT-AA-TAAAATCT
1 TAAAAATTTATTTAAATATAAATTAAAATCT
30054949 T
1 T
30054950 TGATAGCTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.10
29 5 0.10
30 16 0.31
31 25 0.49
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (31 bp):
TAAAAATTTATTTAAATATAAATTAAAATCT
Found at i:30056043 original size:30 final size:31
Alignment explanation
Indices: 30056004--30056062 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
30055994 AAAATTACTC
* *
30056004 ATTATTGATATA-TATCATTTGATTTATTTT
1 ATTAATGATATAGTATCATTTAATTTATTTT
30056034 ATTAATGATATAGTATCATTTAATTTATT
1 ATTAATGATATAGTATCATTTAATTTATT
30056063 AATAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (31 bp):
ATTAATGATATAGTATCATTTAATTTATTTT
Found at i:30056054 original size:26 final size:24
Alignment explanation
Indices: 30056025--30056092 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
30056015 ATATCATTTG
**
30056025 ATTTATTTTATTAATGATATAGTATC
1 ATTTA-TTTATTAATGATATA-TAAA
*
30056051 ATTTAATTTATTAATAATATATAAA
1 ATTT-ATTTATTAATGATATATAAA
*
30056076 ATTTATATATTAATGAT
1 ATTTATTTATTAATGAT
30056093 GTATCTGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 11 0.31
25 6 0.17
26 18 0.50
27 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
ATTTATTTATTAATGATATATAAA
Found at i:30058654 original size:31 final size:30
Alignment explanation
Indices: 30058619--30058698 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
30058609 TTAAAATTAC
***
30058619 ATATTATTTAAAAAATTAAATTAAATTTTCT
1 ATATTATTTAAAAAATTAAA-TAAAAACTCT
30058650 ATATTCATTT-AAAAATTAAATAAAAACTCT
1 ATATT-ATTTAAAAAATTAAATAAAAACTCT
*
30058680 ATATCTATTTAAAATATTA
1 ATAT-TATTTAAAAAATTA
30058699 TGTAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 15 0.36
31 23 0.55
32 4 0.10
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATTATTTAAAAAATTAAATAAAAACTCT
Found at i:30060403 original size:20 final size:21
Alignment explanation
Indices: 30060366--30060415 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
30060356 TTTGAAATTA
30060366 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
30060387 ATAAAATATTA-TTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
30060407 AT-AAATATT
1 ATAAAATATT
30060416 TAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.24
20 11 0.38
21 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:30060417 original size:14 final size:16
Alignment explanation
Indices: 30060388--30060442 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 16
30060378 TTTTTAAATA
*
30060388 TAAA-ATATTATT-TT
1 TAAATATATAATTATT
30060402 TAAATATA-AA-TATT
1 TAAATATATAATTATT
*
30060416 TAAATATATAATTATA
1 TAAATATATAATTATT
30060432 TAAATATATAA
1 TAAATATATAA
30060443 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 1 0.03
14 15 0.43
15 5 0.14
16 14 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATATAATTATT
Found at i:30060421 original size:8 final size:8
Alignment explanation
Indices: 30060405--30060443 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
30060395 TTATTTTTAA
30060405 ATATAAAT
1 ATATAAAT
*
30060413 ATTTAAAT
1 ATATAAAT
*
30060421 ATATAATT
1 ATATAAAT
30060429 ATATAAAT
1 ATATAAAT
30060437 ATATAAA
1 ATATAAA
30060444 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:30070666 original size:22 final size:22
Alignment explanation
Indices: 30070638--30070681 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30070628 GCTGTTCACG
30070638 TTCAACGCCAAGTTGCAACTCC
1 TTCAACGCCAAGTTGCAACTCC
30070660 TTCAACGCCAAGTTGCAACTCC
1 TTCAACGCCAAGTTGCAACTCC
30070682 ATATCCTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (22 bp):
TTCAACGCCAAGTTGCAACTCC
Found at i:30075999 original size:2 final size:2
Alignment explanation
Indices: 30075992--30076024 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30075982 CGCTCAAATT
*
30075992 TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30076025 TCCCATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30081474 original size:4 final size:4
Alignment explanation
Indices: 30081458--30081519 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
30081448 ATTTATATAC
* * *
30081458 TTAA TTAA GTAA TTAA TT-A TT-A TATAA TTAA ATAA TTAA TTAA TAAA
1 TTAA TTAA TTAA TTAA TTAA TTAA T-TAA TTAA TTAA TTAA TTAA TTAA
30081505 TT-A -TAA TTTAA TTAA
1 TTAA TTAA -TTAA TTAA
30081520 ACAAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
2 1 0.02
3 7 0.15
4 34 0.72
5 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:30081507 original size:31 final size:31
Alignment explanation
Indices: 30081459--30081520 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
30081449 TTTATATACT
* *
30081459 TAATTAAGTAATTAATTATTATATAATTAAA
1 TAATTAAGTAATAAATTATAATATAATTAAA
* *
30081490 TAATTAATTAATAAATTATAATTTAATTAAA
1 TAATTAAGTAATAAATTATAATATAATTAAA
30081521 CAAAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (31 bp):
TAATTAAGTAATAAATTATAATATAATTAAA
Found at i:30082652 original size:3 final size:3
Alignment explanation
Indices: 30082644--30082719 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
30082634 TGTTTCCGCC
* * *
30082644 TCT TCT TCT TCT TCT TCT TCT CCT TCCT GC- TCT TCT TTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT
* * *
30082689 CCT T-G TCT TCCT TCT ACT TCT TACT T-T TCT T
1 TCT TCT TCT T-CT TCT TCT TCT T-CT TCT TCT T
30082720 TCTCTTCTCC
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
2 4 0.07
3 43 0.78
4 8 0.15
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:30082702 original size:24 final size:23
Alignment explanation
Indices: 30082646--30082710 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
30082636 TTTCCGCCTC
30082646 TTCTT-CTTCTTCTTCTTCTCCT
1 TTCTTCCTTCTTCTTCTTCTCCT
* * *
30082668 TCCTGCTCTTCTTTTTCTTCTCCT
1 TTCTTC-CTTCTTCTTCTTCTCCT
*
30082692 TGTCTTCCTTCTACTTCTT
1 T-TCTTCCTTCTTCTTCTT
30082711 ACTTTTCTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 3 0.09
24 27 0.82
25 3 0.09
ACGTcount: A:0.02, C:0.35, G:0.03, T:0.60
Consensus pattern (23 bp):
TTCTTCCTTCTTCTTCTTCTCCT
Found at i:30082703 original size:39 final size:38
Alignment explanation
Indices: 30082656--30082729 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
30082646 TTCTTCTTCT
* * *
30082656 TCTTCTTCTCCTTCCTGCTCTTCTTTTTCTTCTCCTTG
1 TCTTCTTCTACTTCCTACTCTTCTTTCTCTTCTCCTTG
* *
30082694 TCTTCCTTCTACTTCTTACTTTTCTTTCTCTTCTCC
1 TCTT-CTTCTACTTCCTACTCTTCTTTCTCTTCTCC
30082730 CCAAACACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 4 0.13
39 26 0.87
ACGTcount: A:0.03, C:0.36, G:0.03, T:0.58
Consensus pattern (38 bp):
TCTTCTTCTACTTCCTACTCTTCTTTCTCTTCTCCTTG
Found at i:30094611 original size:26 final size:26
Alignment explanation
Indices: 30094559--30094612 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
30094549 AAATAGTAAT
* * *
30094559 AAAAATTATCATAATTATGATTGAAA
1 AAAAATTATCATAAATATAATTAAAA
* *
30094585 AAAAATTATTATAAATGTAATTAAAA
1 AAAAATTATCATAAATATAATTAAAA
30094611 AA
1 AA
30094613 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAATTATCATAAATATAATTAAAA
Found at i:30100653 original size:26 final size:25
Alignment explanation
Indices: 30100616--30100667 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
30100606 TCATTTATAA
30100616 ATATTAAATAAATATGTTTACGAAC
1 ATATTAAATAAATATGTTTACGAAC
*
30100641 ATATATAAATAAATATGTTTATGAAC
1 ATAT-TAAATAAATATGTTTACGAAC
30100667 A
1 A
30100668 ATAAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (25 bp):
ATATTAAATAAATATGTTTACGAAC
Found at i:30101197 original size:35 final size:35
Alignment explanation
Indices: 30101157--30101226 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
30101147 TTGAAGTGAT
30101157 TTTAGAGACTGTTTGCTATGGCCCCCTTTGAAGAC
1 TTTAGAGACTGTTTGCTATGGCCCCCTTTGAAGAC
* *
30101192 TTTAGAGATTGTTTGCTATGGCCTCCTTTGAAGAC
1 TTTAGAGACTGTTTGCTATGGCCCCCTTTGAAGAC
30101227 CCACCGCCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (35 bp):
