Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015085.1 Kokia drynarioides strain JFW-HI SEQ_130129, 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: 897486
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 584 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:476341 original size:24 final size:24
Alignment explanation
Indices: 476313--476363 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
476303 AGTTTGACTC
* *
476313 AAACAAATAAACATAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
*
476337 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAACTG
476361 AAA
1 AAA
476364 AATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:478328 original size:24 final size:23
Alignment explanation
Indices: 478257--478331 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
478247 AGTTTGACTC
*
478257 AAATAAATAAATAAAGTTTAATTA
1 AAATAAATAAAT-AAGTTTAATTG
*
478281 AAACAAATAAATAGAGTTTAATTG
1 AAATAAATAAATA-AGTTTAATTG
*
478305 AAATAAATAAACAATGTTTAATTG
1 AAATAAATAAATAA-GTTTAATTG
478329 AAA
1 AAA
478332 GATTATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.04
24 43 0.96
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (23 bp):
AAATAAATAAATAAGTTTAATTG
Found at i:479156 original size:18 final size:17
Alignment explanation
Indices: 479131--479185 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
479121 TACATTGTTA
479131 TTTA-ATTTTATAATTAT
1 TTTATATTTTATAATT-T
479148 TTTATATTTTA-ATATTT
1 TTTATATTTTATA-ATTT
*
479165 TTTCTATTTTTATAATTT
1 TTTATA-TTTTATAATTT
479183 TTT
1 TTT
479186 GTAAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 11 0.33
18 21 0.64
19 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTTTATAATTT
Found at i:479167 original size:17 final size:18
Alignment explanation
Indices: 479131--479185 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
479121 TACATTGTTA
479131 TTTA-ATTTT-ATAATTAT
1 TTTATATTTTAATAATT-T
479148 TTTATATTTTAAT-ATTT
1 TTTATATTTTAATAATTT
* *
479165 TTTCTATTTTTATAATTT
1 TTTATATTTTAATAATTT
479183 TTT
1 TTT
479186 GTAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 16 0.48
18 15 0.45
19 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATTTTAATAATTT
Found at i:480486 original size:21 final size:22
Alignment explanation
Indices: 480462--480502 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
480452 TCACTCTTAC
*
480462 TTTCTC-ACGAGTTTATTTTCT
1 TTTCTCTACAAGTTTATTTTCT
*
480483 TTTCTCTACAAGTTTCTTTT
1 TTTCTCTACAAGTTTATTTT
480503 AACCTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTCTCTACAAGTTTATTTTCT
Found at i:482348 original size:21 final size:21
Alignment explanation
Indices: 482310--482349 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
482300 GATTGGTTCA
* **
482310 AAGGACAAGAAGGGGAAGCGC
1 AAGGACAAAAAGAAGAAGCGC
482331 AAGGACAAAAAGAAGAAGC
1 AAGGACAAAAAGAAGAAGC
482350 ACAATGAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.35, T:0.00
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCGC
Found at i:483141 original size:13 final size:13
Alignment explanation
Indices: 483101--483142 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
483091 AATGTTGAAT
*
483101 GAGAAAAGGAAAA
1 GAGAAAAGAAAAA
*
483114 GAAAAAAAGAAAAA
1 G-AGAAAAGAAAAA
483128 GAGAAAAGAAAAA
1 GAGAAAAGAAAAA
483141 GA
1 GA
483143 AATATTGCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAGAAAAGAAAAA
Found at i:495746 original size:40 final size:40
Alignment explanation
Indices: 495612--495804 Score: 181
Period size: 40 Copynumber: 4.8 Consensus size: 40
495602 ATAACATCGA
* * * * * *
495612 CACGAAACCTGCTAGGCTCAAAGCCTGATAGTATACACCGA
1 CACGAAACCTACTAGGCACTAAGCCCGATA-AATACACCGG
** * * *
495653 CACGAAGTCTACTAGGCACAAAGCTCGATAAATACACCAG
1 CACGAAACCTACTAGGCACTAAGCCCGATAAATACACCGG
* * *
495693 CATGAAGA-TTACTAGGCACTAAGCCCGATAAATACACTGG
1 CACGAA-ACCTACTAGGCACTAAGCCCGATAAATACACCGG
* * *
495733 CACGAAACCTACTAGGCATTAAGCCCAATAAATACACTGG
1 CACGAAACCTACTAGGCACTAAGCCCGATAAATACACCGG
* * *
495773 CACGAAGCCTGCAAGGCACTAAGCCCGATAAA
1 CACGAAACCTACTAGGCACTAAGCCCGATAAA
495805 CATCGAGGAA
Statistics
Matches: 125, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.80
41 24 0.19
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (40 bp):
CACGAAACCTACTAGGCACTAAGCCCGATAAATACACCGG
Found at i:501836 original size:27 final size:27
Alignment explanation
Indices: 501806--501891 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
501796 CCTTTCAAAA
* * *
501806 TTTGTCATACAGGCATTCTCTTCATAT
1 TTTGCCATAAAGGCATTCTTTTCATAT
*
501833 TTTGCCATAAAGGCATTTTTTTTCATAT
1 TTTGCCATAAAGGCA-TTCTTTTCATAT
* *
501861 CTTGCCATAAAGACATTCCTTTTCATAT
1 TTTGCCATAAAGGCATT-CTTTTCATAT
501889 TTT
1 TTT
501892 TTGTCACAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 15 0.31
28 34 0.69
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTGCCATAAAGGCATTCTTTTCATAT
Found at i:503023 original size:78 final size:78
Alignment explanation
Indices: 502873--503023 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 78
502863 CAAAATGCAT
* * *
502873 CAAAAATGCCCTCAAATTTTTTCAAAAAAAAAAATTAATCCCCTAATTTTATTTTGCACTCAATT
1 CAAAAAGGCCCTCAAACTTTTTCAAAAAAAAAAATTAA-CCCCT-ATTGTATTTTGCACTCAATT
502938 AGGTACTTCAACTTA
64 AGGTACTTCAACTTA
*
502953 CAAAAAGGCCCTCAAACTTTTTCAAAAAATAAATAATTAA-GCCT-TTGGT-TTTTGCACTCAAT
1 CAAAAAGGCCCTCAAACTTTTTCAAAAAA-AAA-AATTAACCCCTATT-GTATTTTGCACTCAAT
*
503015 TGGGTACTT
63 TAGGTACTT
503024 GAACCACTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
78 23 0.37
79 1 0.02
80 30 0.48
81 3 0.05
82 6 0.10
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (78 bp):
CAAAAAGGCCCTCAAACTTTTTCAAAAAAAAAAATTAACCCCTATTGTATTTTGCACTCAATTAG
GTACTTCAACTTA
Found at i:505173 original size:38 final size:37
Alignment explanation
Indices: 505130--505220 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
505120 AAAAGCAAGA
*
505130 GAAGAAAAAGAAAAGGAGAAAGAAAAACAAGGAATGAT
1 GAAGAAAGAGAAAA-GAGAAAGAAAAACAAGGAATGAT
* * * * *
505168 GAAGAAAGTGAAGCAGAGAAAGAAAAATAGGGATTGAT
1 GAAGAAAGAGAA-AAGAGAAAGAAAAACAAGGAATGAT
505206 GAAGATAAGAGAAAA
1 GAAGA-AAGAGAAAA
505221 CAAGTGCAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 36 0.84
39 7 0.16
ACGTcount: A:0.60, C:0.02, G:0.29, T:0.09
Consensus pattern (37 bp):
GAAGAAAGAGAAAAGAGAAAGAAAAACAAGGAATGAT
Found at i:506252 original size:17 final size:17
Alignment explanation
Indices: 506230--506263 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
506220 TAATGTTAAA
506230 GCTTTAATCTAAAATTG
1 GCTTTAATCTAAAATTG
506247 GCTTTAATCTAAAATTG
1 GCTTTAATCTAAAATTG
506264 TTATACTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
GCTTTAATCTAAAATTG
Found at i:514622 original size:70 final size:70
Alignment explanation
Indices: 514465--514622 Score: 253
Period size: 70 Copynumber: 2.3 Consensus size: 70
514455 TGATTTTTGG
* *
514465 AGACTTTTACCGGTACTTGTTGAAAAAGTATCGGTAGTTGTCAAGTCGATAAATAGTTCAAGAAC
1 AGACTTTTACCGGTACTTATTGAAAAAGTATCGATAGTTGTCAAGTCGATAAATAGTTCAAGAAC
514530 AGTGC
66 AGTGC
* * *
514535 AGACTTCTACCGGTACTTATTGAACAAGTATCGATAGTTGTTAAGTCGATAAATAGTTCAAGAAC
1 AGACTTTTACCGGTACTTATTGAAAAAGTATCGATAGTTGTCAAGTCGATAAATAGTTCAAGAAC
514600 AGTGC
66 AGTGC
* *
514605 AGACTTTTATCGATACTT
1 AGACTTTTACCGGTACTT
514623 GAGACAATAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 80 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (70 bp):
AGACTTTTACCGGTACTTATTGAAAAAGTATCGATAGTTGTCAAGTCGATAAATAGTTCAAGAAC
AGTGC
Found at i:515641 original size:52 final size:52
Alignment explanation
Indices: 515560--515850 Score: 424
Period size: 52 Copynumber: 5.6 Consensus size: 52
515550 TTCCAATTTA
* * * *
515560 ATACTCATGATGACACAAAGTCATCGGACCTTA-AATCCATAAAAGGA-TCTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTC-AT
* * *
515612 ATGCTCATGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** **
515664 ATACTCACGATGACACATAGCCATCAAACCTCATAATATGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
515716 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
515768 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
515820 ATACTCACAATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
515851 TTTCCATTTA
Statistics
Matches: 217, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
52 209 0.96
53 8 0.04
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:521234 original size:52 final size:52
Alignment explanation
Indices: 521137--521323 Score: 227
Period size: 52 Copynumber: 3.6 Consensus size: 52
521127 TTCCCATTTA
* * * *
