Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold183
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: 471943
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:187552 original size:15 final size:15
Alignment explanation
Indices: 187514--187570 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
187504 GTTATATACT
187514 TTTAATTTTTTAAAA
1 TTTAATTTTTTAAAA
* *
187529 -ATATGTTTTTTAAAA
1 TTTA-ATTTTTTAAAA
187544 TTTAA-TTTTTAATAA
1 TTTAATTTTTTAA-AA
187559 TTTAATATTTTT
1 TTTAAT-TTTTT
187571 CTTTATTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.27
15 17 0.52
16 2 0.06
17 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTAATTTTTTAAAA
Found at i:187764 original size:30 final size:28
Alignment explanation
Indices: 187695--187771 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
187685 TCCTTAAATT
*
187695 TTTATAAAAATACACTTACCTTCCTAATG
1 TTTA-AAAAATACACTTACCTTCCTAAGG
*
187724 TTTAAAAAATACACTTACCTT-CTACGG
1 TTTAAAAAATACACTTACCTTCCTAAGG
187751 TTTAGCCAAAAATACACTTAC
1 TTTA---AAAAATACACTTAC
187772 TCCTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 8 0.19
28 17 0.40
29 4 0.09
30 14 0.33
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (28 bp):
TTTAAAAAATACACTTACCTTCCTAAGG
Found at i:189094 original size:28 final size:29
Alignment explanation
Indices: 189063--189128 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
189053 AATAAATTAG
189063 TAATATAAATATTAAAAAAATTTAAA-AA
1 TAATATAAATATTAAAAAAATTTAAATAA
* *
189091 TAATTTATAA-ATTAAATAAATTTAAATAA
1 TAATATA-AATATTAAAAAAATTTAAATAA
189120 -AATA-AAATA
1 TAATATAAATA
189129 AAAGAGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 24 0.75
29 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TAATATAAATATTAAAAAAATTTAAATAA
Found at i:189122 original size:15 final size:16
Alignment explanation
Indices: 189087--189125 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
189077 AAAAAATTTA
*
189087 AAAATAATTTATAAAT
1 AAAATAAATTATAAAT
*
189103 TAAATAAATT-TAAAT
1 AAAATAAATTATAAAT
189118 AAAATAAA
1 AAAATAAA
189126 ATAAAAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAAATTATAAAT
Found at i:189470 original size:31 final size:31
Alignment explanation
Indices: 189429--189525 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
189419 AAATAGATAT
* *
189429 AATTATTTATAAATTTAATTAATATTAAAAA
1 AATTACTTATAAATTTAATAAATATTAAAAA
* *
189460 AATTACTTATAAATTTAATAAATATTATATAT
1 AATTACTTATAAATTTAATAAATATTA-AAAA
* *
189492 AATTACTCATAAATTTAA-CAATCA-TAAAAA
1 AATTACTTATAAATTTAATAAAT-ATTAAAAA
189522 AATT
1 AATT
189526 TTAGTTTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 6 0.11
31 30 0.54
32 20 0.36
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (31 bp):
AATTACTTATAAATTTAATAAATATTAAAAA
Found at i:189684 original size:11 final size:12
Alignment explanation
Indices: 189658--189686 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
189648 TTTTAAAGTG
189658 ATAAAAATTTTA
1 ATAAAAATTTTA
189670 ATAAAAATTTT-
1 ATAAAAATTTTA
189681 ATAAAA
1 ATAAAA
189687 TTAATATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAAAATTTTA
Found at i:191159 original size:34 final size:34
Alignment explanation
Indices: 191111--191184 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
191101 ACAAGGAATG
* *
191111 ATAATTTCATGAGCCTGCCTATGTGCTGAGTTTA
1 ATAATTTCAAGAGCCTGCCTATGTACTGAGTTTA
*
191145 ATAATTTCAAGAGCCTGCCTATGTACTGATTTTA
1 ATAATTTCAAGAGCCTGCCTATGTACTGAGTTTA
*
191179 GTAATT
1 ATAATT
191185 CGCTAGCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (34 bp):
ATAATTTCAAGAGCCTGCCTATGTACTGAGTTTA
Found at i:193737 original size:15 final size:15
Alignment explanation
Indices: 193719--193766 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
193709 AACAAAAGTC
*
193719 AACAGTTTAAAATTA
1 AACAATTTAAAATTA
193734 AACAATTTAAAATTAA
1 AACAATTTAAAATT-A
* *
193750 AATAATTTAAATTTA
1 AACAATTTAAAATTA
193765 AA
1 AA
193767 TTATGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (15 bp):
AACAATTTAAAATTA
Found at i:193758 original size:16 final size:16
Alignment explanation
Indices: 193719--193766 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
193709 AACAAAAGTC
*
193719 AACAGTTTAAAATT-A
1 AACAATTTAAAATTAA
193734 AACAATTTAAAATTAA
1 AACAATTTAAAATTAA
* *
193750 AATAATTTAAATTTAA
1 AACAATTTAAAATTAA
193766 A
1 A
193767 TTATGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
AACAATTTAAAATTAA
Found at i:194294 original size:33 final size:33
Alignment explanation
Indices: 194257--194361 Score: 103
Period size: 33 Copynumber: 3.2 Consensus size: 33
194247 GATCATATCT
*
194257 ATTTAAATAAAACGAATATTCAGATATGCAAGA
1 ATTTAAATAAAACGAATATTCAAATATGCAAGA
* **
194290 ATTT-AA-AAATC-AAGTATT-AAATGAT-CATATCT
1 ATTTAAATAAAACGAA-TATTCAAAT-ATGCA-A-GA
194322 ATTTAAATAAAACGAATATTCAAATATGCAAGA
1 ATTTAAATAAAACGAATATTCAAATATGCAAGA
194355 ATTTAAA
1 ATTTAAA
194362 AATCAAGTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
30 7 0.12
31 11 0.20
32 6 0.11
33 13 0.23
34 11 0.20
35 8 0.14
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (33 bp):
ATTTAAATAAAACGAATATTCAAATATGCAAGA
Found at i:194315 original size:65 final size:65
Alignment explanation
Indices: 194239--194369 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
194229 CATAAAAGTT
*
194239 TATTAAATGATCATATCTATTTAAATAAAACGAATATTCAGATATGCAAGAATTTAAAAATCAAG
1 TATTAAATGATCATATCTATTTAAATAAAACGAATATTCAAATATGCAAGAATTTAAAAATCAAG
194304 TATTAAATGATCATATCTATTTAAATAAAACGAATATTCAAATATGCAAGAATTTAAAAATCAAG
1 TATTAAATGATCATATCTATTTAAATAAAACGAATATTCAAATATGCAAGAATTTAAAAATCAAG
194369 T
1 T
194370 CAGATTGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (65 bp):
TATTAAATGATCATATCTATTTAAATAAAACGAATATTCAAATATGCAAGAATTTAAAAATCAAG
Found at i:194406 original size:23 final size:22
Alignment explanation
Indices: 194379--194451 Score: 58
Period size: 25 Copynumber: 3.1 Consensus size: 22
194369 TCAGATTGAT
194379 ATTTATTTTTATTAAAAATTATA
1 ATTTATTTTTATTAAAAATT-TA
* *
194402 ATTTATATATTTTTTAAAATATTTT
1 ATTTAT-T-TTTATTAAAA-ATTTA
* *
194427 ATATA-TTTTAATAAAAATTTTA
1 ATTTATTTTTATTAAAAA-TTTA
194449 ATT
1 ATT
194452 AAATCTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.03
22 13 0.33
23 7 0.18
24 1 0.03
25 14 0.36
26 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATTTTTATTAAAAATTTA
Found at i:194427 original size:21 final size:21
Alignment explanation
Indices: 194403--194448 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
194393 AAAATTATAA
*
194403 TTTATATATTTT-TTAAAATAT
1 TTTATATATTTTAATAAAA-AT
194424 TTTATATATTTTAATAAAAAT
1 TTTATATATTTTAATAAAAAT
194445 TTTA
1 TTTA
194449 ATTAAATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATATATTTTAATAAAAAT
Found at i:194476 original size:28 final size:27
Alignment explanation
Indices: 194437--194490 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
194427 ATATATTTTA
*
194437 ATAAAAATTTTAATTAAATCTAATTTG
1 ATAAAAAATTTAATTAAATCTAATTTG
* *
194464 ATAAAATAATTTATTTAAATTTAATTT
1 ATAAAA-AATTTAATTAAATCTAATTT
194491 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATAAAAAATTTAATTAAATCTAATTTG
Found at i:194706 original size:17 final size:17
Alignment explanation
Indices: 194663--194708 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
194653 TTTGAAATGT
* *
194663 AAATAATTCAAACAAAA
1 AAATAACTCGAACAAAA
194680 AAATAACTCGAACAAAA
1 AAATAACTCGAACAAAA
194697 AAATAACTCGAA
1 AAATAACTCGAA
194709 ATTTTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (17 bp):
AAATAACTCGAACAAAA
Found at i:199941 original size:11 final size:12
Alignment explanation
Indices: 199916--199949 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
199906 ATAATATTAA
*
199916 AAAATTTTAATT
1 AAAATTTAAATT
*
199928 TAAATTTAAATT
1 AAAATTTAAATT
199940 AAAATTTAAA
1 AAAATTTAAA
199950 AATAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:199951 original size:32 final size:31
Alignment explanation
Indices: 199915--199986 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
199905 TATAATATTA
* * *
199915 AAAAATTTTAATTTAAATTTAAATTAAAATTT
1 AAAAATTATAA-TTAAATTTAAAATAAAATAT
* *
199947 AAAAATAAATAATTAAGTTTAAAATAAAATAT
1 AAAAAT-TATAATTAAATTTAAAATAAAATAT
199979 AAAAATTA
1 AAAAATTA
199987 ACTTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.03
32 29 0.88
33 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAAATTATAATTAAATTTAAAATAAAATAT
Found at i:199962 original size:21 final size:19
Alignment explanation
Indices: 199936--199974 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
199926 TTTAAATTTA
199936 AATTAAAATTTAAAAATAAAT
1 AATT-AAATTT-AAAATAAAT
*
199957 AATTAAGTTTAAAATAAA
1 AATTAAATTTAAAATAAA
199975 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATTAAATTTAAAATAAAT
Found at i:202682 original size:13 final size:13
Alignment explanation
Indices: 202650--202687 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
202640 TTTTTTAATT
202650 AATTAAAATTTTC
1 AATTAAAATTTTC
202663 -ATATAAAATTTTC
1 AAT-TAAAATTTTC
*
202676 AATTAAACTTTT
1 AATTAAAATTTT
