Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:245608 original size:496 final size:459
Alignment explanation
Indices: 244705--245660 Score: 1254
Period size: 462 Copynumber: 2.0 Consensus size: 459
244695 TGTTGTTATG
* * *
244705 AATAAGTAATAATAAAACTAAAAAATAAATCTATTTGCATTAGTGCTAGTCCAATTACATTAGTT
1 AATAAGTAATAATAAAACCAAAAAATAAATCTACTTGCATTAGTGCTAGTCCAATTACATTAGCT
* * *
244770 TACGTAGGCCCAATATATAAGCCTACTCTTTTATTACAAATATATAAGCATTAGTGCTAGTCCAT
66 TACATAGGCCCAATATATAAGCCCACTCTTTTATTACAAATATATAAGCATTAATGCTAGTCCAT
* *
244835 TTACATTAGGGTTTATGGTTTAGGATTTACGGTTTAGTATGTAAGGTTTGAAGTTTAGGTTTTAG
131 TTACATTAGGGCTTATGGTTTAGGATTTACGCTTTAGTATGTAAGGTTTGAAGTTTAGGTTTTAG
244900 GGTTTCTATAAAATATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATA
196 GGTTTCTATAAAATATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATA
*
244965 TAAGTAATAATATATATATATATATATAGGTTATATATATATATAGTTTATATATATAGTTTATA
261 TAAGTAATAATATATATATATATATATAGATTATATATATATATAGTTTATATATATAGTTTATA
245030 TACATACATATTATATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATTAAT
326 TACATACATATTATATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATTAAT
* *
245095 AATTATGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATATTAAATAGCAGTAC
391 AATTAGGTGTAAAATAATTAGTATGTCACATTGCATATTATATGGTTC--A-TAAATAGCAGTAC
245160 ATGTCAT
453 ATGTCAT
* ** *
245167 AATAAGTAATAATAAAACCCAAAAATAGGTCTACTTGCATTAGTGCTAGTCCACTTACATTAGCT
1 AATAAGTAATAATAAAACCAAAAAATAAATCTACTTGCATTAGTGCTAGTCCAATTACATTAGCT
*
245232 TACATAGGCCCAATATATAAGCCCACTCTTTTATTACAAATATATATGCATTAATGCTAGTCCAT
66 TACATAGGCCCAATATATAAGCCCACTCTTTTATTACAAATATATAAGCATTAATGCTAGTCCAT
* * * *
245297 TTATATTAGGGCTTATGGTTTAGGGTTT-TGTCTTTAGTATGTATGGTTTGAAGTTTAGGTTTTA
131 TTACATTAGGGCTTATGGTTTAGGATTTACG-CTTTAGTATGTAAGGTTTGAAGTTTAGGTTTTA
* *
245361 GGGTTTAGAGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTGTGCATAGTGTTTCTAT
195 --G----G-GTTTCTATAAAATATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTAT
*
245426 GAAA-TATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATATAGTTTATATATA
253 -AAACTATATAAGTAA--TA----ATATA---TATATATATATATAGAT-TATA---TATATATA
* *
245490 TAGTTTATATATACTA-TACATGGTTTATACATACATATTATATAAAATTATTTAATAACATTAA
304 TAGTTTATATATA-TAGT---T--TATATACATACATATTATATAAAATTATTTAATAAAATT-A
* * *
245554 TAAAAAAAATTAAATGTAAATTATTTAAATC-TTGATTAATTAGGTGTAAAATAATTAGTATGTC
362 T--------TTAAATGTAAATTATATAAAACATT-AATAATTAGGTGTAAAATAATTAGTATGTC
*
245618 ACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
418 ACATTGCATATTATATGGTTCATAAATAGCAGTACATGTCAT
245660 A
1 A
245661 TTAATTTCAT
Statistics
Matches: 427, Mismatches: 29, Indels: 45
0.85 0.06 0.09
Matches are distributed among these distances:
461 1 0.00
462 175 0.41
464 1 0.00
468 1 0.00
469 65 0.15
470 3 0.01
471 2 0.00
475 5 0.01
478 15 0.04
479 4 0.01
482 22 0.05
483 2 0.00
485 1 0.00
487 37 0.09
488 2 0.00
493 20 0.05
494 1 0.00
495 2 0.00
496 68 0.16
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (459 bp):
AATAAGTAATAATAAAACCAAAAAATAAATCTACTTGCATTAGTGCTAGTCCAATTACATTAGCT
TACATAGGCCCAATATATAAGCCCACTCTTTTATTACAAATATATAAGCATTAATGCTAGTCCAT
TTACATTAGGGCTTATGGTTTAGGATTTACGCTTTAGTATGTAAGGTTTGAAGTTTAGGTTTTAG
GGTTTCTATAAAATATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATA
TAAGTAATAATATATATATATATATATAGATTATATATATATATAGTTTATATATATAGTTTATA
TACATACATATTATATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATTAAT
AATTAGGTGTAAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGCAGTACATG
TCAT
Found at i:245900 original size:7 final size:7
Alignment explanation
Indices: 245888--245936 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
245878 TAGGGTCTAT
245888 TGTTTAG
1 TGTTTAG
*
245895 TGTTTAA
1 TGTTTAG
245902 TGTTTAG
1 TGTTTAG
245909 TGTTTA-
1 TGTTTAG
245915 TGGTTTAG
1 T-GTTTAG
*
245923 AGTTTAG
1 TGTTTAG
*
245930 GGTTTAG
1 TGTTTAG
245937 GATTTCTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 1 0.03
7 35 0.97
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (7 bp):
TGTTTAG
Found at i:246036 original size:15 final size:15
Alignment explanation
Indices: 246016--246067 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
246006 TAATTTATTT
246016 TATATAGTTTATATA
1 TATATAGTTTATATA
*
246031 TATATAGGTTATATA
1 TATATAGTTTATATA
246046 TATATAGTTTATATA
1 TATATAGTTTATATA
246061 TACTATA
1 TA-TATA
246068 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:246258 original size:560 final size:556
Alignment explanation
Indices: 245167--247024 Score: 2689
Period size: 545 Copynumber: 3.3 Consensus size: 556
245157 TACATGTCAT
* * *
245167 AATAAGTAATAATAAAACCCAAAAATAGGTCTACTTGCATTAGTGCTAGTCCACTTACATTAGCT
1 AATAAGTAATAATAAAACCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTACATTAGTT
* *
245232 TACATAGGCCCAATATATAAGCCCACTCTTTTATTACAAATATATATGCATTAATGCTAGTCCAT
66 TACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCAT
* ** * * *
245297 TTATATTAGGGCTTATGGTTTAGGGTTTTGTCTTTAGTATGTATGGTTTGAAGTTTAGGTTTTAG
131 TTACATTAGGGC-TATGGTTTAGGGTTTAATGTTTAGTGTTTATGGTTT-AAG--TA-G-TTTAG
* *
245362 GGTTTA-GAGTTTCTATAAACTATATACTTTATTACTTTATATAGTTTGTGCATAGTGTTTCTAT
190 GGTTTAGGA-TTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAATGTTTCTAT
*
245426 GAAATATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATATAGTTTATATATAT
254 AAAATATATAAGTAATTTA-TTTATATAG----T-T-TATATATATATAT-TA---TATATATAT
245491 AGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAACATTAATA
308 AGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAA-ATTAATA
** * * * * *
245556 AAAAAAATTAAATGTAAATTATTTAAATCTTGATTAATTAGGTGTAAAATAATTAGTATGTCACA
372 AAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACA
*
245621 TTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTAT
437 TTGCATATTATATGCTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTAT
*
245686 TTTAGTTGCATGTTAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATG
502 TTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATG
* * *
245741 AATAAGTTATAA-AAAACCCCCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAG
1 AATAAGTAATAATAAAA--CCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTACATTAG
* * *
245805 TTTACATAGGCCCAAAACGTAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCT
64 TTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCC
* *
245870 ATTTACATTAGGGTCTATTGTTTAGTGTTTAATGTTTAGTGTTTATGGTTT-AG-AGTTTAGGGT
129 ATTTACATTAGGG-CTATGGTTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAGTAGTTTAGGGT
*
245933 TTAGGATTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAAA
193 TTAGGATTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAAA
245998 TATATAAGTAATTTATTTTATATAGTTTATATATATATAGGTTATATATATATAGTTTATATATA
258 TATATAAGTAATTTA-TTTATATAGTTTATATATATATA--TTATATATATATAGTTTATATATA
246063 CTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAA
320 CTATACATGGTTTATACATACATATTATATAAAATTATTTAAT-AAATTAATAAAATTATTTAAA
* *
246128 TGTAAATTATATAAAACATGATTAATTAGTTGTTAAAGAATTAGTATGTCACATTGCATATTATA
384 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
*
246193 TGCTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTTGTTGCATG
449 TGCTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
246258 TTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATG
514 TTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATG
* *
246301 AATAAGTAATAATAAAACCCAAAACTAAGTCTATTTGCATTAGTACTAGTCCACTTACATTAGTT
1 AATAAGTAATAATAAAACCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTACATTAGTT
*
246366 TACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTAT
66 TACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCAT
* * *
246431 TTACATTTGGGCTTATGCTTTAGGGTTTAGTGTTTAGTGTGTT-TGGTTTTAAGTTTAAAGTTTA
131 TTACATTAGGGC-TATGGTTTAGGGTTTAATGTTTAGTGT-TTATGG-TTTAAG--T--AGTTTA
* * * *
246495 GGGTTTAGGGTTTCTATAAACTAAATACTTTATTACTTTATATAGCTTATGCATAATGTTTCTGT
189 GGGTTTAGGATTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAATGTTTCTAT
* *
246560 AAACTATATAAGTAATTTA-CT-T-TA---TAT-TATAT-TA-TATATATATATAGTTTATATAT
254 AAAATATATAAGTAATTTATTTATATAGTTTATATATATATATTATATATATATAGTTTATATAT
* *
246616 ACTATACATGGTTTATACATAAATATTATAT-AAA--A-TT-AT---CTAATAAAATTATTTAAA
319 ACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAATTAATAAAATTATTTAAA
246673 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
384 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
* * * *
246738 TGTTTCATAAATAGTAGTACATGTCATAATAATTTTATTTGCATAATTAGTATTTTAGTTTCATG
449 TGCTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
*
246803 TTAAGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATG
514 TTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATG
* *
246846 AATAAGTAATAATGAAACCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTGCATTAGTT
1 AATAAGTAATAATAAAACCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTACATTAGTT
* * *
246911 TACATAGGCCCAATACATATGCCCACTCCTTTATTACAAATATATATGTATTAGTGCTAGTCCAT
66 TACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCAT
* ** *
246976 TTATATTAGAGTTTAGGGTTTAGGGTTTAATGTTTAGTGTTTATGGTTT
131 TTACATTAG-GGCTATGGTTTAGGGTTTAATGTTTAGTGTTTATGGTTT
247025 GTGTAACACC
Statistics
Matches: 1185, Mismatches: 80, Indels: 68
0.89 0.06 0.05
Matches are distributed among these distances:
544 5 0.00
545 338 0.29
546 1 0.00
549 2 0.00
550 2 0.00
551 1 0.00
553 3 0.00
554 52 0.04
557 2 0.00
558 6 0.01
559 146 0.12
560 260 0.22
561 8 0.01
562 14 0.01
