Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007902.1 Hibiscus syriacus cultivar Beakdansim tig00110293_pilon, 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: 611524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:289391 original size:25 final size:25
Alignment explanation
Indices: 289363--289422 Score: 113
Period size: 24 Copynumber: 2.4 Consensus size: 25
289353 CAAAATTGGT
289363 TAAAGTTAAAATACGTTTAAAAGAG
1 TAAAGTTAAAATACGTTTAAAAGAG
289388 TAAAGTT-AAATACGTTTAAAAGAG
1 TAAAGTTAAAATACGTTTAAAAGAG
289412 TAAAGTTAAAA
1 TAAAGTTAAAA
289423 AATATCTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.28
Consensus pattern (25 bp):
TAAAGTTAAAATACGTTTAAAAGAG
Found at i:289928 original size:2 final size:2
Alignment explanation
Indices: 289912--289946 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
289902 GTACTTACCC
* *
289912 TA TA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
289947 TATTCCGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:295479 original size:22 final size:24
Alignment explanation
Indices: 295453--295496 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
295443 GAAAACTGGT
295453 TGGTCAAC-G-TAAAACATTTTTC
1 TGGTCAACAGATAAAACATTTTTC
*
295475 TGGTCAACAGATAAAATATTTT
1 TGGTCAACAGATAAAACATTTT
295497 AATATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (24 bp):
TGGTCAACAGATAAAACATTTTTC
Found at i:295577 original size:19 final size:19
Alignment explanation
Indices: 295550--295588 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
295540 ATATTTATTA
*
295550 ATATTTTTAATAATATAAT
1 ATATATTTAATAATATAAT
*
295569 ATATATTTAATATTATAAT
1 ATATATTTAATAATATAAT
295588 A
1 A
295589 AAATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTTAATAATATAAT
Found at i:295581 original size:48 final size:50
Alignment explanation
Indices: 295529--295622 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 50
295519 TAATTATTAA
* * * * *
295529 AATATTAAAATATATTTATTAA-TAT-TTTTAATAATATAATATATATTT
1 AATATTAAAATAAAATAATTAATTATATTATAATAATATAAGATATATTT
*
295577 AATATTATAATAAAATAATTAATTATATTATAATAATATAAGATAT
1 AATATTAAAATAAAATAATTAATTATATTATAATAATATAAGATAT
295623 TATATTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 18 0.47
49 3 0.08
50 17 0.45
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (50 bp):
AATATTAAAATAAAATAATTAATTATATTATAATAATATAAGATATATTT
Found at i:295624 original size:23 final size:23
Alignment explanation
Indices: 295559--295628 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
295549 AATATTTTTA
* * *
295559 ATAATATAATATATATTTAATATT
1 ATAATAAAATAAATAATT-ATATT
*
295583 ATAATAAAATAATTAATTATATT
1 ATAATAAAATAAATAATTATATT
*
295606 ATAATAATATAAGAT-ATTATATT
1 ATAATAAAATAA-ATAATTATATT
295629 TTTATTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 24 0.62
24 15 0.38
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATAATAAAATAAATAATTATATT
Found at i:295656 original size:31 final size:31
Alignment explanation
Indices: 295565--295656 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 31
295555 TTTAATAATA
*
295565 TAATATATATT-TAATATTATAATAAAATA-AT
1 TAAT-TATATTATAATA-TATAATAAATTATAT
* *
295596 TAATTATATTATAATAATATAAGATATTATAT
1 TAATTATATTATAAT-ATATAATAAATTATAT
* *
295628 T-TTTATTTTAATAATATATAATAAATTAT
1 TAATTATATT-ATAATATATAATAAATTAT
295657 TAATAAAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 6 0.12
31 35 0.70
32 9 0.18
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
TAATTATATTATAATATATAATAAATTATAT
Found at i:295661 original size:50 final size:51
Alignment explanation
Indices: 295534--295734 Score: 150
Period size: 53 Copynumber: 3.9 Consensus size: 51
295524 ATTAAAATAT
* *
295534 TAAAATATATTTATTAATATTTTTAATAATATAATATATATTTAATATTATAA
1 TAAAATA-ATTAATTAA-ATTATTAATAATATAATATATATTTAATATTATAA
* * *
295587 TAAAATAATTAATTATATTA-TAATAATATAAGATATTATATTT-TTATTTTAA
1 TAAAATAATTAATTAAATTATTAATAATAT-A-ATA-TATATTTAATATTATAA
* * * * *
295639 TAATAT-A-TAA-TAAATTATTAATAAAAT-CTATATTATTTATTAATT-TCA
1 TAAAATAATTAATTAAATTATTAATAATATAATATA-TATTTAAT-ATTATAA
* *
295687 TAGAAATAATATTATTAAATTATTAATAAT-GAATA-ATATTTAATATTA
1 TA-AAATAAT-TAATTAAATTATTAATAATATAATATATATTTAATATTA
295735 AAAGATTTAA
Statistics
Matches: 118, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
46 2 0.02
47 7 0.06
48 6 0.05
49 12 0.10
50 24 0.20
51 12 0.10
52 25 0.21
53 30 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
TAAAATAATTAATTAAATTATTAATAATATAATATATATTTAATATTATAA
Found at i:303334 original size:23 final size:23
Alignment explanation
Indices: 303307--303361 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
303297 TGAGATCTGT
303307 CGACGATGAGAGGCTGAGAGCTC
1 CGACGATGAGAGGCTGAGAGCTC
303330 CGACGATGAGAGGCTGAGAGCTC
1 CGACGATGAGAGGCTGAGAGCTC
303353 CGACGATGA
1 CGACGATGA
303362 AAGGTTCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (23 bp):
CGACGATGAGAGGCTGAGAGCTC
Found at i:304430 original size:2 final size:2
Alignment explanation
Indices: 304423--304482 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
304413 TATTAATAAT
304423 TA TA TA TA TA 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 TA TA TA TA TA
304465 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
304483 ACTCAATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:304615 original size:2 final size:2
Alignment explanation
Indices: 304608--304637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
304598 AAATAATTTC
304608 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
304638 TATTTTATTT
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:305149 original size:36 final size:37
Alignment explanation
Indices: 305106--305182 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
305096 TTGCAAAGAA
* *
305106 TATTATAATATTAAATTTA-ATTTAAAAATATTTAA-T
1 TATTATAATATTAAAGTTAGATTT-AAAATATTAAACT
*
305142 TATTATAATATTAAAGTTAGCTTTAAAATATTAAACT
1 TATTATAATATTAAAGTTAGATTTAAAATATTAAACT
305179 TATT
1 TATT
305183 TTTATACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 28 0.78
37 8 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (37 bp):
TATTATAATATTAAAGTTAGATTTAAAATATTAAACT
Found at i:305218 original size:20 final size:19
Alignment explanation
Indices: 305114--305218 Score: 54
Period size: 20 Copynumber: 5.5 Consensus size: 19
305104 AATATTATAA
* *
305114 TATTAAATTTAATTTAAAAA
1 TATTAAA-TTAATTTTAAAC
* *
305134 TATTTAATT-ATTAT-AA-
1 TATTAAATTAATTTTAAAC
** *
305150 TATTAAAGTTAGCTTTAAAA
1 TATTAAA-TTAATTTTAAAC
* *
305170 TATTAAACTTATTTTTATAC
1 TATTAAA-TTAATTTTAAAC
* *
305190 AATTGAATTGAATTTTAAAC
1 TATTAAATT-AATTTTAAAC
305210 TATTAAATT
1 TATTAAATT
305219 TATCATTATT
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
16 6 0.10
17 4 0.06
18 5 0.08
19 6 0.10
20 41 0.66
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (19 bp):
TATTAAATTAATTTTAAAC
Found at i:309119 original size:18 final size:18
Alignment explanation
Indices: 309096--309131 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
309086 TTTTCTTATC
*
309096 TATTTTTTATTTAATTTT
1 TATTTTGTATTTAATTTT
309114 TATTTTGTATTTAATTTT
1 TATTTTGTATTTAATTTT
309132 AATAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TATTTTGTATTTAATTTT
Found at i:309660 original size:16 final size:16
Alignment explanation
Indices: 309639--309678 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
309629 ATTATCATCA
309639 TTTTAAA-CTCCTAAAT
1 TTTTAAATCT-CTAAAT
*
309655 TTTTAAATCTTTAAAT
1 TTTTAAATCTCTAAAT
309671 TTTTAAAT
1 TTTTAAAT
309679 ATTCAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATCTCTAAAT
Found at i:330037 original size:166 final size:167
Alignment explanation
Indices: 329732--330062 Score: 531
Period size: 166 Copynumber: 2.0 Consensus size: 167
329722 ATAAGCTACT
* * *
329732 AAAAGATTATTATATCCTTATGTGTAAGGTTCTAAGCTACATTCAGAATAAGAAGTTTTATAATG
1 AAAAGAATATTATATCCTTATGTATAAGGTTCTAAGCTACATTCAGAATAAGAAGTTGTATAATG
* *
329797 AAATAATGAGAAAAGTATTGTGCCTTATTCATGCATGAATGTTGTGATTATATAGTTAAGTTACA
66 AAATAATGAGAAAAGTATTGCGCCTTATTCATGCATGAACGTTGTGATTATATAGTTAAGTTACA
* *
329862 TTGAATAACCTT-AAATGAGAAATGTTGATGTGTGTAG
131 TTGAATAACCTTAAAAT-AAAAACGTTGATGTGTGTAG
329899 AAAAGAATATTATATCCTTATGTATAAGGTTCTAAGCTACATTCAGAATAAGAAGTTGTATAATG
1 AAAAGAATATTATATCCTTATGTATAAGGTTCTAAGCTACATTCAGAATAAGAAGTTGTATAATG
** * * *
329964 -AATTGTGAGAAAAGTCTTGCGCCTTATTCATGCATGAACGTTTTGATTATATGGTTAAGTTACA
66 AAATAATGAGAAAAGTATTGCGCCTTATTCATGCATGAACGTTGTGATTATATAGTTAAGTTACA
330028 TTGAATAACCTTAAAATAAAAACGTTGATGTGTGT
131 TTGAATAACCTTAAAATAAAAACGTTGATGTGTGT
330063 GGTGTGTGGA
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 85 0.56
167 66 0.44
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (167 bp):
AAAAGAATATTATATCCTTATGTATAAGGTTCTAAGCTACATTCAGAATAAGAAGTTGTATAATG
AAATAATGAGAAAAGTATTGCGCCTTATTCATGCATGAACGTTGTGATTATATAGTTAAGTTACA
TTGAATAACCTTAAAATAAAAACGTTGATGTGTGTAG
Found at i:333489 original size:33 final size:33
Alignment explanation
Indices: 333443--333512 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
333433 AATATTTAAC
* *
333443 CTGCTTATTGAGGCATCATCGC-AGCTACTTGGA
1 CTGCTTATAGAGGCATCATCACTA-CTACTTGGA
*
333476 CTGCTTATAGAGGCATCATCACTACTACTTGGC
1 CTGCTTATAGAGGCATCATCACTACTACTTGGA
333509 CTGC
1 CTGC
333513 ATATGGGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (33 bp):
CTGCTTATAGAGGCATCATCACTACTACTTGGA
Found at i:342351 original size:35 final size:37
Alignment explanation
Indices: 342280--342352 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
342270 GTTGGAAAAT
* *
342280 ATTTATATATTTTCTTTAAAAAAATTCAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
*
342317 ATTTATATATTTT-TTT-ATAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
342352 A
1 A
342353 AAAAAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 6 0.19
37 13 0.41
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:349011 original size:81 final size:82
Alignment explanation
Indices: 348863--349023 Score: 243
Period size: 81 Copynumber: 2.0 Consensus size: 82
348853 AGTCTCTTGC