TTTAGAGACTGTTTGCTATGGCCCCCTTTGAAGAC
Found at i:30103336 original size:21 final size:20
Alignment explanation
Indices: 30103311--30103350 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30103301 AAGATTAAAA
30103311 TAAAATAATTTATTTATTAAT
1 TAAAATAA-TTATTTATTAAT
* *
30103332 TAAAATTATTATTTTTTAA
1 TAAAATAATTATTTATTAA
30103351 AATTTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAATAATTATTTATTAAT
Found at i:30109299 original size:14 final size:15
Alignment explanation
Indices: 30109280--30109308 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30109270 TTGCCATCTT
30109280 CTCTGTTTT-TTCTC
1 CTCTGTTTTGTTCTC
30109294 CTCTGTTTTGTTCTC
1 CTCTGTTTTGTTCTC
30109309 TACTCTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.28, G:0.10, T:0.62
Consensus pattern (15 bp):
CTCTGTTTTGTTCTC
Found at i:30117222 original size:6 final size:6
Alignment explanation
Indices: 30117213--30117240 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30117203 GAAGAGGAAG
30117213 TGGACA TGGACA TGGACA TGGACA TGGA
1 TGGACA TGGACA TGGACA TGGACA TGGA
30117241 TTTTAATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.36, T:0.18
Consensus pattern (6 bp):
TGGACA
Found at i:30119238 original size:72 final size:72
Alignment explanation
Indices: 30119162--30119307 Score: 274
Period size: 72 Copynumber: 2.0 Consensus size: 72
30119152 TAGGTTTTCA
30119162 TTCTTTTTCATTGTTTAAAAAATCAAGGACTCCTATATATTTTTTGTTTATATGGGATATTGTTT
1 TTCTTTTTCATTGTTTAAAAAATCAAGGACTCCTATATATTTTTTGTTTATATGGGATATTGTTT
30119227 ATTTTTT
66 ATTTTTT
*
30119234 TTCTTTTTCATTTTTTAAAAAATCAAGGACTCCTATATATTTTTTGTTTATATGGGATATTGTTT
1 TTCTTTTTCATTGTTTAAAAAATCAAGGACTCCTATATATTTTTTGTTTATATGGGATATTGTTT
*
30119299 TTTTTTT
66 ATTTTTT
30119306 TT
1 TT
30119308 TTCTCTGTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (72 bp):
TTCTTTTTCATTGTTTAAAAAATCAAGGACTCCTATATATTTTTTGTTTATATGGGATATTGTTT
ATTTTTT
Found at i:30121490 original size:17 final size:17
Alignment explanation
Indices: 30121449--30121493 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
30121439 TTTATCTTTT
*
30121449 TTTATTCAAAAATTTTAA
1 TTTA-TCAACAATTTTAA
**
30121467 TGAATCAACAATTTTAA
1 TTTATCAACAATTTTAA
30121484 TTTATCAACA
1 TTTATCAACA
30121494 TGAATGACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTATCAACAATTTTAA
Found at i:30133952 original size:49 final size:48
Alignment explanation
Indices: 30133882--30133974 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
30133872 TTTTGATAAT
*
30133882 ATTTATAACTCTATTAAAAGAATTCTTAAA-GGATTAGAGAGTGACAC
1 ATTTATAACTCTATTAAAAGAATTCTTAAAGGGATTAGAAAGTGACAC
*
30133929 ATTTATAATTCTCTATTTAAAGAATTCTTAAAGGGATTAGAAAGTG
1 ATTTATAA--CTCTATTAAAAGAATTCTTAAAGGGATTAGAAAGTG
30133975 CCAAACGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 8 0.20
49 21 0.51
50 12 0.29
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (48 bp):
ATTTATAACTCTATTAAAAGAATTCTTAAAGGGATTAGAAAGTGACAC
Found at i:30134470 original size:31 final size:31
Alignment explanation
Indices: 30134431--30134494 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
30134421 CAAGACTATT
30134431 TTTTTCT-TTTC-AACATTATAAAATAATCA
1 TTTTTCTCTTTCTAACATTATAAAATAATCA
* *
30134460 TTTTTCTCTTTCTAATATTATAAAATGATCA
1 TTTTTCTCTTTCTAACATTATAAAATAATCA
30134491 TTTT
1 TTTT
30134495 AACTTTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
30 4 0.13
31 20 0.65
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (31 bp):
TTTTTCTCTTTCTAACATTATAAAATAATCA
Found at i:30134499 original size:301 final size:298
Alignment explanation
Indices: 30134159--30134722 Score: 855
Period size: 297 Copynumber: 1.9 Consensus size: 298
30134149 AATGATCATT
* *
30134159 TTTTTCTCTTTCTAATATTATAAAATAATCATTTTAACTTGTAATGAAAAATGACCTAAAATGTT
1 TTTTTCTCTTTCTAATATTATAAAATAATCATTTTAACTTGTAACGAAAAATAACCTAAAATGTT
* * * *
30134224 AATAATAAAAATTTTAAAATATGTTAAAAGAATTCCCAAAGAGATTGTATTTTAACACTTGTTTA
66 AATAATAAAAAATTTAAAATA---T-AAAGAATTCCCAAAGAGATTATATTTTAACACCTGTTCA
* * * * *
30134289 ACATTATAAAATGATCATTTTATCCTTTAATGAAAAA-AGAATAACCTAAAATGTAAATAGTAAA
127 AAATTATAAAATGATCATTTTACCCTTTAAT-AAAAATAAAATAACCTAAAATGGAAATAATAAA
* *
30134353 ATAATAA-AAATATGAAAATT-AAAAAAACAGATATAAAAACTTTTAAAATCCCTAAGGGTATCA
191 ATAATAATAAATATGAAAATTAAAAAAAAAAGATAT-AAAACTTTTAAAATCCCTAAAGGTATCA
30134416 TATTGCAAGACTATTTTTTTCTTTTCAACATTATAAAATAATCA
255 TATTGCAAGACTATTTTTTTCTTTTCAACATTATAAAATAATCA
* *
30134460 TTTTTCTCTTTCTAATATTATAAAATGATCATTTTAACTTTTAACGAAAAATAACCTAAAATGTT
1 TTTTTCTCTTTCTAATATTATAAAATAATCATTTTAACTTGTAACGAAAAATAACCTAAAATGTT
* *
30134525 AATAATAAAAAATTTAAAATATAAAGAATTTCCAAAGAGATTATATTTTATCACCTGTTCAAAAT
66 AATAATAAAAAATTTAAAATATAAAGAATTCCCAAAGAGATTATATTTTAACACCTGTTCAAAAT
*
30134590 TATAAAATGATTATTTTACCCTTTAATAAAAATAAAATAACCTAAAATGGAAATAATAAAATAAT
131 TATAAAATGATCATTTTACCCTTTAATAAAAATAAAATAACCTAAAATGGAAATAATAAAATAAT
* * *
30134655 AATAAATATGAAAATTAAAAAAAAAAAGATATATAACTTTTAAAATCCTTAAAGGTATTATATTG
196 AATAAATATGAAAATT-AAAAAAAAAAGATATAAAACTTTTAAAATCCCTAAAGGTATCATATTG
30134720 CAA
260 CAA
30134723 AACCCGTGCA
Statistics
Matches: 238, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
296 5 0.02
297 93 0.39
298 14 0.06
299 32 0.13
300 13 0.05
301 81 0.34
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (298 bp):
TTTTTCTCTTTCTAATATTATAAAATAATCATTTTAACTTGTAACGAAAAATAACCTAAAATGTT
AATAATAAAAAATTTAAAATATAAAGAATTCCCAAAGAGATTATATTTTAACACCTGTTCAAAAT
TATAAAATGATCATTTTACCCTTTAATAAAAATAAAATAACCTAAAATGGAAATAATAAAATAAT
AATAAATATGAAAATTAAAAAAAAAAGATATAAAACTTTTAAAATCCCTAAAGGTATCATATTGC
AAGACTATTTTTTTCTTTTCAACATTATAAAATAATCA
Found at i:30134834 original size:22 final size:21
Alignment explanation
Indices: 30134794--30134837 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
30134784 TCTTTAATCA
*
30134794 AAATAAAATAATTTAAAATAT
1 AAATAAAAAAATTTAAAATAT
*
30134815 AAATAATAAAAATTTTAAATAT
1 AAATAA-AAAAATTTAAAATAT
30134837 A
1 A
30134838 TATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAAAAAAATTTAAAATAT
Found at i:30134892 original size:30 final size:30
Alignment explanation
Indices: 30134856--30134914 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
30134846 ATACCTGTCC
* * *
30134856 AACATTATAGATTAATTATTTTATTTTTTT
1 AACATTATAAAATAATCATTTTATTTTTTT
*
30134886 AACATTATAAAATGATCATTTTATTTTTT
1 AACATTATAAAATAATCATTTTATTTTTT
30134915 AATGAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (30 bp):
AACATTATAAAATAATCATTTTATTTTTTT
Found at i:30143543 original size:20 final size:18
Alignment explanation
Indices: 30143510--30143549 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
30143500 ATTTATCCCT
30143510 CAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAA
30143528 CAAAAGAAATAAAAAAAAAA
1 CAAAA-AAA-AAAAAAAAAA
30143548 CA
1 CA
30143550 TTGTAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 12 0.60
ACGTcount: A:0.88, C:0.07, G:0.03, T:0.03
Consensus pattern (18 bp):
CAAAAAAAAAAAAAAAAA
Found at i:30144574 original size:20 final size:20
Alignment explanation
Indices: 30144546--30144583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30144536 TTATAAAATA
30144546 TTTAATTTAAAATAATATTT
1 TTTAATTTAAAATAATATTT
* *
30144566 TTTATTTTAATATAATAT
1 TTTAATTTAAAATAATAT
30144584 ATTAGTTAAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTAAAATAATATTT
Found at i:30144706 original size:32 final size:31
Alignment explanation
Indices: 30144661--30144778 Score: 77
Period size: 32 Copynumber: 3.8 Consensus size: 31
30144651 ATCCTTTTGA
*
30144661 AAAAATTTCATA-TTATTT-TGAAAAGTTAAGT
1 AAAAATTTCATATTTATTTAT-AAAA-TTAAAT
*
30144692 AAAATTTTCTATATTTATTTATAAAATTAAAT
1 AAAAATTTC-ATATTTATTTATAAAATTAAAT
* * * *
30144724 AAAAAATCCATA-TCATTT-TAAAATTTTAAGT
1 AAAAATTTCATATTTATTTATAAAA--TTAAAT
*
30144755 AAAAAATTTCAT-GTTATTT-TAAAA
1 -AAAAATTTCATATTTATTTATAAAA
30144779 AAGCTATTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