563 4 0.00
564 3 0.00
566 84 0.07
568 90 0.08
569 3 0.00
570 1 0.00
573 6 0.01
574 11 0.01
575 142 0.12
576 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (556 bp):
AATAAGTAATAATAAAACCCAAAAATAAGTCTATTTGCATTAGTGCTAGTCCACTTACATTAGTT
TACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCAT
TTACATTAGGGCTATGGTTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAGTAGTTTAGGGTTTA
GGATTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAAATAT
ATAAGTAATTTATTTATATAGTTTATATATATATATTATATATATATAGTTTATATATACTATAC
ATGGTTTATACATACATATTATATAAAATTATTTAATAAATTAATAAAATTATTTAAATGTAAAT
TATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGCTTCA
TAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTT
AATTCACATTAATAGCCCATTTATTTTGTTGTTATG
Found at i:246621 original size:20 final size:19
Alignment explanation
Indices: 246592--246632 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
246582 TATATTATAT
*
246592 TATATATATATATAGTTTA
1 TATATATATACATAGTTTA
*
246611 TATATACTATACATGGTTTA
1 TATATA-TATACATAGTTTA
246631 TA
1 TA
246633 CATAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATATATACATAGTTTA
Found at i:247170 original size:25 final size:25
Alignment explanation
Indices: 247121--247170 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
247111 AGTATAAAAG
** *
247121 TTCAGTCGGAAGTATCGTCGTTAAT
1 TTCAGTCGGAAGTATCACCGGTAAT
*
247146 TTCATTCGGAAGTATCACCGGTAAT
1 TTCAGTCGGAAGTATCACCGGTAAT
247171 AACTCGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (25 bp):
TTCAGTCGGAAGTATCACCGGTAAT
Found at i:249166 original size:24 final size:24
Alignment explanation
Indices: 249139--249206 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
249129 TATTACTTGT
* *
249139 ATTCTGTTCTGATTTTTGATCTGG
1 ATTCTGTTCTGATTTCTGATCTGA
* * *
249163 ATTCTTTTCTGATATCTGTTCTGA
1 ATTCTGTTCTGATTTCTGATCTGA
*
249187 ATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATTTCTGAT
249207 ATCTCCGTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.15, C:0.13, G:0.16, T:0.56
Consensus pattern (24 bp):
ATTCTGTTCTGATTTCTGATCTGA
Found at i:249203 original size:12 final size:12
Alignment explanation
Indices: 249140--249204 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
249130 ATTACTTGTA
249140 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
249152 TTTTGATCTGGA-
1 TTCTGTTCT-GAT
*
249164 TTCTTTTCTGAT
1 TTCTGTTCTGAT
* *
249176 ATCTGTTCTGAA
1 TTCTGTTCTGAT
*
249188 TTCTGTTTTGAT
1 TTCTGTTCTGAT
249200 TTCTG
1 TTCTG
249205 ATATCTCCGT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 36 0.90
13 2 0.05
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:252852 original size:12 final size:12
Alignment explanation
Indices: 252834--252895 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
252824 ACCTGAATTA
252834 TGTTCTGATTTC
1 TGTTCTGATTTC
*
252846 TGATCTGGA-TTC
1 TGTTCT-GATTTC
** *
252858 TGTTCCAATATC
1 TGTTCTGATTTC
*
252870 TGTTCTGAATTC
1 TGTTCTGATTTC
*
252882 TGTTTTGATTTC
1 TGTTCTGATTTC
252894 TG
1 TG
252896 ATATCTCCGT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
11 1 0.03
12 34 0.92
13 2 0.05
ACGTcount: A:0.15, C:0.16, G:0.18, T:0.52
Consensus pattern (12 bp):
TGTTCTGATTTC
Found at i:252861 original size:24 final size:24
Alignment explanation
Indices: 252826--252897 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
252816 GATAAATTAC
*
252826 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* ** * *
252850 CTGGATTCTGTTCCAATATCTGTT
1 CTGAATTCTGTTCTGATTTCTGAT
*
252874 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
252898 ATCTCCGTTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:255020 original size:32 final size:32
Alignment explanation
Indices: 254979--255058 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
254969 GCGTTGACCA
254979 TTGACCGACGTTGACCACAGTTGACCAAAACT
1 TTGACCGACGTTGACCACAGTTGACCAAAACT
*
255011 TTGACCGACGTTGACCATAGTTGACCAAAACT
1 TTGACCGACGTTGACCACAGTTGACCAAAACT
255043 TTGACC-AGCGTTGACC
1 TTGACCGA-CGTTGACC
255059 GGGCATTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 1 0.02
32 45 0.98
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (32 bp):
TTGACCGACGTTGACCACAGTTGACCAAAACT
Found at i:256500 original size:26 final size:26
Alignment explanation
Indices: 256454--256506 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
256444 TGACCCAAGA
* *
256454 ATATCATCAAGCTCAGGAATGATTGG
1 ATATCATCAAGCTCAGAAATGAATGG
* *
256480 ATATCCTCAAGCTCTGAAATGAATGG
1 ATATCATCAAGCTCAGAAATGAATGG
256506 A
1 A
256507 ATAAAACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (26 bp):
ATATCATCAAGCTCAGAAATGAATGG
Found at i:260468 original size:26 final size:26
Alignment explanation
Indices: 260422--260474 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
260412 TGACCCAAGA
*
260422 ATATCATCAAGCTCAAGAATGATTAG
1 ATATCATCAAGCTCAAGAATGAATAG
* *
260448 ATATCATCGAGCTC-TGAAATGAATAG
1 ATATCATCAAGCTCAAG-AATGAATAG
260474 A
1 A
260475 ATAAAACTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (26 bp):
ATATCATCAAGCTCAAGAATGAATAG
Found at i:261534 original size:12 final size:12
Alignment explanation
Indices: 261492--261548 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
261482 ATACATTACC
*
261492 TGAATTTTGTTA
1 TGAATTCTGTTA
* * *
261504 TGATTTCTGATC
1 TGAATTCTGTTA
*
261516 TGGATTCTGTTA
1 TGAATTCTGTTA
*
261528 TGAATTCTGTTT
1 TGAATTCTGTTA
*
261540 TGATTTCTG
1 TGAATTCTG
261549 ATATCTCCGT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.18, C:0.09, G:0.19, T:0.54
Consensus pattern (12 bp):
TGAATTCTGTTA
Found at i:262736 original size:3 final size:3
Alignment explanation
Indices: 262721--262780 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
262711 TTTATCCCAG
* * * **
262721 TTA TTA TTT TTA TTA -TA GTAA TTA TAA TTA CGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
262766 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
262781 AATAATTTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.93
4 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:264945 original size:6 final size:6
Alignment explanation
Indices: 264929--264961 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
264919 TATATTCTTC
*
264929 TTTATT ATTATT TTTA-T TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
264962 GATATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:264949 original size:17 final size:17
Alignment explanation
Indices: 264929--264961 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
264919 TATATTCTTC
264929 TTTATTATTATTTTTAT
1 TTTATTATTATTTTTAT
*
264946 TTTATTTTTATTTTTA
1 TTTATTATTATTTTTA
264962 GATATTAAAT
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTATTATTTTTAT
Found at i:264952 original size:11 final size:11
Alignment explanation
Indices: 264929--264959 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
264919 TATATTCTTC
264929 TTTATTATTATT
1 TTTATT-TTATT
264941 TTTATTTTATT
1 TTTATTTTATT
264952 TTTATTTT
1 TTTATTTT
264960 TAGATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:271891 original size:36 final size:36
Alignment explanation
Indices: 271841--271938 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
271831 ATGATTCATG
** *
271841 TGGGGCATCCTGAAGGCCCATGTCAGTATGAATATT
1 TGGGGCATTTTGAAGGCTCATGTCAGTATGAATATT
* * *
271877 TGGGGCATTTTGAAGGCTCACGGCAATATGAATATT
1 TGGGGCATTTTGAAGGCTCATGTCAGTATGAATATT
* *
271913 T-GGGCATTCTTGGAGGCTCATCTCAG
1 TGGGGCATT-TTGAAGGCTCATGTCAG
271939 CAAGAAGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
35 7 0.14
36 43 0.86
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (36 bp):
TGGGGCATTTTGAAGGCTCATGTCAGTATGAATATT
Found at i:273492 original size:22 final size:21
Alignment explanation
Indices: 273442--273494 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
273432 ATCTACACTC
273442 TTCAAAGATGATAGATTCTCT
1 TTCAAAGATGATAGATTCTCT
*
273463 CTCTAAAGATGATAGATTCTCTT
1 TTC-AAAGATGATAGATTCTC-T
273486 TTCAAAGAT
1 TTCAAAGAT
273495 AAAAGCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TTCAAAGATGATAGATTCTCT
Found at i:274051 original size:113 final size:113
Alignment explanation
Indices: 273854--274309 Score: 532
Period size: 113 Copynumber: 4.0 Consensus size: 113
273844 TTAGAAAAGA
* * * *
273854 TTTGAATCCATTACTCA-ATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCT
1 TTTGAATTCATCACT-AGATGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCT
* *
273917 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTT
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTT
* * *
273966 TTTGAATTCATCATTTGATGGATCAACATTACCAGGCAGAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTAGATGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTG
274031 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTT
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTT
* * * *
274078 GTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTTATC
1 -TTTGAATTCATCACTAGATGGATCAACATTACCAG-GAAGAGTTCATAATGAGAAGAACTCATC
* * * *
274143 TGAAG-ATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACC-TTTG
64 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTT
* * * *
274191 TTT-AACTCTATCACAGAAGGAGATAGATCAACATCAATATTTCCA-GAAGTGTTCATAATGAGA
1 TTTGAATTC-ATCAC-----TAGATGGATCAACAT---TA---CCAGGAAGAGTTCATAATGAGA
274254 AGAACTCATCTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
54 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
274310 GCCTTAATTT
Statistics