* * *
348863 ACAACCGGCTCGGTAGCTTTATGCTCTACACCTCTGTGTGAGAGCTTGTCGATCCGCCATTTCGT
1 ACAACCGGCTCAGTAACTTCATGCTCTACACCTC-GTGTGAGAGCTTGTCGATCCGCCATTTCGT
348928 GTGCGAACCATTCTCGGT
65 GTGCGAACCATTCTCGGT
* * * *
348946 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTC-TGTGAGAGCTTGTTGCTCCGCTATTTCGTG
1 ACAACCGGCTCAGTAACTTCATGCTCTACACCTCGTGTGAGAGCTTGTCGATCCGCCATTTCGTG
349010 TGCGAACCATTCTC
66 TGCGAACCATTCTC
349024 TGTAACTCGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
81 41 0.58
83 30 0.42
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.30
Consensus pattern (82 bp):
ACAACCGGCTCAGTAACTTCATGCTCTACACCTCGTGTGAGAGCTTGTCGATCCGCCATTTCGTG
TGCGAACCATTCTCGGT
Found at i:349367 original size:109 final size:110
Alignment explanation
Indices: 349139--349383 Score: 291
Period size: 109 Copynumber: 2.2 Consensus size: 110
349129 TAGAATTAAC
* *
349139 GATTGAGCACCTTTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGTTTAAAAAATGACTGAGC
1 GATTGAGCACCTATGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG-TCAAAAAATGACTGAGC
*** *
349204 ACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGAT
65 ACCTCTGTGCTTCAGCCAAAAGCTAACACCTCTGTGCAGCTAAGAT
* *
349250 GATTGAGCACCTATGTTCTTCAATCGAG-GACTGACACCTCTGTGCAG-CCAAAAATGACTGAGC
1 GATTGAGCACCTATGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGTCAAAAAATGACTGAGC
* * ** *
349313 ACCTCTGTGCTTCAGTCTAAAATCTGGCACCTCTGTGCA--TTAGAAT
65 ACCTCTGTGCTTCAG-CCAAAAGCTAACACCTCTGTGCAGCTAAG-AT
* *
349359 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTATGTGCTTCAATC
349384 TAAAATCAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
108 3 0.03
109 53 0.46
110 16 0.14
111 43 0.37
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (110 bp):
GATTGAGCACCTATGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGTCAAAAAATGACTGAGCA
CCTCTGTGCTTCAGCCAAAAGCTAACACCTCTGTGCAGCTAAGAT
Found at i:349398 original size:54 final size:54
Alignment explanation
Indices: 349302--349433 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 54
349292 TGCAGCCAAA
* * *** *
349302 AATGACTGAGCACCTCTGTGCTTCAGTCTAAAATCTGGCACCTCTGTGCATTAG
1 AATGACTGAGCACCTCTGTGCTACAATCTAAAATCAAACACCTCAGTGCATTAG
* * *
349356 AATGATTGAGCACCTCTGTGCTACAATCTAAAATCAAACACCTCAGTGCTTTTACA
1 AATGACTGAGCACCTCTGTGCTACAATCTAAAATCAAACACCTCAGTGC-ATTA-G
* *
349412 AATGACCGAGCACCTCCGTGCT
1 AATGACTGAGCACCTCTGTGCT
349434 GCGATCTGCG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 42 0.66
55 3 0.05
56 19 0.30
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (54 bp):
AATGACTGAGCACCTCTGTGCTACAATCTAAAATCAAACACCTCAGTGCATTAG
Found at i:350815 original size:15 final size:15
Alignment explanation
Indices: 350795--350882 Score: 88
Period size: 15 Copynumber: 5.5 Consensus size: 15
350785 TAATAAGGTT
350795 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
350810 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
350825 AATTATTATAAAATATGGATA
1 ATTTATT-T-TAA-A---ATA
350846 GATTTATTTTAAAATA
1 -ATTTATTTTAAAATA
350862 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
350876 ATTTATT
1 ATTTATT
350883 AGTATTGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
14 12 0.19
15 30 0.48
16 4 0.06
17 2 0.03
18 1 0.02
19 1 0.02
20 2 0.03
21 4 0.06
22 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:350876 original size:14 final size:14
Alignment explanation
Indices: 350847--350914 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
350837 ATATGGATAG
350847 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
350862 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
350876 ATTTATTAGTATTGATTT
1 ATTTA-T--T-TTAAATA
350894 ATTTATTTTAAATA
1 ATTTATTTTAAATA
350908 ATTTATT
1 ATTTATT
350915 AGTATGAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 21 0.49
15 11 0.26
17 2 0.05
18 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:350901 original size:32 final size:32
Alignment explanation
Indices: 350862--350937 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
350852 TTTTAAAATA
*
350862 ATTTATTTTAAATAATTTATTAGTATTGATTT
1 ATTTATTTTAAATAATTTATTAGTATTGATTG
350894 ATTTATTTTAAATAATTTATTAGTA-TGAATTG
1 ATTTATTTTAAATAATTTATTAGTATTG-ATTG
350926 ATTTATTTTAAA
1 ATTTATTTTAAA
350938 ATATGGATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATTGATTG
Found at i:351006 original size:32 final size:32
Alignment explanation
Indices: 350964--351506 Score: 332
Period size: 32 Copynumber: 17.7 Consensus size: 32
350954 TATTGTAGTT
*
350964 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
350996 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
351019 -TATGGATAAATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
351050 GTATAGATTGATTTATTTTAAAATATGTAAAATAATTTATTA
1 GTATGGATTGATTTA---T----T-T-T-AAATAATTTATTA
351092 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* **
351124 GTATGAATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * *
351155 G-ATTTATT-ATTGTAGTTGTATGAATTGATTTAATTTA
1 GTATGGATTGATT-TA-TT-T-T-AAATAATTT-A-TTA
* * * * * * *
351192 -AAT-AATTTA-TTAGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTA-AATAATTTA--TT--A
* **
351226 ATATGGATAAATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
351258 GTATAGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
351284 G--T--ATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
351312 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
351344 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
351367 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
351398 GTATGGATTGATTTATTTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
351422 -TATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
351453 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
351485 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
351507 ATATGGATTG
Statistics
Matches: 407, Mismatches: 36, Indels: 136
0.70 0.06 0.23
Matches are distributed among these distances:
22 39 0.10
23 26 0.06
24 4 0.01
25 2 0.00
26 13 0.03
27 2 0.00
28 9 0.02
29 9 0.02
30 10 0.02
31 17 0.04
32 202 0.50
33 2 0.00
34 9 0.02
35 7 0.02
36 16 0.04
37 9 0.02
39 2 0.00
40 1 0.00
41 1 0.00
42 27 0.07
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:351022 original size:22 final size:22
Alignment explanation
Indices: 350997--351039 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
350987 AATTTATTAG
**
350997 TATGGATTGATTTATTTTAAAA
1 TATGGATAAATTTATTTTAAAA
351019 TATGGATAAATTTATTTTAAA
1 TATGGATAAATTTATTTTAAA
351040 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (22 bp):
TATGGATAAATTTATTTTAAAA
Found at i:351043 original size:54 final size:54
Alignment explanation
Indices: 350974--351333 Score: 345
Period size: 54 Copynumber: 6.8 Consensus size: 54
350964 GTATGAATTG
350974 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
*
351028 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-G----
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
** *
351077 ---TA----AAATAATTTATTAGTATGGATTGATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATAA
* * * * ** * * * ** * *
351124 GTATGAATTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGT-TGTATGAA
1 AT-TTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATGGAT-AA
* *
351179 TTGATTTAATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATAA
1 ---ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
* * **
351236 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
351290 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
351334 TAATTTATTT
Statistics
Matches: 253, Mismatches: 31, Indels: 44
0.77 0.09 0.13
Matches are distributed among these distances:
41 4 0.02
42 33 0.13
46 2 0.01
51 1 0.00
53 1 0.00
54 161 0.64
55 10 0.04
56 2 0.01
57 18 0.07
58 21 0.08
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAA
Found at i:351106 original size:74 final size:78
Alignment explanation
Indices: 351019--351237 Score: 283
Period size: 80 Copynumber: 2.9 Consensus size: 78
351009 TATTTTAAAA
**
351019 TATGGATAAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG-T-A-AA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATGATAA
351081 ATAATT-TA-TTAG
66 ATAATTGTAGTT-G
351093 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATAT-GA-TGA
** *
351157 TTTATTATTGTAGTTG
63 TAAATAATTGTAGTTG
* *
351173 TATGAATTGATTTAATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG--GATAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATGATAA
351236 AT
66 AT
351238 TTATTTTAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 16
0.84 0.06 0.11
Matches are distributed among these distances:
73 1 0.01
74 53 0.42
75 1 0.01
76 5 0.04
77 1 0.01
78 1 0.01
79 6 0.05
80 56 0.44
81 3 0.02
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (78 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATGATAA
ATAATTGTAGTTG
Found at i:351107 original size:18 final size:18
Alignment explanation
Indices: 351084--351140 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
351074 ATGTAAAATA
*
351084 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
* *
351102 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
351116 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
351134 ATTTATT
1 ATTTATT
351141 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 1 0.03
18 17 0.57
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:351229 original size:208 final size:210
Alignment explanation
Indices: 350846--351603 Score: 924
Period size: 208 Copynumber: 3.5 Consensus size: 210
350836 AATATGGATA
* *
350846 GATTTATTTTAAAATAAT-TTATTTTAAATAATTTATTAGTATTGATTTATTTATTTTAAATAAT
1 GATTTATTTTAAAAT-ATGTTA---TAAATAATTTATTAGTATGGATTGATTTATTTTAAATAAT
350910 TTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGA
62 TTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGA
*
350975 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATAAATTTATTTTAAA
127 TTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATAAATTTATTTTAAA
351040 TAATTTATTAGTATAGATT