521137 ATACTCACGATGACACAAAGTCATC-GAACCTTA-AATCCTTAAAAGGA-TCTAT
1 ATACTCACAATGACACATAGTCATCAG-ACCTCATAATCCGT-AAAGGATTC-AT
* * *
521189 ATTCTCACAATGACACATAGTCATTAGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
**
521241 ATACTCATGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
521293 ATACTTACAATGACACATAGTCATCGGACCT
1 ATACTCACAATGACACATAGTCATCAGACCT
521324 TTTTCATTTA
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
52 107 0.92
53 9 0.08
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (52 bp):
ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:531057 original size:3 final size:3
Alignment explanation
Indices: 531044--531086 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
531034 GTGCATAAAA
*
531044 AAT ATAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
531087 TAAATACTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:531584 original size:2 final size:2
Alignment explanation
Indices: 531577--531609 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
531567 CACTCAAGAA
531577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
531610 ACACCATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:533220 original size:10 final size:9
Alignment explanation
Indices: 533181--533335 Score: 66
Period size: 9 Copynumber: 16.6 Consensus size: 9
533171 CATATGAAAA
533181 AAAAATTAT
1 AAAAATTAT
533190 AAAAA--AT
1 AAAAATTAT
**
533197 AAAAACCAAT
1 AAAAA-TTAT
*
533207 AAAAGTTAT
1 AAAAATTAT
533216 AAAAATTATT
1 AAAAATTA-T
**
533226 AAATTTTAAT
1 AAAAATT-AT
533236 AAAAA-TAT
1 AAAAATTAT
533244 AAAAATATATTT
1 AAAAAT-TA--T
**
533256 AAATTTTATT
1 AAAAATTA-T
533266 AAAAATTAT
1 AAAAATTAT
* *
533275 AAATATTGT
1 AAAAATTAT
* *
533284 AAATATTGT
1 AAAAATTAT
*
533293 AAAATTTTAT
1 AAAA-ATTAT
*
533303 AAAAATCAT
1 AAAAATTAT
*
533312 AACAAAATAT
1 AA-AAATTAT
533322 -AAAATGTAT
1 AAAAAT-TAT
533331 AAAAA
1 AAAAA
533336 AGACCCTTTA
Statistics
Matches: 111, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
7 7 0.06
8 10 0.09
9 44 0.40
10 42 0.38
11 3 0.03
12 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:533236 original size:29 final size:30
Alignment explanation
Indices: 533204--533277 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
533194 AATAAAAACC
533204 AATAAAAGTTATAAAAAT-TA-TTAAATTTT
1 AATAAAA-TTATAAAAATATATTTAAATTTT
*
533233 AATAAAAATATAAAAATATATTTAAATTTT
1 AATAAAATTATAAAAATATATTTAAATTTT
*
533263 ATTAAAAATTATAAA
1 AAT-AAAATTATAAA
533278 TATTGTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 9 0.23
29 9 0.23
30 11 0.28
31 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
AATAAAATTATAAAAATATATTTAAATTTT
Found at i:533572 original size:9 final size:9
Alignment explanation
Indices: 533555--533742 Score: 55
Period size: 9 Copynumber: 20.3 Consensus size: 9
533545 TTTGTATTTC
*
533555 TTTACAATT
1 TTTATAATT
533564 TTTATAATT
1 TTTATAATT
*
533573 TTCT-TACAGT
1 TT-TATA-ATT
*
533583 TTTATAAAT
1 TTTATAATT
533592 TTTATAATT
1 TTTATAATT
* * *
533601 TTTTTCCTATA
1 TTTAT--AATT
533612 TTT-TAATAT
1 TTTATAAT-T
* *
533621 ATTAT-TTT
1 TTTATAATT
*
533629 TTTATGATT
1 TTTATAATT
533638 TTTATAAATT
1 TTTAT-AATT
**
533648 TTTCCAATT
1 TTTATAATT
* *
533657 TGTAATAAAT
1 T-TTATAATT
*
533667 TTTAAATATT
1 TTTATA-ATT
533677 TTTAT-ATT
1 TTTATAATT
*
533685 TTTATTAAAAT
1 TTTA-T-AATT
* *
533696 TTAATCATT
1 TTTATAATT
*
533705 TTTATAACT
1 TTTATAATT
*
533714 TTTATTGATT
1 TTTA-TAATT
533724 TTTAT--TT
1 TTTATAATT
*
533731 TTTATCATT
1 TTTATAATT
533740 TTT
1 TTT
533743 GCCACATATC
Statistics
Matches: 129, Mismatches: 33, Indels: 34
0.66 0.17 0.17
Matches are distributed among these distances:
7 7 0.05
8 14 0.11
9 64 0.50
10 34 0.26
11 10 0.08
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:533579 original size:20 final size:20
Alignment explanation
Indices: 533521--533594 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 20
533511 TAGTACGATC
*
533521 ATTTTTATAATTTATTTTACGA
1 ATTTTTATAATTT-TCTTAC-A
*
533543 A-TTTTGT-A-TTTCTTTACA
1 ATTTTTATAATTTTC-TTACA
533561 ATTTTTATAATTTTCTTAC-
1 ATTTTTATAATTTTCTTACA
*
533580 AGTTTTATAAATTTT
1 ATTTTTAT-AATTTT
533595 ATAATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.07
19 18 0.42
20 12 0.28
21 9 0.21
22 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATTTTCTTACA
Found at i:541750 original size:24 final size:24
Alignment explanation
Indices: 541718--541763 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
541708 CTAATTAGAT
* *
541718 TTTATAAATAATTAATATTAATTA
1 TTTAAAAATAATTAAAATTAATTA
*
541742 TTTAAAAATATTTAAAATTAAT
1 TTTAAAAATAATTAAAATTAAT
541764 AGTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTAATTA
Found at i:548153 original size:2 final size:2
Alignment explanation
Indices: 548146--548174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
548136 AAATTCACAC
548146 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 T
548175 GGGGTTGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:548391 original size:17 final size:17
Alignment explanation
Indices: 548356--548398 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
548346 CTCCCTTAAC
* *
548356 CTTTAACCTTCCATCTT
1 CTTTAACTTTCCATATT
*
548373 CTTTAACTTTTCATATT
1 CTTTAACTTTCCATATT
548390 CTTGTAACT
1 CTT-TAACT
548399 ATTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (17 bp):
CTTTAACTTTCCATATT
Found at i:548524 original size:16 final size:17
Alignment explanation
Indices: 548503--548535 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
548493 TTCAATACAA
548503 ATTCTCATATT-ATCAT
1 ATTCTCATATTCATCAT
548519 ATTCTCATATTCATCAT
1 ATTCTCATATTCATCAT
548536 TTATCTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTCTCATATTCATCAT
Found at i:549024 original size:22 final size:23
Alignment explanation
Indices: 548972--549024 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
548962 TAAGGATCCA
* *
548972 AATTAAATTGTAATTTTTACTAT
1 AATTAAATTGTAATTTTTACAAG
*
548995 AATAAAATTGTAATTTTTA-AAG
1 AATTAAATTGTAATTTTTACAAG
*
549017 GATTAAAT
1 AATTAAAT
549025 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (23 bp):
AATTAAATTGTAATTTTTACAAG
Found at i:553341 original size:30 final size:30
Alignment explanation
Indices: 553297--553421 Score: 137
Period size: 30 Copynumber: 4.2 Consensus size: 30
553287 ATTAAAATCC
*
553297 GGTC-AATTTGAATTTTTAGAAAGTTCAAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* *
553326 GGTCAAATTGGAATTTTTGGAAAGTTCGA-
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* * * **
553355 GGTCACATTTGAATTTTTTGAAATTTTGAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
* *
553385 GGTAAAATTTGAATTTTTGGAAAGTTTAAG
1 GGTCAAATTTGAATTTTTGGAAAGTTCAAG
*
553415 AGTCAAA
1 GGTCAAA
553422 ACATAATTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
29 28 0.35
30 51 0.65
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTGGAAAGTTCAAG
Found at i:553399 original size:59 final size:58
Alignment explanation
Indices: 553297--553410 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
553287 ATTAAAATCC
*
553297 GGTCAATTTGAATTTTTAGAAAGTTCAAGGGTCAAATTGGAATTTTTGGAAAGTTCGA
1 GGTCAATTTGAATTTTTAGAAAGTTCAAGGGTAAAATTGGAATTTTTGGAAAGTTCGA
* * ** *
553355 GGTCACATTTGAATTTTTTGAAATTTTGAGGGTAAAATTTGAATTTTTGGAAAGTT
1 GGTCA-ATTTGAATTTTTAGAAAGTTCAAGGGTAAAATTGGAATTTTTGGAAAGTT
553411 TAAGAGTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 5 0.10
59 44 0.90
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (58 bp):
GGTCAATTTGAATTTTTAGAAAGTTCAAGGGTAAAATTGGAATTTTTGGAAAGTTCGA
Found at i:554635 original size:4 final size:4
Alignment explanation
Indices: 554618--554661 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
554608 ATTTATATTT
* *
554618 ATAA ATAG ATAA ATAA ATAA ATAA A-AA TTAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
554662 ATTTAAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 33 0.94
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:554651 original size:19 final size:19
Alignment explanation
Indices: 554627--554669 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
554617 TATAAATAGA
554627 TAAATAAATAAATAAAAAT
1 TAAATAAATAAATAAAAAT
*
554646 TAAATAAATAAATAAAATT
1 TAAATAAATAAATAAAAAT
554665 TAAAT
1 TAAAT
554670 GGAATTGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAATAAATAAATAAAAAT
Found at i:554721 original size:5 final size:5
Alignment explanation
Indices: 554711--554740 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
554701 TTATTTTGGG
*