Matches: 296, Mismatches: 29, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
111 4 0.01
112 37 0.12
113 141 0.48
114 32 0.11
117 11 0.04
120 1 0.00
121 64 0.22
122 3 0.01
123 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTGAATTCATCACTAGATGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTT
Found at i:276273 original size:141 final size:139
Alignment explanation
Indices: 276024--276282 Score: 344
Period size: 140 Copynumber: 1.8 Consensus size: 139
276014 AAATCATATT
* * * * *
276024 TTAATATTTATTTATTTTTCAATATTAAGAAAGGAATGTCTTAAAGCAACTGGATGTCCATTTTC
1 TTAATATTTATTTATTTTTCAATATAAAGAAAAGAATATCTTAAAGCAACTAGAAGTCCATTTTC
* *
276089 TGATATTTTAAATAAATAAATATCTTACTTTTATAAATTATATGTATTT-TTAATTATTTTTAGT
66 TGATATTTTAAATAAATAAATATCTTAC-TTAAAAAATTATATGT-TTTCTTAATTATTTTTAGT
276153 TAAATTTTTTA
129 TAAATTTTTTA
* * *
276164 TTAATATTTATTTATTTTTTAATATAAAGAAAAGATATATCTTAAAGCACCTAGAAG-CCCTTTT
1 TTAATATTTATTTATTTTTCAATATAAAGAAAAGA-ATATCTTAAAGCAACTAGAAGTCCATTTT
*
276228 TTGATATTTCTAAATAAATAAATATCTTA-TTAAAAAATATAATATGTTTTCTTAA
65 CTGATATTT-TAAATAAATAAATATCTTACTTAAAAAAT-T-ATATGTTTTCTTAA
276283 AATTATAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
139 7 0.07
140 50 0.49
141 46 0.45
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (139 bp):
TTAATATTTATTTATTTTTCAATATAAAGAAAAGAATATCTTAAAGCAACTAGAAGTCCATTTTC
TGATATTTTAAATAAATAAATATCTTACTTAAAAAATTATATGTTTTCTTAATTATTTTTAGTTA
AATTTTTTA
Found at i:276762 original size:57 final size:55
Alignment explanation
Indices: 276679--276858 Score: 170
Period size: 57 Copynumber: 3.2 Consensus size: 55
276669 AATATTTACT
* * *
276679 AAAATATCACCAGTTTCAAAATAATTACTAAAATGCATCTTTTCAAAACAATTACGA
1 AAAATACCACCATTTTCAAAATAATTACCAAAAT-CATCTTTTCAAAA-AATTACGA
* * * *
276736 AAAATACCACCTTTTTTCAAAA-AATTACGAAATTATCACCTTATT-AAAAAAATACG-
1 AAAATACCACC-ATTTTCAAAATAATTACCAAA--ATCATCTT-TTCAAAAAATTACGA
* *
276792 AAAATAACACCATTTTCAAAATAATTACCAAAATACATCAATTTCAAAATAATTAC-A
1 AAAATACCACCATTTTCAAAATAATTACCAAAAT-CATC-TTTTCAAAA-AATTACGA
276849 AAAATACCAC
1 AAAATACCAC
276859 TCAGTTAACG
Statistics
Matches: 100, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
54 2 0.02
55 14 0.14
56 24 0.24
57 39 0.39
58 17 0.17
59 4 0.04
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (55 bp):
AAAATACCACCATTTTCAAAATAATTACCAAAATCATCTTTTCAAAAAATTACGA
Found at i:276802 original size:27 final size:29
Alignment explanation
Indices: 276720--276826 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 29
276710 AATGCATCTT
* * *
276720 TTCAAAACAATTACGAAAAATACCACCTTTT
1 TTCAAAA-AAATACG-AAAATAACACCTTTA
* * *
276751 TTCAAAAAATTACGAAATTATCACC-TTA
1 TTCAAAAAAATACGAAAATAACACCTTTA
*
276779 TT-AAAAAAATACGAAAATAACACCATT-
1 TTCAAAAAAATACGAAAATAACACCTTTA
* *
276806 TTCAAAATAATTACCAAAATA
1 TTCAAAA-AAATACGAAAATA
276827 CATCAATTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
27 21 0.32
28 10 0.15
29 20 0.31
30 7 0.11
31 7 0.11
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (29 bp):
TTCAAAAAAATACGAAAATAACACCTTTA
Found at i:278997 original size:12 final size:12
Alignment explanation
Indices: 278972--279041 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
278962 ACGGAGATAT
* *
278972 CAGAAATCAAAA
1 CAGAATTCAGAA
278984 CAGAATTCAGAA
1 CAGAATTCAGAA
278996 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
279008 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
279020 CAGAAATCATAA
1 CAGAATTCAGAA
279032 CAGAATTCAG
1 CAGAATTCAG
279042 GTCATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:279052 original size:24 final size:24
Alignment explanation
Indices: 278970--279064 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
278960 AAACGGAGAT
* *
278970 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
278994 AACAGATATCAGAACAGAATCCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
279018 ATCAGAAATCATAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
279042 GTCATG-TATCAGAACAAAATTCA
1 ATCA-GATATCAGAACAGAATTCA
279065 AGTCAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:279075 original size:48 final size:48
Alignment explanation
Indices: 278970--279076 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
278960 AAACGGAGAT
* * *
278970 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAAAAATCAAAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
* * **
279018 ATCAGAAATCATAACAGAATTCAGGTCATG-TATCAGAACAAAATTCAAG
1 ATCAAAAATCAAAACAGAATTCAGAACA-GATATCAGAACAAAA-TCAAG
279067 -TCAAAAATCA
1 ATCAAAAATCA
279077 GATAAAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
48 46 0.90
49 5 0.10
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (48 bp):
ATCAAAAATCAAAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
Found at i:279954 original size:29 final size:28
Alignment explanation
Indices: 279920--280117 Score: 215
Period size: 29 Copynumber: 7.0 Consensus size: 28
279910 CCGTTGACCG
279920 GGTGATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTT-AAAAT
*
279949 GGTGATATTTTTGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTT-AAAAT
* * * *
279978 GGTGCTATTTTTGTGATTTTTTTAAAA-
1 GGTGATATTTTAGTAATTATTTTAAAAT
*
280005 GAGTGATAATTTTA-TAATTTTTTTAAAGA-
1 G-GTGAT-ATTTTAGTAATTATTTTAAA-AT
280034 GGTGATATTTTAGTAATTATTTTAGAAAT
1 GGTGATATTTTAGTAATTATTTTA-AAAT
* *
280063 GGTGCTATTTTGGTAATTAATTTTAAAAT
1 GGTGATATTTTAGTAATT-ATTTTAAAAT
* *
280092 GGTGCTATTTT-GTAATTGTTTTAAAA
1 GGTGATATTTTAGTAATTATTTTAAAA
280118 AATATTAATT
Statistics
Matches: 151, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.10
28 42 0.28
29 88 0.58
30 6 0.04
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (28 bp):
GGTGATATTTTAGTAATTATTTTAAAAT
Found at i:280065 original size:85 final size:85
Alignment explanation
Indices: 279920--280117 Score: 242
Period size: 85 Copynumber: 2.3 Consensus size: 85
279910 CCGTTGACCG
* *
279920 GGTGATATTTTAGTAATTATTTTGAAAATGGTGATATTTTTGTAATTATTTTGAAAATGGTGCTA
1 GGTGATATTTTA-TAATT-TTTTTAAAATGGTGATATTTTAGTAATTATTTTGAAAATGGTGCTA
* * *
279985 TTTTTGTGATT-TTTTTAAAA-
64 TTTTGGTAATTAATTTTAAAAT
280005 GAGTGATAATTTTATAATTTTTTTAAAGA-GGTGATATTTTAGTAATTATTTT-AGAAATGGTGC
1 G-GTGAT-ATTTTATAATTTTTTTAAA-ATGGTGATATTTTAGTAATTATTTTGA-AAATGGTGC
280068 TATTTTGGTAATTAATTTTAAAAT
62 TATTTTGGTAATTAATTTTAAAAT
* * *
280092 GGTGCTATTTTGTAATTGTTTTAAAA
1 GGTGATATTTTATAATTTTTTTAAAA
280118 AATATTAATT
Statistics
Matches: 99, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
84 2 0.02
85 67 0.68
86 23 0.23
87 7 0.07
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (85 bp):
GGTGATATTTTATAATTTTTTTAAAATGGTGATATTTTAGTAATTATTTTGAAAATGGTGCTATT
TTGGTAATTAATTTTAAAAT
Found at i:281098 original size:42 final size:42
Alignment explanation
Indices: 281051--281255 Score: 283
Period size: 42 Copynumber: 4.8 Consensus size: 42
281041 GAAGTATTAT
281051 CAGGTCCCTTTGCTGTGTGCTAA-GGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTCC
*
281093 CAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACA-TATTCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT-TTCC
281135 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
*
281177 CAGGTCCCTTTGCTGTGTGCAAGGGTAAACCTTACAGTTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCC
* * *
281220 TAGGCTCCAC--TGCTTTGTGCATAGGTTAAGCCTTAC
1 CAGG-TCC-CTTTGCTGTGTGCA-AGGGTAAGCCTTAC
281256 TGGTGTATAG
Statistics
Matches: 149, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
41 3 0.02
42 111 0.74
43 19 0.13
44 15 0.10
45 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
Found at i:287929 original size:28 final size:28
Alignment explanation
Indices: 287862--287932 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
287852 TTAAAGAAAT
*
287862 ATTTACTAAAATATCATCATTTTCAAAA
1 ATTTACTAAAATATAATCATTTTCAAAA
* *
287890 TTATTAATAAAATATAAT-ATTTTCAAAAA
1 AT-TTACTAAAATATAATCATTTTC-AAAA
*
287919 ATTTACGAAAATAT
1 ATTTACTAAAATAT
287933 CACTTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.39
Consensus pattern (28 bp):
ATTTACTAAAATATAATCATTTTCAAAA
Found at i:287940 original size:28 final size:29
Alignment explanation
Indices: 287922--287980 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
287912 TCAAAAAATT
* *
287922 TACGAAAATATCACTTTTTTTTAAAAAAA
1 TACGAAAATATCACCTTTTTTAAAAAAAA
*
287951 TACGAAATTATCACC-TTTTTAAAAAAAA
1 TACGAAAATATCACCTTTTTTAAAAAAAA
287979 TA
1 TA
287981 TAGCATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (29 bp):
TACGAAAATATCACCTTTTTTAAAAAAAA
Found at i:290163 original size:24 final size:24
Alignment explanation
Indices: 290132--290200 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
290122 CGGAGATATT
290132 AGAAATCAAAACAGAATTCAGAAC
1 AGAAATCAAAACAGAATTCAGAAC
* * * * *
290156 TGATATCAGAACAGAATCCAGATC
1 AGAAATCAAAACAGAATTCAGAAC
*
290180 AGAAATCATAACAGAATTCAG
1 AGAAATCAAAACAGAATTCAG
290201 GTCATGTATC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (24 bp):
AGAAATCAAAACAGAATTCAGAAC
Found at i:290177 original size:12 final size:11
Alignment explanation
Indices: 290135--290196 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
290125 AGATATTAGA
*
290135 AATCAAAACAG
1 AATCAGAACAG
*
290146 AATTCAGAACTG
1 AA-TCAGAACAG
290158 ATATCAGAACAG
1 A-ATCAGAACAG
*
290170 AATCCAGATCAG
1 AAT-CAGAACAG
*
290182 AAATCATAACAG
1 -AATCAGAACAG
290194 AAT
1 AAT
290197 TCAGGTCATG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 7 0.17
12 30 0.73
13 4 0.10
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.18