202688 ATAAATAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTAAAATTTTC
Found at i:202728 original size:27 final size:27
Alignment explanation
Indices: 202650--202853 Score: 130
Period size: 27 Copynumber: 7.4 Consensus size: 27
202640 TTTTTTAATT
* *
202650 AATTAAAATTTT-CATATAAAATTTTC
1 AATTAAACTTTTACATAAAAAATTTTC
*
202676 AATTAAACTTTT--ATAAATAAGGTTTTC
1 AATTAAACTTTTACATAAA-AA-ATTTTC
*
202703 AATTAAACTTTTACATAAAAAATTTTT
1 AATTAAACTTTTACATAAAAAATTTTC
* * * *
202730 AAATAAACTCTTCACATATAAAATTTTT
1 AATTAAACT-TTTACATAAAAAATTTTC
* * ** *
202758 AACTAGAATTTTTACAAGTAAAACTTTTTT
1 AATTA-AACTTTTAC-A-TAAAAAATTTTC
* * *
202788 AATTAAATTTTTACTCATGAAAAA--TTA
1 AATTAAACTTTTA--CATAAAAAATTTTC
* **
202815 AATTGAACTTTTACATATGAAATTTTC
1 AATTAAACTTTTACATAAAAAATTTTC
202842 AATTAAACTTTT
1 AATTAAACTTTT
202854 TTACATATAA
Statistics
Matches: 140, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
25 10 0.07
26 13 0.09
27 55 0.39
28 26 0.19
29 21 0.15
30 14 0.10
31 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (27 bp):
AATTAAACTTTTACATAAAAAATTTTC
Found at i:202747 original size:28 final size:27
Alignment explanation
Indices: 202706--202759 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
202696 GGTTTTCAAT
*
202706 TAAACTTTTACATAAAAAATTTTTAAA
1 TAAACTTTCACATAAAAAATTTTTAAA
*
202733 TAAACTCTTCACATATAAAATTTTTAA
1 TAAACT-TTCACATAAAAAATTTTTAA
202760 CTAGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAACTTTCACATAAAAAATTTTTAAA
Found at i:204202 original size:17 final size:16
Alignment explanation
Indices: 204182--204221 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
204172 TTGTTTTCTC
204182 TCTTTTTCCTT-TTCCTT
1 TCTTTTTCCTTCTT--TT
204199 TCTTTTTCCTTCTTTT
1 TCTTTTTCCTTCTTTT
204215 TCTTTTT
1 TCTTTTT
204222 TTTTTCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 11 0.50
18 2 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTTTTCCTTCTTTT
Found at i:204205 original size:11 final size:11
Alignment explanation
Indices: 204186--204227 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
204176 TTTCTCTCTT
*
204186 TTTCCTTTTCC
1 TTTCTTTTTCC
204197 TTTCTTTTTCC
1 TTTCTTTTTCC
*
204208 -TTCTTTTTCT
1 TTTCTTTTTCC
*
204218 TTTTTTTTTC
1 TTTCTTTTTC
204228 AAGCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTCC
Found at i:204222 original size:17 final size:16
Alignment explanation
Indices: 204175--204221 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
204165 TCTTATTTTG
*
204175 TTTTCTCTCTTTTTCC
1 TTTTCTTTCTTTTTCC
204191 TTTTCCTTTCTTTTTCC
1 TTTT-CTTTCTTTTTCC
204208 TTCTT-TTTCTTTTT
1 TT-TTCTTTCTTTTT
204222 TTTTTCAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 13 0.46
17 13 0.46
18 2 0.07
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTTTCTTTTTCC
Found at i:204795 original size:35 final size:36
Alignment explanation
Indices: 204738--204809 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
204728 AGAAATGAAA
*
204738 AATAGAAAAAAAATAATTACAAGCTCTATGTATTTT
1 AATAGAAAAAAAATAATGACAAGCTCTATGTATTTT
204774 AATAG-AAAAAAATAATGACAAGCTCTATGTATTTT
1 AATAGAAAAAAAATAATGACAAGCTCTATGTATTTT
204809 A
1 A
204810 GTTCTATAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (36 bp):
AATAGAAAAAAAATAATGACAAGCTCTATGTATTTT
Found at i:205386 original size:15 final size:17
Alignment explanation
Indices: 205355--205416 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
205345 AATATATGAT
205355 ATATATAATATTAATTA
1 ATATATAATATTAATTA
205372 ATATATAA-ATT-ATTA
1 ATATATAATATTAATTA
* *
205387 ATATAATGAATAATAATTT
1 ATAT-AT-AATATTAATTA
205406 ATATTATAATA
1 ATA-TATAATA
205417 ATATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 10 0.26
18 6 0.16
19 8 0.21
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATAATATTAATTA
Found at i:206695 original size:12 final size:12
Alignment explanation
Indices: 206678--206702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
206668 ATATTTACAA
206678 TTATTTTAATAT
1 TTATTTTAATAT
206690 TTATTTTAATAT
1 TTATTTTAATAT
206702 T
1 T
206703 ATTACTTTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTTAATAT
Found at i:209348 original size:19 final size:20
Alignment explanation
Indices: 209324--209361 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
209314 ATTTCAATGT
209324 ATACAT-AAAAAATGTATCG
1 ATACATAAAAAAATGTATCG
209343 ATACATAAAAAAATGTATC
1 ATACATAAAAAAATGTATC
209362 AATATGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (20 bp):
ATACATAAAAAAATGTATCG
Found at i:209348 original size:33 final size:29
Alignment explanation
Indices: 209267--209348 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 29
209257 CGATGCATTG
209267 AAAAATGTATCGATACATTTAGATAAAAA
1 AAAAATGTATCGATACATTTAGATAAAAA
* * *
209296 AATAGAATGCATCGATACATTTCAATGTATACATA
1 AA-A-AATGTATCGATACATTT--A-G-ATAAAAA
209331 AAAAATGTATCGATACAT
1 AAAAATGTATCGATACAT
209349 AAAAAAATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 2 0.05
30 1 0.02
31 16 0.37
33 15 0.35
34 2 0.05
35 7 0.16
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (29 bp):
AAAAATGTATCGATACATTTAGATAAAAA
Found at i:210044 original size:12 final size:12
Alignment explanation
Indices: 210027--210051 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
210017 GTGTTTGCAA
210027 TTATTTTAATAT
1 TTATTTTAATAT
210039 TTATTTTAATAT
1 TTATTTTAATAT
210051 T
1 T
210052 ATTACTTTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTTAATAT
Found at i:210108 original size:31 final size:32
Alignment explanation
Indices: 210073--210132 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
210063 AAATTAGATT
210073 TTTCATAAAATAACC-AAACAAAAAAAAAAAC
1 TTTCATAAAATAACCTAAACAAAAAAAAAAAC
* * * *
210104 TTTCATTAAGTCACCTAAACATAAAAAAA
1 TTTCATAAAATAACCTAAACAAAAAAAAA
210133 TATTAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.50
32 12 0.50
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.22
Consensus pattern (32 bp):
TTTCATAAAATAACCTAAACAAAAAAAAAAAC
Found at i:216325 original size:50 final size:50
Alignment explanation
Indices: 216262--216434 Score: 154
Period size: 50 Copynumber: 3.4 Consensus size: 50
216252 ATTTGGTAAG
* * *
216262 GGTGACTTAGTGTCACTTAATAGTTATGCTATGGTAGCGAATAGAGTTTA
1 GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGAATAGAGTTTA
* ** *
216312 GGTGACTTGGTGTCAAATAATGACG--ATGCTATGGTGGC-AATCAAGATTTGGTAA
1 GGTGACTTGGAGTCACTTAAT-A-GTTATGCTATGGTGGCGAAT--AGAGTT--T-A
* * * *
216366 GGGTGACTTGGAGTCACTTAATAGTTATGCCATTGTGGCGATTAAAGTTTA
1 -GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGAATAGAGTTTA
216417 GGTGACTTGGAGTCACTT
1 GGTGACTTGGAGTCACTT
216435 GGAGTCACTG
Statistics
Matches: 99, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
49 3 0.03
50 48 0.48
51 7 0.07
52 2 0.02
53 2 0.02
54 6 0.06
55 29 0.29
56 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (50 bp):
GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGAATAGAGTTTA
Found at i:216344 original size:105 final size:105
Alignment explanation
Indices: 216224--216431 Score: 319
Period size: 105 Copynumber: 2.0 Consensus size: 105
216214 TTAGCATCAC
* *
216224 TAATGATGATGCTATGGTGGCAATCATA-ATTTGGTAAGGGTGACTTAGTGTCACTTAATAGTTA
1 TAATGACGATGCTATGGTGGCAATCA-AGATTTGGTAAGGGTGACTTAGAGTCACTTAATAGTTA
* * *
216288 TGCTATGGTAGCGAATAGAGTTTAGGTGACTTGGTGTCAAA
65 TGCCATGGTAGCGAATAAAGTTTAGGTGACTTGGAGTCAAA
*
216329 TAATGACGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCACTTAATAGTTAT
1 TAATGACGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTAGAGTCACTTAATAGTTAT
* * *
216394 GCCATTGTGGCGATTAAAGTTTAGGTGACTTGGAGTCA
66 GCCATGGTAGCGAATAAAGTTTAGGTGACTTGGAGTCA
216432 CTTGGAGTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 92 0.99
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (105 bp):
TAATGACGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTAGAGTCACTTAATAGTTAT
GCCATGGTAGCGAATAAAGTTTAGGTGACTTGGAGTCAAA
Found at i:216376 original size:55 final size:54
Alignment explanation
Indices: 216224--216381 Score: 152
Period size: 50 Copynumber: 3.0 Consensus size: 54
216214 TTAGCATCAC
* **
216224 TAATGATGATGCTATGGTGGCAATCATA-ATTTGGTAAGGGTGACTTAGTGTCACT
1 TAATGA-GATGCTATGGTGGCAATCA-AGATTTGGTAAGGGTGACTTGGTGTCAAA
* *
216279 TAAT-AGTTATGCTATGGTAGCGAAT--AGAGTT--T-A-GGTGACTTGGTGTCAAA
1 TAATGAG--ATGCTATGGTGGC-AATCAAGATTTGGTAAGGGTGACTTGGTGTCAAA
*
216329 TAATGACGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCA
1 TAATGA-GATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGTGTCA
216382 CTTAATAGTT
Statistics
Matches: 83, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
49 3 0.04
50 30 0.36
51 7 0.08
52 2 0.02
53 3 0.04
54 5 0.06
55 30 0.36
56 3 0.04
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.32
Consensus pattern (54 bp):
TAATGAGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGTGTCAAA
Found at i:224243 original size:13 final size:13
Alignment explanation
Indices: 224225--224250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
224215 TACAGCAAGT
224225 ATGTATCGATACA
1 ATGTATCGATACA
224238 ATGTATCGATACA