554711 TATTT TATTT TATTT TAATT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT
554741 ATAAAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:555665 original size:79 final size:79
Alignment explanation
Indices: 555499--555644 Score: 220
Period size: 79 Copynumber: 1.8 Consensus size: 79
555489 CTTTAAAGCT
* * * *
555499 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGGATGATTTTC
1 TTAGGGTAAAAGATTAGATTGCTTCAATCTGCCCTATGGTCGGGGCAAAAGATCGGATGATCTTC
555564 AAGCCACCCTCTAG
66 AAGCCACCCTCTAG
* * * *
555578 TTAGGGTAAAATATTAGATTGCTTCAATTTGCCCTATGGTCGGGGCAAAAGATTGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTGCTTCAATCTGCCCTATGGTCGGGGCAAAAGATCGGATGATCTTC
555643 AA
66 AA
555645 TCTACCCCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (79 bp):
TTAGGGTAAAAGATTAGATTGCTTCAATCTGCCCTATGGTCGGGGCAAAAGATCGGATGATCTTC
AAGCCACCCTCTAG
Found at i:555704 original size:40 final size:40
Alignment explanation
Indices: 555499--555748 Score: 179
Period size: 40 Copynumber: 6.4 Consensus size: 40
555489 CTTTAAAGCT
* *
555499 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
** * * * * * ** *
555538 TCGGGGTAAGAGATCGGATGATTTTCAAGCCACCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
* * * * *
555578 TTAGGGTAAAATATTAGATTG-CTTCAATTTGCCCTATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
** * * *
555617 TCGGGGCAAAAGATTGGATGGTCTTCAATCTACCC-CATGA
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGG
* * * *
555657 TTGGGGTAAGAGATCGGATGGTCTTAAATCTGCCCTCTGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
* * * *
555697 TTAGGGTAAAATATTGGATGG---TCAACCTCCCCTCTGA
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
555734 TTAGGGTAAAAGATT
1 TTAGGGTAAAAGATT
555749 TGGGGTTATA
Statistics
Matches: 154, Mismatches: 53, Indels: 10
0.71 0.24 0.05
Matches are distributed among these distances:
37 26 0.17
39 41 0.27
40 86 0.56
41 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (40 bp):
TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGG
Found at i:561190 original size:30 final size:30
Alignment explanation
Indices: 561156--561370 Score: 188
Period size: 30 Copynumber: 7.3 Consensus size: 30
561146 CATTAAAACT
*
561156 GGGTCAAATTTGAATTTTTGGAAAGTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* **
561186 GGGTCAAATTGGAATTTTTGGAAAG-TTCG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
***
561215 GGGTCAAATTTGAATTTTCAAAAAGTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* * * * *
561245 -GGTTATATTGGAATTTTTGAAAAGTTTGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
*
561274 -GGTCAAATTTGAATTTTTGGAAAATTT-A
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* * * *
561302 GAGGTAAAATTTGGATTTTTTGAAAGTTTGA
1 G-GGTCAAATTTGAATTTTTGGAAAGTTTAA
* * **
561333 GGGTAAAATTAGAATTTTTAAAAAG-TTAGA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTA-A
561363 GGGTCAAA
1 GGGTCAAA
561371 ACATAATTTT
Statistics
Matches: 149, Mismatches: 31, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.01
29 69 0.46
30 77 0.52
31 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAA
Found at i:561231 original size:59 final size:58
Alignment explanation
Indices: 561156--561370 Score: 220
Period size: 59 Copynumber: 3.6 Consensus size: 58
561146 CATTAAAACT
** *
561156 GGGTCAAATTTGAATTTTTGGAAAGTTCAAGGGTCAAATTGGAATTTTTGGAAAGTTCG
1 GGGTCAAATTTGAATTTTTAAAAAGTT-AAGGGTCAAATTGGAATTTTTGGAAAGTTTG
* * * *
561215 GGGTCAAATTTGAATTTTCAAAAAGTTTAA-GGTTATATTGGAATTTTTGAAAAGTTTG
1 GGGTCAAATTTGAATTTTTAAAAAG-TTAAGGGTCAAATTGGAATTTTTGGAAAGTTTG
* * * * *
561273 AGGTCAAATTTGAATTTTTGGAAAA-TTTAGAGGTAAAATTTGG-ATTTTTTGAAAGTTTG
1 GGGTCAAATTTGAATTTTT-AAAAAGTTAAG-GGTCAAA-TTGGAATTTTTGGAAAGTTTG
* *
561332 AGGGTAAAATTAGAATTTTTAAAAAGTTAGAGGGTCAAA
1 -GGGTCAAATTTGAATTTTTAAAAAGTTA-AGGGTCAAA
561371 ACATAATTTT
Statistics
Matches: 127, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
57 3 0.02
58 41 0.32
59 51 0.40
60 30 0.24
61 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (58 bp):
GGGTCAAATTTGAATTTTTAAAAAGTTAAGGGTCAAATTGGAATTTTTGGAAAGTTTG
Found at i:562017 original size:17 final size:17
Alignment explanation
Indices: 561997--562049 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
561987 ATTTGGTTTG
561997 TATTTGTTTATTTTTAT
1 TATTTGTTTATTTTTAT
*
562014 TATTTATTTA-TTTT-T
1 TATTTGTTTATTTTTAT
* *
562029 TATTTGTATATATTTA-
1 TATTTGTTTATTTTTAT
562045 TATTT
1 TATTT
562050 ATAAAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.30
16 12 0.40
17 9 0.30
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (17 bp):
TATTTGTTTATTTTTAT
Found at i:562022 original size:32 final size:31
Alignment explanation
Indices: 561986--562051 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
561976 TGAGTATGTG
* * *
561986 TATTTGGTTTGTATTTGTTTATTTTTATTATT
1 TATTTAGTTTGTATTTGTATATATTTA-TATT
* *
562018 TATTTATTTTTTATTTGTATATATTTATATT
1 TATTTAGTTTGTATTTGTATATATTTATATT
562049 TAT
1 TAT
562052 AAAAAGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (31 bp):
TATTTAGTTTGTATTTGTATATATTTATATT
Found at i:562197 original size:14 final size:14
Alignment explanation
Indices: 562178--562206 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
562168 AAATGATAAG
562178 TAAATAAAATAAAA
1 TAAATAAAATAAAA
562192 TAAATAAAATAAAA
1 TAAATAAAATAAAA
562206 T
1 T
562207 TGGTTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAATAAAATAAAA
Found at i:562876 original size:20 final size:20
Alignment explanation
Indices: 562851--562964 Score: 64
Period size: 20 Copynumber: 5.9 Consensus size: 20
562841 GATGATGATT
562851 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
562871 ATAATTTT---AT-A-TTTA
1 ATAATTTTAAAATAATTTTA
* ** *
562886 AAAAAATTAAATTAATTTTAAA
1 ATAATTTTAAAATAATTTT--A
* *
562908 ATAAATTT--ATTAATTTT-
1 ATAATTTTAAAATAATTTTA
*
562925 ATATTTTTTAAAAATAATTTTA
1 ATA-ATTTT-AAAATAATTTTA
*
562947 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
562965 GCTGACAGGA
Statistics
Matches: 71, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
15 9 0.13
16 1 0.01
17 5 0.07
18 4 0.06
19 1 0.01
20 29 0.41
21 12 0.17
22 10 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:563357 original size:4 final size:4
Alignment explanation
Indices: 563348--563373 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
563338 TATAAAGATA
563348 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
563374 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:564119 original size:60 final size:57
Alignment explanation
Indices: 563990--564175 Score: 185
Period size: 60 Copynumber: 3.2 Consensus size: 57
563980 TTAATATAAG
* * * * *
563990 ATTTGGTATTTAAATTTGACACTTTTTTCTAATTCGGTATCTAAATTTTTTT-ACTCA
1 ATTTGGTACTTGAACTTGACAC-TATTTCTAATTTGGTATCTAAATTTTTTTGACTCA
* *
564047 ATTTGATACTTGAACTTGAGACTATTTCTTAATTTGGTATCTAAATTTTTTTTGGACTCA
1 ATTTGGTACTTGAACTTGACACTATTTC-TAATTTGGTATCTAAA-TTTTTTT-GACTCA
* * * * * *
564107 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGATACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACACTATTT-CTAATTTGGTATCTAA-ATTTTTTT-GACTCA
564167 ATTTGGTAC
1 ATTTGGTAC
564176 CTAAATTTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
56 5 0.05
57 32 0.30
58 7 0.07
60 62 0.58
61 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (57 bp):
ATTTGGTACTTGAACTTGACACTATTTCTAATTTGGTATCTAAATTTTTTTGACTCA
Found at i:566044 original size:36 final size:36
Alignment explanation
Indices: 565997--566066 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
565987 TGAGAAAAAG
*
565997 AGGGCATGATTACATTCCACAGTCTTTGTTGTTTTT
1 AGGGCATGATTACATTCCACAGTCTCTGTTGTTTTT
566033 AGGGCATGATTACATTCCACAGTCTCTGTTGTTT
1 AGGGCATGATTACATTCCACAGTCTCTGTTGTTT
566067 CTACTAGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (36 bp):
AGGGCATGATTACATTCCACAGTCTCTGTTGTTTTT
Found at i:569478 original size:15 final size:16
Alignment explanation
Indices: 569447--569482 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
569437 AAATTTAAAG
*
569447 GTAAATAAGTAAATTA
1 GTAAATAAATAAATTA
569463 GTAAATAAAT-AATTA
1 GTAAATAAATAAATTA
569478 GTAAA
1 GTAAA
569483 AAGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (16 bp):
GTAAATAAATAAATTA
Found at i:570478 original size:20 final size:20
Alignment explanation
Indices: 570453--570499 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
570443 GTCCAGGTAC
**
570453 GCACTCCAATTTCCCTATAT
1 GCACTCCAATGCCCCTATAT
**
570473 GCACTCTGATGCCCCTATAT
1 GCACTCCAATGCCCCTATAT
570493 GCACTCC
1 GCACTCC