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:290211 original size:24 final size:25
Alignment explanation
Indices: 290136--290223 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 25
290126 GATATTAGAA
*
290136 ATCAAAACAGAATTCAGAAC-TGAT
1 ATCAAAACAGAATTCAGATCATGAT
* * *
290160 ATCAGAACAGAATCCAGATCA-GAA
1 ATCAAAACAGAATTCAGATCATGAT
* *
290184 ATCATAACAGAATTCAGGTCATG-T
1 ATCAAAACAGAATTCAGATCATGAT
* *
290208 ATCAAAATAAAATTCA
1 ATCAAAACAGAATTCA
290224 AGTCGGAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (25 bp):
ATCAAAACAGAATTCAGATCATGAT
Found at i:292642 original size:30 final size:29
Alignment explanation
Indices: 292623--292807 Score: 143
Period size: 29 Copynumber: 6.6 Consensus size: 29
292613 CCCTTTTATG
* *
292623 AAATATTTACTAAAATATCATCATTTTCA
1 AAATAATTACTAAAATATCACCATTTTCA
*
292652 AAATAATTACTAAAATATCATC-TTTTCA
1 AAATAATTACTAAAATATCACCATTTTCA
* ** *
292680 AAAAAATTA-TGAAAATATCACTTTTTTTA
1 AAATAATTACT-AAAATATCACCATTTTCA
* * *
292709 AAAAAATTACGAAATTATCACC-TTTT-A
1 AAATAATTACTAAAATATCACCATTTTCA
* *
292736 AAA-AA--A-TGAAAATAGCACAATTTTCA
1 AAATAATTACT-AAAATATCACCATTTTCA
* * * *
292762 AAATAATTACCAAAATACCATCAATTTCA
1 AAATAATTACTAAAATATCACCATTTTCA
*
292791 AAATAATTACAAAAATA
1 AAATAATTACTAAAATA
292808 CCACTCGGTT
Statistics
Matches: 128, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
24 9 0.07
25 4 0.03
26 6 0.05
27 7 0.05
28 27 0.21
29 75 0.59
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATAATTACTAAAATATCACCATTTTCA
Found at i:292868 original size:13 final size:13
Alignment explanation
Indices: 292821--292869 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
292811 CTCGGTTAAC
292821 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
292834 GGTTAACGGGTCG
1 GGTCAACGGGTCG
*
292847 GGTC-A--GGTCA
1 GGTCAACGGGTCG
292857 GGTCAACGGGTCG
1 GGTCAACGGGTCG
292870 TGTCGGGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 1 0.03
13 19 0.66
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:294244 original size:3 final size:3
Alignment explanation
Indices: 294224--294317 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
294214 TCTAGTCCTA
*
294224 ATT ATT -TT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
294271 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
294318 CAAACTTTAC
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:294422 original size:8 final size:8
Alignment explanation
Indices: 294409--294454 Score: 74
Period size: 8 Copynumber: 5.5 Consensus size: 8
294399 TTATAAGAAA
294409 TTTTAAAT
1 TTTTAAAT
294417 TTTTAAAT
1 TTTTAAAT
294425 TTTTAAATT
1 TTTTAAA-T
294434 TTTTAAATT
1 TTTTAAA-T
294443 TTTTAAAT
1 TTTTAAAT
294451 TTTT
1 TTTT
294455 TATATTTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 20 0.54
9 17 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTAAAT
Found at i:294436 original size:9 final size:9
Alignment explanation
Indices: 294409--294461 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
294399 TTATAAGAAA
294409 TTTTAAA-T
1 TTTTAAATT
294417 TTTTAAA-T
1 TTTTAAATT
294425 TTTTAAATT
1 TTTTAAATT
294434 TTTTAAATT
1 TTTTAAATT
294443 TTTTAAATT
1 TTTTAAATT
*
294452 TTTTATATT
1 TTTTAAATT
294461 T
1 T
294462 CTATATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 15 0.35
9 28 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAAATT
Found at i:294814 original size:48 final size:49
Alignment explanation
Indices: 294717--294814 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 49
294707 TGTTTATTTT
* ** * * *
294717 TAATTAAATTTTAAAAAAAAAAATAATTTAATATTAAAATATTTTTAAA
1 TAATAAAATTTTAAAAAAAAAAATAAAATAAAAGTAAAATATTTATAAA
*
294766 TAATAAAATTTT-AAAAAAAAATTAAAATAAAAGTAAAAT-TTCTATAAA
1 TAATAAAATTTTAAAAAAAAAAATAAAATAAAAGTAAAATATT-TATAAA
294814 T
1 T
294815 TTCATGTGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
47 2 0.05
48 28 0.68
49 11 0.27
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (49 bp):
TAATAAAATTTTAAAAAAAAAAATAAAATAAAAGTAAAATATTTATAAA
Found at i:297462 original size:24 final size:24
Alignment explanation
Indices: 297435--297543 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
297425 AAACGGAGAT
* *
297435 ATCAGAAATCAAAACAAAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * * * *
297459 ATCAGATATTAGAATAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAA
*
297483 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* * *
297507 GTCATG-TATCAGAACATAATTCAA
1 ATCA-GAAATCAGAACAGAATTCAA
297531 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
297544 TAAAATATTC
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:300773 original size:123 final size:123
Alignment explanation
Indices: 300548--300795 Score: 349
Period size: 123 Copynumber: 2.0 Consensus size: 123
300538 ATAACAAATC
* * *
300548 CACTAGTATTCACATGATATGTTTAGCACATTTAATAAAGGCTAAACATACGGATGATCATTTAT
1 CACTAGTATTCACATGACATGTTTAGCACATTTAATAAAGACTAAACATACGGATGATCACTTAT
* * *
300613 GTTTGTGTTTTGTCCACTTTTGATGATGGATTTCAAAAACATAGGATATGA-TCACTTT
66 GTTTGTGTTTTGTCCACTTTTGATCATGGATTACAAAAACATAAGATAT-ATTCACTTT
* *
300671 CACTAGTATTCACATGACATGTTTAGCACATTTAAT-AAGATTTAAC-TACAGGGATGATCACTT
1 CACTAGTATTCACATGACATGTTTAGCACATTTAATAAAGACTAAACATAC--GGATGATCACTT
* * *
300734 ATTTTTGTGTTTTGTCCACTTTTGGTCATTGATTACAAAAACATAAGATATATTCACTTT
64 ATGTTTGTGTTTTGTCCACTTTTGATCATGGATTACAAAAACATAAGATATATTCACTTT
300794 CA
1 CA
300796 TTTTTATTTA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
121 3 0.03
122 8 0.07
123 100 0.90
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (123 bp):
CACTAGTATTCACATGACATGTTTAGCACATTTAATAAAGACTAAACATACGGATGATCACTTAT
GTTTGTGTTTTGTCCACTTTTGATCATGGATTACAAAAACATAAGATATATTCACTTT
Found at i:301356 original size:153 final size:158
Alignment explanation
Indices: 301193--301550 Score: 442
Period size: 153 Copynumber: 2.3 Consensus size: 158
301183 AAGCCCCTTT
* * *
301193 GTTTTTACCAAATTTGAACTACATGCTCCTAAGCCATAGTATAATACATGTTTACTTTCAATTTC
1 GTTTTTACCAAATTTGAACTACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAA-TTC
301258 C-CTTTTTGATAAC-AA-TTTTT-TTTTTCAATTTAGTCATT-AATTTTTCATAATCTCCTTATT
65 CTCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCATTCAATTTTTCATAATCTCCTTATT
*
301318 TCTTCAA-TTCATCATTTATTTTAAATCC
130 CCTTCAATTTCATCATTTATTTTAAATCC
** *
301346 GTTTTTACCAAATTTGATA-TGTATACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTC
1 GTTTTTACCAAATTTGA-ACTACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTC
* * *
301410 CTCTTTTTGATTACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCCTTATT
65 CTCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCATTCAATTTTTCATAATCTCCTTATT
* ** * * *
301475 CCTTTAATTTGTTTATTTATTTTAAGTTC
130 CCTTCAATTTCATCATTTATTTTAAATCC
* * * * * * *
301504 GTTTTTACCACATTTAAACCACATGCTCATATACCACAATAGAATAC
1 GTTTTTACCAAATTTGAACTACATGCTCCTAAACCATAGTAGAATAC
301551 CTATATAACT
Statistics
Matches: 171, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
152 4 0.02
153 64 0.37
154 3 0.02
155 5 0.03
156 17 0.10
157 27 0.16
158 51 0.30
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (158 bp):
GTTTTTACCAAATTTGAACTACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCC
TCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCATTCAATTTTTCATAATCTCCTTATTC
CTTCAATTTCATCATTTATTTTAAATCC
Found at i:301575 original size:158 final size:153
Alignment explanation
Indices: 301193--301575 Score: 342
Period size: 158 Copynumber: 2.5 Consensus size: 153
301183 AAGCCCCTTT
* * * * * * * *
301193 GTTTTTACCAAATTTG-AACTACATGCTCCTAAGCCATAGTATAATACATGTTTACTTTCAATTT
1 GTTTTTACCAAATTTGAAAC-ACATACTCATAAACCACAATAGAATACATATATACTTTCAA-TT
* *
301257 CC-CTTTTTGATAACAATTTTTTTTTTCAATTTAGTCATTAATTTTTCATAATCTCCTTATTTCT
64 CCTATTTTTGATAACAATTTTTTTTTTCAATTTAGTCATTAATTTTTCATAATCTCCTTATTCCT
301321 TCAATTCATCATTTATTTTAAATCC
129 TCAATTCATCATTTATTTTAAATCC
* *** * * * * *
301346 GTTTTTACCAAATTTGATATGTATACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCC
1 GTTTTTACCAAATTTGAAACACATACTCATAAACCACAATAGAATACATATATACTTTCAATTCC
* * * *
301411 TCTTTTTGATTACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCCTTATTC
66 TATTTTTGATAAC-AA-TTTTT-TTTTTCAATTTAGTCATT-AATTTTTCATAATCTCCTTATTC
* ** * * *
301476 CTTTAATTTGTTTATTTATTTTAAGTTC
127 CTTCAA-TTCATCATTTATTTTAAATCC
* * * *
301504 GTTTTTACCACATTT-AAACCACATGCTCATATACCACAATAGAATACCTATATAAC-TTCAATT
1 GTTTTTACCAAATTTGAAA-CACATACTCATAAACCACAATAGAATACATATAT-ACTTTCAATT
**
301567 GTTATTTTT
64 CCTATTTTT
301576 TTACTAAAGA
Statistics
Matches: 187, Mismatches: 34, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
152 4 0.02
153 62 0.33
154 3 0.02
155 5 0.03
156 17 0.09
157 28 0.15
158 66 0.35
159 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (153 bp):
GTTTTTACCAAATTTGAAACACATACTCATAAACCACAATAGAATACATATATACTTTCAATTCC
TATTTTTGATAACAATTTTTTTTTTCAATTTAGTCATTAATTTTTCATAATCTCCTTATTCCTTC
AATTCATCATTTATTTTAAATCC
Found at i:304255 original size:3 final size:3
Alignment explanation
Indices: 304188--304242 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
304178 TTCATTTGAA
304188 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
304233 T-T TAT TAT TA
1 TAT TAT TAT TA
304243 ATAAATATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:305602 original size:3 final size:3
Alignment explanation
Indices: 305594--305628 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
305584 ATTTGTAATA
*
305594 TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