192 TAATTTATTAGTATAGATT
351059 GATTTATTTTAAAATATG-TA-AAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTAT
1 GATTTATTTTAAAATATGTTATAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTAT
351122 TAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTA
66 TAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTA
*
351187 ATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATAAATTTATTTTAAATAAT
131 TTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATAAATTTATTTTAAATAAT
351252 TTATTAGTATAGATT
196 TTATTAGTATAGATT
351267 GATTTATTTTAAAATATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA
1 GATTTATTTT-AAA-A--TA-TG--TTA---TAAATAATTTATTAGTATGGATTGATTTATTTTA
* * *
351332 AATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-T
56 AATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGT
* * * * * * *
351396 TAGTATGGATTGATTTATTTTTAA-AA--TA-T-GAATTGATTTATTTTAAATAATTTATTAGTA
115 T-GTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGA-TTT--AT--TTTA-AAATA
** * *
351456 TGGATTGATTTATTTTAAATAATTTATTTGTATGGATT
173 TGGATAAATTTATTTTAAATAATTTATTAGTATAGATT
** * *
351494 GATTTATTTTAAAATATGGATTGATTTATTATTGTAATT-GTATAGATTGATTTATTTTAAATAA
1 GATTTATTTTAAAATAT-G-TT-ATAAATAATT-T-ATTAGTATGGATTGATTTATTTTAAATAA
* * * *
351558 TTTATTAGTACGGATTAATTTATTTTAAAATATAGATTGATTTATT
61 TTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
351604 TTAAATAATT
Statistics
Matches: 487, Mismatches: 28, Indels: 54
0.86 0.05 0.09
Matches are distributed among these distances:
208 194 0.40
209 3 0.01
210 1 0.00
212 6 0.01
213 17 0.03
216 2 0.00
219 2 0.00
220 86 0.18
221 73 0.15
222 12 0.02
223 6 0.01
224 4 0.01
225 5 0.01
226 29 0.06
227 47 0.10
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (210 bp):
GATTTATTTTAAAATATGTTATAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTAT
TAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTA
TTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATAAATTTATTTTAAATAAT
TTATTAGTATAGATT
Found at i:351370 original size:22 final size:22
Alignment explanation
Indices: 351345--351387 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
351335 AATTTATTTG
351345 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
351367 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
351388 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:351371 original size:54 final size:54
Alignment explanation
Indices: 351313--351618 Score: 359
Period size: 54 Copynumber: 5.6 Consensus size: 54
351303 AATTTATTAG
*
351313 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
351367 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAA
*
351422 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * * **
351475 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAATTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TAA-AA
* * *
351534 TATAGATTGATTTATTTTAAATAATTTATTAGTACGGATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
351588 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
351619 TTGTAGTTGT
Statistics
Matches: 215, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
50 16 0.07
52 2 0.01
53 5 0.02
54 95 0.44
55 57 0.27
56 4 0.02
57 2 0.01
58 14 0.07
59 2 0.01
60 2 0.01
62 16 0.07
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:351560 original size:80 final size:82
Alignment explanation
Indices: 351371--351603 Score: 328
Period size: 80 Copynumber: 2.8 Consensus size: 82
351361 TTAAAATATG
*
351371 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGAATTGATTTA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAATATGGATTGATTTA
* *
351436 TTTTAAATAATTTATTAGTATG
65 --TT-AAT-ATTAATTAGTATA
*
351458 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
351523 T-AT-TGTAATT-GTATA
66 TAATAT-TAATTAGTATA
* * *
351538 GATTGATTTATTTTAAATAATTTATTAGTACGGATTAATTTATTTTAAAATATAGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
351603 T
66 T
351604 TTAAATAATT
Statistics
Matches: 137, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
80 67 0.49
81 4 0.03
82 2 0.01
84 2 0.01
86 21 0.15
87 41 0.30
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (82 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TAATATTAATTAGTATA
Found at i:351668 original size:31 final size:31
Alignment explanation
Indices: 351633--351691 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
351623 AGTTGTATGG
* *
351633 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
351664 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
351692 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:358439 original size:3 final size:3
Alignment explanation
Indices: 358433--358470 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
358423 ACTGATTTGC
358433 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
358471 CAAATCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:361232 original size:29 final size:31
Alignment explanation
Indices: 361160--361232 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
361150 CATGAACGTC
* * *
361160 AAAGACCTAGGTTTTGTTTTCTTTAATAGTT
1 AAAGACCTAAGTTTTGTTTTCTTAAATAGTG
*
361191 AAAGACCTGAGTTTT-TTTT-TTAAATAGTG
1 AAAGACCTAAGTTTTGTTTTCTTAAATAGTG
*
361220 AAAGACCAAAGTT
1 AAAGACCTAAGTT
361233 ATAACTAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 19 0.53
30 4 0.11
31 13 0.36
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (31 bp):
AAAGACCTAAGTTTTGTTTTCTTAAATAGTG
Found at i:370602 original size:223 final size:224
Alignment explanation
Indices: 370205--370651 Score: 823
Period size: 223 Copynumber: 2.0 Consensus size: 224
370195 AATAATTAAC
370205 CAATTTCACCAAAACCCGTGAAAATTCTCAACTATAAATCCAAAGAGGGAAAAAAAACCTATCAA
1 CAATTTCACCAAAACCCGTGAAAATTCTCAACTATAAATCCAAAGAGGGAAAAAAAACCTATCAA
370270 ACCTCAAAGGAAAACAAGTTAAACCGCAATTACTCTCGCAGCAACTAAAACCCAAAATTCATAAA
66 ACCTCAAAGGAAAACAAGTTAAACCGCAATTACTCTCGCAGCAACTAAAACCCAAAATTCATAAA
370335 ATCCACCCACCACGTCAAATTCAAATCAATCTGAACTAAATCTTACAAACAACGCAATAATATAA
131 ATCCACCCACCACGTCAAATTCAAATCAATCTGAACTAAATCTTAC-AACAACGCAATAATAT-A
370400 AAAACTGAAATTAACAGGCTTGAAACAGATG
194 AAAACTGAAATTAACAGGCTTGAAACAGATG
370431 CAATTTCACCAAAACCCGTGAAAATTCTCAACTATAAATCC-AAGA-GG-AAAAAAACCTATCAA
1 CAATTTCACCAAAACCCGTGAAAATTCTCAACTATAAATCCAAAGAGGGAAAAAAAACCTATCAA
370493 A-CTCAAAGGAAAACAAAGTTAAACCGCAATTACTCTCGCAGCAACTAAAACCCAAAATTCATAA
66 ACCTCAAAGGAAAAC-AAGTTAAACCGCAATTACTCTCGCAGCAACTAAAACCCAAAATTCATAA
370557 AATCCACCCACCACGTCAAATTCAAATCAGATCTGAACT-AATCTTACAACAACGCAATAATATA
130 AATCCACCCACCACGTCAAATTCAAATCA-ATCTGAACTAAATCTTACAACAACGCAATAATATA
370621 AAAACTGAAATTAACAGGCTTGAAACAGATG
194 AAAACTGAAATTAACAGGCTTGAAACAGATG
370652 AGGAAAAAGA
Statistics
Matches: 219, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
221 32 0.15
222 29 0.13
223 102 0.47
224 11 0.05
225 4 0.02
226 41 0.19
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.19
Consensus pattern (224 bp):
CAATTTCACCAAAACCCGTGAAAATTCTCAACTATAAATCCAAAGAGGGAAAAAAAACCTATCAA
ACCTCAAAGGAAAACAAGTTAAACCGCAATTACTCTCGCAGCAACTAAAACCCAAAATTCATAAA
ATCCACCCACCACGTCAAATTCAAATCAATCTGAACTAAATCTTACAACAACGCAATAATATAAA
AACTGAAATTAACAGGCTTGAAACAGATG
Found at i:372017 original size:19 final size:21
Alignment explanation
Indices: 371978--372022 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
371968 CTTTAATATT
*
371978 TATAAATATTAAAATTAATAA
1 TATAAATATAAAAATTAATAA
371999 TATAAATA-AAAAATT-ATAA
1 TATAAATATAAAAATTAATAA
*
372018 CATAA
1 TATAA
372023 CATTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAATATAAAAATTAATAA
Found at i:372417 original size:30 final size:31
Alignment explanation
Indices: 372332--372417 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
372322 GGTCATATTC
* *
372332 AGGGTCAATTTGATA-TTTAT-TCAAATTTTA
1 AGGGTCAAATTGATATTTTATCT-AAAATTTA
* **
372362 AGGGTTAAATTGATATTTTGCCTAAAATTT-
1 AGGGTCAAATTGATATTTTATCTAAAATTTA
*
372392 AGGGTCAAATTAATATTTTATCTAAA
1 AGGGTCAAATTGATATTTTATCTAAA
372418 CTATAAGAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
30 35 0.78
31 9 0.20
32 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (31 bp):
AGGGTCAAATTGATATTTTATCTAAAATTTA
Found at i:374327 original size:28 final size:29
Alignment explanation
Indices: 374265--374329 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
374255 AATAAAAGAG
*
374265 TAAATAAAAAAATAAGAAGAAAATACAAA
1 TAAATAAAAAAATAAAAAGAAAATACAAA
* *
374294 TAAATAAAACAAATGAAAAGAAGATA-AAA
1 TAAATAAAA-AAATAAAAAGAAAATACAAA
374323 -AAATAAA
1 TAAATAAA
374330 GATAAGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.22
29 12 0.38
30 13 0.41
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (29 bp):
TAAATAAAAAAATAAAAAGAAAATACAAA
Found at i:374405 original size:3 final size:3
Alignment explanation
Indices: 374386--374427 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
374376 AGAAATAAAT
*
374386 ATA AT- ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
374428 AAGCAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:374510 original size:14 final size:14
Alignment explanation
Indices: 374491--374518 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
374481 AATAAATAAA
374491 ATATATGTATATAT
1 ATATATGTATATAT
374505 ATATATGTATATAT
1 ATATATGTATATAT
374519 GTAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:374711 original size:16 final size:17
Alignment explanation
Indices: 374690--374736 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
374680 ATAAAATGAT
374690 TTAAAATAATAATAA-A
1 TTAAAATAATAATAACA
*
374706 TTAAAAAAATAA-AACA
1 TTAAAATAATAATAACA
374722 TATAAAAT-ATAATAA
1 T-TAAAATAATAATAA
374737 TGATAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 17 0.65
17 7 0.27
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAATAATAATAACA
Found at i:375169 original size:37 final size:37
Alignment explanation
Indices: 375117--375227 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
375107 ATGCTTATGG
*
375117 ATCATA-TTTTAGGAGTTTGAATCTTAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