570500 GGTGCCCTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30
Consensus pattern (20 bp):
GCACTCCAATGCCCCTATAT
Found at i:570514 original size:20 final size:20
Alignment explanation
Indices: 570465--570506 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
570455 ACTCCAATTT
*
570465 CCCTATATGCACTCTGATGC
1 CCCTATATGCACTCCGATGC
*
570485 CCCTATATGCACTCCGGTGC
1 CCCTATATGCACTCCGATGC
570505 CC
1 CC
570507 TTGTATGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.17, T:0.26
Consensus pattern (20 bp):
CCCTATATGCACTCCGATGC
Found at i:571914 original size:24 final size:24
Alignment explanation
Indices: 571882--571938 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
571872 AATATAAACT
571882 AACAGAGTTCGACTGAAACAAATA
1 AACAGAGTTCGACTGAAACAAATA
571906 AACAGAGTTCGACTGAAACAAATA
1 AACAGAGTTCGACTGAAACAAATA
571930 AACAGAGTT
1 AACAGAGTT
571939 AACTAGGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (24 bp):
AACAGAGTTCGACTGAAACAAATA
Found at i:574874 original size:17 final size:17
Alignment explanation
Indices: 574852--574890 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
574842 CTCCACCTTG
*
574852 ACAAGAATTCTCT-ACGA
1 ACAAGAACTCT-TAACGA
574869 ACAAGAACTCTTAACGA
1 ACAAGAACTCTTAACGA
574886 ACAAG
1 ACAAG
574891 TTATCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTTAACGA
Found at i:579222 original size:27 final size:27
Alignment explanation
Indices: 579181--579238 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
579171 AACACTGATT
579181 AAAT-TAATTAAAGAATACA-AAAAATC
1 AAATATAATTAAAGAATA-AGAAAAATC
*
579207 AAATATAATTATAGAATAAGAAAAATC
1 AAATATAATTAAAGAATAAGAAAAATC
579234 AAATA
1 AAATA
579239 CAGTTAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (27 bp):
AAATATAATTAAAGAATAAGAAAAATC
Found at i:587254 original size:44 final size:44
Alignment explanation
Indices: 587204--587293 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
587194 CCAACAAGAT
*
587204 TTGAAAAATCAAAATATTCCAAATCATAATTAATGTAAAAAAAA
1 TTGAAAAATCAAAATATTACAAATCATAATTAATGTAAAAAAAA
587248 TTGAAAAATCAAAATATTACAAATCATAATTAATGTAAAAAAAA
1 TTGAAAAATCAAAATATTACAAATCATAATTAATGTAAAAAAAA
587292 TT
1 TT
587294 CTTACATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (44 bp):
TTGAAAAATCAAAATATTACAAATCATAATTAATGTAAAAAAAA
Found at i:587694 original size:17 final size:18
Alignment explanation
Indices: 587672--587714 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
587662 TCTTTTTGCA
587672 GGTGAGCTCT-CATGT-TT
1 GGTGAGCTCTGCA-GTCTT
587689 GGTGAGCT-TGCAGTCTT
1 GGTGAGCTCTGCAGTCTT
587706 GGTGAGCTC
1 GGTGAGCTC
587715 GCACACTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.12, C:0.19, G:0.35, T:0.35
Consensus pattern (18 bp):
GGTGAGCTCTGCAGTCTT
Found at i:590834 original size:14 final size:15
Alignment explanation
Indices: 590810--590838 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
590800 TTGGCAATAA
590810 ATTTATTTATTTTTC
1 ATTTATTTATTTTTC
590825 ATTT-TTTATTTTTC
1 ATTTATTTATTTTTC
590839 CTTGTAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTATTTTTC
Found at i:597903 original size:3 final size:3
Alignment explanation
Indices: 597895--597941 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
597885 GTTATTTTTA
*
597895 TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
597942 ATTATTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.00, G:0.30, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:597913 original size:12 final size:12
Alignment explanation
Indices: 597871--597944 Score: 76
Period size: 12 Copynumber: 6.2 Consensus size: 12
597861 TGTCGCAACG
* *
597871 TTGTTATTGTCA
1 TTGTTGTTGTTA
* *
597883 TTGTTATTTTTA
1 TTGTTGTTGTTA
*
597895 TTGTTGTTGTTG
1 TTGTTGTTGTTA
* *
597907 TTATTGTTGTTG
1 TTGTTGTTGTTA
*
597919 TTGTTGTTGTTG
1 TTGTTGTTGTTA
597931 TTGTTGTTGTTA
1 TTGTTGTTGTTA
597943 TT
1 TT
597945 ATTATTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.08, C:0.01, G:0.23, T:0.68
Consensus pattern (12 bp):
TTGTTGTTGTTA
Found at i:616259 original size:31 final size:31
Alignment explanation
Indices: 616224--616291 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
616214 TCGGATCAAC
*
616224 TCGAATAAAAAATCAAGTTTTTCGGCTTAAA
1 TCGAATAAAAAATCAAGTTTTTCGACTTAAA
*
616255 TCGAATAAAAAATCAAGTTTTTCGACTTAAC
1 TCGAATAAAAAATCAAGTTTTTCGACTTAAA
616286 TCGAAT
1 TCGAAT
616292 GTGAATTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
TCGAATAAAAAATCAAGTTTTTCGACTTAAA
Found at i:623245 original size:35 final size:35
Alignment explanation
Indices: 623174--623245 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
623164 AAATGTTTAG
623174 TTTAGACATGAAATTATAAAGTAAAAAATATCTAT
1 TTTAGACATGAAATTATAAAGTAAAAAATATCTAT
* * * *
623209 TTTAGATATGGAATTATAAAGTAATAAATATGTAT
1 TTTAGACATGAAATTATAAAGTAAAAAATATCTAT
623244 TT
1 TT
623246 AAATAATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (35 bp):
TTTAGACATGAAATTATAAAGTAAAAAATATCTAT
Found at i:623367 original size:23 final size:21
Alignment explanation
Indices: 623337--623381 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
623327 TTAATATATG
623337 AAATATTAAT-TTAAATATTTTT
1 AAATATTAATATT-AAT-TTTTT
623359 AAATAATTAATATTAATTTTTT
1 AAAT-ATTAATATTAATTTTTT
623381 A
1 A
623382 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATATTAATATTAATTTTTT
Found at i:626520 original size:35 final size:35
Alignment explanation
Indices: 626480--626549 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
626470 TATGACAGAC
*
626480 AATAACAAAAAAAATCTAAACTTGCCATACACTTT
1 AATAACAAAAAAAATCCAAACTTGCCATACACTTT
* * *
626515 AATAACCAAAGAAATCCAAACTTGTCATACACTTT
1 AATAACAAAAAAAATCCAAACTTGCCATACACTTT
626550 GATATAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (35 bp):
AATAACAAAAAAAATCCAAACTTGCCATACACTTT
Found at i:631603 original size:21 final size:21
Alignment explanation
Indices: 631579--631621 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
631569 TATATAAAAC
631579 TATCATAAACATAAATAGTAT
1 TATCATAAACATAAATAGTAT
* *
631600 TATCATAAATATAAATATTAT
1 TATCATAAACATAAATAGTAT
631621 T
1 T
631622 TAATTACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
TATCATAAACATAAATAGTAT
Found at i:633505 original size:30 final size:30
Alignment explanation
Indices: 633471--633588 Score: 139
Period size: 30 Copynumber: 3.9 Consensus size: 30
633461 CATTAAAACC
*
633471 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTAGAAAGTTTAG
* *
633501 GGGTCAAATTGGAATTTTTAGAAAGTTCGAG
1 GGGTCAAATTTGAATTTTTAGAAAGTT-TAG
** *
633532 GGGTCAAATTCAAATTTTTGGAAAGTTTA-
1 GGGTCAAATTTGAATTTTTAGAAAGTTTAG
* * *
633561 AGATCAAATTTGAATTTTTAAAAAGTTT
1 GGGTCAAATTTGAATTTTTAGAAAGTTT
633589 GGGAGTTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
29 22 0.30
30 26 0.35
31 26 0.35
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTAGAAAGTTTAG
Found at i:633537 original size:31 final size:30
Alignment explanation
Indices: 633471--633558 Score: 122
Period size: 31 Copynumber: 2.9 Consensus size: 30
633461 CATTAAAACC
* *
633471 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTCGAATTTTTGGAAAGTTGAG
* *
633501 GGGTCAAATTGGAATTTTTAGAAAGTTCGAG
1 GGGTCAAATTCGAATTTTTGGAAAGTT-GAG
*
633532 GGGTCAAATTCAAATTTTTGGAAAGTT
1 GGGTCAAATTCGAATTTTTGGAAAGTT
633559 TAAGATCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGTCAAATTCGAATTTTTGGAAAGTTGAG
Found at i:634218 original size:22 final size:22
Alignment explanation
Indices: 634193--634236 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
634183 TTTGCTGCTG
*
634193 ATTTTCTATC-AATTTCTTGTAT
1 ATTTT-TATCTAATTTCGTGTAT
*
634215 ATTTTTCTCTAATTTCGTGTAT
1 ATTTTTATCTAATTTCGTGTAT
634237 TTGTGTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTTTATCTAATTTCGTGTAT
Found at i:635360 original size:39 final size:39
Alignment explanation
Indices: 635237--635363 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 39
635227 TATAGCTTTA
* *
635237 GGGGTAAAATATTGGATTGCTTCAATCTACAC-CATGGTC
1 GGGGTAAAAAATTGGATTGCTTCAATCTGC-CTCATGGTC
* * ** * * *
635276 GGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTC-TAGTT
1 GGGGTAAAAAATTGGATTG-CTTCAATCTG-CCTCATGGTC
* *
635316 AGGGTAAAAAATTGGATTGCTTCAATTTGCCTCATGGTC
1 GGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTC
635355 GGGGTAAAA
1 GGGGTAAAA
635364 GATTCGGGGT
Statistics
Matches: 66, Mismatches: 18, Indels: 8
0.72 0.20 0.09
Matches are distributed among these distances:
38 4 0.06
39 34 0.52
40 26 0.39
41 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (39 bp):
GGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTC
Found at i:643746 original size:17 final size:17
Alignment explanation
Indices: 643726--643773 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
643716 ACAACAATGC
643726 AAATGTAATAACAAGTA
1 AAATGTAATAACAAGTA
* * *
643743 AAATGCATTAACAATTA
1 AAATGTAATAACAAGTA
*
643760 AAATGTAATGACAA
1 AAATGTAATAACAA
643774 CTAGATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.25
Consensus pattern (17 bp):
AAATGTAATAACAAGTA
Found at i:643747 original size:34 final size:34
Alignment explanation
Indices: 643709--643773 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
643699 ATATTAATGG
*
643709 AAATGCAACAACAATGCAAATGTAATAACAAGTA
1 AAATGCAACAACAATGAAAATGTAATAACAAGTA
** * *
643743 AAATGCATTAACAATTAAAATGTAATGACAA
1 AAATGCAACAACAATGAAAATGTAATAACAA
643774 CTAGATGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (34 bp):
AAATGCAACAACAATGAAAATGTAATAACAAGTA
Found at i:645497 original size:24 final size:24
Alignment explanation
Indices: 645470--645524 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
645460 CTGCCGACGA
645470 TTTAGCAGCTGGTTTGGACGGGGT
1 TTTAGCAGCTGGTTTGGACGGGGT
645494 TTTAGCAGCTGGTTTGGACGGGGT
1 TTTAGCAGCTGGTTTGGACGGGGT
645518 TTTAGCA
1 TTTAGCA
645525 CTACGAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.13, G:0.38, T:0.35
Consensus pattern (24 bp):
TTTAGCAGCTGGTTTGGACGGGGT
Found at i:658786 original size:18 final size:16
Alignment explanation
Indices: 658741--658787 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
658731 ATTTACAAGT
658741 ATAAATAATAAAAACA
1 ATAAATAATAAAAACA
*
658757 ATATATACATAAAATACA
1 ATAAATA-ATAAAA-ACA
658775 ATAAAATAATAAA
1 AT-AAATAATAAA
658788 TTAAGTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 6 0.23
17 6 0.23
18 10 0.38
19 4 0.15
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAATAATAAAAACA
Found at i:658927 original size:29 final size:29
Alignment explanation
Indices: 658895--659005 Score: 114
Period size: 30 Copynumber: 3.8 Consensus size: 29
658885 AAACCAAGTC
658895 AAATTTGAATTTTTGGAAAGTTTAGGGTT
1 AAATTTGAATTTTTGGAAAGTTTAGGGTT
*** * * *
658924 AAATCAAAATATTTAGAAAGTTTGAAGGTT
1 AAATTTGAATTTTTGGAAAGTTT-AGGGTT
* *
658954 GAATTTGAATTTTTGGAAAGTTTAGGGGTC
1 AAATTTGAATTTTTGGAAAGTTTA-GGGTT
* *
658984 AAATTTGAAGTTTTGAAAAGTT
1 AAATTTGAATTTTTGGAAAGTT
659006 CGAGGATTAA
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
29 19 0.30
30 44 0.70
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.40
Consensus pattern (29 bp):
AAATTTGAATTTTTGGAAAGTTTAGGGTT
Found at i:659356 original size:31 final size:32
Alignment explanation
Indices: 659321--659380 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
659311 TTACTTTTTA
659321 CAAAAAACT-AAAT-TTTCTTT-CTTTTTTCTCT
1 CAAAAAA-TAAAATCTTT-TTTCCTTTTTTCTCT
659352 CAAAAAATAAAATCTTTTTTCCTTTTTTC
1 CAAAAAATAAAATCTTTTTTCCTTTTTTC
659381 ATGGCCGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.04
31 14 0.54
32 11 0.42
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (32 bp):
CAAAAAATAAAATCTTTTTTCCTTTTTTCTCT
Found at i:667423 original size:12 final size:12
Alignment explanation
Indices: 667406--667436 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
667396 ATTTTAATAA
667406 TAACTTAAATTT
1 TAACTTAAATTT
*
667418 TAACTTAACTTT
1 TAACTTAAATTT
667430 TAACTTA
1 TAACTTA
667437 GAAAGGGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (12 bp):
TAACTTAAATTT
Found at i:669658 original size:28 final size:28
Alignment explanation
Indices: 669626--669684 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
669616 TTTTCCCGAT
*
669626 TCAGGTAAAGTTAGAACTAGTGATTTAG
1 TCAGGCAAAGTTAGAACTAGTGATTTAG
669654 TCAGGCAAAGTTAGAACTAGTGATTTAG
1 TCAGGCAAAGTTAGAACTAGTGATTTAG
669682 TCA
1 TCA
669685 ATGTCTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (28 bp):
TCAGGCAAAGTTAGAACTAGTGATTTAG
Found at i:676384 original size:70 final size:70
Alignment explanation
Indices: 676250--676539 Score: 463
Period size: 70 Copynumber: 4.1 Consensus size: 70
676240 CTTGGCCAAG
** * *
676250 GTATCGGTAGAAGTCTTAGGCCACAACTTCTTTGCTCACTAGAGTTTGTTCTACTGATAGAAGTC
1 GTATCGGTAGAAGTCCCAGGTCACAACTTC-TTGCTCACTAGAGTTTGTTCTACCGATAGAAGTC
676315 TTGGTT
65 TTGGTT
* * *
676321 GTATCGGTAGAAGTCCCACGTCACAACTTCTTGCTCACTGGAGTTTGTTCTACCGATAAAAGTCT
1 GTATCGGTAGAAGTCCCAGGTCACAACTTCTTGCTCACTAGAGTTTGTTCTACCGATAGAAGTCT
676386 TGGTT
66 TGGTT
* * * *
676391 GTATCGATAGAAGTCCCAGATCACAACTTCTTTCTCAATAGAGTTTGTTCTACCGATAGAAGTCT
1 GTATCGGTAGAAGTCCCAGGTCACAACTTCTTGCTCACTAGAGTTTGTTCTACCGATAGAAGTCT
676456 TGGTT
66 TGGTT
*
676461 GTATCGGTAGAAGTCCCAGGTCACAACTTCTTTCTCACTAGAGTTTGTTCTACCGATAGAAGTCT
1 GTATCGGTAGAAGTCCCAGGTCACAACTTCTTGCTCACTAGAGTTTGTTCTACCGATAGAAGTCT
676526 TGGTT
66 TGGTT
676531 GTATCGGTA
1 GTATCGGTA
676540 AAACCAAGAG
Statistics
Matches: 202, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
70 176 0.87
71 26 0.13
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (70 bp):
GTATCGGTAGAAGTCCCAGGTCACAACTTCTTGCTCACTAGAGTTTGTTCTACCGATAGAAGTCT
TGGTT
Found at i:679366 original size:19 final size:18
Alignment explanation
Indices: 679311--679378 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
679301 GTAAATTGTA
679311 TATTT-TATACATATATAT
1 TATTTATATACATATAT-T
* *
679329 TGTTTATATATAT-TCATT
1 TATTTATATACATAT-ATT
679347 TATTTCATATACATATATTT
1 TATTT-ATATACATATA-TT
*
679367 TTTTTATATACA
1 TATTTATATACA
679379 AGTTGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 10 0.25
19 23 0.57
20 7 0.17
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (18 bp):
TATTTATATACATATATT
Found at i:679374 original size:17 final size:17
Alignment explanation
Indices: 679313--679374 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
679303 AAATTGTATA
*
679313 TTTTATACATATATATT
1 TTTTATACATATATTTT
* *
679330 GTTTATATATATTCATTTAT
1 TTTTATACATA-T-ATTT-T
*
679350 TTCATATACATATATTTT
1 TT-TTATACATATATTTT
679368 TTTTATA
1 TTTTATA
679375 TACAAGTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 7 0.21
20 3 0.09
21 7 0.21
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATACATATATTTT
Found at i:684587 original size:61 final size:61
Alignment explanation
Indices: 684511--684641 Score: 217
Period size: 61 Copynumber: 2.1 Consensus size: 61
684501 TGTTCACATT
*
684511 GGAACTCATTTCATTTAATACTCACGATGACATATAGTCATCAAACCTTTTGTTCCGTAGA
1 GGAACTCATTTCATTTAATACTCACGATGACATATAGTCATCAAACCTCTTGTTCCGTAGA
** *
684572 GGAACTCATTTCATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATA
1 GGAACTCATTTCATTTAATACTCACGATGACATATAGTCATCAAACCTCTTGTTCCGTAGA
*
684633 GGAATTCAT
1 GGAACTCAT
684642 ATACTCACGA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (61 bp):
GGAACTCATTTCATTTAATACTCACGATGACATATAGTCATCAAACCTCTTGTTCCGTAGA
Found at i:684709 original size:51 final size:51
Alignment explanation
Indices: 684590--684779 Score: 202
Period size: 54 Copynumber: 3.6 Consensus size: 51
684580 TTTCATTTAA
** * * *
684590 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-CTTAATCCATAAAGG-ATTCATT
* * * * *
684643 TACTCACGATGACACTGAGTCATCGTACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCATAAAGGATTCATT
*
684694 TACTCACGATGACACTTAGTCACCACCGGACCCTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGT---CATCGGACCCTTAATCCATAAAGGATTCATT
* *
684748 TACTCACGATGGCACTTAGTCATCGGATCCTT
1 TACTCACGATGACACTTAGTCATCGGACCCTT
684780 TCGTTTATAG
Statistics
Matches: 114, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
51 35 0.31
52 8 0.07
53 25 0.22
54 46 0.40
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTAATCCATAAAGGATTCATT
Found at i:689971 original size:21 final size:21
Alignment explanation
Indices: 689945--689995 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
689935 ATAGATGCCT
*
689945 CAGTTTTCTCTTGAAAATCTA
1 CAGTTTGCTCTTGAAAATCTA
*
689966 CAGTTTGCTTTTGAAAATCTA
1 CAGTTTGCTCTTGAAAATCTA
* *
689987 TAGATTGCT
1 CAGTTTGCT
689996 GCTGAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (21 bp):
CAGTTTGCTCTTGAAAATCTA
Found at i:690001 original size:21 final size:21
Alignment explanation
Indices: 689956--690002 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
689946 AGTTTTCTCT
* **
689956 TGAAAATCTACAGTTTGCTTT
1 TGAAAATCTACAGATTGCTGC
*
689977 TGAAAATCTATAGATTGCTGC
1 TGAAAATCTACAGATTGCTGC
689998 TGAAA
1 TGAAA
690003 TTCAAGAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (21 bp):
TGAAAATCTACAGATTGCTGC
Found at i:691557 original size:16 final size:16
Alignment explanation