1 ATGTATCGATACA
224251 CAAAAAATTG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:226500 original size:21 final size:21
Alignment explanation
Indices: 226467--226511 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
226457 TTACAAGTTG
*
226467 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
226489 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
226509 AAA
1 AAA
226512 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:228333 original size:15 final size:15
Alignment explanation
Indices: 228313--228343 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
228303 TAAAAATGTC
*
228313 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
228328 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
228343 C
1 C
228344 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:230440 original size:13 final size:13
Alignment explanation
Indices: 230422--230473 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
230412 CATTTTTTCT
230422 TTGTATCGATACA
1 TTGTATCGATACA
230435 TTGTATCGATACA
1 TTGTATCGATACA
230448 TTGTATCGATACA
1 TTGTATCGATACA
230461 TTGTATCGATACA
1 TTGTATCGATACA
230474 GGGTGATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:233047 original size:13 final size:13
Alignment explanation
Indices: 233029--233054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
233019 TACAGCAAGT
233029 ATGTATCGATACA
1 ATGTATCGATACA
233042 ATGTATCGATACA
1 ATGTATCGATACA
233055 CAAAAAATTG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:241094 original size:1 final size:1
Alignment explanation
Indices: 241088--241160 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
241078 TCTTTCGTAC
* ** * * *** *
241088 AAAAAAAACAAAAAAAAAACCAAGAAAAAAAAACAAAAAAAACCCAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
241153 CAAAAAAA
1 AAAAAAAA
241161 GGGTATCATC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:241115 original size:23 final size:21
Alignment explanation
Indices: 241087--241160 Score: 96
Period size: 23 Copynumber: 3.4 Consensus size: 21
241077 ATCTTTCGTA
*
241087 CAAAAAAAACAAAAAAAAAAC
1 CAAAAAAAAAAAAAAAAAAAC
241108 CAAGAAAAAAAAACAAAAAAAACC
1 CAA-AAAAAAAAA-AAAAAAAA-C
241132 CAAAAAAAAAAAACAAAAAAA-
1 CAAAAAAAAAAAA-AAAAAAAC
241153 CAAAAAAA
1 CAAAAAAA
241161 GGGTATCATC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 11 0.23
22 9 0.19
23 24 0.50
24 4 0.08
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAAAAAAC
Found at i:241121 original size:25 final size:25
Alignment explanation
Indices: 241088--241152 Score: 105
Period size: 24 Copynumber: 2.6 Consensus size: 25
241078 TCTTTCGTAC
*
241088 AAAAAAAACAAAAAAAAAACCAAGA
1 AAAAAAAACAAAAAAAAAACCAAAA
*
241113 AAAAAAAAC-AAAAAAAACCCAAAA
1 AAAAAAAACAAAAAAAAAACCAAAA
241137 AAAAAAAACAAAAAAA
1 AAAAAAAACAAAAAAA
241153 CAAAAAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 22 0.59
25 15 0.41
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAAACAAAAAAAAAACCAAAA
Found at i:241160 original size:24 final size:23
Alignment explanation
Indices: 241088--241160 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
241078 TCTTTCGTAC
*
241088 AAAAAAAACAAAAAAAAAACCAAGA
1 AAAAAAAACAAAAAAAAAA--AAAA
**
241113 AAAAAAAACAAAAAAAACCCAAAA
1 AAAAAAAACAAAAAAAA-AAAAAA
*
241137 AAAAAAAACAAAAAAACAAAAAA
1 AAAAAAAACAAAAAAAAAAAAAA
241160 A
1 A
241161 GGGTATCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 5 0.12
24 19 0.46
25 17 0.41
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAAAAAAAA
Found at i:242375 original size:14 final size:14
Alignment explanation
Indices: 242355--242392 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
242345 CAATTTGCCA
242355 TTTGTCAAGAAA-T
1 TTTGTCAAGAAACT
242368 TATTGTCAA-AAACT
1 T-TTGTCAAGAAACT
242382 TTTGTCAAGAA
1 TTTGTCAAGAA
242393 CGTTCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (14 bp):
TTTGTCAAGAAACT
Found at i:242434 original size:28 final size:28
Alignment explanation
Indices: 242403--242913 Score: 475
Period size: 28 Copynumber: 18.1 Consensus size: 28
242393 CGTTCATCTC
* * *
242403 TTCAAAGCCCACAGGTCAATGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
242431 TTCAAATCTCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
242459 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * *
242487 TTCAAAACCCACAAGTTAGTTGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
242515 TTCAAAGCCCAC-A---AGT--CATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
242537 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
242564 CTTCAAAAGACCACAAGTCAGTGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* * *
242594 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
242622 TTCAAAGCCCACAACTAAGTGGTATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * * * *
242652 TTTAAAGCCCACACAAATTAATGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* * *
242682 TCCAAAGCCTACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
242710 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
242738 TTCAAAGCCCATAAGTCAGTAGTATCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
242766 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
242794 TTCAAAGCCCATAAGTCAGTGGCATACTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CCT
242823 TTCAAAGCCCACAAGTCAGTGGCA-CACT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
242851 TTCAAAGCCCACACAAGTTAGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* *
242883 TTCAAAACCTACACAAGTTAGTGGCA-CCT
1 TTCAAAGCC--CACAAGTCAGTGGCATCCT
242912 TT
1 TT
242914 TTTTTTAAAA
Statistics
Matches: 401, Mismatches: 59, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
22 18 0.04
23 1 0.00
24 3 0.01
26 3 0.01
27 5 0.01
28 240 0.60
29 59 0.15
30 32 0.08
31 6 0.01
32 33 0.08
33 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:242537 original size:22 final size:22
Alignment explanation
Indices: 242509--242554 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
242499 AAGTTAGTTG
242509 CATCCTTTCAAAGCCCACAAGT
1 CATCCTTTCAAAGCCCACAAGT
242531 CATCCTTTCAAAGCCCACAAGT
1 CATCCTTTCAAAGCCCACAAGT
242553 CA
1 CA
242555 GTGGCATCTC
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:0.33, C:0.37, G:0.09, T:0.22
Consensus pattern (22 bp):
CATCCTTTCAAAGCCCACAAGT
Found at i:242737 original size:116 final size:112
Alignment explanation
Indices: 242461--242863 Score: 460
Period size: 116 Copynumber: 3.6 Consensus size: 112
242451 GGCATCTTTT
* * *
242461 CAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAACCCACAAGTTAGTTGCATCCTTTCAAAG-CC
1 CAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
* * * * *
242524 -C-AC-AAGT--CATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTC
65 ACAACTAAGTAGTATCCCTTCAAAGCCCACAAATCAATGGCA-CCCTTC
* * * *
242568 AAAAGACCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCA
1 CAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
* * *
242633 CAACTAAGTGGTATACCCTTTTAAAGCCCACACAAATTAATGGCACCCTTC
66 CAACTAAGTAGTAT-CCC-TTCAAAG-CC-CACAAATCAATGGCACCCTTC
* *
242684 CAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
1 CAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
* * * * *
242749 TAAGTCAGTAGTATCCCTTCAAAGCCCACAAGTCAATGGCACCCTTT
66 CAACTAAGTAGTATCCCTTCAAAGCCCACAAATCAATGGCACCCTTC
* * * *
242796 CAAAGCCCATAAGTCAGTGGCATACTTTTCAAAGCCCACAAGTCAGTGGCACACTTTCAAAGCCC
1 CAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
242861 ACA
65 ACA
242864 CAAGTTAGTG
Statistics
Matches: 250, Mismatches: 34, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
107 51 0.20
108 4 0.02
109 1 0.00
110 2 0.01
111 4 0.02
112 38 0.15
113 44 0.18
114 8 0.03
115 9 0.04
116 77 0.31
117 12 0.05
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (112 bp):
CAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCA
CAACTAAGTAGTATCCCTTCAAAGCCCACAAATCAATGGCACCCTTC
Found at i:253553 original size:55 final size:56
Alignment explanation
Indices: 253423--253554 Score: 135
Period size: 55 Copynumber: 2.4 Consensus size: 56
253413 ATCAGAGAGA
* * * *
253423 TTTGGTGGTC-AGGAGTATAACAATTGTGTGACTAGCCATTCTGGTGGTTAGAGAGG
1 TTTGGTGGTCAAGGA-TATAACAATTGTGCGACTAGCCATTCTGATGGTAAGAGAAG
* * * * *
253479 TTTGATGATTAGAGG-TATAACAATTGTGCG-CTAGTCATTTTGATGGTAAGAGAAG
1 TTTGGTGGTCA-AGGATATAACAATTGTGCGACTAGCCATTCTGATGGTAAGAGAAG
*
253534 TTTGGCGGTCAAGGATATAAC
1 TTTGGTGGTCAAGGATATAAC
253555 GATATATATA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
54 3 0.05
55 33 0.55
56 21 0.35
58 3 0.05
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (56 bp):
TTTGGTGGTCAAGGATATAACAATTGTGCGACTAGCCATTCTGATGGTAAGAGAAG
Found at i:254802 original size:33 final size:32
Alignment explanation
Indices: 254722--254802 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
254712 ATATTTAAAT
* * *
254722 TTTTAAGTTTGAATCATTTTAATTTTGAGTAA
1 TTTTAAATTTGAATCATTTCAATTTCGAGTAA
* * * * *
254754 TTTCAAATTTAAATCATTTCGATTTCCGATTTA
1 TTTTAAATTTGAATCATTTCAATTT-CGAGTAA
254787 TTTTAAATTTGAATCA
1 TTTTAAATTTGAATCA
254803 ATTTTTATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 20 0.53