375153 ATCATATTTTTAGGAGTTTGAATCATAATAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
375190 ATCTTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
375227 A
1 A
375228 ACGTTATGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 6 0.09
37 63 0.91
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:375975 original size:84 final size:84
Alignment explanation
Indices: 375885--376907 Score: 1094
Period size: 84 Copynumber: 12.3 Consensus size: 84
375875 GTTTGCCTCT
* * *
375885 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
375950 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
375969 GAGCTGAGTGTAGTCAAACTCGAAGGTC-TT--TTGGCAGATAGCCCTTCTCAACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
376031 CTGTAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * * *
376050 GAGCTGAGCATAGTCAAACTCAAAAGTCTTTGGTTGGCAGATAACCTTTATCGACTTAAGTTTTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
376115 CTACAGATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * *
376134 GGGCTGAGCGTAGTCGAACTCGAATGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* * *
376198 GTTGTAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* * * * * * *
376219 AAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCATATAGA-CCTTTTCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA-ACCCTTCTCGACTTAAGTTAT
* * *
376279 GCTGTAAATGATGTACCTTA
65 GCTGCAAATGATGTGCCTTG
* *
376299 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
376364 CTGCAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
376383 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACATATAACCCTTTCTAGCCTTGAGTTA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCC-TTCTCGACTTAAGTTA
* *
376447 TGCTGTAAATGATGTGCCCTCG
64 TGCTGCAAATGATGTG-CCTTG
* * * * * *
376469 AAGCTAAGTGTAATCGAACTCGATGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
376530 ATGTAAATGATGTGCCTTA
66 CTGCAAATGATGTGCCTTG
* * *
376549 GAGCTGAGCGTAG-CTGAACTCGAAGGACTTTGATTGGAAGATAACCCTTCTCGACTTAAGTTAT
1 GAGCTGAGCGTAGTC-GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
376613 GCTGCAAATGATATGCCTTA
65 GCTGCAAATGATGTGCCTTG
** * * *
376633 GAGCTGAGTATAGTCGAACTCGAAGGTC-TT--TTGGCAGATAGCCCTTCTCAACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
376695 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
376714 GAGATAAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
376779 CTGCAAATGATATGCCTTA
66 CTGCAAATGATGTGCCTTG
* * * * * * *
376798 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGGCAAATAGCTCTTCTAGCCTTGAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
376862 GCTGCAAATGATGTGCCTTA
65 GCTGCAAATGATGTGCCTTG
* * *
376882 AAGCTAAGCATAGTCGAACTCGAAGG
1 GAGCTGAGCGTAGTCGAACTCGAAGG
376908 ACTTGGCTCA
Statistics
Matches: 777, Mismatches: 136, Indels: 52
0.81 0.14 0.05
Matches are distributed among these distances:
79 1 0.00
80 49 0.06
81 201 0.26
82 18 0.02
83 6 0.01
84 407 0.52
85 68 0.09
86 27 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:376089 original size:165 final size:165
Alignment explanation
Indices: 375885--376907 Score: 1166
Period size: 165 Copynumber: 6.2 Consensus size: 165
375875 GTTTGCCTCT
* *
375885 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
* * * *
375950 CTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTTGGCAGATAGCCCTT
66 CTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCCCTT
*
376015 CTCAACTTAAGTTATGCTGTAAATGATGTGCCTTG
131 CTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * * * *
376050 GAGCTGAGCATAGTCAAACTCAAAAGTCTTTGGTTGGCAGATAACCTTTATCGACTTAAGTTTTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
* * * * * *
376115 CTACAGATGATATGCCTTGGGGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-G-G-CAGATAGCC
* * * * *
376180 CTTCT-AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCG
128 CTTCTCA-ACTTAAGTTATGCTGCAAATGATGTG-CCTTG
* * * * * *
376219 AAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCATATAGACCTTT-TCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA-ACCTTTCTCGACTTAAGTTAT
* * * * *
376279 GCTGTAAATGATGTACCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGATTGGCAGATAAC
65 GCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT--TTGGCAGATAGC
* *
376344 CCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
127 CCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * * *
376383 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACATATAACCCTTTCTAGCCTTGAGTTA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAA-CCTTTCTCGACTTAAGTTA
* * * * * * * *
376447 TGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCGATGGTC-TTTGGCAGATAGCC
64 TGCTGCAAATGATATGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCC
* * * *
376511 CTTCTCGACTTAAGTTATGATGTAAATGATGTGCCTTA
128 CTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * *
376549 GAGCTGAGCGTAG-CTGAACTCGAAGGACTTTGATTGGAAGATAACCCTTCTCGACTTAAGTTAT
1 GAGCTGAGCGTAGTC-GAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTAT
**
376613 GCTGCAAATGATATGCCTTAGAGCTGAGTATAGTCGAACTCGAAGGTCTTTTGGCAGATAGCCCT
65 GCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCCCT
*
376678 TCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTG
130 TCTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * *
376714 GAGATAAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
* *
376779 CTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAAATAGCT
66 CTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT--TGGCAGATAGCC
* * * *
376844 CTTCT-AGCCTTGAGCTATGCTGCAAATGATGTGCCTTA
128 CTTCTCA-ACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * *
376882 AAGCTAAGCATAGTCGAACTCGAAGG
1 GAGCTGAGCGTAGTCGAACTCGAAGG
376908 ACTTGGCTCA
Statistics
Matches: 724, Mismatches: 108, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
164 51 0.07
165 382 0.53
166 92 0.13
167 7 0.01
168 118 0.16
169 52 0.07
170 22 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (165 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATG
CTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCCCTT
CTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
Found at i:376253 original size:249 final size:248
Alignment explanation
Indices: 375885--376907 Score: 1232
Period size: 249 Copynumber: 4.1 Consensus size: 248
375875 GTTTGCCTCT
* * * * *
375885 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTAT
* * * * * *
375949 GCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTTGGCAGATAGCCCT
65 GCTGCAAATGATGTGCCTCGAAGCTAAGTGTAATCGAACTCGAGGGTC-TTTGGCAGATAGCCCT
* * * * *
376014 TCTCAACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCAAAAGTCT
129 TCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* * * * * *
376079 TTGGTTGGCAGATAACCTTTATCGACTTAAGTTTTGCTACAGATGATATGCCTTG
194 TTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
* * * *
376134 GGGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
* * * * *
376199 TTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCATATAGACCTT
66 CTGCAAATGATGTG-CCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTT
* * *
376264 TTCGACTTAAGCTATGCTGTAAATGATGTACCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
130 CTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
376329 TGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
195 TGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
* * *
376383 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACATATAACCCTTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCC-TTCTAGACTTAAGTTAT
* *
376448 GCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCGATGGTCTTTGGCAGATAGCCCT
65 GCTGCAAATGATGTG-CCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
* * *
376513 TCTCGACTTAAGTTATGATGTAAATGATGTGCCTTAGAGCTGAGCGTAG-CTGAACTCGAAGGAC
129 TCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTC-GAACTCAAAGGTC
* *
376577 TTTGATTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTA
193 TTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
** * *
376633 GAGCTGAGTATAGTCGAACTCGAAGGTCTTTT-G-G-CAGATAGCCCTTCTCA-ACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCT-AGACTTAAGTTAT
* * * * * * * *
376694 GCTGCAAATGATGTGCCTTGGAGATAAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAAC
65 GCTGCAAATGATGTGCCTCGAAGCTAAGTGTAATCGAACTCG-AGG-GTCT--TTGGCAGATAGC
* * * *
376759 CTTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGG
126 CCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGG
* * * * * * * * * *
376824 TCTTTTG-GTGGCAAATAGCTCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTA
191 TC-TTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
* * *
376882 AAGCTAAGCATAGTCGAACTCGAAGG
1 GAGCTGAGCGTAGTCGAACTCGAAGG
376908 ACTTGGCTCA
Statistics
Matches: 680, Mismatches: 83, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
245 22 0.03
246 28 0.04
247 11 0.02
248 1 0.00
249 363 0.53
250 255 0.38
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (248 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATGTGCCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTC
TCGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
GATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
Found at i:378280 original size:95 final size:94
Alignment explanation
Indices: 378108--378303 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 94
378098 AGATAGTTCA
* * * * ** *
378108 ATATGTAAACACCTTTATCAGGTTAACTGAATCTTATCCATAAAGTTGTGGCATTTAACCAATTA
1 ATATATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGAGGCATTTAACCAATTA
* *
378173 CCTTTGAGGGACAACTCAATCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTTATTGT
* ** *
378202 ATAGTATAATCACCTTTATTAGGCTAGGTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGAGGCATTTAACCAATT
*
378267 -GCTCTAGAGGGACAACTCAAGCTTTATTGT
65 ACCT-TAGAGGGACAACTCAAGCTTTATTGT
378297 ATATATA
1 ATATATA
378304 TAATATTATA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 9 0.10
95 77 0.90
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGAGGCATTTAACCAATTA
CCTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:387869 original size:13 final size:13
Alignment explanation
Indices: 387847--387880 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
387837 TATATATATA
387847 TATA-ATAATACG
1 TATAGATAATACG
387859 TATAGATAATACG
1 TATAGATAATACG
387872 TATAGATAA
1 TATAGATAA
387881 ATAATATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (13 bp):
TATAGATAATACG
Found at i:388470 original size:37 final size:37
Alignment explanation
Indices: 388404--388515 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 37
388394 ATGCTTATGG
* * *
388404 ATCTTATTTTTAGGTGTTTAAATCTTAGTAAAACTCT
1 ATCTTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
388441 ATTTTATTTTTAGGAATTTGAATCATAGTAAAATTCT
1 ATCTTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
388478 ATCCTATTTTTAGGAGTTTGAATCATAATAAAACTCT
1 ATCTTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
388515 A
1 A
388516 ACGTTATGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.46
Consensus pattern (37 bp):
ATCTTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:391088 original size:64 final size:64
Alignment explanation
Indices: 390984--391114 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
390974 ACGATAACCA
* *
390984 TTCTCTCCTTCCAAAAGCAAACTCATTTCTATTTTTATATGAGTAAACATCCATTTATCATTGT
1 TTCTCTCATTCCAAAAGCAAACTCATTTCTATTTTAATATGAGTAAACATCCATTTATCATTGT
*
391048 TTCTCTCATTCCAAAAGCAAATTCATTTCTATTTTAATATGAGTAAACATCCATTTATCATTGT
1 TTCTCTCATTCCAAAAGCAAACTCATTTCTATTTTAATATGAGTAAACATCCATTTATCATTGT
391112 TTC
1 TTC
391115 CATCAATAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.43
Consensus pattern (64 bp):
TTCTCTCATTCCAAAAGCAAACTCATTTCTATTTTAATATGAGTAAACATCCATTTATCATTGT
Found at i:401424 original size:23 final size:22
Alignment explanation
Indices: 401389--401431 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
401379 TAAATCTTTC
401389 GATTATTACATAAATAGTTAAAT
1 GATTATTACATAAATA-TTAAAT
**
401412 GATTATTTTATAAATATTAA
1 GATTATTACATAAATATTAA
401432 CAATTAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTATTACATAAATATTAAAT
Found at i:402610 original size:33 final size:35
Alignment explanation
Indices: 402572--402657 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
402562 AGGTTTACAT
* *
402572 AGTAAACTATTTCA-TGGTTA-TGTA-TTGTTATTA
1 AGTAAACTATTTCACT-GTAAGTGTATTTATTATTA
* *
402605 AGTAAACTATTTTACTGTAAGTTTATTTATTATTA
1 AGTAAACTATTTCACTGTAAGTGTATTTATTATTA
402640 AGTAAACTATTTCACTGT
1 AGTAAACTATTTCACTGT
402658 CAGTTTGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 16 0.36
34 4 0.09
35 25 0.56
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (35 bp):
AGTAAACTATTTCACTGTAAGTGTATTTATTATTA
Found at i:404059 original size:37 final size:36
Alignment explanation
Indices: 403995--404083 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 36
403985 AATCACTTCG
* * **
403995 ATTCAAACTGTTTTTTATTATTATCAATATTCATTA
1 ATTCAAACTATTTTTTATCATTATCAATATTCACCA
404031 ATTCAAACTATTTTCTTATCATTATCAATATTCACCA
1 ATTCAAACTATTTT-TTATCATTATCAATATTCACCA
* *
404068 ATTCAACCTGTTTTTT
1 ATTCAAACTATTTTTT
404084 TATTGAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 15 0.33
37 31 0.67
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.49
Consensus pattern (36 bp):
ATTCAAACTATTTTTTATCATTATCAATATTCACCA
Found at i:410439 original size:35 final size:34
Alignment explanation
Indices: 410354--410440 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
410344 ATTTGGTATT
*
410354 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
410388 TAAATGATAACCAAATTACAATAACTGATATTAAAT-G
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
*
410425 TTAATA-AACAAAATTA
1 TAAATACAACAAAATTA
410441 ATTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 7 0.16
38 7 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:411209 original size:20 final size:20
Alignment explanation
Indices: 411186--411255 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
411176 GTTTCCAGAT
411186 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
**
411206 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
* *
411227 TCGCAACTCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
411247 TCGCAACGC
1 TCGCAACGC
411256 TGAATTTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:413275 original size:21 final size:21
Alignment explanation
Indices: 413251--413318 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
413241 GAAAACCGCA
413251 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTATTATCGCG
* **
413272 TTGCGA--TAGTCAGAATCGCG
1 TTGCGATTTTGT-ATTATCGCG
*
413292 TTGCGATTATGTATTATCGCG
1 TTGCGATTTTGTATTATCGCG
413313 TTGCGA
1 TTGCGA
413319 ATCTAGAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 13 0.35
21 19 0.51
22 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGCGATTTTGTATTATCGCG
Found at i:413337 original size:41 final size:41
Alignment explanation
Indices: 413251--413339 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
413241 GAAAACCGCA
* * *
413251 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTATGTATTATCGCGTTGCGATAGTCAGAAACGAG
*
413292 TTGCGATTATGTATTATCGCGTTGCGA-A-TCTAGAAACTGAT
1 TTGCGATTATGTATTATCGCGTTGCGATAGTC-AGAAAC-GAG
413333 TTGCGAT
1 TTGCGAT
413340 ACTGGAGATC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.05
40 6 0.14
41 34 0.81
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCGTTGCGATAGTCAGAAACGAG
Found at i:413368 original size:19 final size:19
Alignment explanation
Indices: 413344--413380 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
413334 TGCGATACTG
*
413344 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
413363 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
413381 TGTTTATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:419082 original size:41 final size:41
Alignment explanation
Indices: 419025--419106 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
419015 CACTTCCATT
419025 TTGCTGGTAAAAGATGGAATGGTTAATGCATGCATGAAGAA
1 TTGCTGGTAAAAGATGGAATGGTTAATGCATGCATGAAGAA
419066 TTGCTGGTAAAAGATGGAATGGTTAATGCATGCATGAAGAA
1 TTGCTGGTAAAAGATGGAATGGTTAATGCATGCATGAAGAA
419107 ATGTTGTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.27
Consensus pattern (41 bp):
TTGCTGGTAAAAGATGGAATGGTTAATGCATGCATGAAGAA
Found at i:419146 original size:14 final size:15
Alignment explanation
Indices: 419129--419161 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
419119 TATTTTGTCT
419129 TTAAG-ATTTAGAAA
1 TTAAGAATTTAGAAA
*
419143 TTAAGAATTTAGAAT
1 TTAAGAATTTAGAAA
419158 TTAA
1 TTAA
419162 TGTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (15 bp):
TTAAGAATTTAGAAA
Found at i:420371 original size:48 final size:48
Alignment explanation
Indices: 420317--420429 Score: 199
Period size: 48 Copynumber: 2.4 Consensus size: 48
420307 TAATTTAACG
420317 TAATACAGAAATATTTGAAATTAAATCTATTATTATATCAAACTAGCA
1 TAATACAGAAATATTTGAAATTAAATCTATTATTATATCAAACTAGCA
* *
420365 TAATACAGAAATATTTGAAATTAAATTTATTATTATATCAAATTAGCA
1 TAATACAGAAATATTTGAAATTAAATCTATTATTATATCAAACTAGCA
*
420413 TAATACATAAATATTTG
1 TAATACAGAAATATTTG
420430 GGGCTAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (48 bp):
TAATACAGAAATATTTGAAATTAAATCTATTATTATATCAAACTAGCA
Found at i:420811 original size:18 final size:17
Alignment explanation
Indices: 420775--420817 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
420765 CAAAAAGAAG
*
420775 ATAAATAAAATTTTAAA
1 ATAAATAAAATTGTAAA
*
420792 ATAAATATAATATGTAAA
1 ATAAATAAAAT-TGTAAA
420810 ATAAATAA
1 ATAAATAA
420818 TTAATCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAATAAAATTGTAAA
Found at i:421160 original size:17 final size:17
Alignment explanation
Indices: 421135--421183 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
421125 TGGTAAATAT
*
421135 AAAATAATATTTATTTA
1 AAAAAAATATTTATTTA
*
421152 AAAAAAATATTCATTTA
1 AAAAAAATATTTATTTA
**
421169 ATATCAAATATTTAT
1 A-AAAAAATATTTAT
421184 ATATATGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAAAATATTTATTTA
Found at i:429013 original size:12 final size:12
Alignment explanation
Indices: 428998--429022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
428988 TTTTTTTTTC
428998 AAATTTTATTAT
1 AAATTTTATTAT
429010 AAATTTTATTAT
1 AAATTTTATTAT
429022 A
1 A
429023 TTATTTGATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTTTATTAT
Found at i:435623 original size:14 final size:14
Alignment explanation
Indices: 435604--435647 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
435594 TTTGATTTAG
*
435604 GATTTATGGTTCAT
1 GATTTATGGTTCAA
*
435618 GATTTAGGGTTCCAA
1 GATTTATGGTT-CAA
435633 G-TTTATGGTTCAA
1 GATTTATGGTTCAA
435646 GA
1 GA
435648 GGTTAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 4 0.16
14 18 0.72
15 3 0.12
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (14 bp):
GATTTATGGTTCAA
Found at i:435691 original size:21 final size:21
Alignment explanation
Indices: 435633--435691 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
435623 AGGGTTCCAA
*
435633 GTTTATGGTTCAAGAGGTTAATG
1 GTTTAAGGTT-AAG-GGTTAATG
* *
435656 GTTT-AGGATATAGGGTTAATT
1 GTTTAAGGTTA-AGGGTTAATG
435677 GTTTAAGGTTAAGGG
1 GTTTAAGGTTAAGGG
435692 GTTAGGGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 16 0.53
22 10 0.33
23 4 0.13
ACGTcount: A:0.27, C:0.02, G:0.32, T:0.39
Consensus pattern (21 bp):
GTTTAAGGTTAAGGGTTAATG
Found at i:435729 original size:20 final size:21
Alignment explanation
Indices: 435685--435736 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
435675 TTGTTTAAGG
* * *
435685 TTAAGGGGTTAGGGTTAACAG
1 TTAAGGGTTTAGGGTGAACAC
435706 TTAAGGGTTTAGGGTGAA-AC
1 TTAAGGGTTTAGGGTGAACAC
*
435726 TTAAGGATTTA
1 TTAAGGGTTTA
435737 ATACCAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.33
Consensus pattern (21 bp):
TTAAGGGTTTAGGGTGAACAC
Found at i:442199 original size:2 final size:2
Alignment explanation
Indices: 442192--442224 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
442182 GGATCATAAC
*
442192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