Indices: 691522--691561 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
691512 ATCTGAGGAA
*
691522 AAATTAAAAGAAAATT
1 AAATTAAAAGAAAATG
691538 AAATTAAAAG-AAATAG
1 AAATTAAAAGAAAAT-G
691554 AAATTAAA
1 AAATTAAA
691562 GGAGTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATTAAAAGAAAATG
Found at i:696025 original size:16 final size:16
Alignment explanation
Indices: 696004--696055 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
695994 TGTATACATG
696004 AATTTTGATTTTATGC
1 AATTTTGATTTTATGC
** **
696020 AATTTT-A-TACATTA
1 AATTTTGATTTTATGC
696034 AATTTTGATTTTATGC
1 AATTTTGATTTTATGC
696050 AATTTT
1 AATTTT
696056 ATACATGAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTTTGATTTTATGC
Found at i:696077 original size:35 final size:30
Alignment explanation
Indices: 695988--696074 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
695978 TGGTTTAATG
*
695988 TGCAATTGTATACATG-AATTTTGATTTTA
1 TGCAATTTTATACATGAAATTTTGATTTTA
*
696017 TGCAATTTTATACATTAAATTTTGATTTTA
1 TGCAATTTTATACATGAAATTTTGATTTTA
696047 TGCAATTTTATACATGAAATTTTGATTT
1 TGCAATTTTATACATGAAATTTTGATTT
696075 GATCTAATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 14 0.26
30 40 0.74
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (30 bp):
TGCAATTTTATACATGAAATTTTGATTTTA
Found at i:700907 original size:3 final size:3
Alignment explanation
Indices: 700899--700926 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
700889 ATCTAAAGCT
700899 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
700927 GTACTTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:707873 original size:3 final size:3
Alignment explanation
Indices: 707865--707899 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
707855 TAACGCTTAT
707865 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
707900 TAATCTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:708377 original size:14 final size:14
Alignment explanation
Indices: 708358--708389 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
708348 TTAATAATTG
708358 AATAATACAAAGAA
1 AATAATACAAAGAA
*
708372 AATAATGCAAAGAA
1 AATAATACAAAGAA
708386 AATA
1 AATA
708390 TTATTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.16
Consensus pattern (14 bp):
AATAATACAAAGAA
Found at i:711120 original size:30 final size:30
Alignment explanation
Indices: 711069--711125 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
711059 TATAATTCAT
711069 AAAAATTAATAAAAATATTTTAAAAAAATA
1 AAAAATTAATAAAAATATTTTAAAAAAATA
* *
711099 AAAAAGTTCATAAAAA-CTTTTAAAAAA
1 AAAAA-TTAATAAAAATATTTTAAAAAA
711126 TTTATCTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAAATTAATAAAAATATTTTAAAAAAATA
Found at i:711598 original size:18 final size:19
Alignment explanation
Indices: 711566--711605 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
711556 TTTTACACCA
* *
711566 AATTTTAATTAATAATTGT
1 AATTTAAATTAATAATTAT
711585 AATTTAAATT-ATAATTAT
1 AATTTAAATTAATAATTAT
711603 AAT
1 AAT
711606 AGCTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AATTTAAATTAATAATTAT
Found at i:711700 original size:18 final size:20
Alignment explanation
Indices: 711663--711703 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
711653 CATTAGCATA
711663 ATTTTAAAATAAATTATAATT
1 ATTTTAAAAT-AATTATAATT
711684 ATTTTAAAAT-ATT-TAATT
1 ATTTTAAAATAATTATAATT
711702 AT
1 AT
711704 CATAATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
21 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATAATTATAATT
Found at i:719628 original size:15 final size:17
Alignment explanation
Indices: 719605--719637 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
719595 TGTAAATTTT
719605 AAATAATTTAAA-AGTA
1 AAATAATTTAAAGAGTA
719621 AAAT-ATTTAAAGAGTA
1 AAATAATTTAAAGAGTA
719637 A
1 A
719638 TGTTAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
AAATAATTTAAAGAGTA
Found at i:720237 original size:16 final size:15
Alignment explanation
Indices: 720216--720258 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
720206 AGCAAAGTTG
720216 AAAAAATTAAAAGGT
1 AAAAAATTAAAAGGT
* * *
720231 GAGAAAATGAAAGGGT
1 -AAAAAATTAAAAGGT
720247 AAAAAATTAAAA
1 AAAAAATTAAAA
720259 AGATGAAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (15 bp):
AAAAAATTAAAAGGT
Found at i:730805 original size:13 final size:13
Alignment explanation
Indices: 730789--730813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
730779 AAAAAATTGG
730789 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
730802 AAAAAAAAAAAA
1 AAAAAAAAAAAA
730814 AATTATAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:731006 original size:17 final size:18
Alignment explanation
Indices: 730979--731013 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
730969 TTAGGCTTTG
*
730979 TTTTGTTTTTTTGTTTCA
1 TTTTGTTTTTTTATTTCA
730997 TTTT-TTTTTTTATTTCA
1 TTTTGTTTTTTTATTTCA
731014 CCAAAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTGTTTTTTTATTTCA
Found at i:731459 original size:26 final size:28
Alignment explanation
Indices: 731414--731466 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
731404 GTAAGGACAA
*
731414 AAAAGATAAAAACAACAC-AAATTTGTC
1 AAAAGATAAAAACAAAACAAAATTTGTC
731441 AAAAGA-AAAAACAAAACAAAATTTGT
1 AAAAGATAAAAACAAAACAAAATTTGT
731467 TGGGTGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (28 bp):
AAAAGATAAAAACAAAACAAAATTTGTC
Found at i:744125 original size:34 final size:34
Alignment explanation
Indices: 744070--744134 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
744060 ATATATATGG
** *
744070 AAATGCAACTACAATGCAAATGCGTTGACAAATA
1 AAATGCAACTACAATAAAAATGCGATGACAAATA
*
744104 AAATGCAA-TGACAATAAAAATGTGATGACAA
1 AAATGCAACT-ACAATAAAAATGCGATGACAA
744135 CTACATGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 1 0.04
34 25 0.96
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (34 bp):
AAATGCAACTACAATAAAAATGCGATGACAAATA
Found at i:744593 original size:24 final size:21
Alignment explanation
Indices: 744541--744594 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
744531 CGACAGGAAC
*
744541 TTCCTCTTTCTTTTCTTTTCT
1 TTCCTCTTCCTTTTCTTTTCT
*
744562 TTCATCTTCCTTTTCTTCTTCCT
1 TTCCTCTTCCTTTTCTT-TT-CT
744585 TCTCCTCTTC
1 T-TCCTCTTC
744595 GATACCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.56
22 2 0.07
23 3 0.11
24 7 0.26
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCCTCTTCCTTTTCTTTTCT
Found at i:749525 original size:9 final size:9
Alignment explanation
Indices: 749511--749535 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
749501 TTTGAAATGT
749511 AAAATGCTA
1 AAAATGCTA
749520 AAAATGCTA
1 AAAATGCTA
749529 AAAATGC
1 AAAATGC
749536 AATGCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (9 bp):
AAAATGCTA
Found at i:751618 original size:6 final size:6
Alignment explanation
Indices: 751607--751658 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
751597 TTCCTTATCT
* * * *
751607 TCTTCA TCTTCA TCTTCA TCTTCA CCTCCA -CCTCTA TCTTGA TCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC-A TCTTCA TCTTCA
751655 TCTT
1 TCTT
751659 GTTCTTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 2 0.05
6 33 0.89
7 2 0.05
ACGTcount: A:0.15, C:0.37, G:0.02, T:0.46
Consensus pattern (6 bp):
TCTTCA
Found at i:754175 original size:31 final size:31
Alignment explanation
Indices: 754137--754199 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
754127 AAAAAAATGA
754137 ATAAATCAACTAGCTTAGCACCAAGTTCACC
1 ATAAATCAACTAGCTTAGCACCAAGTTCACC
754168 ATAAATCAACTAGCTTAGCACCAAGTTCACC
1 ATAAATCAACTAGCTTAGCACCAAGTTCACC
754199 A
1 A
754200 ATCTGTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.22
Consensus pattern (31 bp):
ATAAATCAACTAGCTTAGCACCAAGTTCACC
Found at i:755235 original size:38 final size:38
Alignment explanation
Indices: 755168--755245 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 38
755158 TTAAAATTAA
* * * *
755168 TTTTTAAAATATAAAATTATTATATTTATTATATTATT
1 TTTTTAAAATATAAAATTATTAAAATTATTAAATAATT
* * *
755206 TTTTTGAACTATAAAATTGTTAAAATTATTAAATAATT
1 TTTTTAAAATATAAAATTATTAAAATTATTAAATAATT
755244 TT
1 TT
755246 AACCTCATCG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (38 bp):
TTTTTAAAATATAAAATTATTAAAATTATTAAATAATT
Found at i:758558 original size:24 final size:24
Alignment explanation
Indices: 758530--758616 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
758520 TAGACTAATA
*
758530 AGAGTTTGACTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
*
758554 AGAGTTTAACTAAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* *