33 18 0.47
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (32 bp):
TTTTAAATTTGAATCATTTCAATTTCGAGTAA
Found at i:255965 original size:19 final size:19
Alignment explanation
Indices: 255929--255967 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
255919 ATATTAATTT
*
255929 AATTTTAAATGTTAATAAA
1 AATTTTAAATATTAATAAA
* *
255948 AATTTTAATTATTTATAAA
1 AATTTTAAATATTAATAAA
255967 A
1 A
255968 CATATAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTTTAAATATTAATAAA
Found at i:259833 original size:15 final size:15
Alignment explanation
Indices: 259815--259845 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
259805 TACGTTGCTA
259815 TTCACAAAATCAAAT
1 TTCACAAAATCAAAT
259830 TTCACAAAATCAAAT
1 TTCACAAAATCAAAT
259845 T
1 T
259846 AAGTAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
TTCACAAAATCAAAT
Found at i:260211 original size:16 final size:16
Alignment explanation
Indices: 260190--260223 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
260180 AATATAAAAA
260190 TACTAAATTTAAATAT
1 TACTAAATTTAAATAT
260206 TACTAAATTTAAATAT
1 TACTAAATTTAAATAT
260222 TA
1 TA
260224 TATGCTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TACTAAATTTAAATAT
Found at i:260903 original size:13 final size:13
Alignment explanation
Indices: 260885--260912 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
260875 TTTATAATTG
260885 CTTTTAAGGTAGT
1 CTTTTAAGGTAGT
260898 CTTTTAAGGTAGT
1 CTTTTAAGGTAGT
260911 CT
1 CT
260913 AAAACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (13 bp):
CTTTTAAGGTAGT
Found at i:262561 original size:16 final size:16
Alignment explanation
Indices: 262511--262554 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
262501 AAGGTTTTAG
*
262511 GTTTTCGATTTTTGCTT
1 GTTTT-GATATTTGCTT
262528 GTTTTGATATTTGCTT
1 GTTTTGATATTTGCTT
262544 GTTTTGATATT
1 GTTTTGATATT
262555 ATTTTGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.11, C:0.07, G:0.18, T:0.64
Consensus pattern (16 bp):
GTTTTGATATTTGCTT
Found at i:265187 original size:34 final size:34
Alignment explanation
Indices: 265142--265215 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
265132 CATGAGACTC
*
265142 TTTTGTAAATATTATTTTATGAAAGAAAGTTGTT
1 TTTTCTAAATATTATTTTATGAAAGAAAGTTGTT
265176 TTTTCTAAATATTATTTTATGAAAGAAAGTTGTT
1 TTTTCTAAATATTATTTTATGAAAGAAAGTTGTT
265210 TTTTCT
1 TTTTCT
265216 TTCACTATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (34 bp):
TTTTCTAAATATTATTTTATGAAAGAAAGTTGTT
Found at i:265516 original size:54 final size:54
Alignment explanation
Indices: 265415--265555 Score: 135
Period size: 54 Copynumber: 2.6 Consensus size: 54
265405 TTAATATGTC
* * * *
265415 TGACTTAGTATCATTAATGGTGATG-TAGTGGTGGCAAGTAGATTTTGGTAAGCA
1 TGACTTAGTGTCACTAATGATGATGCTA-TGGTGGCAAGTAGAATTTGGTAAGCA
* * **
265469 TGACTTAGCGTCACTAATGATGATGCTATGGTGGCAA-TCATAATTTGGTAAGGG
1 TGACTTAGTGTCACTAATGATGATGCTATGGTGGCAAGT-AGAATTTGGTAAGCA
* *
265523 TGACTTGGTGTCACGTAAT-AGTTATGCTATGGT
1 TGACTTAGTGTCAC-TAATGA-TGATGCTATGGT
265556 AACGATTAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.01
54 54 0.75
55 17 0.24
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (54 bp):
TGACTTAGTGTCACTAATGATGATGCTATGGTGGCAAGTAGAATTTGGTAAGCA
Found at i:265609 original size:105 final size:105
Alignment explanation
Indices: 265483--265690 Score: 310
Period size: 105 Copynumber: 2.0 Consensus size: 105
265473 TTAGCGTCAC
*
265483 TAATGATGATGCTATGGTGGCAATCATA-ATTTGGTAAGGGTGACTTGGTGTCACGTAATAGTTA
1 TAATGATGATGCTATGGTGGCAATCA-AGATTTGGTAAGGGTGACTTGGAGTCACGTAATAGTTA
* * * * *
265547 TGCTATGGTAACGATTAGAGTTTAGGTGACTTGGTGTCAAA
65 TGCCATGATAACGATTAAAATTTAGGTGACTTGGAGTCAAA
*
265588 TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCACTTAATAGTTAT
1 TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCACGTAATAGTTAT
* **
265653 GCCATTATGGCGATTAAAATTTAGGTGACTTGGAGTCA
66 GCCATGATAACGATTAAAATTTAGGTGACTTGGAGTCA
265691 CTGATAATGA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 1 0.01
105 91 0.99
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (105 bp):
TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCACGTAATAGTTAT
GCCATGATAACGATTAAAATTTAGGTGACTTGGAGTCAAA
Found at i:265635 original size:55 final size:55
Alignment explanation
Indices: 265483--265640 Score: 168
Period size: 50 Copynumber: 3.0 Consensus size: 55
265473 TTAGCGTCAC
**
265483 TAATGATGATGCTATGGTGGCAATCATA-ATTTGGTAAGGGTGACTTGGTGTCACG
1 TAATGATGATGCTATGGTGGCAATCA-AGATTTGGTAAGGGTGACTTGGTGTCAAA
* ** * * *
265538 TAAT-AGTTATGCTATGGTAACGAT-TAGAGTT--T-A-GGTGACTTGGTGTCAAA
1 TAATGA-TGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGTGTCAAA
*
265588 TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGAGTCA
1 TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGTGTCA
265641 CTTAATAGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
50 33 0.41
51 7 0.09
52 1 0.01
53 2 0.03
54 5 0.06
55 32 0.40
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (55 bp):
TAATGATGATGCTATGGTGGCAATCAAGATTTGGTAAGGGTGACTTGGTGTCAAA
Found at i:269085 original size:19 final size:19
Alignment explanation
Indices: 269049--269087 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
269039 ATATTAATTT
*
269049 AATTTTAAATGTTAATAAA
1 AATTTTAAATATTAATAAA
* *
269068 AATTTTAATTATTTATAAA
1 AATTTTAAATATTAATAAA
269087 A
1 A
269088 CATATAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTTTAAATATTAATAAA
Found at i:275103 original size:17 final size:17
Alignment explanation
Indices: 275055--275118 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
275045 TTAATTATAT
275055 TAAAAATATAAATATTTAA
1 TAAAAATAT--ATATTTAA
*
275074 T-ATAATA-ATTATTTAA
1 TAAAAATATA-TATTTAA
275090 TAAAAATATATATTTAA
1 TAAAAATATATATTTAA
* *
275107 TTAAATTATATA
1 TAAAAATATATA
275119 ATTTTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.03
16 8 0.21
17 22 0.58
18 6 0.16
19 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATATATTTAA
Found at i:275755 original size:37 final size:37
Alignment explanation
Indices: 275714--275821 Score: 98
Period size: 37 Copynumber: 3.3 Consensus size: 37
275704 ATATCATATT
275714 TATATTTAAAGTATTATATATCTATAATAAATTTTGA
1 TATATTTAAAGTATTATATATCTATAATAAATTTTGA
*
275751 TATATTT--ATTATT-TATATC----AT--A---T-A
1 TATATTTAAAGTATTATATATCTATAATAAATTTTGA
* *
275775 TATATTTAAAGCATTATATATTTATAATAAATTTTGA
1 TATATTTAAAGTATTATATATCTATAATAAATTTTGA
275812 TATATTTAAA
1 TATATTTAAA
275822 CTTTAAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 26
0.64 0.05 0.31
Matches are distributed among these distances:
24 8 0.15
25 1 0.02
26 4 0.07
27 5 0.09
28 1 0.02
30 2 0.04
31 2 0.04
33 1 0.02
34 6 0.11
35 5 0.09
36 1 0.02
37 18 0.33
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (37 bp):
TATATTTAAAGTATTATATATCTATAATAAATTTTGA
Found at i:275769 original size:61 final size:62
Alignment explanation
Indices: 275691--275819 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 62
275681 ATGGTATAGG
* *
275691 TATTTATTTATTCATATCATATTTATATTTAAAGTATTATATATCTATAATAAATTTTGATA
1 TATTTATTTATTCATATCATATATATATTTAAAGCATTATATATCTATAATAAATTTTGATA
* *
275753 TATTTA-TTATTTATATCATATATATATTTAAAGCATTATATATTTATAATAAATTTTGATA
1 TATTTATTTATTCATATCATATATATATTTAAAGCATTATATATCTATAATAAATTTTGATA
275814 TATTTA
1 TATTTA
275820 AACTTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 57 0.90
62 6 0.10
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (62 bp):
TATTTATTTATTCATATCATATATATATTTAAAGCATTATATATCTATAATAAATTTTGATA
Found at i:276185 original size:26 final size:26
Alignment explanation
Indices: 276155--276223 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
276145 GACAGATGAA
*
276155 AAATTTGATAAAATTAAAAAAAAATT
1 AAATTTAATAAAATTAAAAAAAAATT
* * *
276181 AAATTTAATTAAATTTAAAAAATATT
1 AAATTTAATAAAATTAAAAAAAAATT
*
276207 ATA-TTAA-AAAATCTAAA
1 AAATTTAATAAAAT-TAAA
276224 TATTAATTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
24 4 0.11
25 7 0.20
26 24 0.69
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
AAATTTAATAAAATTAAAAAAAAATT
Found at i:276607 original size:23 final size:23
Alignment explanation
Indices: 276530--276607 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 23
276520 TTATATGAGT
*
276530 TTAATTTATTTTTATTTGTAAAAGT
1 TTAATTTATTTTTATTTGT--AAGA
* *
276555 TTAAATTT-GTGTTATTT-TAA-A
1 TT-AATTTATTTTTATTTGTAAGA
*
276576 GTATGATTTATTTTTATTTGTAAGA
1 -T-TAATTTATTTTTATTTGTAAGA
276601 TTAATTT
1 TTAATTT
276608 GATTAAAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 7 0.17
23 13 0.32
24 5 0.12
25 10 0.25
26 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (23 bp):
TTAATTTATTTTTATTTGTAAGA
Found at i:276711 original size:25 final size:26
Alignment explanation
Indices: 276679--276735 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
276669 ATGATTTTAA
276679 ATTTTTATTTAT-GATAGTAT-AATTT
1 ATTTTTATTTATAGA-AGTATAAATTT
* *
276704 ATTTTTATTTGTAGAAGTTTAAATTT
1 ATTTTTATTTATAGAAGTATAAATTT
276730 ATTTTT
1 ATTTTT
276736 TTTGATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (26 bp):