29 5 0.07
30 5 0.07
31 16 0.23
32 33 0.47
33 10 0.14
34 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (31 bp):
AAAAATTTCATATTTATTTATAAAATTAAAT
Found at i:30153232 original size:14 final size:13
Alignment explanation
Indices: 30153213--30153285 Score: 61
Period size: 14 Copynumber: 5.9 Consensus size: 13
30153203 TGAAATAAAA
30153213 AAATACAAAATACG
1 AAATACAAAATA-G
30153227 AAATAC-AAA-A-
1 AAATACAAAATAG
30153237 AAATACAAAATATG
1 AAATACAAAATA-G
30153251 AAATACAAAA-A-
1 AAATACAAAATAG
*
30153262 AAATATAAAA-A-
1 AAATACAAAATAG
30153273 ATAATACAAAATA
1 A-AATACAAAATA
30153286 CCAAAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
10 6 0.12
11 14 0.27
12 10 0.20
13 5 0.10
14 16 0.31
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (13 bp):
AAATACAAAATAG
Found at i:30153241 original size:24 final size:24
Alignment explanation
Indices: 30153209--30153263 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
30153199 AATATGAAAT
30153209 AAAAAAATACAAAATACGAAATAC
1 AAAAAAATACAAAATACGAAATAC
*
30153233 AAAAAAATACAAAATATGAAATAC
1 AAAAAAATACAAAATACGAAATAC
30153257 AAAAAAA
1 AAAAAAA
30153264 ATATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAAAAATACAAAATACGAAATAC
Found at i:30153271 original size:11 final size:11
Alignment explanation
Indices: 30153209--30153283 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 11
30153199 AATATGAAAT
30153209 AAAAAAATACA
1 AAAAAAATACA
30153220 AAATACGAAATAC-
1 AAA-A--AAATACA
30153233 AAAAAAATACA
1 AAAAAAATACA
30153244 AAATATGAAATACA
1 AAA-A--AAATACA
*
30153258 AAAAAAATATA
1 AAAAAAATACA
30153269 AAAAATAATACA
1 AAAAA-AATACA
30153281 AAA
1 AAA
30153284 TACCAAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
10 6 0.11
11 17 0.31
12 11 0.20
13 4 0.07
14 16 0.30
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAAAATACA
Found at i:30154285 original size:10 final size:10
Alignment explanation
Indices: 30154270--30154294 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30154260 AAAAAAAATT
30154270 TTTTTTTTAA
1 TTTTTTTTAA
30154280 TTTTTTTTAA
1 TTTTTTTTAA
30154290 TTTTT
1 TTTTT
30154295 ATATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:30156095 original size:6 final size:7
Alignment explanation
Indices: 30156078--30156104 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30156068 CTCAAAACAC
30156078 AAAAAAT
1 AAAAAAT
30156085 AAAAAAT
1 AAAAAAT
30156092 AAAAAAT
1 AAAAAAT
30156099 AAAAAA
1 AAAAAA
30156105 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:30166790 original size:96 final size:96
Alignment explanation
Indices: 30166674--30166916 Score: 283
Period size: 96 Copynumber: 2.5 Consensus size: 96
30166664 TTTTGAGAAA
* * * *
30166674 AAATGAGATTTTAAAATTGTTGAACCTCTGTTGAGAGGAG-CTTTTTCAAGATAAAATTTTAAA-
1 AAATGAGATTTTAAAGTTGTTGAGCATCTGCTGAGAGGAGCCTTTTTCAAGAT-AAATTTTAAAG
* * * *
30166737 TTATTGAGCCTCTGCTGAGAGAAGCTCTTTTC
65 TTATTAAGCCTCTGCTAAGAAAAGCCCTTTTC
* * * *
30166769 TAAATGAGATTTTAAAGTTGTTGAGCTTCTGCTGAAAGGAGCCCTTTTCAAGATGAATTTTAAAG
1 -AAATGAGATTTTAAAGTTGTTGAGCATCTGCTGAGAGGAGCCTTTTTCAAGATAAATTTTAAAG
* *
30166834 TTGTTAAGCCTCTGTTAAGAAAAGCCCTTTTC
65 TTATTAAGCCTCTGCTAAGAAAAGCCCTTTTC
* * *
30166866 AAGATGAAATTTTTAAAGTTGTTGAGCATCTGCTGAGATGAGTCTTTTTCA
1 AA-ATGAGA-TTTTAAAGTTGTTGAGCATCTGCTGAGAGGAGCCTTTTTCA
30166917 TATTTTAAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
96 46 0.37
97 42 0.34
98 36 0.29
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (96 bp):
AAATGAGATTTTAAAGTTGTTGAGCATCTGCTGAGAGGAGCCTTTTTCAAGATAAATTTTAAAGT
TATTAAGCCTCTGCTAAGAAAAGCCCTTTTC
Found at i:30166800 original size:49 final size:49
Alignment explanation
Indices: 30166676--30166903 Score: 248
Period size: 48 Copynumber: 4.7 Consensus size: 49
30166666 TTGAGAAAAA
* * * * * *
30166676 ATGAGATTTTAAAATTGTTGAACCTCTGTTGAGAGGAG-CTTTTTCAAG
1 ATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCCTTTTCAAG
* * *
30166724 ATAAAATTTTAAA-TTATTGAGCCTCTGCTGAGAGAAGCTCTTTTCTAA-
1 ATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCCTTTTC-AAG
* * * *
30166772 ATGAGATTTTAAAGTTGTTGAGCTTCTGCTGAAAGGAGCCCTTTTCAAG
1 ATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCCTTTTCAAG
* * * *
30166821 ATG-AATTTTAAAGTTGTTAAGCCTCTGTTAAGAAAAGCCCTTTTCAAG
1 ATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCCTTTTCAAG
*
30166869 ATGAAATTTTTAAAGTTGTTGAGCATCTGCTGAGA
1 ATGAAA-TTTTAAAGTTGTTGAGCCTCTGCTGAGA
30166904 TGAGTCTTTT
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
47 20 0.14
48 69 0.47
49 34 0.23
50 24 0.16
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (49 bp):
ATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCCTTTTCAAG
Found at i:30167193 original size:24 final size:25
Alignment explanation
Indices: 30167158--30167211 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
30167148 TACGAAATAC
*
30167158 AAAAATACAAAATAT-GAAATACAAA
1 AAAAATACAAAAAATAG-AATACAAA
*
30167183 AAAAATA-AAAAAATAGAATAGAAA
1 AAAAATACAAAAAATAGAATACAAA
30167207 AAAAA
1 AAAAA
30167212 AATCGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.13
Consensus pattern (25 bp):
AAAAATACAAAAAATAGAATACAAA
Found at i:30167316 original size:29 final size:29
Alignment explanation
Indices: 30167257--30167316 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
30167247 CGCCACCATG
* *
30167257 CCTTACACCCTTCTGACCACCATGCCCTA
1 CCTTACACCCCTCTGACCACCATACCCTA
* *
30167286 CCTTCCACCCCTCTGACCACCATACCTTA
1 CCTTACACCCCTCTGACCACCATACCCTA
30167315 CC
1 CC
30167317 ACTTATCCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.05, T:0.23
Consensus pattern (29 bp):
CCTTACACCCCTCTGACCACCATACCCTA
Found at i:30170536 original size:26 final size:23
Alignment explanation
Indices: 30170500--30170556 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 23
30170490 AAATTAAACA
*
30170500 AAATAAATATATTTATGAATATATAT
1 AAATAAATATATTCAT-AA-ATA-AT
30170526 AAATAAATATATTCATAAATAAT
1 AAATAAATATATTCATAAATAAT
30170549 AAATAAAT
1 AAATAAAT
30170557 TTAAATAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 2 0.07
26 15 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATAAATATATTCATAAATAAT
Found at i:30176777 original size:15 final size:15
Alignment explanation
Indices: 30176746--30176779 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30176736 TTTCATAAAA
* *
30176746 AATTATTTTTCATTG
1 AATTATTTTTAAGTG
30176761 AATTATTTTTAAGTG
1 AATTATTTTTAAGTG
30176776 AATT
1 AATT
30176780 CAATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (15 bp):
AATTATTTTTAAGTG
Found at i:30177376 original size:25 final size:23
Alignment explanation
Indices: 30177348--30177407 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
30177338 AAATTATGGC
30177348 TTTTTTAATATTTAAAAATCTT-A
1 TTTTTTAATATTTAAAAAT-TTAA
* * *
30177371 TTTTTTCATATTTTAAAATTTTTTA
1 TTTTTTAATA-TTTAAAA-ATTTAA
30177396 TTTTTTAATATT
1 TTTTTTAATATT
30177408 ACAAATAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 9 0.29
24 11 0.35
25 11 0.35
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTAATATTTAAAAATTTAA
Found at i:30177381 original size:23 final size:24
Alignment explanation
Indices: 30177348--30177407 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
30177338 AAATTATGGC
30177348 TTTTTTAATATTTAAAA-ATCTTA
1 TTTTTTAATATTTAAAATATCTTA
* * *
30177371 TTTTTTCATATTTTAAAATTTTTTA
1 TTTTTTAATA-TTTAAAATATCTTA
30177396 TTTTTTAATATT
1 TTTTTTAATATT
30177408 ACAAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 9 0.29
24 9 0.29
25 13 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTTAATATTTAAAATATCTTA
Found at i:30177401 original size:17 final size:18
Alignment explanation
Indices: 30177370--30177403 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30177360 TAAAAATCTT
30177370 ATTTTTTCATATTTTAAA
1 ATTTTTTCATATTTTAAA
*
30177388 ATTTTTT-ATTTTTTAA
1 ATTTTTTCATATTTTAA