305629 CATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:306459 original size:29 final size:30
Alignment explanation
Indices: 306426--306490 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
306416 TTAATTTTTA
* *
306426 ATTATTTCTTTTCAAAATTTTTATATATAT
1 ATTATTTATTTTCAAAATATTTATATATAT
* *
306456 -TTA-TTATTTTCATAATATTTATATGTAT
1 ATTATTTATTTTCAAAATATTTATATATAT
306484 ATTATTT
1 ATTATTT
306491 TATTAATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 21 0.72
29 6 0.21
30 2 0.07
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (30 bp):
ATTATTTATTTTCAAAATATTTATATATAT
Found at i:306473 original size:18 final size:19
Alignment explanation
Indices: 306442--306477 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
306432 TCTTTTCAAA
*
306442 ATTTTTATATATATTTATT
1 ATTTTCATATATATTTATT
306461 ATTTTCATA-ATATTTAT
1 ATTTTCATATATATTTAT
306478 ATGTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTCATATATATTTATT
Found at i:309721 original size:15 final size:15
Alignment explanation
Indices: 309701--309732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
309691 GATCAATACC
309701 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
309716 TTTTGCATACATTCA
1 TTTTGCATACATGCA
309731 TT
1 TT
309733 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:318812 original size:113 final size:113
Alignment explanation
Indices: 318614--319059 Score: 612
Period size: 113 Copynumber: 3.9 Consensus size: 113
318604 GATTCAAATC
* * *
318614 CATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGA
1 CATCATTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
318679 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
318727 CATCATTCGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCGTCTGAAGAAGG
1 CATCATTCGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
318791 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
65 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * * * ** * **
318840 CATCACTCGGTGGATCAGCAGTGCTAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
1 CATCATTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGG
* *
318905 AAGAAGAAA-TTCATAATGAGAAGAAGTTGTTCAACCTTTTGCTTAAATT
65 AAGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
318954 CATCACTT-GATGGATCAA-ATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CATCA-TTCGATGGATCAACA-TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* * *
319017 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
64 GAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
319060 ATGACTCTAT
Statistics
Matches: 291, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
112 3 0.01
113 193 0.66
114 91 0.31
115 4 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:319018 original size:227 final size:226
Alignment explanation
Indices: 318645--319059 Score: 674
Period size: 227 Copynumber: 1.8 Consensus size: 226
318635 TTCCAGAGAA
** *
318645 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
318710 AACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGA
66 AACCTTTTGCTTAAATTCATCATTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGA
*
318775 ACTCGTCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
131 ACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
318840 CATCACTCGGTGGATCAGCAGTGCTAGTTAG
196 CATCACTCGGTGGATCAGCAGTGCTAGTTAG
*
318871 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAAGAAGAAATTCATAATGAGAAGAAGTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAA-AAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTT
*
318936 CAACCTTTTGCTTAAATTCATCACTT-GATGGATCAA-ATTTTCCAGAG-AAAGTTCATAATGAG
65 CAACCTTTTGCTTAAATTCATCA-TTCGATGGATCAACA-TTGCCAG-GTAAAGTTCATAATGAG
* * *
318998 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
127 AAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
319060 ATGACTCTAT
Statistics
Matches: 174, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
226 29 0.17
227 142 0.82
228 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (226 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTAAATTCATCATTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
CATCACTCGGTGGATCAGCAGTGCTAGTTAG
Found at i:320806 original size:32 final size:32
Alignment explanation
Indices: 320764--320947 Score: 250
Period size: 32 Copynumber: 5.8 Consensus size: 32
320754 TAGATAACTT
*
320764 TCCATATGTCCCGAAAGACATAGGTAATATTA
1 TCCATATGTCCCGAAAGACATAGGTAATATTG
* *
320796 TCCATTTGTCCTGAAAGAC--AGGTAAT-TCTG
1 TCCATATGTCCCGAAAGACATAGGTAATAT-TG
*
320826 TCTATATGTCCCGAAAGACATAGGTAATA-TG
1 TCCATATGTCCCGAAAGACATAGGTAATATTG
**
320857 TCCATATGTCCCGAAAGACATAGGTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATATTG
* *
320889 TCAATAAGTCCCGAAAGACATAGGTAATATTG
1 TCCATATGTCCCGAAAGACATAGGTAATATTG
*
320921 TCCATATGTCCCGTAAGACATAGGTAA
1 TCCATATGTCCCGAAAGACATAGGTAA
320948 CCCTCGACTC
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.01
30 24 0.18
31 29 0.22
32 78 0.59
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATATTG
Found at i:320874 original size:93 final size:94
Alignment explanation
Indices: 320764--320947 Score: 255
Period size: 93 Copynumber: 2.0 Consensus size: 94
320754 TAGATAACTT
* * ** *
320764 TCCATATGTCCCGAAAGACATAGGTAATATTATCCATTTGTCCTGAAAGAC-AGGTAAT-TCTGT
1 TCCATATGTCCCGAAAGACATAGGTAATACTATCAATAAGTCCCGAAAGACAAGGTAATAT-TGT
*
320827 CTATATGTCCCGAAAGACATAGGTAATATG
65 CCATATGTCCCGAAAGACATAGGTAATATG
* *
320857 TCCATATGTCCCGAAAGACATAGGTAATCCTGTCAATAAGTCCCGAAAGACATAGGTAATATTGT
1 TCCATATGTCCCGAAAGACATAGGTAATACTATCAATAAGTCCCGAAAGACA-AGGTAATATTGT
*
320922 CCATATGTCCCGTAAGACATAGGTAA
65 CCATATGTCCCGAAAGACATAGGTAA
320948 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 44 0.56
95 34 0.43
96 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (94 bp):
TCCATATGTCCCGAAAGACATAGGTAATACTATCAATAAGTCCCGAAAGACAAGGTAATATTGTC
CATATGTCCCGAAAGACATAGGTAATATG
Found at i:320910 original size:63 final size:64
Alignment explanation
Indices: 320771--320947 Score: 270
Period size: 63 Copynumber: 2.8 Consensus size: 64
320761 CTTTCCATAT
* * * * * *
320771 GTCCCGAAAGACATAGGTAATATTATCCATTTGTCCTGAAAGAC--AGGTAATTCTGTCTATAT
1 GTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGTAATCCTGTCAATAA
320833 GTCCCGAAAGACATAGGTAATA-TGTCCATATGTCCCGAAAGACATAGGTAATCCTGTCAATAA
1 GTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGTAATCCTGTCAATAA
*
320896 GTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGTAAGACATAGGTAA
1 GTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGTAA
320948 CCCTCGACTC
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
61 18 0.17
62 22 0.21
63 37 0.35
64 28 0.27
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
GTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGTAATCCTGTCAATAA
Found at i:322781 original size:33 final size:33
Alignment explanation
Indices: 322734--322806 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
322724 GGATTAGAAT
322734 TTAATAAAAATATTAATAAAATAAATTTGAGTTA
1 TTAAT-AAAATATTAATAAAATAAATTTGAGTTA
322768 TTAATAAAATATTAATAAAATAAATTTGAGTTA
1 TTAATAAAATATTAATAAAATAAATTTGAGTTA
322801 TTAATA
1 TTAATA
322807 TATGCCATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 34 0.87
34 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (33 bp):
TTAATAAAATATTAATAAAATAAATTTGAGTTA
Found at i:323680 original size:25 final size:24
Alignment explanation
Indices: 323652--323732 Score: 60
Period size: 25 Copynumber: 3.4 Consensus size: 24
323642 GTATAAATTC
* *
323652 TTAAATTCATAATATTTTATATATA
1 TTAAATTAAAAATATTTT-TATATA
*
323677 TTAACTTAAAAATA-TTTT-TATA
1 TTAAATTAAAAATATTTTTATATA
* *
323699 TTAACTTATTAAATATATTTTAT-TA
1 TTAAATTA-AAAATAT-TTTTATATA
*
323724 TTAACTTAA
1 TTAAATTAA
323733 TTTAAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 12 0.26
23 6 0.13
24 3 0.06
25 25 0.53
26 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAATTAAAAATATTTTTATATA
Found at i:323701 original size:22 final size:23
Alignment explanation
Indices: 323673--323732 Score: 86
Period size: 22 Copynumber: 2.6 Consensus size: 23
323663 ATATTTTATA
323673 TATATTAACTTAAAAATAT-TTT
1 TATATTAACTTAAAAATATATTT
*
323695 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
323719 TATTATTAACTTAA
1 TA-TATTAACTTAA
323733 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
23 6 0.18
24 5 0.15
25 10 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Found at i:323737 original size:27 final size:25
Alignment explanation
Indices: 323662--323748 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 25
323652 TTAAATTCAT
323662 AATATTTTATATATATTAACTTAA--A
1 AATATTTT-TAT-TATTAACTTAATTA
323687 AATATTTTTA-TATTAACTT-ATTA
1 AATATTTTTATTATTAACTTAATTA
323710 AATATATTTTATTATTAACTTAATTTA
1 AATAT-TTTTATTATTAACTTAA-TTA
*
323737 AAAATATTTTAT
1 AATAT-TTTTAT
323749 GCGAACATTG
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
21 1 0.02
22 9 0.16
23 6 0.11
24 7 0.13
25 17 0.31
26 1 0.02
27 14 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTTTATTATTAACTTAATTA
Found at i:337081 original size:8 final size:8
Alignment explanation
Indices: 337068--337107 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
337058 TCATTTTCAT
337068 AGAATTTG
1 AGAATTTG
337076 AGAATTT-
1 AGAATTTG
*
337083 AGAGTTTG
1 AGAATTTG
*
337091 GGAATTTG
1 AGAATTTG
337099 AGAATTTG
1 AGAATTTG
337107 A
1 A
337108 AAGCTTGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
AGAATTTG