ATTTTTATTTATAGAAGTATAAATTT
Found at i:278696 original size:15 final size:17
Alignment explanation
Indices: 278665--278726 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
278655 AATATATGAT
278665 ATATATAATATTAATTA
1 ATATATAATATTAATTA
278682 ATATATAA-ATT-ATTA
1 ATATATAATATTAATTA
* *
278697 ATATAATGAATAATAATTT
1 ATAT-AT-AATATTAATTA
278716 ATATTATAATA
1 ATA-TATAATA
278727 ATATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 10 0.26
18 6 0.16
19 8 0.21
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATAATATTAATTA
Found at i:282313 original size:50 final size:51
Alignment explanation
Indices: 282213--282327 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
282203 AATTAACTAG
* ** * *
282213 ATGTATCGATGCATTGAAAAATGTATCGATACATTTGGATAAAAAAACAGA
1 ATGTATCGATACATCAAAAAATGTATCGATAAATCTGGATAAAAAAACAGA
*
282264 ATGTATCGATACATCAAAAAATGTATCGATAAATCTGGGT-AAAAAACAGA
1 ATGTATCGATACATCAAAAAATGTATCGATAAATCTGGATAAAAAAACAGA
*
282314 TTGTATCGATACAT
1 ATGTATCGATACAT
282328 GTATTGTTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 23 0.40
51 34 0.60
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATCAAAAAATGTATCGATAAATCTGGATAAAAAAACAGA
Found at i:282992 original size:12 final size:12
Alignment explanation
Indices: 282975--282999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282965 GTGTTTATAA
282975 TTATTTTAATAT
1 TTATTTTAATAT
282987 TTATTTTAATAT
1 TTATTTTAATAT
282999 T
1 T
283000 GTTACTTTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTTAATAT
Found at i:283155 original size:2 final size:2
Alignment explanation
Indices: 283148--283177 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
283138 ACCAACCATC
283148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283178 GCCAAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284887 original size:16 final size:16
Alignment explanation
Indices: 284843--284887 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
284833 GTTTAAAATT
* *
284843 AAAATAATTTGAATTA
1 AAAATAATTTAAATAA
* *
284859 AAAAGAATCTAAATAA
1 AAAATAATTTAAATAA
284875 AAAATAATTTAAA
1 AAAATAATTTAAA
284888 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AAAATAATTTAAATAA
Found at i:286468 original size:16 final size:16
Alignment explanation
Indices: 286449--286482 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
286439 GTTTTCGGTT
*
286449 TTTGCTTTTTTTGATA
1 TTTGCTTGTTTTGATA
286465 TTTGCTTGTTTTGATA
1 TTTGCTTGTTTTGATA
286481 TT
1 TT
286483 ATTTTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (16 bp):
TTTGCTTGTTTTGATA
Found at i:288036 original size:17 final size:17
Alignment explanation
Indices: 288010--288043 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
288000 AGCCTTGGAT
*
288010 AGGTTGAGAGAGATGGC
1 AGGTTAAGAGAGATGGC
288027 AGGTTAAGAGAGATGGC
1 AGGTTAAGAGAGATGGC
288044 TACCTACCAA
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:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (17 bp):
AGGTTAAGAGAGATGGC
Found at i:289064 original size:54 final size:54
Alignment explanation
Indices: 289005--289111 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
288995 TTTAATATGT
* * *
289005 ATGACTCAGTATCATTAATCG-TGATG-TCATGGTGGCAAGCATATTTTGGTAAGC
1 ATGACTCAGCATCACTAAT-GATGATGCT-ATGGTGGCAAGCATAATTTGGTAAGC
* *
289059 ATGACTTAGCATCACTAATGATGATGCTATGGTGGCAATCATAATTTGGTAAG
1 ATGACTCAGCATCACTAATGATGATGCTATGGTGGCAAGCATAATTTGGTAAG
289112 GGTGACTTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.02
54 44 0.96
55 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (54 bp):
ATGACTCAGCATCACTAATGATGATGCTATGGTGGCAAGCATAATTTGGTAAGC
Found at i:289172 original size:50 final size:50
Alignment explanation
Indices: 289112--289283 Score: 168
Period size: 50 Copynumber: 3.4 Consensus size: 50
289102 ATTTGGTAAG
* *
289112 GGTGACTTGGTGTCACTTAATAGTTATGCTATGGTAGCGATTAGAGTTTA
1 GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGATTAGAGTTTA
* ** * * *
289162 GGTGACTTGGTGTCAAGTAAT-GATGATGCTATGGTGGCGATCAAGAATTGGTGA
1 GGTGACTTGGAGTCACTTAATAG-TTATGCTATGGTGGCGAT-TAGAGTT--T-A
* * *
289216 GGGTGACTTGGAGTCACTTAATAGTTATGCCATTGTGGCGATTAAAGTTTA
1 -GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGATTAGAGTTTA
*
289267 GATGACTT-GAGTCACTT
1 GGTGACTTGGAGTCACTT
289284 GGAGTCACTA
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
49 10 0.10
50 42 0.42
51 6 0.06
52 1 0.01
53 1 0.01
54 5 0.05
55 33 0.33
56 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (50 bp):
GGTGACTTGGAGTCACTTAATAGTTATGCTATGGTGGCGATTAGAGTTTA
Found at i:289199 original size:105 final size:105
Alignment explanation
Indices: 289074--289275 Score: 307
Period size: 105 Copynumber: 1.9 Consensus size: 105
289064 TTAGCATCAC
* *
289074 TAATGATGATGCTATGGTGGCAATCATA-ATTTGGTAAGGGTGACTTGGTGTCACTTAATAGTTA
1 TAATGATGATGCTATGGTGGCAATCA-AGAATTGGTAAGGGTGACTTGGAGTCACTTAATAGTTA
* * *
289138 TGCTATGGTAGCGATTAGAGTTTAGGTGACTTGGTGTCAAG
65 TGCCATGGTAGCGATTAAAGTTTAGATGACTTGGTGTCAAG
* *
289179 TAATGATGATGCTATGGTGGCGATCAAGAATTGGTGAGGGTGACTTGGAGTCACTTAATAGTTAT
1 TAATGATGATGCTATGGTGGCAATCAAGAATTGGTAAGGGTGACTTGGAGTCACTTAATAGTTAT
* *
289244 GCCATTGTGGCGATTAAAGTTTAGATGACTTG
66 GCCATGGTAGCGATTAAAGTTTAGATGACTTG
289276 AGTCACTTGG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 86 0.99
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (105 bp):
TAATGATGATGCTATGGTGGCAATCAAGAATTGGTAAGGGTGACTTGGAGTCACTTAATAGTTAT
GCCATGGTAGCGATTAAAGTTTAGATGACTTGGTGTCAAG
Found at i:289256 original size:55 final size:53
Alignment explanation
Indices: 289082--289257 Score: 171
Period size: 55 Copynumber: 3.3 Consensus size: 53
289072 ACTAATGATG
* * *
289082 ATGCTATGGTGGCAATCATAATTTGGTAAGGGTGACTTGGTGTCACTTAATAGTT
1 ATGCTATGGTGGCGATAAGAA-TTGGT-AGGGTGACTTGGTGTCACTTAATAGTT
* * * ** *
289137 ATGCTATGGTAGCGATTAGAGTT--TA-GGTGACTTGGTGTCAAGTAAT-GATG
1 ATGCTATGGTGGCGATAAGAATTGGTAGGGTGACTTGGTGTCACTTAATAG-TT
*
289187 ATGCTATGGTGGCGATCAAGAATTGGTGAGGGTGACTTGGAGTCACTTAATAGTT
1 ATGCTATGGTGGCGAT-AAGAATTGGT-AGGGTGACTTGGTGTCACTTAATAGTT
* *
289242 ATGCCATTGTGGCGAT
1 ATGCTATGGTGGCGAT
289258 TAAAGTTTAG
Statistics
Matches: 97, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
49 1 0.01
50 35 0.36
51 6 0.06
52 1 0.01
53 1 0.01
54 3 0.03
55 49 0.51
56 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.34
Consensus pattern (53 bp):
ATGCTATGGTGGCGATAAGAATTGGTAGGGTGACTTGGTGTCACTTAATAGTT
Found at i:291519 original size:13 final size:13
Alignment explanation
Indices: 291501--291525 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291491 CATAAAGTGT
291501 TGTATCGATACAA
1 TGTATCGATACAA
291514 TGTATCGATACA
1 TGTATCGATACA
291526 TTTTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:291605 original size:13 final size:13
Alignment explanation
Indices: 291587--291611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291577 ATCACTTAAA
291587 TGTATCGATACAT
1 TGTATCGATACAT
291600 TGTATCGATACA
1 TGTATCGATACA
291612 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:291676 original size:52 final size:52
Alignment explanation
Indices: 291620--291748 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
291610 CACTGATCTT
*
291620 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
291672 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
291724 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
291749 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:299479 original size:56 final size:56
Alignment explanation
Indices: 299407--299519 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
299397 TGCACTAGGT
* * *
299407 GACCAACCATTTTGGTGATCAGAGAGATTTGGTGGTCAG-GAGTATAACAATTGTGC
1 GACCAACCATTCTGGTGATCAGAGAGATTTGATGATCAGAGA-TATAACAATTGTGC
* * * *
299463 GACCAACCATTCTGGTGGTTAGAGAGGTTTGATGATTAGAGATATAACAATTGTGC
1 GACCAACCATTCTGGTGATCAGAGAGATTTGATGATCAGAGATATAACAATTGTGC
299519 G
1 G
299520 CTAGTCATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
56 47 0.96
57 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (56 bp):
GACCAACCATTCTGGTGATCAGAGAGATTTGATGATCAGAGATATAACAATTGTGC
Found at i:306285 original size:17 final size:17
Alignment explanation
Indices: 306237--306300 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
306227 TTAATTATAT
306237 TAAAAATATAAATATTTAA
1 TAAAAATAT--ATATTTAA
*
306256 T-ATAATA-ATTATTTAA
1 TAAAAATATA-TATTTAA
306272 TAAAAATATATATTTAA
1 TAAAAATATATATTTAA
* *
306289 TTAAATTATATA
1 TAAAAATATATA
306301 ATTTTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.03
16 8 0.21
17 22 0.58
18 6 0.16
19 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATATATTTAA
Found at i:307234 original size:13 final size:13
Alignment explanation
Indices: 307216--307241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307206 CATTATTCAA
307216 TGTATCGATACAT
1 TGTATCGATACAT
307229 TGTATCGATACAT
1 TGTATCGATACAT
307242 CTATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:307238 original size:33 final size:33
Alignment explanation
Indices: 307196--307261 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