30177404 TATTACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTCATATTTTAAA
Found at i:30177426 original size:23 final size:24
Alignment explanation
Indices: 30177399--30177468 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
30177389 TTTTTTATTT
* *
30177399 TTTAATATTACAAATAA-TGAAAC
1 TTTAATATTAAAAATAATTGAAAA
* *
30177422 TTTAATTTTATAAAA-AATTTAAAA
1 TTTAATATTA-AAAATAATTGAAAA
30177446 TTTAATATTAAAAAT-ATT-AAAA
1 TTTAATATTAAAAATAATTGAAAA
30177468 T
1 T
30177469 AAAAAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.13
23 18 0.46
24 16 0.41
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
TTTAATATTAAAAATAATTGAAAA
Found at i:30178117 original size:2 final size:2
Alignment explanation
Indices: 30178112--30178145 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
30178102 CCCCCCCCCC
*
30178112 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30178146 TTTTTTGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:30180412 original size:2 final size:2
Alignment explanation
Indices: 30180405--30180453 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
30180395 CTAAAGTGAA
*
30180405 AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30180445 AT AT AT AT A
1 AT AT AT AT A
30180454 GGACAAACGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30180454 original size:20 final size:21
Alignment explanation
Indices: 30180405--30180454 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
30180395 CTAAAGTGAA
30180405 ATATATATA-ATATAATATAT
1 ATATATATAGATATAATATAT
30180425 ATATATATAGATAT-ATATAT
1 ATATATATAGATATAATATAT
30180445 ATATATATAG
1 ATATATATAG
30180455 GACAAACGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATATATATAGATATAATATAT
Found at i:30180852 original size:19 final size:19
Alignment explanation
Indices: 30180828--30180868 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
30180818 TAATGAATGA
30180828 AATAATTTT-TTAAAATAAT
1 AATAATTTTCTTAAAAT-AT
*
30180847 AATAATTTTCTTCAAATAT
1 AATAATTTTCTTAAAATAT
30180866 AAT
1 AAT
30180869 TATAAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTTTCTTAAAATAT
Found at i:30181570 original size:14 final size:13
Alignment explanation
Indices: 30181532--30181578 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
30181522 ATATGAAACT
30181532 TAATTA-ATTTATA
1 TAATTATATTTA-A
*
30181545 TAATTATTTTTAA
1 TAATTATATTTAA
30181558 TAATTGATATTTAA
1 TAATT-ATATTTAA
30181572 TAATTAT
1 TAATTAT
30181579 GAAATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 14 0.47
14 16 0.53
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TAATTATATTTAA
Found at i:30183639 original size:20 final size:21
Alignment explanation
Indices: 30183599--30183641 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
30183589 AAGTTAAATT
*
30183599 TTCAAAATCTTTTTGAAAAAA
1 TTCAAAATCATTTTGAAAAAA
*
30183620 TTCAATATCATTTT-AAAAAA
1 TTCAAAATCATTTTGAAAAAA
30183640 TT
1 TT
30183642 AACTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (21 bp):
TTCAAAATCATTTTGAAAAAA
Found at i:30192978 original size:20 final size:21
Alignment explanation
Indices: 30192950--30192991 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30192940 AATTTTTTAA
*
30192950 TTATCAAATTAATTAATATAT
1 TTATCAAATTAAATAATATAT
*
30192971 TTAT-AAATTAAATATTATAT
1 TTATCAAATTAAATAATATAT
30192991 T
1 T
30192992 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATCAAATTAAATAATATAT
Found at i:30192998 original size:20 final size:20
Alignment explanation
Indices: 30192955--30192999 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30192945 TTTAATTATC
* * *
30192955 AAATTAATTAATATATTTAT
1 AAATTAAATAATATATTAAA
*
30192975 AAATTAAATATTATATTAAA
1 AAATTAAATAATATATTAAA
30192995 AAATT
1 AAATT
30193000 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTAAATAATATATTAAA
Found at i:30202574 original size:3 final size:3
Alignment explanation
Indices: 30202566--30202599 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
30202556 TAAGGATGAG
*
30202566 ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30202600 GAAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:30204850 original size:23 final size:23
Alignment explanation
Indices: 30204823--30204874 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
30204813 TTGATGAGCA
*
30204823 TTTTTAGAACACTCTTTAAGGTT
1 TTTTTAAAACACTCTTTAAGGTT
* **
30204846 TTTTTAAAATACTCTTTGTGGTT
1 TTTTTAAAACACTCTTTAAGGTT
30204869 TTTTTA
1 TTTTTA
30204875 TACACTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTTTAAAACACTCTTTAAGGTT
Found at i:30206680 original size:22 final size:22
Alignment explanation
Indices: 30206655--30206701 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
30206645 AAATTTCATA
30206655 AGAGATCTGTTT-AAGATTTGTT
1 AGAGATCTGTTTGAA-ATTTGTT
*
30206677 AGAGATTTGTTTGAAATTTGTT
1 AGAGATCTGTTTGAAATTTGTT
30206699 AGA
1 AGA
30206702 TATTACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (22 bp):
AGAGATCTGTTTGAAATTTGTT
Found at i:30209604 original size:28 final size:28
Alignment explanation
Indices: 30209573--30209632 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
30209563 AATTAATATA
* *
30209573 TTTATAATTTAAATATTATATTAAAAAT
1 TTTAAAATTTAAATAATATATTAAAAAT
* * *
30209601 TTTAAAATTTATATAATATATTTAATAT
1 TTTAAAATTTAAATAATATATTAAAAAT
30209629 TTTA
1 TTTA
30209633 CTATAATTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAAAATTTAAATAATATATTAAAAAT
Found at i:30212243 original size:17 final size:17
Alignment explanation
Indices: 30212221--30212254 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30212211 ACCATTTCAA
30212221 AATCATTTAAAACATAG
1 AATCATTTAAAACATAG
30212238 AATCATTTAAAACATAG
1 AATCATTTAAAACATAG
30212255 GCTATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
AATCATTTAAAACATAG
Found at i:30216133 original size:27 final size:29
Alignment explanation
Indices: 30216103--30216158 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30216093 ATTAATTCCA
30216103 TATTCTTT-CATTTTAAC-ATTAATAATT
1 TATTCTTTCCATTTTAACTATTAATAATT
* *
30216130 TATTCTTTCCTTTTTAACTTTTAATAATT
1 TATTCTTTCCATTTTAACTATTAATAATT
30216159 AAAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 8 0.32
29 9 0.36
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTCTTTCCATTTTAACTATTAATAATT
Found at i:30217789 original size:18 final size:18
Alignment explanation
Indices: 30217761--30217800 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
30217751 CATTTTTACT
30217761 TTTTATAATTTATCTTTTA
1 TTTTATAATTTAT-TTTTA
30217780 TTTT-TAATTTATTTTTA
1 TTTTATAATTTATTTTTA
30217797 TTTT
1 TTTT
30217801 CATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATAATTTATTTTTA
Found at i:30223183 original size:5 final size:5
Alignment explanation
Indices: 30223163--30223197 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
30223153 TTTTTAGCTC
30223163 TATA- TATAT ATATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT
30223198 AAATATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:30226015 original size:36 final size:36
Alignment explanation
Indices: 30225963--30226049 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
30225953 ATAATTGATT
* * *
30225963 AAAA-TTAATTAGTGTTTAGTGACACTGGTTAGGGA
1 AAAAGTTAATTAATGTTTAGTGACACTGGTAAAGGA
*
30225998 AAAAGTTAATTAATGTTTAGTGACATTGGTAAAGGA
1 AAAAGTTAATTAATGTTTAGTGACACTGGTAAAGGA
*
30226034 AAATGTTAATTAATGT
1 AAAAGTTAATTAATGT
30226050 CTATAAGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 4 0.09
36 42 0.91
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (36 bp):
AAAAGTTAATTAATGTTTAGTGACACTGGTAAAGGA
Found at i:30235856 original size:128 final size:128
Alignment explanation
Indices: 30235628--30235884 Score: 496
Period size: 128 Copynumber: 2.0 Consensus size: 128
30235618 ATTGAAGTAA
*
30235628 AAACCCAAACATCCATTTTTCACAGAAAAATTACATATTCACTCCCAGATTACAAATTATATACC
1 AAACCCAAACATCCATTTTTCACAGAAAAATTACATATTCACTCCCAGATTACAAAATATATACC