Found at i:337090 original size:15 final size:15
Alignment explanation
Indices: 337067--337107 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
337057 CTCATTTTCA
337067 TAGAATTTGAGAATT
1 TAGAATTTGAGAATT
* *
337082 TAGAGTTTGGGAATT
1 TAGAATTTGAGAATT
337097 TGAGAATTTGA
1 T-AGAATTTGA
337108 AAGCTTGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (15 bp):
TAGAATTTGAGAATT
Found at i:337521 original size:128 final size:128
Alignment explanation
Indices: 337188--337793 Score: 1081
Period size: 128 Copynumber: 4.7 Consensus size: 128
337178 ACTATTCACA
337188 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
337253 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
337316 TGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *
337380 TTATGCCACTCATGTCCCTTGGGGACACTAGAT-ATTTCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
337443 TGAAGGTGCGTTCCCGGGGGGGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
337508 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
337571 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
337636 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCATGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
337699 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
337764 TTATGTCACTCATGTCCCTCTGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
337794 GATGGATTGT
Statistics
Matches: 455, Mismatches: 20, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
127 121 0.27
128 334 0.73
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:338197 original size:34 final size:34
Alignment explanation
Indices: 338158--338264 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
338148 TAAGTTGAAA
* *
338158 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
338192 TTTAATTTTAAATTTCGAATAATATTATTTTTAAT
1 TTTAATTTTAAATTTCGAATAATATAATTTAT-AT
* *
338227 TTT-ATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
338260 TTTAA
1 TTTAA
338265 AAACATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 5 0.08
34 54 0.84
35 5 0.08
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:338839 original size:21 final size:21
Alignment explanation
Indices: 338785--338878 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
338775 TATGGTATAA
*
338785 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
338806 AA-CCTGGCAGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
338827 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
338848 AACCCTACGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
338869 AACCCTGCGG
1 AACCCTGCGG
338879 AGATGGCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.28, G:0.31, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:338908 original size:21 final size:21
Alignment explanation
Indices: 338882--338929 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
338872 CCTGCGGAGA
*
338882 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
338903 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
338924 GGGCAT
1 TGGCAT
338930 GTACCCCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:340719 original size:31 final size:33
Alignment explanation
Indices: 340654--340733 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
340644 TTAATAATTC
* *
340654 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
340688 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
340719 TATAAAATATAATAA
1 TA-AAAAAATAATAA
340734 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:342109 original size:30 final size:31
Alignment explanation
Indices: 342061--342128 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
342051 TATTTATTTA
* * * *
342061 TTTATTTTTCAGCACTTTAGA-TTCCATCAT
1 TTTATTTTCCAACACTTTAAATTTCCAACAT
* *
342091 TTTATTTTCCAACCCTTTAAATTTTCAACAT
1 TTTATTTTCCAACACTTTAAATTTCCAACAT
342122 TTTATTT
1 TTTATTT
342129 GAATCCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTATTTTCCAACACTTTAAATTTCCAACAT
Found at i:346936 original size:6 final size:6
Alignment explanation
Indices: 346925--346955 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
346915 GATTATATGT
*
346925 TAATGA TAATGA TAATGA TAATGA CAATGA T
1 TAATGA TAATGA TAATGA TAATGA TAATGA T
346956 GTAATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.32
Consensus pattern (6 bp):
TAATGA
Found at i:347805 original size:20 final size:20
Alignment explanation
Indices: 347776--347825 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
347766 TTCTAGAAAA
* * *
347776 GTAAAGCCTCCAGGTGATTT
1 GTAAAACCTCCAGGTCATCT
*
347796 GTAAAACCTCCGGGTCATCT
1 GTAAAACCTCCAGGTCATCT
347816 GTAAAACCTC
1 GTAAAACCTC
347826 AGGGTAGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
GTAAAACCTCCAGGTCATCT
Found at i:347884 original size:119 final size:119
Alignment explanation
Indices: 347673--347905 Score: 421
Period size: 119 Copynumber: 2.0 Consensus size: 119
347663 TTTCCCACAA
*
347673 ATTTGAAAAACCTCCGGGTCATCTTTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGAAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
*
347738 AGTGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAGTAAAGCCTCCAGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAGTAAAGCCTCCAGGTG
*
347792 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGAAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
* *
347857 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCC
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAGTAAAGCCTCC
347906 GGGTAGGATG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 109 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (119 bp):
ATTTGAAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAGTAAAGCCTCCAGGTG
Found at i:348172 original size:11 final size:11
Alignment explanation
Indices: 348143--348191 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
348133 TTTTTTGTTT
*
348143 TTATATAATTA
1 TTATATTATTA
*
348154 TATATATTACTA
1 T-TATATTATTA
348166 TTATATTTATTA
1 TTATA-TTATTA
348178 TTATATTATTA
1 TTATATTATTA
348189 TTA
1 TTA
348192 CAAATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 14 0.42
12 19 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATTATTA
Found at i:366300 original size:50 final size:50
Alignment explanation
Indices: 366246--366345 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
366236 GCGCACGCTA
366246 TCCACATTGAGATATGCTCCATGTGACCTTTTTTTCAACCTCAAATTCTG
1 TCCACATTGAGATATGCTCCATGTGACCTTTTTTTCAACCTCAAATTCTG
366296 TCCACATTGAGATATGCTCCATGTGACCTTTTTTTCAACCTCAAATTCTG
1 TCCACATTGAGATATGCTCCATGTGACCTTTTTTTCAACCTCAAATTCTG
366346 CCGTTTTCCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (50 bp):
TCCACATTGAGATATGCTCCATGTGACCTTTTTTTCAACCTCAAATTCTG
Found at i:371053 original size:45 final size:46
Alignment explanation
Indices: 370983--371075 Score: 152
Period size: 45 Copynumber: 2.0 Consensus size: 46
370973 ATGTACATAC
* * *
370983 TTACACCAGTGTAAGTATGTGTTAAGTGTTGCATTTTTTTATTTTA
1 TTACACCAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTA
371029 TTACACCAGTGT-AGTATGTGTTAAGTGCTACACTTTTTTATTTTA
1 TTACACCAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTA
371074 TT
1 TT
371076 CACTTACACC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 32 0.73
46 12 0.27
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (46 bp):
TTACACCAGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTA
Found at i:371066 original size:46 final size:45
Alignment explanation
Indices: 370983--371116 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
370973 ATGTACATAC
* *
370983 TTACACCAGTGTAAGTATGTGTTAAGTGTTGCATTTTTTTATTTTA
1 TTACACCAGTGTAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTA
371029 TTACACCAGTGT-AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
1 TTACACCAGTGTAAGTATGTGTTAAGTGCTACA-TTTTTTA--TT-TT-A
* * * *
371078 CTTACACCGGTGTAAATATGTGTTAAATACTACATTTTT
1 -TTACACCAGTGTAAGTATGTGTTAAGTGCTACATTTTT
371117 GTAGTATAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
45 25 0.33
46 12 0.16
47 2 0.03
48 2 0.03
49 1 0.01
50 16 0.21
51 17 0.23
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (45 bp):
TTACACCAGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTA
Found at i:374052 original size:46 final size:46
Alignment explanation
Indices: 373959--374078 Score: 116
Period size: 46 Copynumber: 2.6 Consensus size: 46
373949 TTAAAAGAAA
* *
373959 AACTAGCTTAGGAGCGTCAAACCCTTTCGAGATTTCATTAGAGGGTG
1 AACTCGCTTAGGAGCATCAAA-CCTTTCGAGATTTCATTAGAGGGTG
* * * * * * *
374006 AGCTTGCTTGGGAGCCTCAAACCTTTTGAAGA-TTCGTTGGAGGGTG
1 AACTCGCTTAGGAGCATCAAACCTTTCG-AGATTTCATTAGAGGGTG
*
374052 AACTCGCTTTGGAGCATCAAAACCTTT
1 AACTCGCTTAGGAGCATC-AAACCTTT
374079 ATGTATTTCT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
46 32 0.53
47 28 0.47
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (46 bp):
AACTCGCTTAGGAGCATCAAACCTTTCGAGATTTCATTAGAGGGTG
Found at i:374163 original size:46 final size:46
Alignment explanation
Indices: 374113--374310 Score: 209
Period size: 46 Copynumber: 4.3 Consensus size: 46
374103 CATTTGGAAA
* * * *
374113 TGTCAAACCCTTTGGAGATTTGTTGGAGGGTGAGCTCACTTAGGAG
1 TGTCAAACCCTTTGGAGATTTTTTAGAGGGCGAGCTCACTTGGGAG
*
374159 TGTCACACCCTTTGGAGATTTTTTAGAGGGCGAGCTCACTTGGGAG
1 TGTCAAACCCTTTGGAGATTTTTTAGAGGGCGAGCTCACTTGGGAG
* * * * **
374205 AGTCAAAACTTTTAGAGATTTCTTTA-AGGGCGAGCTCACTTGAAAG
1 TGTCAAACCCTTTGGAGATTT-TTTAGAGGGCGAGCTCACTTGGGAG
** * * *
374251 CATCAAACCCTATGGAGATTTCTTTAGAGGGTGAGCTCACTTGGGAA