307186 GCCAAGGAAA
307196 TGTATCGATACAT-TATTCAATGTATCGATACAT
1 TGTATCGATACATCTA-TCAATGTATCGATACAT
**
307229 TGTATCGATACATCTATCTTTGTATCGATACAT
1 TGTATCGATACATCTATCAATGTATCGATACAT
307262 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATCTATCAATGTATCGATACAT
Found at i:307346 original size:40 final size:40
Alignment explanation
Indices: 307280--307393 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
307270 TTTACCCAGA
* * *
307280 TGTATCGATACATTTTGCATTATATCGATACATTGCTCAT
1 TGTATCGATACATTTTACATTGTATCGATACATTACTCAT
* *
307320 TGTATCGATACATTGCT-CATTGTATCGAAACATTACTCAT
1 TGTATCGATACATT-TTACATTGTATCGATACATTACTCAT
* *
307360 TGTATCGATATATTTTACAATGTATCGATACATT
1 TGTATCGATACATTTTACATTGTATCGATACATT
307394 TAGGTATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.02
40 62 0.97
41 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (40 bp):
TGTATCGATACATTTTACATTGTATCGATACATTACTCAT
Found at i:307394 original size:20 final size:20
Alignment explanation
Indices: 307280--307393 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
307270 TTTACCCAGA
*
307280 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
307300 TATATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
307320 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
307340 TGTATCGAAACATTACTCAT
1 TGTATCGATACATTGCTCAT
* * *
307360 TGTATCGATATATT-TTACAA
1 TGTATCGATACATTGCT-CAT
307380 TGTATCGATACATT
1 TGTATCGATACATT
307394 TAGGTATTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 80 0.98
21 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:309708 original size:51 final size:51
Alignment explanation
Indices: 309617--309954 Score: 244
Period size: 51 Copynumber: 6.5 Consensus size: 51
309607 TAAATTTCTA
* * * **
309617 AATTTTTCAC-CTCGGAGATACTCCAA-TCCCGGTTCCATTTCCAAAACATC
1 AATTTTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATC
** * * * *
309667 AATTTTTCTTAATCGGGGATACTCCTACTCTGATTTTATTTCTAAAGCATC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* ** * *
309718 GATTTACCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* * * *
309769 AATTTTTCACAATTGGGGATACTCCAAC-CC--TGTTATTTCATCGGGGATAC-TCC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC--C---AAAACAT-C
* * *
309822 AACCCCGTTATTTC-CAA--GGGGATACTCCAACTCCGATTTTATTTCTAAAATACC
1 AA-----TT-TTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* * *
309876 AATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* *
309927 AATTTTTCATAATTGGGGATACTCCAAC
1 AATTTTTCACAATCGGGGATACTCCAAC
309955 CCTGTTATTT
Statistics
Matches: 223, Mismatches: 44, Indels: 41
0.72 0.14 0.13
Matches are distributed among these distances:
48 10 0.04
49 5 0.02
50 11 0.05
51 152 0.68
52 1 0.00
53 6 0.03
54 5 0.02
56 14 0.06
57 2 0.01
58 5 0.02
59 12 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
Found at i:309815 original size:28 final size:28
Alignment explanation
Indices: 309783--309852 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
309773 TTTCACAATT
* *
309783 GGGGATACTCCAACCCTGTTATTT-CATC
1 GGGGATACTCCAACCCCGTTATTTCCA-A
309811 GGGGATACTCCAACCCCGTTATTTCCAA
1 GGGGATACTCCAACCCCGTTATTTCCAA
309839 GGGGATACTCCAAC
1 GGGGATACTCCAAC
309853 TCCGATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:309899 original size:158 final size:158
Alignment explanation
Indices: 309681--310010 Score: 561
Period size: 158 Copynumber: 2.1 Consensus size: 158
309671 TTTCTTAATC
* * * * *
309681 GGGGATACTCCTACTCTGATTTTATTTCTAAAGCATCGATTTACCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCGGGGATACTCCAAC
*
309746 TCCGATTTTATTTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAACCCTGTTATTTCATC
66 TCCGATTTTATTTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAACCCTGTTATTTAATC
309811 GGGGATACTCCAACCCCGTTATTTCCAA
131 GGGGATACTCCAACCCCGTTATTTCCAA
* *
309839 GGGGATACTCCAACTCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCGGGGATACTCCAAC
*
309904 TCCGATTTTATTTTCAAAACACCAATTTTTCATAATTGGGGATACTCCAACCCTGTTATTTAATC
66 TCCGATTTTATTTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAACCCTGTTATTTAATC
* *
309969 GGGGATACTCCAACCCCGTTATTTTCGA
131 GGGGATACTCCAACCCCGTTATTTCCAA
309997 GGGGATACTCCAAC
1 GGGGATACTCCAAC
310011 CTCGGCTTTA
Statistics
Matches: 161, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 161 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCGGGGATACTCCAAC
TCCGATTTTATTTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAACCCTGTTATTTAATC
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:309972 original size:28 final size:28
Alignment explanation
Indices: 309936--310011 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
309926 CAATTTTTCA
* *
309936 TAATTGGGGATACTCCAACCCTGTTATT
1 TAATCGGGGATACTCCAACCCCGTTATT
309964 TAATCGGGGATACTCCAACCCCGTTATT
1 TAATCGGGGATACTCCAACCCCGTTATT
309992 T--TCGAGGGGATACTCCAACC
1 TAATC--GGGGATACTCCAACC
310012 TCGGCTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.05
28 42 0.95
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (28 bp):
TAATCGGGGATACTCCAACCCCGTTATT
Found at i:310002 original size:107 final size:106
Alignment explanation
Indices: 309890--310169 Score: 364
Period size: 108 Copynumber: 2.6 Consensus size: 106
309880 TTCCACAATC
* * *
309890 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAAC-CCGATTTTATTTTCAAAATACCAATTTTTTATAATCGGGGATACTCCAAC
*
309955 CCTGTTATTTAATCGGGGATACTCCAACCCCGTTATTTTCGA
65 CCCGTTATTTAATCGGGGATACTCCAACCCCGTTATTTTCGA
** * * ** * *
309997 GGGGATACTCCAACCTCGGCTTTATATCTAAAAATATTATTTTTTTATAATCGGGGGTACTCCAA
1 GGGGATACTCCAACC-CGATTTTAT-TTTCAAAATACCAATTTTTTATAATCGGGGATACTCCAA
* *
310062 CCCCGTTATTTCATCGGGGATACTCCAATCCCGTTATTTTCGA
64 CCCCGTTATTTAATCGGGGATACTCCAACCCCGTTATTTTCGA
* *
310105 GGGGATATTCCAACCCGGATTTTA-TTTCTAAAATACCAATTTTTTACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCC-GATTTTATTTTC-AAAATACCAATTTTTTATAATCGGGGATACTCCAA
310169 C
64 C
310170 TCTGATTTTA
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
106 3 0.02
107 53 0.37
108 89 0.61
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (106 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTTATAATCGGGGATACTCCAACC
CCGTTATTTAATCGGGGATACTCCAACCCCGTTATTTTCGA
Found at i:310079 original size:28 final size:28
Alignment explanation
Indices: 310046--310100 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
310036 TTTTTTTATA
*
310046 ATCGGGGGTACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
310074 ATCGGGGATACTCCAATCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
310101 TCGAGGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:310108 original size:28 final size:26
Alignment explanation
Indices: 310048--310121 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
310038 TTTTTATAAT
*
310048 CGGGGGTACTCCAACCCCGTTATTTCA
1 CGGGGATACTCCAA-CCCGTTATTTCA
310075 TCGGGGATACTCCAATCCCGTTATTTTCGA
1 -CGGGGATACTCCAA-CCCGTTA-TTTC-A
*
310105 -GGGGATATTCCAACCCG
1 CGGGGATACTCCAACCCG
310122 GATTTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 32 0.78
29 4 0.10
30 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (26 bp):
CGGGGATACTCCAACCCGTTATTTCA
Found at i:310168 original size:51 final size:51
Alignment explanation
Indices: 310105--310222 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
310095 TTATTTTCGA
* * * *
310105 GGGGATATTCCAACCCGGATTTTA-TTTCTAAAATACCAATTTTTTACAATC
1 GGGGATACTCCAACCCGGATTTTATTTTC-AAAACACCAATTTCTCACAATC
* *
310156 GGGGATACTCCAACTCTGATTTTATTTTCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCGGATTTTATTTTCAAAACACCAATTTCTCACAATC
310207 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
310223 CGTTATTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 55 0.93
52 4 0.07
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCGGATTTTATTTTCAAAACACCAATTTCTCACAATC
Found at i:310238 original size:79 final size:79
Alignment explanation
Indices: 310155--310302 Score: 235
Period size: 79 Copynumber: 1.9 Consensus size: 79
310145 TTTTTACAAT
* * *
310155 CGGGGATACTCCAACTCTGATTTTATTTTCAAAACACCAA-TTTCTCACAATCGGGGATACTCCA
1 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCT-ACAATCAGGGATACTCCA
310219 ACCCCGTTATTTTCG
65 ACCCCGTTATTTTCG
* *
310234 CGGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCTATAATCAGGGATACTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAA
310299 CCCC
66 CCCC
310303 AATTTTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 58 0.92
80 5 0.08
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAA
CCCCGTTATTTTCG
Found at i:310298 original size:51 final size:52
Alignment explanation
Indices: 310236--310346 Score: 145
Period size: 52 Copynumber: 2.2 Consensus size: 52
310226 TATTTTCGCG
* * *
310236 GGGATACTCCAACCCCGA-TTTTATTT-TCAAAATACCAATTTTCTATAATCA
1 GGGATACTCCAACCCCAATTTTTATTTCT-AAAACACCAATTTTCCATAATCA
* * *
310287 GGGATACTCCAACCCCAATTTTTATTTCTAGAACACCGATTTTCCATAATCG
1 GGGATACTCCAACCCCAATTTTTATTTCTAAAACACCAATTTTCCATAATCA
310339 GGGATACT
1 GGGATACT