758578 AAAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
758602 A-ATGTTTAACTGAAA
1 AGA-GTTTAACTGAAA
758617 GATTATTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 1 0.02
24 55 0.98
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:759512 original size:30 final size:30
Alignment explanation
Indices: 759471--759582 Score: 90
Period size: 30 Copynumber: 3.7 Consensus size: 30
759461 GTAAATTACA
759471 AAAAATCATAAAAACTTATAAATATTATTC
1 AAAAATCATAAAAACTTATAAATATTATTC
* * *
759501 AAAAATGATAAAAGAATTA-ATATATT-TT-
1 AAAAATCATAAAA-ACTTATAAATATTATTC
*
759529 AATAAATCATTAAAAACTATATAAA-ATTA-AC
1 AA-AAATCA-TAAAAACT-TATAAATATTATTC
* *
759560 AAAATTTTATAAAAACTTATAAA
1 AAAA-ATCATAAAAACTTATAAA
759583 AATTCATCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
28 2 0.03
29 15 0.23
30 38 0.58
31 10 0.15
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAATCATAAAAACTTATAAATATTATTC
Found at i:759851 original size:15 final size:14
Alignment explanation
Indices: 759815--759865 Score: 70
Period size: 15 Copynumber: 3.7 Consensus size: 14
759805 TTTTAATTGA
759815 TAAATTTTTATTTT
1 TAAATTTTTATTTT
759829 T--ATTTTTATTTT
1 TAAATTTTTATTTT
759841 TAAATTTTTTATTTT
1 TAAA-TTTTTATTTT
*
759856 CAAATTTTTA
1 TAAATTTTTA
759866 AGTACAGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.36
14 8 0.24
15 13 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TAAATTTTTATTTT
Found at i:759855 original size:6 final size:6
Alignment explanation
Indices: 759818--759842 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
759808 TAATTGATAA
759818 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
759843 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:760986 original size:12 final size:12
Alignment explanation
Indices: 760965--760999 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
760955 AATAACTCCA
*
760965 AACAACAAAAAT
1 AACAACAAAAAC
*
760977 AACAATAAAAAC
1 AACAACAAAAAC
760989 AACAACAAAAA
1 AACAACAAAAA
761000 ATAGAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:761016 original size:22 final size:22
Alignment explanation
Indices: 760991--761064 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
760981 ATAAAAACAA
760991 CAACAAAAAATAGAAAAAATAG
1 CAACAAAAAATAGAAAAAATAG
* * *
761013 CAACAAAAAAAACAAAAAA-AA
1 CAACAAAAAATAGAAAAAATAG
* * *
761034 CAGCATCAAAATAGTAAAAATAG
1 CAACA-AAAAATAGAAAAAATAG
*
761057 CACCAAAA
1 CAACAAAA
761065 CAGAAACCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
21 5 0.13
22 29 0.74
23 5 0.13
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.08
Consensus pattern (22 bp):
CAACAAAAAATAGAAAAAATAG
Found at i:761022 original size:24 final size:24
Alignment explanation
Indices: 760967--761044 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
760957 TAACTCCAAA
* * *
760967 CAACAAAAATAACAATAAAAACAA
1 CAACAAAAAAAACAAAAAAAACAG
* * *
760991 CAAC--AAAAAATAGAAAAAATAG
1 CAACAAAAAAAACAAAAAAAACAG
761013 CAACAAAAAAAACAAAAAAAACAG
1 CAACAAAAAAAACAAAAAAAACAG
*
761037 CATCAAAA
1 CAACAAAA
761045 TAGTAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 16 0.38
24 26 0.62
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.06
Consensus pattern (24 bp):
CAACAAAAAAAACAAAAAAAACAG
Found at i:761031 original size:44 final size:46
Alignment explanation
Indices: 760967--761064 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 46
760957 TAACTCCAAA
*
760967 CAACAAAAATAACAATAAAAACAACAACA-AAAAATAGAAAAAATAG
1 CAACAAAAAAAACAATAAAAA-AACAACATAAAAATAGAAAAAATAG
* * *
761013 CAACAAAAAAAAC-A-AAAAAAACAGCATCAAAATAGTAAAAATAG
1 CAACAAAAAAAACAATAAAAAAACAACATAAAAATAGAAAAAATAG
*
761057 CACCAAAA
1 CAACAAAA
761065 CAGAAACCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.13
44 27 0.59
45 1 0.02
46 12 0.26
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.08
Consensus pattern (46 bp):
CAACAAAAAAAACAATAAAAAAACAACATAAAAATAGAAAAAATAG
Found at i:761033 original size:46 final size:44
Alignment explanation
Indices: 760967--761064 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 44
760957 TAACTCCAAA
* *
760967 CAACAAAAATAACAATAAAAACAACAACAAAAAATAGAAAAAATAG
1 CAACAAAAAAAACAAAAAAAACAACAAC--AAAATAGAAAAAATAG
* * *
761013 CAACAAAAAAAACAAAAAAAACAGCATCAAAATAGTAAAAATAG
1 CAACAAAAAAAACAAAAAAAACAACAACAAAATAGAAAAAATAG
*
761057 CACCAAAA
1 CAACAAAA
761065 CAGAAACCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 22 0.48
46 24 0.52
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.08
Consensus pattern (44 bp):
CAACAAAAAAAACAAAAAAAACAACAACAAAATAGAAAAAATAG
Found at i:761093 original size:30 final size:30
Alignment explanation
Indices: 761048--761140 Score: 82
Period size: 30 Copynumber: 3.0 Consensus size: 30
761038 ATCAAAATAG
761048 TAAAAATAGCACCAAAACAGAAACCAAAACAA
1 TAAAAA-A-CACCAAAACAGAAACCAAAACAA
*
761080 TAAAAAACACCAAAACAGTAAA--AACACAA
1 TAAAAAACACCAAAACAG-AAACCAAAACAA
* * * *
761109 TACCAAAACAGCAAAAATAGCAACCAAAACAA
1 TA-AAAAACA-CCAAAACAGAAACCAAAACAA
761141 CAATATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 8 0.16
30 19 0.38
31 11 0.22
32 12 0.24
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.06
Consensus pattern (30 bp):
TAAAAAACACCAAAACAGAAACCAAAACAA
Found at i:761113 original size:22 final size:21
Alignment explanation
Indices: 761061--761139 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 21
761051 AAATAGCACC
* *
761061 AAAACAGAAACCAAAACAATA
1 AAAACACAAACCAAAACAGTA
761082 AAAA-AC--ACCAAAACAGTA
1 AAAACACAAACCAAAACAGTA
*
761100 AAAACACAATACCAAAACAGCA
1 AAAACACAA-ACCAAAACAGTA
*
761122 AAAATAGC-AACCAAAACA
1 AAAACA-CAAACCAAAACA
761140 ACAATATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 15 0.31
19 2 0.04
20 1 0.02
21 13 0.27
22 17 0.35
23 1 0.02
ACGTcount: A:0.67, C:0.23, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAACACAAACCAAAACAGTA
Found at i:761694 original size:19 final size:18
Alignment explanation
Indices: 761670--761929 Score: 73
Period size: 20 Copynumber: 14.2 Consensus size: 18
761660 CCAGTTCAAG
761670 TTTTTATGATTTGTTATAA
1 TTTTTATGATTT-TTATAA
* *
761689 TTTTTATAAGTTTATATCAA
1 TTTTTATGA-TTTTTAT-AA
* * *
761709 ATTTAAT-ATTTTTTATAT
1 TTTTTATGA-TTTTTATAA
761727 TTTTTATGATTTTCTATAAA
1 TTTTTATGATTTT-TAT-AA
* *
761747 GTTTTAAGAATTTTTATACA
1 TTTTTATG-ATTTTTATA-A
761767 TTTTTAT-A-----A-AA
1 TTTTTATGATTTTTATAA
* *
761778 TTTTAAAT-ATTTTTTTAA
1 TTTT-TATGATTTTTATAA
761796 -TTTTATAGAATTTATTATAA
1 TTTTTAT-G-ATTT-TTATAA
*
761816 TTTATTA-GTTTTATTAT-A
1 TTT-TTATGATTT-TTATAA
* *
761834 TTTTTATAATATTTATAAA
1 TTTTTATGATTTTTAT-AA
*
761853 TTTTTTATTATTTTTTATAA
1 -TTTTTATGA-TTTTTATAA
761873 TTTTTAT-ATGTTTATATCAA
1 TTTTTATGAT-TTT-TAT-AA
**
761893 TTTGAAT-ATTTTTA-AA
1 TTTTTATGATTTTTATAA
* * *
761909 TATTTATAATTTTTATTA
1 TTTTTATGATTTTTATAA
761927 TTT
1 TTT
761930 AATAATTTTA
Statistics
Matches: 180, Mismatches: 31, Indels: 61
0.66 0.11 0.22
Matches are distributed among these distances:
11 5 0.03
12 4 0.02
13 1 0.01
16 8 0.04
17 18 0.10
18 28 0.16
19 49 0.27
20 51 0.28
21 13 0.07
22 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTATGATTTTTATAA
Found at i:761697 original size:9 final size:9
Alignment explanation
Indices: 761670--761938 Score: 129
Period size: 9 Copynumber: 28.4 Consensus size: 9
761660 CCAGTTCAAG
*
761670 TTTTTATGA
1 TTTTTATAA
761679 TTTGTTATAA
1 TTT-TTATAA
761689 TTTTTATAA
1 TTTTTATAA
*
761698 GTTTATATCAA
1 -TTTTTAT-AA
* * *
761709 ATTTAATAT
1 TTTTTATAA
*
761718 TTTTTATAT
1 TTTTTATAA
*
761727 TTTTTATGA
1 TTTTTATAA
761736 TTTTCTATAAA
1 TTTT-TAT-AA
* *
761747 GTTTTAAGAA
1 -TTTTTATAA
761757 TTTTTATACA
1 TTTTTATA-A
761767 TTTTTATAAA
1 TTTTTAT-AA
* *
761777 ATTTTAAATA
1 TTTTTATA-A
*
761787 TTTTTTTAA
1 TTTTTATAA
*
761796 TTTTATAGAA
1 TTTT-TATAA
761806 TTTATTATAA
1 TTT-TTATAA
761816 TTTATTAGT--
1 TTT-TTA-TAA
761825 TTTATTAT-A
1 TTT-TTATAA
761834 TTTTTATAA
1 TTTTTATAA
*
761843 TATTTATAAA
1 TTTTTAT-AA
*
761853 TTTTTTATTAT
1 -TTTTTA-TAA
761864 TTTTTATAA
1 TTTTTATAA
761873 TTTTTAT-A
1 TTTTTATAA
761881 TGTTTATATCAA
1 T-TTT-TAT-AA
**
761893 TTTGAAT-A
1 TTTTTATAA
761901 TTTTTA-AA
1 TTTTTATAA
*
761909 TATTTATAA
1 TTTTTATAA
*
761918 TTTTTATTA
1 TTTTTATAA
*
761927 -TTTAATAA
1 TTTTTATAA
761935 TTTT
1 TTTT
761939 ATGAAAAAAT
Statistics
Matches: 200, Mismatches: 36, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
8 24 0.12
9 81 0.41
10 73 0.37
11 15 0.08
12 7 0.04
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:761780 original size:11 final size:10