1 TGTCAAACCCTTTGGAGATTT-TTTAGAGGGCGAGCTCACTTGGGAG
* *
374298 TGTCGAATCCTTT
1 TGTCAAACCCTTT
374311 AAAGATTCAT
Statistics
Matches: 123, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
46 95 0.77
47 28 0.23
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (46 bp):
TGTCAAACCCTTTGGAGATTTTTTAGAGGGCGAGCTCACTTGGGAG
Found at i:374211 original size:139 final size:137
Alignment explanation
Indices: 373974--374325 Score: 332
Period size: 139 Copynumber: 2.5 Consensus size: 137
373964 GCTTAGGAGC
* ** ** *
373974 GTCAAACCCTTTCGAGATTTCATTAGAGGGTGAGCTTGCTTGGGAGCCTCAAACCTTTTGAAGAT
1 GTCAAACCCTTTGGAGATTTCATTAGAGGGTGAGCTCACTTGGGAGTGTCAAACCCTTTGAAGAT
* * * * * *
374039 TCGTTGGAGGGTGAACTCGCTTTGGAGCATCAAAACCTTTATG-TATTTCTTTAAAGAAAGATCT
66 TCGTTAGAGGGCGAACTCACTTGGGAGCATCAAAACCTTTA-GAGATTTCTTT-AAGAAAGAGCT
*
374103 CATTTGGAAA
129 CACTT-GAAA
* * * * *
374113 TGTCAAACCCTTTGGAGATTT-GTTGGAGGGTGAGCTCACTTAGGAGTGTCACACCCTTTGGAGA
1 -GTCAAACCCTTTGGAGATTTCATTAGAGGGTGAGCTCACTTGGGAGTGTCAAACCCTTTGAAGA
** * * ***
374177 TTTTTTAGAGGGCGAGCTCACTTGGGAG-AGTCAAAACTTTTAGAGATTTCTTTAAGGGCGAGCT
65 TTCGTTAGAGGGCGAACTCACTTGGGAGCA-TCAAAACCTTTAGAGATTTCTTTAAGAAAGAGCT
374241 CACTTGAAA
129 CACTTGAAA
* * * * * *
374250 GCATCAAACCCTATGGAGATTTCTTTAGAGGGTGAGCTCACTTGGGAATGTCGAATCCTTTAAAG
1 G--TCAAACCCTTTGGAGATTTCATTAGAGGGTGAGCTCACTTGGGAGTGTCAAACCCTTTGAAG
*
374315 ATTCATTAGAG
64 ATTCGTTAGAG
374326 AGTTCGCTCG
Statistics
Matches: 170, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
136 1 0.01
137 4 0.02
138 31 0.18
139 115 0.68
140 19 0.11
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (137 bp):
GTCAAACCCTTTGGAGATTTCATTAGAGGGTGAGCTCACTTGGGAGTGTCAAACCCTTTGAAGAT
TCGTTAGAGGGCGAACTCACTTGGGAGCATCAAAACCTTTAGAGATTTCTTTAAGAAAGAGCTCA
CTTGAAA
Found at i:375087 original size:19 final size:20
Alignment explanation
Indices: 375046--375097 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
375036 TATATAGTAT
375046 AAATAATATATAATTTTTGA
1 AAATAATATATAATTTTTGA
* * *
375066 AAATATTATATGATTTTTAA
1 AAATAATATATAATTTTTGA
375086 AAATACATATAT
1 AAATA-ATATAT
375098 TCTTCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
AAATAATATATAATTTTTGA
Found at i:375220 original size:25 final size:25
Alignment explanation
Indices: 375169--375232 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
375159 GAAAACGTAT
* *
375169 TATAATTT-TGAAAAACATTTTATA
1 TATAGTTTCTGAAAAACATTATATA
*
375193 TATGGTTTCTGAAAAACA-TATATAA
1 TATAGTTTCTGAAAAACATTATAT-A
*
375218 TATAGTTTTTGAAAA
1 TATAGTTTCTGAAAA
375233 TAATTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (25 bp):
TATAGTTTCTGAAAAACATTATATA
Found at i:375287 original size:59 final size:61
Alignment explanation
Indices: 375170--375291 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 61
375160 AAAACGTATT
* * *
375170 ATAATTTTGAAAAACATTTTATATATGGTTTCTGAAAAACATATATAATATAGTTTTTGAAA
1 ATAATTTT-AAAAACATATTATATATAGTTTCTGAAAAACATATATAATATAGCTTTTGAAA
*
375232 ATAATTTT-AAAACATATTATATA-AGTTT-TTAAAAGACATAT-TACATATAGCTTTTGAAA
1 ATAATTTTAAAAACATATTATATATAGTTTCTGAAAA-ACATATATA-ATATAGCTTTTGAAA
375291 A
1 A
375292 CGTATACAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
58 7 0.13
59 25 0.46
60 14 0.26
62 8 0.15
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (61 bp):
ATAATTTTAAAAACATATTATATATAGTTTCTGAAAAACATATATAATATAGCTTTTGAAA
Found at i:375291 original size:26 final size:24
Alignment explanation
Indices: 375243--375291 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
375233 TAATTTTAAA
* *
375243 ACATATTATATAAGTTTTTAAAAG
1 ACATATTACATAAGTTTTGAAAAG
375267 ACATATTACATATAGCTTTTGAAAA
1 ACATATTACATA-AG-TTTTGAAAA
375292 CGTATACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 2 0.10
26 8 0.38
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (24 bp):
ACATATTACATAAGTTTTGAAAAG
Found at i:375327 original size:3 final size:3
Alignment explanation
Indices: 375319--375371 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
375309 TGAAAAATAG
* * * *
375319 TAT TAT TAT TAT TAT TAT TGT TGT TGT ATCT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
375365 TAT TAT T
1 TAT TAT T
375372 TATTTATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:383039 original size:14 final size:14
Alignment explanation
Indices: 383020--383052 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
383010 TTTAGGATAT
383020 TATTTTTATATTT-
1 TATTTTTATATTTG
*
383033 TATTTTTATCTTTG
1 TATTTTTATATTTG
383047 TATTTT
1 TATTTT
383053 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TATTTTTATATTTG
Found at i:383089 original size:75 final size:77
Alignment explanation
Indices: 382933--383097 Score: 246
Period size: 76 Copynumber: 2.2 Consensus size: 77
382923 TTAAACTCAA
*
382933 ATTTAGGATAATA-TTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
382997 ATTTTAATTAAG
66 ATTTTAATTAAG
* * **
383009 TTTTAGGATATTATTTTTATATTTTAT-TTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
1 ATTTAGGATATTATTTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
*
383072 ATTTTAATTAGG
66 ATTTTAATTAAG
*
383084 ATTTAGAATATTAT
1 ATTTAGGATATTAT
383098 ATTATTATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 30 0.38
76 40 0.50
77 10 0.12
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (77 bp):
ATTTAGGATATTATTTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
ATTTTAATTAAG
Found at i:383107 original size:75 final size:77
Alignment explanation
Indices: 382955--383118 Score: 244
Period size: 75 Copynumber: 2.1 Consensus size: 77
382945 ATTTTAAACA
* *
382955 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
*
383020 TATTTTTATATT
66 TATTTATATATT
*
383032 TTAT-TTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
383095 TATATTAT-TATT
66 TAT-TTATATATT
383107 TTAGGTATTTTA
1 TTA--TATTTTA
383119 GTTTAAATAG
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
75 37 0.47
76 32 0.41
77 5 0.06
78 5 0.06
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.60
Consensus pattern (77 bp):
TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
TATTTATATATT
Found at i:383771 original size:21 final size:22
Alignment explanation
Indices: 383746--383786 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
383736 CTTTAATTTA
383746 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
383767 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
383787 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:391008 original size:51 final size:51
Alignment explanation
Indices: 390953--391137 Score: 246
Period size: 51 Copynumber: 3.6 Consensus size: 51
390943 TGATAAGTCT
* * *
390953 GCTCCCTATTTCTTCAGAGAGTATAGAACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGATCTTCAAAAAACGTGTCC
* * * **
391004 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGATCTTCAA-AAAACGTGTCC
*
391056 GCTCCCTATTCCTTCAGAGAGTATA-ATACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGATCTTCAAAAAACGTGTCC
* *
391107 GCTCCCTATTGCTTCAGAGAGTATGGAACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
391138 AAACGTCTTC
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
51 70 0.61
52 45 0.39
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGATCTTCAAAAAACGTGTCC
Found at i:391074 original size:103 final size:103
Alignment explanation
Indices: 390952--391139 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 103
390942 ATGATAAGTC
* *
390952 TGCTCCCTATTTCTTCAGAGAGTATAGA-ACTTGATCTTCAACAAACGTGTCCGCTCCCTATTCC
1 TGCTCCCTATTCCTTCAGAGAGTATA-ATACTCGATCTTCAACAAACGTGTCCGCTCCCTATTCC
391016 TTCAGAGAGTATAGG-ACTCAATCTTCAATAAAATGTGTA
65 TTCAGAGAGTAT-GGAACTCAATCTTCAATAAAATGTGTA
* *
391055 TGCTCCCTATTCCTTCAGAGAGTATAATACTCGATCTTCAATAAACGTGTCCGCTCCCTATTGCT
1 TGCTCCCTATTCCTTCAGAGAGTATAATACTCGATCTTCAACAAACGTGTCCGCTCCCTATTCCT
391120 TCAGAGAGTATGGAACTCAA
66 TCAGAGAGTATGGAACTCAA
391140 ACGTCTTCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
102 3 0.04
103 76 0.96
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (103 bp):
TGCTCCCTATTCCTTCAGAGAGTATAATACTCGATCTTCAACAAACGTGTCCGCTCCCTATTCCT
TCAGAGAGTATGGAACTCAATCTTCAATAAAATGTGTA
Found at i:391167 original size:54 final size:54
Alignment explanation
Indices: 391125--391476 Score: 562
Period size: 54 Copynumber: 6.5 Consensus size: 54
391115 TTGCTTCAGA
* * *
391125 GAGTATGGAACTCAAACGTCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * *
391179 GAGTATAGAACTCGAACATCTTATTCTTACGGATTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
391233 GAGTATGGAACTCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * *
391287 GAGTATGGAATTCGAACATTTTCTTCTTACGGGTTCGTTCCCTCTTTCTATAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
391341 GAGTATGGAACTCGAACATCTTCTTCTTACGGGATT-TCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGG-TTCGCTCCCTCTTTCTCTAGG
*
391395 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
391449 GAGTATGGAACTCGAACATCTTCTTCTT
1 GAGTATGGAACTCGAACATCTTCTTCTT
391477 TACCACTTTC
Statistics
Matches: 271, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
53 2 0.01
54 267 0.99
55 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:391924 original size:36 final size:37
Alignment explanation
Indices: 391849--391972 Score: 142
Period size: 37 Copynumber: 3.4 Consensus size: 37
391839 TTACTCTAAC
* * * *
391849 ACTCTTCTGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
391886 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* * * * *
391922 ACTCTTTGGTGAAGGCTCAAAATGGATTTTCTTAATT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