310347 TTAGCCCAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 17 0.33
52 34 0.65
53 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGATACTCCAACCCCAATTTTTATTTCTAAAACACCAATTTTCCATAATCA
Found at i:310308 original size:130 final size:131
Alignment explanation
Indices: 310074--310346 Score: 374
Period size: 130 Copynumber: 2.1 Consensus size: 131
310064 CCGTTATTTC
* * *
310074 ATCGGGGATACTCCAATCCCGTTATTTTCGAGGGGATATTCCAACCCGGATTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
* * * **
310139 ACCAATTTTTTACAATCGGGGATACTCCAACTCTGA-TTTTATTT-TCAAAACACCAA-TTTCTC
66 ACCAATTTTCTACAATCAGGGATACTCCAACCCCAATTTTTATTTCT-AAAACACCAATTTTC-C
310201 ACA
129 ACA
*
310204 ATCGGGGATACTCCAACCCCGTTATTTTCGCGGGGATACTCCAACCCCGATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCT-AAAA
* * *
310268 TACCAATTTTCTATAATCAGGGATACTCCAACCCCAATTTTTATTTCTAGAACACCGATTTTCCA
65 TACCAATTTTCTACAATCAGGGATACTCCAACCCCAATTTTTATTTCTAAAACACCAATTTTCCA
*
310333 TA
130 CA
310335 ATCGGGGATACT
1 ATCGGGGATACT
310347 TTAGCCCAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
129 1 0.01
130 89 0.71
131 31 0.25
132 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (131 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
ACCAATTTTCTACAATCAGGGATACTCCAACCCCAATTTTTATTTCTAAAACACCAATTTTCCAC
A
Found at i:322765 original size:1 final size:1
Alignment explanation
Indices: 322759--322861 Score: 62
Period size: 1 Copynumber: 103.0 Consensus size: 1
322749 CTTCTCTTCT
* * * * * * * * * *
322759 AAAAAAAAATAAAACAAAAACAAAAACAAAAAAAAAGACAAAAACAAAAACAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
322824 AAAAAAAACAAAACAAAGAAAAAAGAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
322862 GAACTTGCTT
Statistics
Matches: 70, Mismatches: 32, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:322778 original size:6 final size:6
Alignment explanation
Indices: 322769--322840 Score: 98
Period size: 6 Copynumber: 12.3 Consensus size: 6
322759 AAAAAAAAAT
322769 AAAACA AAAACA AAAACA AAAA-A AAAGACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAA-ACA AAAACA AAAACA AAAACA
322817 AAAA-A ACAAA-A AAAAC- AAAACA AA
1 AAAACA A-AAACA AAAACA AAAACA AA
322841 GAAAAAAGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
5 14 0.23
6 43 0.70
7 4 0.07
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:322790 original size:18 final size:17
Alignment explanation
Indices: 322759--322847 Score: 103
Period size: 17 Copynumber: 5.2 Consensus size: 17
322749 CTTCTCTTCT
* *
322759 AAAA-AAAAATAAAACA
1 AAAACAAAAACAAAAAA
322775 AAAACAAAAACAAAAAA
1 AAAACAAAAACAAAAAA
322792 AAAGACAAAAACAAAAACA
1 AAA-ACAAAAACAAAAA-A
322811 AAAACAAAAA-AACAAAA
1 AAAACAAAAACAA-AAAA
322828 AAAAC-AAAACAAAGAAA
1 AAAACAAAAACAAA-AAA
322845 AAA
1 AAA
322848 GAGAAAAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.14
17 29 0.45
18 23 0.35
19 4 0.06
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (17 bp):
AAAACAAAAACAAAAAA
Found at i:322854 original size:18 final size:17
Alignment explanation
Indices: 322781--322854 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 17
322771 AACAAAAACA
322781 AAAACAAAAAAAAAGAC
1 AAAACAAAAAAAAAGAC
322798 AAAAACAAAAACAAAA-AC
1 -AAAACAAAAA-AAAAGAC
*
322816 AAAA-AAACAAAAAAAAC
1 AAAACAAA-AAAAAAGAC
*
322833 AAAACAAAGAAAAAAGAG
1 AAAACAAA-AAAAAAGAC
322851 AAAA
1 AAAA
322855 AAGAAAAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
16 7 0.14
17 12 0.24
18 26 0.53
19 4 0.08
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAAAAAGAC
Found at i:323954 original size:55 final size:55
Alignment explanation
Indices: 323894--324198 Score: 337
Period size: 55 Copynumber: 5.3 Consensus size: 55
323884 TTCACCCTTT
*
323894 AGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
* * *
323949 AGTCCTCAAAGAGCAAGACACCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
* *
324004 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
* ** * *
324059 AGTCCTCAAAGAGTAGGACGCCTTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCA-CCTTC
1 AGTCCTCAAAGAGCAGGACGCC---TTTC----AAAGCCCACACGAGTTGGTGGCACCCTCC
* *
324120 AGTCCTCAAAGAGCA-GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
1 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACGAGTTGGTGGCACCCTCC
*
324179 TAGTCCTCAAAAAGCAGGAC
1 -AGTCCTCAAAGAGCAGGAC
324199 ACTCTCCCCT
Statistics
Matches: 221, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
55 125 0.57
57 2 0.01
58 4 0.02
59 29 0.13
60 20 0.09
61 21 0.10
62 20 0.09
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
Found at i:324370 original size:61 final size:61
Alignment explanation
Indices: 324241--324474 Score: 289
Period size: 61 Copynumber: 3.9 Consensus size: 61
324231 GCAGGATGCC
* * * * *
324241 TTTT-AAAGCCCACACAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTCGCC
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT-TCT
* *
324301 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGATG-CTTTCT
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
* * * * *
324360 TTTTGCAAAGCCCGCACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGTAGGACGCCTTT-T
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
*
324421 CTTTTCAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
1 -TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
324475 ACACTTCCTT
Statistics
Matches: 149, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.03
60 29 0.19
61 107 0.72
62 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
Found at i:324380 original size:215 final size:215
Alignment explanation
Indices: 324005--324413 Score: 585
Period size: 215 Copynumber: 1.9 Consensus size: 215
323995 GCACCCTCCA
* * *
324005 GTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAG
1 GTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGCTAGTGGCACCCTCCAGTCCTCAAAG
* *** *
324070 AGTAGGACGCCTTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 AGCAGGACGCCTTTCGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCA
324135 GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAAAGCAGGAC
131 GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAAAGCAGGAC
324199 ACTCTCCCCTTTCGCCTCTTT
195 ACTCTCCCCTTTCGCCTCTTT
* * *
324220 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTAGTGGCA-CCTTCAGTCCTCAAAG
1 GTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGCTAGTGGCACCCTCCAGTCCTCAAAG
* *
324284 AGCAGGACGCC-TTCGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
66 AGCAGGACGCCTTTCGCCTTTTAAAGCCCACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGC
* * * *
324348 AAGATG-CTT-TCTTTTTGCAAAGCCCGCACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGTAG
130 -AGACGCCTTCTCCTTTT--AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAG
324411 GAC
192 GAC
324414 GCCTTTTCTT
Statistics
Matches: 172, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
213 35 0.20
214 45 0.26
215 87 0.51
216 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (215 bp):
GTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGCTAGTGGCACCCTCCAGTCCTCAAAG
AGCAGGACGCCTTTCGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCA
GACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACA
CTCTCCCCTTTCGCCTCTTT
Found at i:324434 original size:122 final size:121
Alignment explanation
Indices: 324245--324470 Score: 355
Period size: 122 Copynumber: 1.9 Consensus size: 121
324235 GATGCCTTTT
*
324245 AAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTTAAAGC
1 AAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAAAGCAGGACGCCTTCGCCTTTTAAAGC
324310 CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGATGCTTTCTTTTTGC
66 CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGATGCTTTCTTTTTGC
* * * * **
324366 AAAGCCCGCACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGTAGGACGCCTT-TTCTTTTCAAA
1 AAAGCCCACACAAGCTAGTGGCACCTT-CAGTCCTCAAAAAGCAGGACGCCTTCGCCTTTT-AAA
*
324430 GCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
64 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
324471 GGACACACTT
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
121 29 0.31
122 66 0.69
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (121 bp):
AAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAAAGCAGGACGCCTTCGCCTTTTAAAGC
CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGATGCTTTCTTTTTGC
Found at i:324538 original size:45 final size:44
Alignment explanation
Indices: 324457--324596 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 44
324447 GCACTTTTCA
* ** *
324457 GTCCTCAAAGAGCAGGACACACTTCCTTCCCTTTTTTTCTCTTTT
1 GTCCTCAAAAAGCAGGACACACTTTTTTTCC-TTTTTTCTCTTTT
*
324502 GTCCTCAAAAAGCAGAACACACTTTATTTTCC--TTTT-TCTTTT
1 GTCCTCAAAAAGCAGGACACACTTT-TTTTCCTTTTTTCTCTTTT
* * **
324544 GTCCTCAGAGAGCAGGACGTA-TTTTGTTTCCTTTTTTC-C-TTT
1 GTCCTCAAAAAGCAGGACACACTTTT-TTTCCTTTTTTCTCTTTT
324586 GTCCTCAAAAA
1 GTCCTCAAAAA
324597 ATGGGACGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
40 1 0.01
41 8 0.10
42 34 0.44
43 9 0.12
45 22 0.28
46 4 0.05
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (44 bp):