30235693 CATATACTCCTGATTCAAGTTTTCAACTCTTTCTCTGTTCGATCTTTGAAACCCAAACTGATC
66 CATATACTCCTGATTCAAGTTTTCAACTCTTTCTCTGTTCGATCTTTGAAACCCAAACTGATC
30235756 AAACCCAAACATCCATTTTTCACAGAAAAATTACATATTCACTCCCAGATTACAAAATATATACC
1 AAACCCAAACATCCATTTTTCACAGAAAAATTACATATTCACTCCCAGATTACAAAATATATACC
*
30235821 CATATACTCCTGATTCAAGTTTTCAACTCTTTCTCTGTTCGATCTTTGAAACTCAAACTGATC
66 CATATACTCCTGATTCAAGTTTTCAACTCTTTCTCTGTTCGATCTTTGAAACCCAAACTGATC
30235884 A
1 A
30235885 TTAGCAATGG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (128 bp):
AAACCCAAACATCCATTTTTCACAGAAAAATTACATATTCACTCCCAGATTACAAAATATATACC
CATATACTCCTGATTCAAGTTTTCAACTCTTTCTCTGTTCGATCTTTGAAACCCAAACTGATC
Found at i:30237188 original size:23 final size:23
Alignment explanation
Indices: 30237162--30237211 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
30237152 ATAAAATATA
*
30237162 AAATATATATTTTAATTTTTAT-T
1 AAATATATA-TATAATTTTTATGT
*
30237185 AAATTTATATATAATTTTTATGT
1 AAATATATATATAATTTTTATGT
30237208 AAAT
1 AAAT
30237212 TTTAATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AAATATATATATAATTTTTATGT
Found at i:30237450 original size:51 final size:51
Alignment explanation
Indices: 30237387--30237488 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
30237377 TACACTATTT
* **
30237387 TGGTTGATATCACCCCATTATACCTTTCTAAAAAGAATTTTAATTGCAAAG
1 TGGTTGACATCACCCCATTATACCTTTCTAAAAAGAATGCTAATTGCAAAG
*
30237438 TGGTTGACATCACCCCATTATACCTTTTTAAAAAGAATGCTAATTGCAAAG
1 TGGTTGACATCACCCCATTATACCTTTCTAAAAAGAATGCTAATTGCAAAG
30237489 CATGATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (51 bp):
TGGTTGACATCACCCCATTATACCTTTCTAAAAAGAATGCTAATTGCAAAG
Found at i:30245268 original size:15 final size:16
Alignment explanation
Indices: 30245237--30245274 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
30245227 ATTAATTTAT
*
30245237 ATAATTTTAACATTCA
1 ATAAATTTAACATTCA
30245253 ATAAATTTAA-ATTCA
1 ATAAATTTAACATTCA
*
30245268 AGAAATT
1 ATAAATT
30245275 GTATAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAAATTTAACATTCA
Found at i:30245700 original size:23 final size:23
Alignment explanation
Indices: 30245669--30245717 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
30245659 TTTGTTAAGT
* *
30245669 ATAATAAAAAATGAATTTAAAA-A
1 ATAAAAAAAAAT-AATGTAAAATA
30245692 ATAAAAAAAAATAATGTAAAATA
1 ATAAAAAAAAATAATGTAAAATA
30245715 ATA
1 ATA
30245718 TATTCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
ATAAAAAAAAATAATGTAAAATA
Found at i:30252833 original size:2 final size:2
Alignment explanation
Indices: 30252826--30252861 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
30252816 AGCTACTTGA
* *
30252826 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30252862 TAGTACTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:30253589 original size:13 final size:13
Alignment explanation
Indices: 30253571--30253596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30253561 TAATCGATAT
30253571 CATTTCTGATAAA
1 CATTTCTGATAAA
30253584 CATTTCTGATAAA
1 CATTTCTGATAAA
30253597 TCCACCTATA
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
CATTTCTGATAAA
Found at i:30262702 original size:3 final size:3
Alignment explanation
Indices: 30262694--30262724 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30262684 ATCATAACAC
30262694 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
30262725 CGACGGCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:30262861 original size:70 final size:70
Alignment explanation
Indices: 30262779--30262920 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
30262769 GGGGCTCTTC
30262779 TACTTCCACACACAGATGGATAAGTCGAGTATCAATTAAAATTATAAAAATAATAGTTATACAAA
1 TACTTCCACACACAGATGGATAAGTCGAGTATCAATTAAAATTATAAAAATAATAGTTATACAAA
30262844 TTAAT
66 TTAAT
30262849 TACTTCCACACACAGATGGATAAGTCGAGTATCAATTAAAATTATAAAAATAATAGTTATACAAA
1 TACTTCCACACACAGATGGATAAGTCGAGTATCAATTAAAATTATAAAAATAATAGTTATACAAA
30262914 TTAAT
66 TTAAT
30262919 TA
1 TA
30262921 TATTCCAGGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (70 bp):
TACTTCCACACACAGATGGATAAGTCGAGTATCAATTAAAATTATAAAAATAATAGTTATACAAA
TTAAT
Found at i:30263400 original size:2 final size:2
Alignment explanation
Indices: 30263388--30263418 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30263378 ATCTATGTAA
*
30263388 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30263419 AACAAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30269074 original size:2 final size:2
Alignment explanation
Indices: 30269067--30269098 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30269057 CAAAAGCAAG
30269067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30269099 AACTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30270492 original size:47 final size:47
Alignment explanation
Indices: 30270412--30270503 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
30270402 CTAACTTTAC
*
30270412 ATATATATATATATGATGAGAAATTTTAAAGAAATGACCATATATAT
1 ATATATATATATATGATGAGAAATTTTAAAGAAATGACCAGATATAT
30270459 ATATATATATATATGATGAGAAATTTTAAAGAAATGACCAGATAT
1 ATATATATATATATGATGAGAAATTTTAAAGAAATGACCAGATAT
30270504 CTACAACGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (47 bp):
ATATATATATATATGATGAGAAATTTTAAAGAAATGACCAGATATAT
Found at i:30272988 original size:23 final size:21
Alignment explanation
Indices: 30272951--30272997 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
30272941 TTTTTCTTAT
30272951 TTTATTTAAAAAAATT-AGTAC
1 TTTATTTAAAAAAATTGA-TAC
30272972 TTTATTTAAAAAAAAATTGATAC
1 TTTATTT--AAAAAAATTGATAC
30272995 TTT
1 TTT
30272998 TCAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (21 bp):
TTTATTTAAAAAAATTGATAC
Found at i:30273177 original size:47 final size:47
Alignment explanation
Indices: 30273126--30273228 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 47
30273116 ATTTTATAAG
30273126 AAAAATTGATA-TT-TTTTCCTTAAAACCTTTTTTTATTTTTTTATTTA
1 AAAAATTGATATTTATTTTCCTTAAAA--TTTTTTTATTTTTTTATTTA
*
30273173 AAAAATTGATACTTTTAACTTTTTCTTAAAATTTTTTTATTTTTTTATTTA
1 AAAAATTGATA--TTT-A-TTTTCCTTAAAATTTTTTTATTTTTTTATTTA
30273224 AAAAA
1 AAAAA
30273229 AATTAGTACT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
47 11 0.22
50 2 0.04
51 25 0.51
53 11 0.22
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (47 bp):
AAAAATTGATATTTATTTTCCTTAAAATTTTTTTATTTTTTTATTTA
Found at i:30273278 original size:48 final size:49
Alignment explanation
Indices: 30273153--30273300 Score: 169
Period size: 48 Copynumber: 3.0 Consensus size: 49
30273143 CCTTAAAACC
* * *
30273153 TTTTTTTATTTTTTTATTT--AAAAAATTGATACTTTTAACTTTTTCTT
1 TTTTTTTATATTTTTATTTAAAAAAAATTGATACTTTCAACTTTTCCTT
* *
30273200 AAAATTTTTTTATTTTTTTATTTAAAAAAAATT-AGTACTTTCAATTTTTCCTT
1 ----TTTTTTTATATTTTTATTTAAAAAAAATTGA-TACTTTCAACTTTTCCTT
*
30273253 TTTTTTTA-ATTTTTATTTAAGAAAAATTGATACTTTCAACTTTTCCTT
1 TTTTTTTATATTTTTATTTAAAAAAAATTGATACTTTCAACTTTTCCTT
30273301 AAAAATATTT
Statistics
Matches: 87, Mismatches: 6, Indels: 11
0.84 0.06 0.11
Matches are distributed among these distances:
48 35 0.40
49 9 0.10
51 19 0.22
52 1 0.01
53 23 0.26
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (49 bp):
TTTTTTTATATTTTTATTTAAAAAAAATTGATACTTTCAACTTTTCCTT
Found at i:30273439 original size:55 final size:58
Alignment explanation
Indices: 30273339--30273448 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 58
30273329 TTGAAAAAAA
* * ** *
30273339 TTTTATTTTCTAAGGAAAATTGATATTTTTAACTTTTCTTTAAAAATAT-TTTTTATT
1 TTTTATTTTCTAAGAAAAATTGATACTTTTAACTTTTCTCAAAAAAAATATTTTTATT
30273396 TTTTATTTT-TAA-AAAAATTGATACTTTTAACTTTTCTCAAAAAAAATATTTTT
1 TTTTATTTTCTAAGAAAAATTGATACTTTTAACTTTTCTCAAAAAAAATATTTTT
30273449 CTTAAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
55 30 0.64
56 8 0.17
57 9 0.19
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (58 bp):
TTTTATTTTCTAAGAAAAATTGATACTTTTAACTTTTCTCAAAAAAAATATTTTTATT