442225 GTATGAAAAA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:442729 original size:19 final size:19
Alignment explanation
Indices: 442705--442822 Score: 76
Period size: 20 Copynumber: 5.9 Consensus size: 19
442695 AAATGACCAA
442705 CAAAATCGCAACGCGATAT
1 CAAAATCGCAACGCGATAT
*
442724 CAAAATCGCAACGCGATTT
1 CAAAATCGCAACGCGATAT
* * * * *
442743 AAAAAAACGCAACGTTGAAAA
1 -CAAAATCGCAACG-CGATAT
* * *
442764 GAATATCGCAACGCGATCTTT
1 CAAAATCGCAACGCGA--TAT
*
442785 CAAGAATCGCAATGCGAT-T
1 CAA-AATCGCAACGCGATAT
442804 CAGAAAATCGCAACGCGAT
1 C--AAAATCGCAACGCGAT
442823 CTTCCAAGAA
Statistics
Matches: 74, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
19 22 0.30
20 35 0.47
21 6 0.08
22 11 0.15
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (19 bp):
CAAAATCGCAACGCGATAT
Found at i:442796 original size:22 final size:22
Alignment explanation
Indices: 442768--442833 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
442758 TGAAAAGAAT
442768 ATCGCAACGCGATCTTTCAAGA
1 ATCGCAACGCGATCTTTCAAGA
* *
442790 ATCGCAATGCGA---TTCAGAAA
1 ATCGCAACGCGATCTTTCA-AGA
*
442810 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATCTTTCAAGA
442832 AT
1 AT
442834 TTTCTCTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
22 15 0.43
23 3 0.09
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (22 bp):
ATCGCAACGCGATCTTTCAAGA
Found at i:442893 original size:6 final size:6
Alignment explanation
Indices: 442882--442947 Score: 132
Period size: 6 Copynumber: 11.0 Consensus size: 6
442872 GACACGTATT
442882 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
442930 ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG
442948 GCGGCGGCGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:443433 original size:6 final size:6
Alignment explanation
Indices: 443422--443478 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
443412 TCTCGTCTCG
443422 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
443470 GGTCGT GGT
1 GGTCGT GGT
443479 AATGGTAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:443484 original size:6 final size:6
Alignment explanation
Indices: 443475--443505 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
443465 GTCGTGGTCG
443475 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
443506 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:443654 original size:20 final size:20
Alignment explanation
Indices: 443629--443989 Score: 328
Period size: 20 Copynumber: 17.9 Consensus size: 20
443619 ACAATTGTTG
443629 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
443649 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
*
443669 GAAACGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* * *
443689 GAATCGAGTTGCGAATCTT-G
1 GAATCGCGTTGCG-ATTTTCT
*
443709 GAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
*
443729 GAAACGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
443749 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
443769 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
*
443789 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
* * *
443809 TAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
443829 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
443849 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
443869 GAAGATCGCGTTGCGATTTTCT
1 G-A-ATCGCGTTGCGATTTTCT
* *
443891 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
443911 GAAGATCGCGTTGCGATTTTCT
1 G-A-ATCGCGTTGCGATTTTCT
** * *
443933 -TTTCAACGTTGCGTTTTTCT
1 GAATC-GCGTTGCGATTTTCT
*
443953 AAATCGCGTTGCGA-TTT-T
1 GAATCGCGTTGCGATTTTCT
443971 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
443990 GTTGGTCATT
Statistics
Matches: 277, Mismatches: 43, Indels: 42
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.01
19 27 0.10
20 199 0.72
21 22 0.08
22 27 0.10
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTTTCT
Found at i:443670 original size:40 final size:40
Alignment explanation
Indices: 443626--443932 Score: 390
Period size: 40 Copynumber: 7.6 Consensus size: 40
443616 GGAACAATTG
443626 TTGGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
1 TTGGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
* *
443666 TTGGAAACGCGTTGCGATTTTCTGAATCG-AGTTGCGAATC
1 TTGGAATCGCGTTGCGATTTTCTGAATCGCA-TTGCGATTC
* * *
443706 TTGGAATCGCGTTGCGATTCTT-GGAAACGCGTTGCGATT-
1 TTGGAATCGCGTTGCGATT-TTCTGAATCGCATTGCGATTC
* * * *
443745 TTCTGAATCGCATTGCGATTCTT-GGAATCGCGTTGCGATT-
1 TT-GGAATCGCGTTGCGATT-TTCTGAATCGCATTGCGATTC
* * *
443785 TTCTGAATCGCGTTGCGATTCTCTTAATCGCATTGCGATTC
1 TT-GGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
443826 TTGGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
1 TTGGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
443866 TTGGAAGATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
1 TTGG-A-ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
443908 TTGGAAGATCGCGTTGCGATTTTCT
1 TTGG-A-ATCGCGTTGCGATTTTCT
443933 TTTCAACGTT
Statistics
Matches: 241, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.02
40 172 0.71
41 5 0.02
42 60 0.25
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (40 bp):
TTGGAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTC
Found at i:446599 original size:21 final size:21
Alignment explanation
Indices: 446573--446674 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 21
446563 GTTTCCAGAT
446573 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
446594 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
446615 TCGCAATGCGAAACGCGAACTTCGACTA
1 T--C---GC--AACGCGAACTTCGACTA
* *
446643 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
446664 TCGCAATGCGA
1 TCGCAACGCGA
446675 TTTACATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
21 47 0.67
23 3 0.04
26 3 0.04
28 17 0.24
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:446641 original size:28 final size:28
Alignment explanation
Indices: 446598--446654 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
446588 CGACTATCGC
*
446598 AACGCGAACTTGGACTATCGCAATGCGA
1 AACGCGAACTTCGACTATCGCAATGCGA
446626 AACGCGAACTTCGACTATCGCAATGCGA
1 AACGCGAACTTCGACTATCGCAATGCGA
446654 A
1 A
446655 CTTGGACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (28 bp):
AACGCGAACTTCGACTATCGCAATGCGA
Found at i:446654 original size:49 final size:49
Alignment explanation
Indices: 446577--446674 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
446567 CCAGATTCGC
446577 AACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGA
1 AACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGA
*
446626 AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGA
1 AACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGA
446675 TTTACATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (49 bp):
AACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGA
Found at i:446713 original size:21 final size:22
Alignment explanation
Indices: 446683--446939 Score: 180
Period size: 21 Copynumber: 12.6 Consensus size: 22
446673 GATTTACATA
*
446683 TTCGCATTGCGATAGTTC-AAG
1 TTCGCGTTGCGATAGTTCGAAG
446704 TTCGCGTTGCGATAG-TCGAAG
1 TTCGCGTTGCGATAGTTCGAAG
* * *
446725 TTCGCGTTGCGAT-TTTCCAAA
1 TTCGCGTTGCGATAGTTCGAAG
446746 TT--CGTTGCGATAG-TCGAAG
1 TTCGCGTTGCGATAGTTCGAAG
* * *
446765 TTCGCGTTGCGAT-TTTCCAAA
1 TTCGCGTTGCGATAGTTCGAAG
446786 TT--CGTTGCGATAG-TCGAAG
1 TTCGCGTTGCGATAGTTCGAAG
* * *
446805 TTCGCGTTGCGAT-TTTCCAAA
1 TTCGCGTTGCGATAGTTCGAAG
*
446826 TT--CGTTACGATAG-TCGAAG
1 TTCGCGTTGCGATAGTTCGAAG
* * *
446845 TTCGCGTTGCGAT-TTTCCAAA
1 TTCGCGTTGCGATAGTTCGAAG
446866 TT--CGTTGCGATAG-TCGAAG
1 TTCGCGTTGCGATAGTTCGAAG
* *
446885 TTCGCGTTGCGATTTA-TTCAAAA
1 TTCGCGTTGCGA--TAGTTCGAAG
*
446908 TT--CGTTGCGATAG-TCCAAG
1 TTCGCGTTGCGATAGTTCGAAG
*
446927 TTAGCGTTGCGAT
1 TTCGCGTTGCGAT
446940 TTATTCCAAA
Statistics
Matches: 182, Mismatches: 31, Indels: 46
0.70 0.12 0.18
Matches are distributed among these distances:
19 67 0.37
20 2 0.01
21 105 0.58
23 8 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (22 bp):
TTCGCGTTGCGATAGTTCGAAG
Found at i:446759 original size:40 final size:40
Alignment explanation
Indices: 446708--446964 Score: 442
Period size: 40 Copynumber: 6.3 Consensus size: 40
446698 TTCAAGTTCG
446708 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
446748 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
446788 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
446828 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
446868 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* *
446910 CGTTGCGATAGTCCAAGTTAGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
446952 CGTTGCGATAGTC
1 CGTTGCGATAGTC
446965 CAAAATCGTA
Statistics
Matches: 209, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 147 0.70
41 2 0.01
42 60 0.29
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:446955 original size:21 final size:20
Alignment explanation
Indices: 446729--446973 Score: 150
Period size: 19 Copynumber: 12.2 Consensus size: 20
446719 TCGAAGTTCG
446729 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
446748 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
446767 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGATTATTCCAAATT
* * *
446788 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
446807 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGATTATTCCAAATT
* * * *
446828 CGTTACGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
446847 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGATTATTCCAAATT
* * *
446868 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
*
446887 CGCGTTGCGATTTATTCAAAATT
1 --CGTTGCGA-TTATTCCAAATT
* *
446910 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
446929 AGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
* *
446952 CGTTGCGA-TAGTCCAAAAT
1 CGTTGCGATTATTCCAAATT
446971 CGT
1 CGT
446974 AATGACTGGT
Statistics
Matches: 172, Mismatches: 33, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
18 4 0.02
19 75 0.44