GTCCTCAAAAAGCAGGACACACTTTTTTTCCTTTTTTCTCTTTT
Found at i:324669 original size:119 final size:117
Alignment explanation
Indices: 324487--324718 Score: 263
Period size: 119 Copynumber: 2.0 Consensus size: 117
324477 ACTTCCTTCC
* * * * *
324487 CTTTTTTTCTCTTTTGTCCTCAAAAAGCAGAACACACTTTATTTTCCTTTTTCTTTTGTCCTC-A
1 CTTTTTTTCACTTTTGTCCTCAAAAAGCAG-ACACACTTTATTTTCCCTCTTCCTTGGTCCTCAA
* * ** *
324551 GAGAGCAGGACGTATTTTGTTTCCTTTTTTCCTTTGTCCTCAAAAAATGGGACGTA
65 G-GAGCAAGACCTA-TTTCATT-CTCTTTTCCTTTGTCCTCAAAAAATGGGACGTA
* * *
324607 CTTTTTTTCAC-TTTGTCCTCAAGAAGCAG-GACACTTTCCTTTTCTCCTCTTCCTTGGTCCTCA
1 CTTTTTTTCACTTTTGTCCTCAAAAAGCAGACACACTTT-ATTTTC-CCTCTTCCTTGGTCCTCA
*
324670 AGGAGCAAGACCTATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTGGG
64 AGGAGCAAGACCTATTTCATTCTCTTTTCCTTTGTCCTCAAAAAATGGG
324719 GCACCCTTTC
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
117 33 0.35
118 10 0.11
119 40 0.42
120 12 0.13
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.42
Consensus pattern (117 bp):
CTTTTTTTCACTTTTGTCCTCAAAAAGCAGACACACTTTATTTTCCCTCTTCCTTGGTCCTCAAG
GAGCAAGACCTATTTCATTCTCTTTTCCTTTGTCCTCAAAAAATGGGACGTA
Found at i:325552 original size:20 final size:19
Alignment explanation
Indices: 325527--325600 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
325517 TTTACCCAGA
325527 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
325547 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
325567 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
325587 TGTATCGATACATT
1 TGTATCGATACATT
325601 CAGCCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:327173 original size:30 final size:27
Alignment explanation
Indices: 327094--327162 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
327084 ATGAACATGC
*
327094 GATACTCCAACCCCGTTATTT-CATCGGG
1 GATACTCCAACCCCGTTATTTCCA--AGG
327122 GATACTCCAACCCCGTTATTTCCAAGG
1 GATACTCCAACCCCGTTATTTCCAAGG
327149 GATACTCCAACCCC
1 GATACTCCAACCCC
327163 AATTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 16 0.41
28 21 0.54
29 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (27 bp):
GATACTCCAACCCCGTTATTTCCAAGG
Found at i:327210 original size:51 final size:51
Alignment explanation
Indices: 327146--327263 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
327136 GTTATTTCCA
*
327146 AGGGATACTCCAACCCCAATTTTA-TTTCTAAAATACCAATAATCCACAATC
1 AGGGATACTCCAACCCCAATTTTATTTTC-AAAACACCAATAATCCACAATC
* * ** * *
327197 AGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATT
1 AGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATAATCCACAATC
*
327248 GGGGATACTCCAACCC
1 AGGGATACTCCAACCC
327264 TGTTATTTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (51 bp):
AGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATAATCCACAATC
Found at i:327386 original size:28 final size:27
Alignment explanation
Indices: 327353--327429 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
327343 TTTTTTTATA
327353 ATCGGGGGTACTCCAACCCCGTTATTT
1 ATCGGGGGTACTCCAACCCCGTTATTT
* * * **
327380 CATCGGGGATTCTCCAATCTTGTTATTT
1 -ATCGGGGGTACTCCAACCCCGTTATTT
327408 -TCGAGGGGATACTCCAACCCCG
1 ATCG-GGGG-TACTCCAACCCCG
327430 ATTTTATTTC
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 31 0.84
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (27 bp):
ATCGGGGGTACTCCAACCCCGTTATTT
Found at i:327387 original size:108 final size:107
Alignment explanation
Indices: 327198--327476 Score: 339
Period size: 108 Copynumber: 2.6 Consensus size: 107
327188 TCCACAATCA
* * * * *
327198 GGGATACTCCAACTCCGATTTTAT-TTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATATCT-AAAATACCAATTTTTCACAATCGGGGATACTCCAAC
*
327262 CCTGTTATTTCACCGGGGATACTCCAATGC-CGTTATTTTCGAG
65 CCCGTTATTTCACCGGGGATACTCCAAT-CTCGTTATTTTCGAG
* ** * * * *
327305 GGGATACTCTAACCCC-AGCTTTATATCTAAAAATATTATTTTTTTATAATCGGGGGTACTCCAA
1 GGGATACTCCAACCCCGA-CTTTATATCT-AAAATACCAATTTTTCACAATCGGGGATACTCCAA
* * *
327369 CCCCGTTATTTCATCGGGGATTCTCCAATCTTGTTATTTTCGAG
64 CCCCGTTATTTCACCGGGGATACTCCAATCTCGTTATTTTCGAG
* *
327413 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATATCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
327477 TCCGATTTTA
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
106 1 0.01
107 50 0.35
108 90 0.63
109 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (107 bp):
GGGATACTCCAACCCCGACTTTATATCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCACCGGGGATACTCCAATCTCGTTATTTTCGAG
Found at i:327475 original size:51 final size:51
Alignment explanation
Indices: 327412--327526 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
327402 TTATTTTCGA
* *
327412 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTCTCACAATC
*
327463 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
327514 GGGGATACTCCAA
1 GGGGATACTCCAA
327527 TCCCATTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 56 0.93
52 4 0.07
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
Found at i:327546 original size:79 final size:77
Alignment explanation
Indices: 327463--327681 Score: 280
Period size: 79 Copynumber: 2.8 Consensus size: 77
327453 TTTCACAATC
* *
327463 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCCAAT
1 GGGGATACTCCAAC-CCGATTTTATTTTCAAAACACCGATTT-TCATAATCGGGGATACTCCAA-
*
327528 CCC-ATTATTTTCGT
63 CCCTATTATTTTCGA
* *
327542 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCGATTTTC-ATAATCGGGGATACTCCAAC
327607 CCTATTATTTTCGA
64 CCTATTATTTTCGA
* *
327621 GGGGATACTCCAACCCTAATTTT-TATTTCTAGAACACCGATTTTCCATAATCGGGGATACT
1 GGGGATACTCCAACCC-GATTTTAT-TTTC-AAAACACCGATTTT-CATAATCGGGGATACT
327682 TTAGCCCAGT
Statistics
Matches: 124, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 9 0.07
79 87 0.70
80 27 0.22
81 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (77 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAACACCGATTTTCATAATCGGGGATACTCCAACCC
TATTATTTTCGA
Found at i:328794 original size:61 final size:62
Alignment explanation
Indices: 328708--328826 Score: 188
Period size: 61 Copynumber: 1.9 Consensus size: 62
328698 ATGATATAGG
328708 TATTTATTTATTCATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAATA
1 TATTTATTTATTCATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAATA
* * *
328770 TATTTATTCT-TT-ATATCATATTTATATTTAAAGTATTATTTATTTATAATAAATTTT
1 TATTTATT-TATTCATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTT
328827 GACATGTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 42 0.79
62 10 0.19
63 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (62 bp):
TATTTATTTATTCATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAATA
Found at i:328843 original size:61 final size:61
Alignment explanation
Indices: 328721--328843 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 61
328711 TTATTTATTC
* **
328721 ATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAATATATTTATTCTTT
1 ATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAACATATTTAAACTTT
* * * * *
328782 ATATCATATTTATATTTAAAGTATTATTTATTTATAATAAATTTTGACATGTTTAAACTTT
1 ATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAACATATTTAAACTTT
328843 A
1 A
328844 AATATTTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (61 bp):
ATATCATATTTATATTTAAAATATTATATATCTATAATAAATTTTAACATATTTAAACTTT
Found at i:329466 original size:13 final size:13
Alignment explanation
Indices: 329448--329472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329438 AGATTGCACA
329448 GTATCGATACATT
1 GTATCGATACATT
329461 GTATCGATACAT
1 GTATCGATACAT
329473 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:329485 original size:20 final size:21
Alignment explanation
Indices: 329460--329512 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
329450 ATCGATACAT
*
329460 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
329480 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
329501 TGTATCGATACA
1 TGTATCGATACA
329513 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:329597 original size:20 final size:20
Alignment explanation
Indices: 329554--329605 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
329544 CTTAACTGTT
*
329554 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
329573 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
329593 TGTATCGATACAT
1 TGTATCGATACAT
329606 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:335524 original size:8 final size:8
Alignment explanation
Indices: 335511--335536 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
335501 ATTTGATTAA
335511 ATTTTGTG
1 ATTTTGTG
335519 ATTTTGTG
1 ATTTTGTG
335527 ATTTTGTG
1 ATTTTGTG
335535 AT
1 AT
335537 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:335757 original size:13 final size:13
Alignment explanation
Indices: 335739--335777 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
335729 CAGCATTCTC
335739 TGTATCGATACAA
1 TGTATCGATACAA
*
335752 TGTATCGATACAG
1 TGTATCGATACAA
335765 TGTATCGATACAA
1 TGTATCGATACAA
335778 AGGGTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.