Found at i:30274920 original size:78 final size:79
Alignment explanation
Indices: 30274827--30274988 Score: 238
Period size: 78 Copynumber: 2.1 Consensus size: 79
30274817 GAACCGAAGT
* * * * *
30274827 CTAAAATGAATAACTTGGACTAAGTCGAAAAGAGATCTAACATAAGCTGAAA-TCTGAAAACAAA
1 CTAAAATGAATAACTTAGACAAAGCCAAAAAAAGATCTAACATAAGCTGAAATTC-GAAAACAAA
*
30274891 ATGA-CTGGATCGAA
65 ATGACCTGAATCGAA
*
30274905 CTAAAATGAATAACTTAGACAAAGCCAAAAAAAGATCTGACATAAGCTGAAATTCGAAAACAAAA
1 CTAAAATGAATAACTTAGACAAAGCCAAAAAAAGATCTAACATAAGCTGAAATTCGAAAACAAAA
30274970 TGACCTGAATCGAA
66 TGACCTGAATCGAA
30274984 CTAAA
1 CTAAA
30274989 GTCTAAAATG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 59 0.79
79 16 0.21
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (79 bp):
CTAAAATGAATAACTTAGACAAAGCCAAAAAAAGATCTAACATAAGCTGAAATTCGAAAACAAAA
TGACCTGAATCGAA
Found at i:30275057 original size:164 final size:165
Alignment explanation
Indices: 30274768--30275065 Score: 399
Period size: 164 Copynumber: 1.8 Consensus size: 165
30274758 GGACTAAGTC
* * * * *
30274768 AAAAAAGATTTGGCATAAGCTAAAATCTGAAAACATAATGACCTAAATTGAACCGAAGTCTAAAA
1 AAAAAAGATCTGACATAAGCTAAAATCTGAAAACAAAATGACCTAAATCGAACCAAAGTCTAAAA
* * *
30274833 TGAATAACTTGGACTAAGTCGAAAAGAGATCTAACATAAGCTGAAATCTGAAAACAAAATGA-CT
66 TGAATAACTTGGACTAACTCGAAAAGAGATATAACATAAGCTAAAATCTGAAAACAAAATGACCT
30274897 GGATCGAACTAAAATGAATAACTTAGACAAAGCCA
131 GGATCGAACTAAAATGAATAACTTAGACAAAGCCA
* * *
30274932 AAAAAAGATCTGACATAAGCTGAAAT-TCGAAAACAAAATGACCTGAATCGAACTAAAGTCTAAA
1 AAAAAAGATCTGACATAAGCTAAAATCT-GAAAACAAAATGACCTAAATCGAACCAAAGTCTAAA
* * *
30274996 ATGAATAATTTGGACTAAACT-GAAGAAG-GATATGACATGAGCTAAAATCT-AAAAGCAAAATG
65 ATGAATAACTTGGACT-AACTCGAA-AAGAGATATAACATAAGCTAAAATCTGAAAA-CAAAATG
30275058 ACCTGGAT
127 ACCTGGAT
30275066 TGAATCGAAG
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
163 5 0.04
164 98 0.85
165 12 0.10
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (165 bp):
AAAAAAGATCTGACATAAGCTAAAATCTGAAAACAAAATGACCTAAATCGAACCAAAGTCTAAAA
TGAATAACTTGGACTAACTCGAAAAGAGATATAACATAAGCTAAAATCTGAAAACAAAATGACCT
GGATCGAACTAAAATGAATAACTTAGACAAAGCCA
Found at i:30275082 original size:86 final size:85
Alignment explanation
Indices: 30274781--30275168 Score: 350
Period size: 86 Copynumber: 4.6 Consensus size: 85
30274771 AAAGATTTGG
* * *
30274781 CATAAGCTAAAATCTGAAAACATAATGACCTAAATTGAACCGAAGTCTAAAATGAATAACTTGGA
1 CATAAGCTAAAATCT-AAAACAAAATGACCTGAATTGAATCGAAGTCTAAAATGAATAACTTGGA
* *
30274846 CT-AAGTCGAA-AAGAGATCTAA
65 CTAAACT-GAAGAAG-GATCTGA
* *
30274867 CATAAGCTGAAATCTGAAAACAAAATGA-CTG----G-ATCGAA--CTAAAATGAATAACTTAGA
1 CATAAGCTAAAATCT-AAAACAAAATGACCTGAATTGAATCGAAGTCTAAAATGAATAACTTGGA
** * *
30274924 C-AAAGCCAAAAAAAGATCTGA
65 CTAAA-CTGAAGAAGGATCTGA
* * * * *
30274945 CATAAGCTGAAATTCGAAAACAAAATGACCTGAATCGAA-CTAAAGTCTAAAATGAATAATTTGG
1 CATAAGCT-AAAATCTAAAACAAAATGACCTGAATTGAATC-GAAGTCTAAAATGAATAACTTGG
*
30275009 ACTAAACTGAAGAAGGATATGA
64 ACTAAACTGAAGAAGGATCTGA
* * * *
30275031 CATGAGCTAAAATCTAAAAGCAAAATGACCTGGATTGAATCGAAGTTTAAAATGAATAACTTAGA
1 CATAAGCTAAAATCTAAAA-CAAAATGACCTGAATTGAATCGAAGTCTAAAATGAATAACTTGGA
** *
30275096 CTAAGTTGAAGAAGGATCTGG
65 CTAAACTGAAGAAGGATCTGA
* * * * *
30275117 CATAGGCCAAAATCCAAAAATAAAATGATCTGAATTGAATCGAAGTCTAAAA
1 CATAAGCTAAAAT-CTAAAACAAAATGACCTGAATTGAATCGAAGTCTAAAA
30275169 GTAAACAATC
Statistics
Matches: 243, Mismatches: 42, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
78 49 0.20
79 9 0.04
80 5 0.02
81 1 0.00
83 2 0.01
84 3 0.01
85 11 0.05
86 154 0.63
87 9 0.04
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.22
Consensus pattern (85 bp):
CATAAGCTAAAATCTAAAACAAAATGACCTGAATTGAATCGAAGTCTAAAATGAATAACTTGGAC
TAAACTGAAGAAGGATCTGA
Found at i:30286639 original size:23 final size:24
Alignment explanation
Indices: 30286604--30286655 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
30286594 TCTTTTCTTA
* *
30286604 TTTTATTTAAAAAATATTAG-TAC
1 TTTTATCTAAAAAAAATTAGATAC
* *
30286627 TTTTATCTGAAAAAAATTTGATAC
1 TTTTATCTAAAAAAAATTAGATAC
30286651 TTTTA
1 TTTTA
30286656 ACTTTTCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTTATCTAAAAAAAATTAGATAC
Found at i:30287006 original size:62 final size:58
Alignment explanation
Indices: 30286830--30287112 Score: 231
Period size: 62 Copynumber: 4.8 Consensus size: 58
30286820 TTTATTTAAA
*** *
30286830 AAAATTGATACTTTCAAC-TTTTAAAAAAAAAAATTTTTTTGAAATTATTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAATT-TTA-TTTTAAGG
* * *** * *
30286889 AAAATTGATA--TTCAACTTTTCCT-TAAATTCA-TCTTTTGAAATATTCATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAAT-TTTATTT-TAAGG
30286945 AAAATTGATACTTTCAACTTTTTCTCAAAAAAAAATATTTTTTGAAAATTTTATCTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAAAAAT-TTTTTTG-AAATTTTAT-TTTAAGG
* * * * * *
30287007 AAAATTGATACTTTCTATTTTTTCTCAAACAACATTTTTTTAAAAATTTTAGTTTTTAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAAAAATTTTTTT-GAAATTTTA-TTTTAAGG
* * * *
30287067 AAAATTGATA-TTTCAA-TCTTTC-CTAAGAAAATTGTTTTGAAATTTT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAATTTT
30287113 CTTTAGAAAG
Statistics
Matches: 181, Mismatches: 30, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
55 3 0.02
56 33 0.18
57 23 0.13
58 20 0.11
59 15 0.08
60 34 0.19
61 8 0.04
62 39 0.22
63 6 0.03
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAATTTTATTTTAAGG
Found at i:30287075 original size:60 final size:62
Alignment explanation
Indices: 30286940--30287087 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 62
30286930 TATTCATTTC
*
30286940 TAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAATATTTTTTGAAAATTTTATCTT
1 TAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAATATTTTTTAAAAATTTTATCTT
* * * *
30287002 TAAGGAAAATTGATACTTTCTATTTTTTCTC-AAACAACAT-TTTTTTAAAAATTTTAGT-TT
1 TAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAATATTTTTTAAAAATTTTA-TCTT
*
30287062 TTAGGAAAATTGATA-TTTCAATCTTT
1 TAAGGAAAATTGATACTTTCAA-CTTT
30287088 CCTAAGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 5 0.07
60 34 0.45
61 8 0.11
62 29 0.38
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (62 bp):
TAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAATATTTTTTAAAAATTTTATCTT
Found at i:30287139 original size:13 final size:13
Alignment explanation
Indices: 30287101--30287142 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
30287091 AAGAAAATTG
30287101 TTTTGAAAT-TTT
1 TTTTGAAATATTT
*
30287113 CTTTAGAAAGTATTT
1 -TTTTGAAA-TATTT
30287128 TTTTGAAATATTT
1 TTTTGAAATATTT
30287141 TT
1 TT
30287143 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 14 0.56
14 8 0.32
15 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (13 bp):
TTTTGAAATATTT
Found at i:30287270 original size:4 final size:4
Alignment explanation
Indices: 30287261--30287292 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
30287251 ATTTTATGAC
30287261 AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
30287293 GTGAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:30288333 original size:30 final size:30
Alignment explanation
Indices: 30288264--30288352 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
30288254 TTATCCGATC
* * *
30288264 AAAAGCTT-AATTTGATAAAAATATATATTT
1 AAAAG-TTCAATTAGATAAAAATATATGTTG
*
30288294 AAAAGTTCAATTAGGTAAAAATATATGTTCG
1 AAAAGTTCAATTAGATAAAAATATATGTT-G
* *
30288325 AAAA-TTCAATTATATAAAAATAAATGTT
1 AAAAGTTCAATTAGATAAAAATATATGTT
30288353 TAAAGTTTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.04
30 44 0.88
31 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (30 bp):
AAAAGTTCAATTAGATAAAAATATATGTTG
Found at i:30288906 original size:19 final size:19
Alignment explanation
Indices: 30288882--30288952 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 19
30288872 TTGTTTCTTC
30288882 TATTTTGCTATTTTTATTT
1 TATTTTGCTATTTTTATTT
** **
30288901 TATTTTTTTATTTTGGTTT
1 TATTTTGCTATTTTTATTT