21 73 0.42
22 3 0.02
23 17 0.10
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:447689 original size:42 final size:42
Alignment explanation
Indices: 447627--447803 Score: 304
Period size: 42 Copynumber: 4.3 Consensus size: 42
447617 TGCGATTTTG
447627 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
447669 GATTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
447711 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
447753 GACTATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
447793 GACTATCGCAA
1 GACTATCGCAA
447804 TGCGAATATG
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 28 0.22
41 3 0.02
42 97 0.76
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:447800 original size:21 final size:20
Alignment explanation
Indices: 447624--447809 Score: 119
Period size: 21 Copynumber: 8.9 Consensus size: 20
447614 CGTTGCGATT
* *
447624 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
447643 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* *
447666 TTCGATTATCGCAA-CGAAC
1 TTGGAATATCGCAAGCGAAC
447685 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* * *
447708 TTCGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
447727 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* * * *
447750 CTCGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
* *
447769 TTGAAAAATCGCAACGCGAAC
1 TTGGAATATCGCAA-GCGAAC
*
447790 TTGGACTATCGCAATGCGAA
1 TTGGAATATCGCAA-GCGAA
447810 TATGTAAATC
Statistics
Matches: 127, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
19 38 0.30
21 62 0.49
23 27 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
TTGGAATATCGCAAGCGAAC
Found at i:447810 original size:42 final size:41
Alignment explanation
Indices: 447627--447828 Score: 284
Period size: 42 Copynumber: 4.9 Consensus size: 41
447617 TGCGATTTTG
447627 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTC
* *
447669 GATTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAA-TTTGAATAAATCGCAACGCGAACTTC
*
447711 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTC
*
447753 GACTATCGCAACGAATTTGAA-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTC
* *
447793 GACTATCGCAATGCGAATATG--TAAATCGCAATGCGA
1 GACTATCGCAA--CGAATTTGAATAAATCGCAACGCGA
447829 TAGTCGAAGT
Statistics
Matches: 146, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
40 28 0.19
41 18 0.12
42 98 0.67
43 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTC
Found at i:451203 original size:2 final size:2
Alignment explanation
Indices: 451196--451221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
451186 TAACTTGTTA
451196 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
451222 CACAAGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453847 original size:2 final size:2
Alignment explanation
Indices: 453840--453865 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
453830 ACTGCCATGC
453840 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
453866 ACAAGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:455508 original size:22 final size:23
Alignment explanation
Indices: 455480--455527 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
455470 CAAATACAAA
455480 ACCTAAAAAT-AGAGTAAGAAGT
1 ACCTAAAAATAAGAGTAAGAAGT
455502 ACCTAAAAATAGAGAGTAAGAAGT
1 ACCTAAAAATA-AGAGTAAGAAGT
455526 AC
1 AC
455528 AATTTTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.42
24 14 0.58
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (23 bp):
ACCTAAAAATAAGAGTAAGAAGT
Found at i:458932 original size:28 final size:28
Alignment explanation
Indices: 458877--458944 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
458867 CACTAAATTT
* * *
458877 AGTTCTTCAAATATGATGTTGGTAAGTC
1 AGTTCTTGAAATATGATGCTAGTAAGTC
* *
458905 AGTTCTTGAAATATTATGCTAGTGAGTC
1 AGTTCTTGAAATATGATGCTAGTAAGTC
458933 AGTGT-TTGAAAT
1 AGT-TCTTGAAAT
458945 CAATGACGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (28 bp):
AGTTCTTGAAATATGATGCTAGTAAGTC
Found at i:459376 original size:25 final size:24
Alignment explanation
Indices: 459322--459377 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
459312 TTTATTATAA
*
459322 AATTTT-ATAATTATTAATAATGT
1 AATTTTAATAATTATTAATAATAT
* *
459345 ATTTTTAATATATTTTTAATAATAT
1 AATTTTAATA-ATTATTAATAATAT
459370 AATTTTAA
1 AATTTTAA
459378 AAACATCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.19
24 3 0.11
25 19 0.70
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
AATTTTAATAATTATTAATAATAT
Found at i:465301 original size:60 final size:57
Alignment explanation
Indices: 465216--465401 Score: 146
Period size: 60 Copynumber: 3.1 Consensus size: 57
465206 CATACGTCCT
* *
465216 CAAATTATGACTCTT-ATTTTAAATTAGTCTCTAAACTTTTAAATATTTCAATTTCATTC
1 CAAACTATGAC-CTTCATTCTAAATTAGTC-CTAAACTTTTAAA-ATTTCAATTTCATTC
* * * * *
465275 CTAAACTATGA-CTGTCGTTCTAAATTAATCCTCAAAGTTTTGAAAATCTCATTTTCACTCTC
1 C-AAACTATGACCT-TCATTCTAAATTAGTCCT-AAACTTTT-AAAATTTCAATTTCA-T-TC
* * * *
465337 C-AACTATGACCTTCATTCTAAATTGGTCC-AAACTTTTTGAACATTTCAATTGCATCC
1 CAAACTATGACCTTCATTCTAAATTAGTCCTAAAC-TTTT-AAAATTTCAATTTCATTC
465394 CAAACTAT
1 CAAACTAT
465402 ACTAATCACA
Statistics
Matches: 101, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
57 2 0.02
58 12 0.12
59 20 0.20
60 58 0.57
61 6 0.06
62 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (57 bp):
CAAACTATGACCTTCATTCTAAATTAGTCCTAAACTTTTAAAATTTCAATTTCATTC
Found at i:465947 original size:36 final size:36
Alignment explanation
Indices: 465907--465978 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
465897 AAAATGTAGC
465907 TTTCTTAATTTCTTTTTGTACTTTTTTTTATATAGT
1 TTTCTTAATTTCTTTTTGTACTTTTTTTTATATAGT
465943 TTTCTTAATTTCTTTTTGTACTTTTTTTTATATAGT
1 TTTCTTAATTTCTTTTTGTACTTTTTTTTATATAGT
465979 GATGGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (36 bp):
TTTCTTAATTTCTTTTTGTACTTTTTTTTATATAGT
Found at i:470489 original size:24 final size:25
Alignment explanation
Indices: 470453--470500 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
470443 ATGCCTCGAA
*
470453 CATCTCATGCATTTT-TGCATTTTG
1 CATCTCATGCATTTTAAGCATTTTG
470477 CATCTACAT-CATTTTAAGCATTTT
1 CATCT-CATGCATTTTAAGCATTTT
470501 CATAAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (25 bp):
CATCTCATGCATTTTAAGCATTTTG
Found at i:471668 original size:19 final size:18
Alignment explanation
Indices: 471637--471684 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
471627 AAAACAAAGA
*
471637 AAAAAGAGAAACAAAATC
1 AAAAAGAAAAACAAAATC
471655 AAAAAGAAAGAACAAAATC
1 AAAAAGAAA-AACAAAATC
471674 AAAAAGAAAAA
1 AAAAAGAAAAA
471685 GGGACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAACAAAATC
Found at i:472314 original size:22 final size:22
Alignment explanation
Indices: 472286--472362 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
472276 ACTACCCCAT
472286 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
*
472308 CAAACCTTTGAACATCAAAT-A
1 CAAACCTTTGAGCATCAAATGA
* *
472329 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
472352 CAAACCTTTGA
1 CAAACCTTTGA
472363 CCAAACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:472794 original size:19 final size:19
Alignment explanation
Indices: 472747--472800 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
472737 TGAGGAATAT
472747 TTGGGGCATC-TTTGGAGA
1 TTGGGGCATCATTTGGAGA
*
472765 TT----CAACATTTGGAGA
1 TTGGGGCATCATTTGGAGA
*
472780 TTGGGGCATCATTTGGGGA
1 TTGGGGCATCATTTGGAGA
472799 TT
1 TT
472801 CAACATCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
18 2 0.07
19 13 0.46
ACGTcount: A:0.20, C:0.11, G:0.33, T:0.35
Consensus pattern (19 bp):
TTGGGGCATCATTTGGAGA
Found at i:473201 original size:36 final size:36
Alignment explanation
Indices: 473092--473229 Score: 154
Period size: 37 Copynumber: 3.8 Consensus size: 36
473082 TTTCCAATAT
* * *
473092 AAATTTTGTCTCGCTTGAGATAGTC-TCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTC-TTTGAAAC
* * * *
473128 AAGATTTTATCTCGCTTGAGATAGTTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGACAG-TCTTCTTTGAAAC
* *
473166 AAATTTCGTCTCCCTTGAGACAGTCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
473202 AAATTTTGTCTCCCTTGAGACAGT-TTCT
1 AAATTTTGTCTCCCTTGAGACAGTCTTCT
473230 CTCCAGACAA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
35 3 0.03
36 36 0.41
37 37 0.42
38 10 0.11
39 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
Found at i:474299 original size:106 final size:106
Alignment explanation
Indices: 473230--474292 Score: 1599
Period size: 106 Copynumber: 10.0 Consensus size: 106
473220 GACAGTTTCT
* * *
473230 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
473295 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * * * ** *
473336 CTCAAGAAAACACAAGCTCAACATCAC-AGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTC
1 CTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
473400 AATTTCAGAGTCAATTTCAACTTTACAGCGAAGGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
473442 CTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
473507 ATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * *
473548 CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
473613 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
473654 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACACACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* * *
473719 ATTTCAGAGCCAAATTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
473760 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
473825 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * *
473866 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACAGCTGGTTGTTAATAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
473931 ATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
473972 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
474037 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * ** *
474078 CTCGAGACGATGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
474143 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGTA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