Alignment explanation
Indices: 761678--761880 Score: 76
Period size: 10 Copynumber: 20.9 Consensus size: 10
761668 AGTTTTTATG
761678 ATTTGTTAT-A
1 ATTT-TTATAA
761688 ATTTTTATAA
1 ATTTTTATAA
* *
761698 GTTTATATCAA
1 ATTTTTAT-AA
*
761709 A-TTTAAT-A
1 ATTTTTATAA
*
761717 TTTTTTAT-A
1 ATTTTTATAA
* *
761726 TTTTTTAT-G
1 ATTTTTATAA
761735 ATTTTCTATAA
1 ATTTT-TATAA
*
761746 AGTTTTA-AGA
1 ATTTTTATA-A
*
761756 ATTTTTATAC
1 ATTTTTATAA
761766 ATTTTTATAA
1 ATTTTTATAA
*
761776 AATTTTA-AA
1 ATTTTTATAA
*
761785 TATTTTT-TTA
1 -ATTTTTATAA
761795 A-TTTTATAGA
1 ATTTTTATA-A
761805 ATTTATTAT-A
1 ATTT-TTATAA
*
761815 A--TTTAT-T
1 ATTTTTATAA
* *
761822 AGTTTTATTAT
1 ATTTTTA-TAA
761833 ATTTTTAT-A
1 ATTTTTATAA
*
761842 ATATTTATAA
1 ATTTTTATAA
*
761852 ATTTTTTATTA
1 A-TTTTTATAA
*
761863 TTTTTTAT-A
1 ATTTTTATAA
761872 ATTTTTATA
1 ATTTTTATA
761881 TGTTTATATC
Statistics
Matches: 147, Mismatches: 26, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.03
8 6 0.04
9 46 0.31
10 63 0.43
11 23 0.16
12 4 0.03
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:761922 original size:17 final size:17
Alignment explanation
Indices: 761900--761938 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
761890 CAATTTGAAT
761900 ATTTTTAAATATTT-ATA
1 ATTTTT-AATATTTAATA
*
761917 ATTTTTATTATTTAATA
1 ATTTTTAATATTTAATA
761934 ATTTT
1 ATTTT
761939 ATGAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTAATATTTAATA
Found at i:763025 original size:29 final size:29
Alignment explanation
Indices: 762853--763417 Score: 431
Period size: 28 Copynumber: 19.9 Consensus size: 29
762843 AATTGTCACT
*
762853 ATTTTACAGTTTTGCCACTAGTTTT--GG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
762880 ATTTTACAATTTTACCACT-GTTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * *
762908 ATTTTGCAATTTTGCCACT-GATTTTCTAG
1 ATTTTACAGTTTTGCCACTAG-TTTTCCAG
* *
762937 GTTTTACAG-TTTGCCAAT-GTTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * *
762964 ATTTTACAATTTTGTCATTA-TTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
762992 ATTTTATAGTTTTGCCATTAGTTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * *
763021 ATTTTACAATTTTGCCACCAATTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * *
763050 ATTTTACAGTTTTACCACTGGTTTTCCAT
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * ** *
763079 ATTTTATAGTTTTACCTTTA-TTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * * *
763107 ATTTTATAGTTTTGCAATTGGTTTTTCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * *
763136 ATTTTATAGTTTTACCACTA-ATTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
763164 ATTTTACAGTTTTGCCATTGGTTTTTTCCAG
1 ATTTTACAGTTTTGCCACTAG--TTTTCCAG
*
763195 ATTTTACAGTTTTGGCACT-GTTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * * * * *
763223 ATTTTAAAATTTTTCCATTGGTTTTTCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * *
763252 ATTTTATAGTTTTACCACTA-TTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * * *
763280 ATTTTATAGTTTTGCCATTGGTTTTTCAT
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * *
763309 ATTTTACATTTTTTCCA-TTGATTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * *
763337 ATTTTACAATTTTGCCA-TTGATTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
763365 ATTTTACA-TTTTGTCACTA-TTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
763392 ATTTTACAATTTTGCCACTATTTTTC
1 ATTTTACAGTTTTGCCACTAGTTTTC
763418 AAAAAAATTA
Statistics
Matches: 430, Mismatches: 93, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
26 5 0.01
27 52 0.12
28 199 0.46
29 150 0.35
30 1 0.00
31 23 0.05
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTAGTTTTCCAG
Found at i:763027 original size:57 final size:57
Alignment explanation
Indices: 762853--763408 Score: 541
Period size: 57 Copynumber: 9.8 Consensus size: 57
762843 AATTGTCACT
* * * * * *
762853 ATTTTACAGTTTTGCCACTAGTTT-TGGATTTTACAATTTTACCACT-GTTTTCCAG
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * *
762908 ATTTTGCAATTTTGCCACTGATTTTCTAGGTTTTACAG-TTTGCCAAT-GTTTTCCAG
1 ATTTTACAATTTTGCCACT-ATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * * *
762964 ATTTTACAATTTTGTCATTATTTTCCAGATTTTATAGTTTTGCCATTAGTTTTCCAG
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * *
763021 ATTTTACAATTTTGCCACCAATTTTCTAGATTTTACAGTTTTACCACTGGTTTTCCAT
1 ATTTTACAATTTTGCCA-CTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * ** * * *
763079 ATTTTATAGTTTTACCTTTATTTTCTAGATTTTATAGTTTTGCAATTGGTTTTTCAG
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * *
763136 ATTTTATAGTTTTACCACTAATTTCTAGATTTTACAGTTTTGCCATTGGTTTTTTCCAG
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGG--TTTTCCAG
* * * * * * * * *
763195 ATTTTACAGTTTTGGCACTGTTTTCCAGATTTTAAAATTTTTCCATTGGTTTTTCAA
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * * * *
763252 ATTTTATAGTTTTACCACTATTTTCTAGATTTTATAGTTTTGCCATTGGTTTTTCAT
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* * * * * *
763309 ATTTTACATTTTTTCCATTGA-TTTCCAGATTTTACAATTTTGCCATT-GATTTCCAG
1 ATTTTACAATTTTGCCACT-ATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
* *
763365 ATTTTAC-ATTTTGTCACTATTTTCTAGATTTTACAATTTTGCCA
1 ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCA
763409 CTATTTTTCA
Statistics
Matches: 415, Mismatches: 77, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
54 1 0.00
55 62 0.15
56 57 0.14
57 202 0.49
58 46 0.11
59 47 0.11
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.51
Consensus pattern (57 bp):
ATTTTACAATTTTGCCACTATTTTCTAGATTTTACAGTTTTGCCATTGGTTTTCCAG
Found at i:764500 original size:32 final size:31
Alignment explanation
Indices: 764426--764516 Score: 119
Period size: 32 Copynumber: 2.9 Consensus size: 31
764416 TAAACATATT
* * *
764426 AAAAGTACAACCTAAATCCCCAAATTATCAA
1 AAAAGTAAAACCTAAATTCCCAAATCATCAA
* *
764457 AAAAGTTAAACCTACATTCCCAAATCATCAAA
1 AAAAGTAAAACCTAAATTCCCAAATCATC-AA
*
764489 AAAAGTAAAACCTAAATTTCCAAATCAT
1 AAAAGTAAAACCTAAATTCCCAAATCAT
764517 TGTTAATAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 24 0.47
32 27 0.53
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.22
Consensus pattern (31 bp):
AAAAGTAAAACCTAAATTCCCAAATCATCAA
Found at i:767371 original size:38 final size:38
Alignment explanation
Indices: 767306--767436 Score: 137
Period size: 36 Copynumber: 3.6 Consensus size: 38
767296 GATAGACCCA
* *
767306 TCTAAGACAAC-CTT-AAAAAGGTTGAGATAAACTTTG
1 TCTAAGACAACATTTAAAAAAAGTTGAGATAAACTTTG
* * *
767342 TCTAAGGCAACCTTTAAAAAATGTTGAGATAGAAC---G
1 TCTAAGACAACATTTAAAAAAAGTTGAGATA-AACTTTG
* * *
767378 ACTAAGACAACATTAAAAAAAAATTGAGATAAACTTTG
1 TCTAAGACAACATTTAAAAAAAGTTGAGATAAACTTTG
*
767416 TCTAAGGCAACATTTAAAAAA
1 TCTAAGACAACATTTAAAAAA
767437 GATCGGGATA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.04
36 36 0.47
37 2 0.03
38 33 0.43
39 3 0.04
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (38 bp):
TCTAAGACAACATTTAAAAAAAGTTGAGATAAACTTTG
Found at i:770855 original size:21 final size:22
Alignment explanation
Indices: 770831--770872 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
770821 TTGATACGTA
*
770831 ACATGGT-TGAACATAAATGAG
1 ACATGGTACGAACATAAATGAG
*
770852 ACATGGTACGTACATAAATGA
1 ACATGGTACGAACATAAATGA
770873 CTATTACTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (22 bp):
ACATGGTACGAACATAAATGAG
Found at i:776251 original size:17 final size:17
Alignment explanation
Indices: 776229--776261 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
776219 ACTCTGGTCA
*
776229 CTGAAATTTTTGGTTAC
1 CTGAAATTTTTCGTTAC
776246 CTGAAATTTTTCGTTA
1 CTGAAATTTTTCGTTA
776262 TAAATAGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (17 bp):
CTGAAATTTTTCGTTAC
Found at i:777767 original size:25 final size:25
Alignment explanation
Indices: 777738--777805 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
777728 TATCGGTACC
777738 TCCTCAAAAGGTATCGATCCGGTAT
1 TCCTCAAAAGGTATCGATCCGGTAT
777763 TCCTCAAAAGGTATCGATCCGGTAT
1 TCCTCAAAAGGTATCGATCCGGTAT
777788 TCCTCAAAAGGTATCGAT
1 TCCTCAAAAGGTATCGAT
777806 ACCGTAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (25 bp):
TCCTCAAAAGGTATCGATCCGGTAT
Found at i:778513 original size:23 final size:23
Alignment explanation
Indices: 778479--778523 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
778469 AGAGATTTTT
*
778479 TTTTGTTTAGAGAGGAAGATTTA
1 TTTTGTTCAGAGAGGAAGATTTA
*
778502 TTTTGTTCAGAGAGGAATATTT
1 TTTTGTTCAGAGAGGAAGATTT
778524 TAGGATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (23 bp):
TTTTGTTCAGAGAGGAAGATTTA
Done.