30288920 TATTTT-C-A---TTATTT
1 TATTTTGCTATTTTTATTT
*
30288934 TATTTTGCT-TTTTTCTTT
1 TATTTTGCTATTTTTATTT
30288952 T
1 T
30288953 CAATTTTCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
17 1 0.03
18 6 0.15
19 21 0.54
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.76
Consensus pattern (19 bp):
TATTTTGCTATTTTTATTT
Found at i:30288934 original size:25 final size:24
Alignment explanation
Indices: 30288893--30288945 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
30288883 ATTTTGCTAT
* *
30288893 TTTTATTTTATTTTTTTATTTTGG
1 TTTTATTTTATTATTTTATTTTGC
30288917 TTTTATTTTCATTATTTTATTTTGC
1 TTTTATTTT-ATTATTTTATTTTGC
30288942 TTTT
1 TTTT
30288946 TTCTTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (24 bp):
TTTTATTTTATTATTTTATTTTGC
Found at i:30289902 original size:13 final size:13
Alignment explanation
Indices: 30289881--30289931 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 13
30289871 TATTATCTAC
30289881 AATAATATAAAAT
1 AATAATATAAAAT
*
30289894 AAT-AT-TATAAT
1 AATAATATAAAAT
30289905 AATAA-ATATAAAT
1 AATAATATA-AAAT
30289918 ATATAATATAAAAT
1 A-ATAATATAAAAT
30289932 TAAACTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.26
12 5 0.16
13 7 0.23
14 8 0.26
15 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATATAAAAT
Found at i:30290120 original size:14 final size:13
Alignment explanation
Indices: 30290103--30290152 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
30290093 GAAATATTAT
30290103 ATATTTTTAATTTA
1 ATATTTTT-ATTTA
*
30290117 ATA--TTTATATA
1 ATATTTTTATTTA
30290128 ATATTTTTATTTA
1 ATATTTTTATTTA
*
30290141 TTTATTTTTATT
1 -ATATTTTTATT
30290153 ATTTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 7 0.23
14 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTTTTATTTA
Found at i:30290126 original size:27 final size:27
Alignment explanation
Indices: 30290096--30290154 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
30290086 AATATACGAA
30290096 ATATTATATATTTTTAATTTA-ATATTT
1 ATATTATATATTTTT-ATTTATATATTT
*
30290123 ATA-TA-ATATTTTTATTTATTTATTT
1 ATATTATATATTTTTATTTATATATTT
*
30290148 TTATTAT
1 ATATTAT
30290155 TTTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 4 0.15
27 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
ATATTATATATTTTTATTTATATATTT
Found at i:30290146 original size:25 final size:22
Alignment explanation
Indices: 30290103--30290165 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 22
30290093 GAAATATTAT
30290103 ATATTTTTAATTTAATATTTATATA
1 ATATTTTT-ATTTAATATTT-T-TA
*
30290128 ATATTTTTATTTATTTATTTTTA
1 ATATTTTTATTTA-ATATTTTTA
*
30290151 TTATTTTTATATTAA
1 ATATTTTTAT-TTAA
30290166 AATAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 11 0.33
24 9 0.27
25 13 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATTTTTATTTAATATTTTTA
Found at i:30292142 original size:51 final size:52
Alignment explanation
Indices: 30292066--30292189 Score: 169
Period size: 51 Copynumber: 2.4 Consensus size: 52
30292056 GGATTCAAGG
* *
30292066 GATTCTTAATAGGTAAGTTTAACTTACAAGAGAAGAATTTTAAAAGGA-AAA
1 GATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAGAAA
* * * **
30292117 GATTCTTAATAGGCAAGTTTGACTTACAGGAGAAGAATTCTAAGAGGAGAGG
1 GATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAGAAA
*
30292169 GATTCTTAATGGGTAAGTTTG
1 GATTCTTAATAGGTAAGTTTG
30292190 TATGGCTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 43 0.68
52 20 0.32
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (52 bp):
GATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTCTAAAAGGAGAAA
Found at i:30292713 original size:31 final size:31
Alignment explanation
Indices: 30292674--30292754 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
30292664 AGGCTTTTAG
30292674 CCCAACAAATGGTATCAGAGCTGTGGTATTC
1 CCCAACAAATGGTATCAGAGCTGTGGTATTC
* *
30292705 TCCAACAAATGGTATCAGAGCTGTGGTGTTC
1 CCCAACAAATGGTATCAGAGCTGTGGTATTC
*
30292736 CCCAACAAGTGGTATCAGA
1 CCCAACAAATGGTATCAGA
30292755 ACTGAAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (31 bp):
CCCAACAAATGGTATCAGAGCTGTGGTATTC
Found at i:30292914 original size:18 final size:18
Alignment explanation
Indices: 30292887--30292922 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
30292877 AAGCAAGTTC
30292887 AGAAAGTTCGA-TTCAAG
1 AGAAAGTTCGAGTTCAAG
30292904 AGAAGAGTTCGAGTTCAAG
1 AGAA-AGTTCGAGTTCAAG
30292923 TTTTGAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
AGAAAGTTCGAGTTCAAG
Found at i:30293245 original size:51 final size:51
Alignment explanation
Indices: 30293145--30293298 Score: 175
Period size: 51 Copynumber: 3.0 Consensus size: 51
30293135 GGACAAGAAG
* * *
30293145 ACTTGCAAAAGAAGAATTCCAAAA-GAAAGAGGATTCTTAATAGGTAAGTTTA
1 ACTTACAAGAGAAGAATTCTAAAAGGAAA-A-GATTCTTAATAGGTAAGTTTA
* * *
30293197 ACTTACAAGAGAAGAATTTTAAAAGGAAAAGATTCTTAATAGGCAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAAAGGAAAAGATTCTTAATAGGTAAGTTTA
* * ** *
30293248 ACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTT
1 ACTTACAAGAGAAGAATTCTAAAAGGA-AAAGATTCTTAATAGGTAAGTTT
30293299 GTATGGCTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 43 0.49
52 40 0.46
53 4 0.05
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (51 bp):
ACTTACAAGAGAAGAATTCTAAAAGGAAAAGATTCTTAATAGGTAAGTTTA
Found at i:30300346 original size:26 final size:26
Alignment explanation
Indices: 30300276--30300346 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
30300266 TTGAATTAAA
* * *
30300276 TTTAAAGAAATTTTTCATCTAAAATT
1 TTTAAAAAAATTTATCATTTAAAATT
** *
30300302 TTTTTAAAAATTTACCATTTAAAA-T
1 TTTAAAAAAATTTATCATTTAAAATT
30300327 TTTAAAAAAATCTTATCATT
1 TTTAAAAAAAT-TTATCATT
30300347 GAATATTGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 10 0.29
26 25 0.71
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (26 bp):
TTTAAAAAAATTTATCATTTAAAATT
Found at i:30301397 original size:30 final size:28
Alignment explanation
Indices: 30301362--30301422 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
30301352 GATAAACCAC
*
30301362 AAAATATTAAAATA-AATAAATAAACAAAAT
1 AAAATAGT-AAATAGAATAAAT--ACAAAAT
*
30301392 AAAATAGTAAATAGGATAAATACAAAAT
1 AAAATAGTAAATAGAATAAATACAAAAT
30301420 AAA
1 AAA
30301423 GTAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 10 0.36
29 5 0.18
30 13 0.46
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (28 bp):
AAAATAGTAAATAGAATAAATACAAAAT
Found at i:30301924 original size:31 final size:31
Alignment explanation
Indices: 30301861--30301950 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
30301851 ATTTTGTGAG
* * * *
30301861 ATTTCAGTTTTGCAAGAATTTGAT-TCTCAAA
1 ATTTTAGTTTCGCAAGAATTT-ATATTTTAAA
30301892 ATTTTAGTTTCGCAAGAATTTATATTTTAAA
1 ATTTTAGTTTCGCAAGAATTTATATTTTAAA
* *
30301923 ATTTTCATTTTCACAAGAATTTA-ATTTT
1 ATTTT-AGTTTCGCAAGAATTTATATTTT
30301951 TCAGATTCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 34 0.67
32 15 0.29
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (31 bp):
ATTTTAGTTTCGCAAGAATTTATATTTTAAA
Found at i:30301994 original size:32 final size:31
Alignment explanation
Indices: 30301953--30302037 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
30301943 TTAATTTTTC
*
30301953 AGATTCGCAAGAATTTGATTCATAAGGATTTA
1 AGATTCGCAAGAATTTGATTCATAA-AATTTA
** *
30301985 AGATTCGCAAGTTTTTAGATTCATAAAATTTT
1 AGATTCGCAAGAATTT-GATTCATAAAATTTA
* **
30302017 AGTTTCATAAGAATTTGATTC
1 AGATTCGCAAGAATTTGATTC
30302038 TCAAGAACTC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
31 5 0.12
32 29 0.67
33 9 0.21
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (31 bp):
AGATTCGCAAGAATTTGATTCATAAAATTTA
Found at i:30302016 original size:16 final size:17
Alignment explanation
Indices: 30301961--30302032 Score: 62
Period size: 16 Copynumber: 4.5 Consensus size: 17
30301951 TCAGATTCGC
30301961 AAGAA-TTT-GATTCAT
1 AAGAATTTTAGATTCAT
* * **
30301976 AAGGATTTAAGATTCGC
1 AAGAATTTTAGATTCAT