** * * * * * * * *
474184 CTTGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCTCG
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
474249 ATTCCATAGCCAATTTCAACTTCAC-GACGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGA
474290 CTC
1 CTC
474293 GGAACAATCC
Statistics
Matches: 867, Mismatches: 87, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
105 2 0.00
106 864 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
Found at i:475222 original size:21 final size:22
Alignment explanation
Indices: 475193--475236 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
475183 ACACGATTTA
*
475193 CACACAAAACACAGAGG-AAAG
1 CACACAAAACACAAAGGCAAAG
* *
475214 CACAGAAAATACAAAGGCAAAG
1 CACACAAAACACAAAGGCAAAG
475236 C
1 C
475237 TATTGTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.23, G:0.18, T:0.02
Consensus pattern (22 bp):
CACACAAAACACAAAGGCAAAG
Found at i:475547 original size:2 final size:2
Alignment explanation
Indices: 475542--475574 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
475532 TTTTAGGTTT
475542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
475575 TTCCTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:487252 original size:29 final size:29
Alignment explanation
Indices: 487217--487298 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
487207 AAACTAAATT
*
487217 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
487246 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
487275 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
487299 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:489410 original size:22 final size:23
Alignment explanation
Indices: 489371--489413 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
489361 TGTGGTGTTG
489371 AGTCTATAACGTATTAAAAGTGT
1 AGTCTATAACGTATTAAAAGTGT
*
489394 AGTCTCTAAC-TATTAAAAGT
1 AGTCTATAACGTATTAAAAGT
489414 TACAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (23 bp):
AGTCTATAACGTATTAAAAGTGT
Found at i:490094 original size:2 final size:2
Alignment explanation
Indices: 490089--490122 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
490079 TACACACATG
490089 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
490123 GTTTCTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:494739 original size:31 final size:31
Alignment explanation
Indices: 494704--494817 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 31
494694 AAATATTATT
494704 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
494735 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
494767 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* *
494794 TATT-TTTATTTTAATAATATATAA
1 TATTATAT-TTTTAATATTATATAA
494818 TAAATTTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
27 4 0.06
28 11 0.16
29 7 0.10
30 7 0.10
31 28 0.41
32 12 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:494742 original size:22 final size:23
Alignment explanation
Indices: 494712--494755 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
494702 TTTATTAATT
494712 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
494735 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
494756 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:494818 original size:54 final size:52
Alignment explanation
Indices: 494721--494823 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
494711 TTATTAATAT
*
494721 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
494773 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
494824 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:494836 original size:23 final size:26
Alignment explanation
Indices: 494718--494843 Score: 68
Period size: 29 Copynumber: 4.8 Consensus size: 26
494708 AATTTATTAA
* *
494718 TATTTATAATAATATAATATTATATTTT
1 TATTT-TAATAATAT-ATAATAAATTTT
* * *
494746 TAATATTATATAA-A-ATAATCAA-TTA
1 T-ATTTTA-ATAATATATAATAAATTTT
*
494771 TATTATAATAATATA-AGATATTATATTTT
1 TATTTTAATAATATATA-ATA--A-ATTTT
494800 TATTTTAATAATATATAATAAATTTT
1 TATTTTAATAATATATAATAAATTTT
*
494826 T-TTTT-AT-ATATTTAATAA
1 TATTTTAATAATATATAATAA
494844 TGAATAATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
23 14 0.18
24 8 0.10
25 10 0.13
26 11 0.14
27 2 0.03
28 5 0.06
29 26 0.34
30 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTTTAATAATATATAATAAATTTT
Found at i:494853 original size:19 final size:19
Alignment explanation
Indices: 494831--494883 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
494821 ATTTTTTTTT
*
494831 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
494850 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
494872 ATAT-TTTAATAA
1 ATATATTTAATAA
494884 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:494904 original size:23 final size:23
Alignment explanation
Indices: 494878--494922 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
494868 AATAATATTT
494878 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
494901 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
494923 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:495097 original size:22 final size:21
Alignment explanation
Indices: 495029--495099 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
495019 TAAAAATACT
* *
495029 ATTTAATAATAAATAAATTAT-
1 ATTTAATAAT-AATTATTTATG
* *
495050 TTTTAATAATAATTTTTTATG
1 ATTTAATAATAATTATTTATG
495071 A-TTAATAAT-ATTATTTATTG
1 ATTTAATAATAATTATTTA-TG
495091 TATTTAATA
1 -ATTTAATA
495100 TTTGTAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 7 0.17
20 17 0.43
21 10 0.25
22 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTAATAATAATTATTTATG
Found at i:495287 original size:15 final size:15
Alignment explanation
Indices: 495269--495320 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
495259 TCATTTTCCA
495269 TAATTCAAATTTCAG
1 TAATTCAAATTTCAG
*
495284 TAATTC-ATTTTCTAG
1 TAATTCAAATTTC-AG
* *
495299 TAATTCAAATTCCAA
1 TAATTCAAATTTCAG
495314 TAATTCA
1 TAATTCA
495321 TTTTTCGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 22 0.71
16 4 0.13
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (15 bp):
TAATTCAAATTTCAG
Found at i:495287 original size:29 final size:30
Alignment explanation
Indices: 495254--495324 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
495244 TTCTAGAAAT
*
495254 GTAATTCATTTTCCA-TAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
495283 GTAATTCATTTTCTAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
495313 ATAATTCATTTT
1 GTAATTCATTTT
495325 TCGGAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:497029 original size:19 final size:19
Alignment explanation
Indices: 497005--497056 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
496995 ACTTTCTAAT
*
497005 AATTTTATTATTTTTTAAC
1 AATTTTAATATTTTTTAAC
* * *
497024 AATTTTAAAATATTTTCAC
1 AATTTTAATATTTTTTAAC
497043 AATTTTAATATTTT
1 AATTTTAATATTTT
497057 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTAATATTTTTTAAC
Found at i:497547 original size:11 final size:11
Alignment explanation
Indices: 497531--497556 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
497521 ATTATACTTT
497531 TAATAAAATTA
1 TAATAAAATTA
497542 TAATAAAATTA
1 TAATAAAATTA
497553 TAAT
1 TAAT
497557 TTTTAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATTA
Found at i:506344 original size:2 final size:2
Alignment explanation
Indices: 506337--506375 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
506327 TATCCTCTCA
506337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
506376 ATTTAAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:509009 original size:37 final size:36
Alignment explanation
Indices: 508939--509010 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
508929 AACGATAGTG
*
508939 ATTATTTTTTTTTTTAAAATTTAATAATAATAAAAT
1 ATTATTTTATTTTTTAAAATTTAATAATAATAAAAT
*
508975 ATTATTTTAATTTTTT-ATATTTAATAATATATAAAA
1 ATTATTTT-ATTTTTTAAAATTTAATAATA-ATAAAA
509011 ATTTATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
ATTATTTTATTTTTTAAAATTTAATAATAATAAAAT
Found at i:511842 original size:69 final size:70
Alignment explanation
Indices: 511721--511861 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 70
511711 AGCCTCACCC
* *
511721 TAGGTACTTGGTAGTGAGTGTCATTTGGATGTTAGATGTTTATGTTGAGTGA-CCAAGTCTCATC
1 TAGGTACTTGGTAGTGAGTGTCATTTGCATGTTAGATGTTGATGTTGAGTGACCCAAGTCTCATC
511785 CAATG
66 CAATG
* * *
511790 TAGGTACTTGGTAGTGAGTGTCATTTGCTTGTTAGATGTTGAT-TCTGTGTGACCCAGGTCTCAT
1 TAGGTACTTGGTAGTGAGTGTCATTTGCATGTTAGATGTTGATGT-TGAGTGACCCAAGTCTCAT
511854 CCAATG
65 CCAATG
511860 TA
1 TA
511862 CCTCTTCGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 1 0.02
69 46 0.71
70 18 0.28
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (70 bp):
TAGGTACTTGGTAGTGAGTGTCATTTGCATGTTAGATGTTGATGTTGAGTGACCCAAGTCTCATC
CAATG
Found at i:513121 original size:2 final size:2
Alignment explanation
Indices: 513116--513198 Score: 141
Period size: 2 Copynumber: 41.5 Consensus size: 2
513106 AATATATTTC
513116 AT AT AT AT AT AT 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 AT AT AT AT AT AT
*
513158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
513199 ATGAGATGAT
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.01
2 75 0.97
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:515224 original size:2 final size:2
Alignment explanation
Indices: 515217--515250 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
515207 GAATCTATCA
515217 AT AT 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 AT AT
515251 GTAATTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516781 original size:23 final size:24
Alignment explanation
Indices: 516746--516801 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
516736 TTAATTTTTA
516746 AAAAATATATATTAAAAAAATACT
1 AAAAATATATATTAAAAAAATACT
*
516770 AAAAATAT-TATTAAAAATATACT
1 AAAAATATATATTAAAAAAATACT
* *
516793 TAATATATA
1 AAAAATATA
516802 CATGTAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAAATATATATTAAAAAAATACT
Done.