*
30301993 AAG-TTTTTAGATTCAT
1 AAGAATTTTAGATTCAT
*
30302009 AA-AATTTTAGTTTCAT
1 AAGAATTTTAGATTCAT
30302025 AAGAATTT
1 AAGAATTT
30302033 GATTCTCAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
15 4 0.09
16 26 0.60
17 13 0.30
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (17 bp):
AAGAATTTTAGATTCAT
Found at i:30302032 original size:88 final size:87
Alignment explanation
Indices: 30301862--30302032 Score: 202
Period size: 88 Copynumber: 2.0 Consensus size: 87
30301852 TTTTGTGAGA
* * * * * *
30301862 TTTCAGTTTTGCAAGAATTTGATTCTCAAAATTTTAGTTTCGCAAGAATTTATATTTTAAAATTT
1 TTTCAGATTCGCAAGAATTTGATTCTCAAAATTTAAGATTCGCAAGAATTTAGATTATAAAATTT
*
30301927 TCATTTTCACAAGAATTTAATT
66 TCAGTTTCACAAGAATTTAATT
* **
30301949 TTTCAGATTCGCAAGAATTTGATTCAT-AAGGATTTAAGATTCGCAAGTTTTTAGATTCATAAAA
1 TTTCAGATTCGCAAGAATTTGATTC-TCAA-AATTTAAGATTCGCAAGAATTTAGATT-ATAAAA
*
30302013 TTTT-AGTTTCATAAGAATTT
63 TTTTCAGTTTCACAAGAATTT
30302033 GATTCTCAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
87 25 0.36
88 36 0.51
89 9 0.13
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (87 bp):
TTTCAGATTCGCAAGAATTTGATTCTCAAAATTTAAGATTCGCAAGAATTTAGATTATAAAATTT
TCAGTTTCACAAGAATTTAATT
Found at i:30302491 original size:23 final size:23
Alignment explanation
Indices: 30302429--30302491 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
30302419 TCAAAGTTCA
* *
30302429 AAAATTCTCA-TTCAAAAACTTT
1 AAAATTCTCATTTAAAAAACTTC
* * **
30302451 AGAGATTCACATAAAAAAAACTTC
1 A-AAATTCTCATTTAAAAAACTTC
30302475 AAAATTCTCATTTAAAA
1 AAAATTCTCATTTAAAA
30302492 CTCAAAGCTT
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
22 1 0.03
23 19 0.66
24 9 0.31
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (23 bp):
AAAATTCTCATTTAAAAAACTTC
Found at i:30303447 original size:16 final size:16
Alignment explanation
Indices: 30303426--30303460 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30303416 TCACTTGCAC
30303426 TTTTTAATTTTTACAT
1 TTTTTAATTTTTACAT
* *
30303442 TTTTTATTTTTTATAT
1 TTTTTAATTTTTACAT
30303458 TTT
1 TTT
30303461 ATAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTAATTTTTACAT
Found at i:30303866 original size:14 final size:15
Alignment explanation
Indices: 30303847--30303875 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30303837 AAGGGTTTTT
30303847 ATTTTTTT-TTTTAC
1 ATTTTTTTCTTTTAC
30303861 ATTTTTTTCTTTTAC
1 ATTTTTTTCTTTTAC
30303876 TCTCTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTTCTTTTAC
Found at i:30308671 original size:11 final size:11
Alignment explanation
Indices: 30308655--30308696 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
30308645 AATCTCATAA
30308655 GAGATTTGTTT
1 GAGATTTGTTT
*
30308666 GAGATTTGTTA
1 GAGATTTGTTT
*
30308677 GAGATTTATTT
1 GAGATTTGTTT
30308688 GAGATTTGT
1 GAGATTTGT
30308697 CAGATATTGC
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:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:30308682 original size:22 final size:22
Alignment explanation
Indices: 30308654--30308696 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30308644 AAATCTCATA
*
30308654 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTATTTGAGATTTGTT
30308676 AGAGATTTATTTGAGATTTGT
1 AGAGATTTATTTGAGATTTGT
30308697 CAGATATTGC
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:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTGAGATTTGTT
Found at i:30308809 original size:52 final size:52
Alignment explanation
Indices: 30308721--30308877 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
30308711 TGGATAAGAA
* * *
30308721 GACTTGCAAAAGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTT
*
30308773 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
** * * * *
30308825 GACTTATACGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
30308877 G
1 G
30308878 TATGGTTATA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 87 0.94
53 6 0.06
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:30309812 original size:4 final size:4
Alignment explanation
Indices: 30309803--30309836 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
30309793 AAAATATTTA
30309803 AAAT AAAT AAAT AAAAT AAAT AAAT -AAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AA
30309837 GACAAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:30309817 original size:13 final size:13
Alignment explanation
Indices: 30309801--30309875 Score: 61
Period size: 13 Copynumber: 6.0 Consensus size: 13
30309791 ACAAAATATT
30309801 TAAAATAAATAAA
1 TAAAATAAATAAA
30309814 TAAAATAAATAAA
1 TAAAATAAATAAA
30309827 T--AATAAATAAGA
1 TAAAATAAATAA-A
* *
30309839 -CAAATACA-AAA
1 TAAAATAAATAAA
*
30309850 TAAAACAAA-AAA
1 TAAAATAAATAAA
*
30309862 CTAAAATGAATAAA
1 -TAAAATAAATAAA
30309876 AACCTTACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 10 0.20
12 11 0.22
13 26 0.52
14 3 0.06
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:30309843 original size:20 final size:20
Alignment explanation
Indices: 30309803--30309853 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
30309793 AAAATATTTA
*
30309803 AAATAAATAAATAAAATAAAT
1 AAAT-AATAAATAAAACAAAT
*
30309824 AAATAATAAATAAGACAAAT
1 AAATAATAAATAAAACAAAT
30309844 ACAA-AATAAA
1 A-AATAATAAA
30309854 ACAAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (20 bp):
AAATAATAAATAAAACAAAT
Found at i:30310622 original size:24 final size:24
Alignment explanation
Indices: 30310569--30310615 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30310559 GATCATTCAA
*
30310569 ATATAATATTAATCATGCAATAAC
1 ATATAATATAAATCATGCAATAAC
*
30310593 ATATAATATAATATCATTCAATA
1 ATATAATATAA-ATCATGCAATA
30310616 TATATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATAATATAAATCATGCAATAAC
Found at i:30310757 original size:21 final size:21
Alignment explanation
Indices: 30310728--30310844 Score: 134
Period size: 21 Copynumber: 5.7 Consensus size: 21
30310718 TTAAATATAT
30310728 AATCATGCAATTAACAATGTA
1 AATCATGCAATTAACAATGTA
* *
30310749 AAACATGCAATTAA-ATATCT-
1 AATCATGCAATTAACA-ATGTA
30310769 AATCATGCAATTAACAATGTA
1 AATCATGCAATTAACAATGTA
* * *
30310790 AAACATGTAATT-A-AATATA
1 AATCATGCAATTAACAATGTA
*
30310809 TAATCATGCAAATAACAATGTA
1 -AATCATGCAATTAACAATGTA
30310831 AATCATGCAATTAA
1 AATCATGCAATTAA
30310845 ATATATAACT
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.06
20 27 0.35
21 41 0.53
22 5 0.06
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (21 bp):
AATCATGCAATTAACAATGTA
Found at i:30310761 original size:41 final size:41
Alignment explanation
Indices: 30310711--30311023 Score: 317
Period size: 41 Copynumber: 7.8 Consensus size: 41
30310701 AATTAATAAT
*
30310711 CATGTAATTAAATATATAATCATGCAATTAACAATGTAAAA
1 CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
*
30310752 CATGCAATTAAATATCTAATCATGCAATTAACAATGTAAAA
1 CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
* * *
30310793 CATGTAATTAAATATATAATCATGCAAATAACAATGTAAAT
1 CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
* *
30310834 CATGCAATTAAATATATAA-CTATGCAAATAA-ATATATTAATAA
1 CATGCAATTAAATATATAATC-ATGCAATTAACA-AT-GTAA-AA
* * * * * * *
30310877 TCATACAATCACACAAATAA--AT-AAATT---AA--T-AAT
1 -CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
* *
30310910 CATGTAATTAAATATATAATCATGCAATTAACAAAGTAAAA
1 CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
* *
30310951 GATGCAATTAAATATCTAATCATGCAATTAACAATGTAAAA
1 CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
30310992 CATGCAATTGACAATATA-AATCATGCAATTAA
1 CATGCAATT-A-AATATATAATCATGCAATTAA
30311024 ATATATTAAT
Statistics
Matches: 225, Mismatches: 31, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
32 13 0.06
33 1 0.00
34 3 0.01
35 5 0.02
38 3 0.01
39 1 0.00
40 3 0.01
41 156 0.69
42 20 0.09
43 6 0.03
44 14 0.06
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (41 bp):
CATGCAATTAAATATATAATCATGCAATTAACAATGTAAAA
Done.