391959 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
391973 ACTTGGCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
36 32 0.43
37 43 0.57
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:393409 original size:125 final size:125
Alignment explanation
Indices: 393204--393429 Score: 353
Period size: 125 Copynumber: 1.8 Consensus size: 125
393194 TGATACAGGC
* * * *
393204 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCTGAATCTT
1 CTTCAAAATACCCCAACACCGCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCCGAATCAT
* * ** *
393269 GTCATTTCATCATGATGTGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGGGT
66 GTAATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGGGT
* *
393329 CTTCAAAATACCCCAACACCGCAAATTGTAAGGCTCATTCTCAATGCCTTCTTTGTCCGAATCAT
1 CTTCAAAATACCCCAACACCGCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCCGAATCAT
393394 GTAATCTCAAAATGATGGGGGTTCAGTCATGCCCCA
66 GTAATCTCAAAATGATGGGGGTTCAGTCATGCCCCA
393430 GTGTGGGTAT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
125 90 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (125 bp):
CTTCAAAATACCCCAACACCGCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCCGAATCAT
GTAATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGGGT
Found at i:396757 original size:72 final size:72
Alignment explanation
Indices: 396640--396790 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
396630 CCCCTAACAG
* *
396640 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTACTATCATCACATTAGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
396705 TTCATCT
66 TTCATAT
* *
396712 GTTCTTGATCATTTACTATCATCACATTAGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTACTATCATCACATTAGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
396777 TTCATAT
66 TTCATAT
*
396784 TTTCTTG
1 GTTCTTG
396791 TGTAATAGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (72 bp):
GTTCTTGATCAGTTACTATCATCACATTAGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:397512 original size:55 final size:55
Alignment explanation
Indices: 397451--397636 Score: 268
Period size: 55 Copynumber: 3.4 Consensus size: 55
397441 AACATCTTCA
* * *
397451 GGATGTCTTTCTTTATGGATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATC
1 GGATGTCTTTCTTCATGAATCGTTCTTCAATCAGTTTCAAATTTCTTCATTCATC
* * *
397506 GGATGTCCTTCTTCATGAATCGTTCTTTAGTCAGTTTCAAATTTCTTCATTCATC
1 GGATGTCTTTCTTCATGAATCGTTCTTCAATCAGTTTCAAATTTCTTCATTCATC
* *
397561 GGATGTCCTTT-TTCATGAATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATC
1 GGATGT-CTTTCTTCATGAATCGTTCTTCAATCAGTTTCAAATTTCTTCATTCATC
397616 GGATGTCCTTT-TTCATGAATC
1 GGATGT-CTTTCTTCATGAATC
397637 ATCTGAACGC
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 116 0.97
56 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (55 bp):
GGATGTCTTTCTTCATGAATCGTTCTTCAATCAGTTTCAAATTTCTTCATTCATC
Found at i:397637 original size:55 final size:55
Alignment explanation
Indices: 397474--397638 Score: 285
Period size: 55 Copynumber: 3.0 Consensus size: 55
397464 TATGGATCGG
* *
397474 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATCGT
1 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
* *
397529 TCTTTAGTCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
1 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
*
397584 TCTTCAATCAGGTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
1 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
397639 CTGAACGCCT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 103 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (55 bp):
TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTTTTCATGAATCAT
Found at i:397980 original size:47 final size:46
Alignment explanation
Indices: 397924--398040 Score: 121
Period size: 47 Copynumber: 2.5 Consensus size: 46
397914 TATCTACCCC
* * *
397924 CATGCCTTGTCATTCACAAAAAATCCTAACCGCATGATATCTAATTCG
1 CATG-CTTGT-ATTCAAAAAAAAACCTAACAGCATGATATCTAATTCG
* * *
397972 CATGCTTGT-TTGATAAAAATAAACCTAACAGCATGATTTCTAGTTCG
1 CATGCTTGTATTCA-AAAAA-AAACCTAACAGCATGATATCTAATTCG
398019 CATGCATT-TATTCAAAAAAAAA
1 CATGC-TTGTATTCAAAAAAAAA
398041 AATTAAATGA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
45 3 0.05
46 7 0.12
47 39 0.67
48 9 0.16
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (46 bp):
CATGCTTGTATTCAAAAAAAAACCTAACAGCATGATATCTAATTCG
Found at i:402727 original size:6 final size:6
Alignment explanation
Indices: 402716--402744 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
402706 TTTCGTTATA
402716 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
402745 TTATTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:404704 original size:76 final size:75
Alignment explanation
Indices: 404613--404777 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
404603 TTAAACTCAA
* *
404613 ATTTAGTATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGAATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
404677 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * * *
404689 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGAATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
404754 TTTAATTAGG
66 TTTAATTAAG
404764 ATTTAGAATATTAT
1 ATTTAGAATATTAT
404778 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.57
Consensus pattern (75 bp):
ATTTAGAATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:404763 original size:19 final size:19
Alignment explanation
Indices: 404735--404797 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
404725 TGTATTTTAG
*
404735 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
404754 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
404773 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
404794 TTTA
1 TTTA
404798 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:407949 original size:13 final size:13
Alignment explanation
Indices: 407949--408024 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
407939 CCGTTGACCC
407949 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
407962 TACCCGACCCATT
1 GACCCGACCCGTT
407975 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
407993 GACCCGACCCGTT
1 GACCCGACCCGTT
*
408006 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
408021 GACC
1 GACC
408025 GTTGACCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:407950 original size:18 final size:18
Alignment explanation
Indices: 407927--408003 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
407917 ACCGGTCACA
407927 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
407945 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
407963 ACCCGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
407976 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
407994 ACCCGACCCG
1 ACCCGACCCG
408004 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.18, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:407970 original size:31 final size:31
Alignment explanation
Indices: 407931--408009 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
407921 GTCACAACCC
407931 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
407962 TACCCGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
407993 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
408010 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:407996 original size:8 final size:8
Alignment explanation
Indices: 407985--408031 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
407975 GACCCGACCC
407985 GACCCGTT
1 GACCCGTT
407993 GACCC---
1 GACCCGTT
407998 GACCCGTT
1 GACCCGTT
408006 GA-CCGTT
1 GACCCGTT
408013 GACCCGTT
1 GACCCGTT
408021 GA-CCGTT
1 GACCCGTT
408028 GACC
1 GACC
408032 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:408013 original size:7 final size:7
Alignment explanation
Indices: 408001--408032 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
407991 TTGACCCGAC
408001 CCGTTGA
1 CCGTTGA
408008 CCGTTGA
1 CCGTTGA
408015 CCCGTTGA
1 -CCGTTGA
408023 CCGTTGA
1 CCGTTGA
408030 CCG
1 CCG
408033 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:408018 original size:15 final size:15
Alignment explanation
Indices: 407985--408031 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
407975 GACCCGACCC
*
407985 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
407998 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
408013 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
408028 GACC
1 GACC
408032 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:409370 original size:18 final size:18
Alignment explanation
Indices: 409344--409379 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
409334 TCGAAAGGAC
*
409344 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
409362 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
409380 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:410542 original size:24 final size:24
Alignment explanation
Indices: 410448--410547 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
410438 ATATTTTATC
* *
410448 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
410472 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
410496 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
410520 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
410544 TGAT
1 TGAT
410548 TTTTGATATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:412712 original size:13 final size:13
Alignment explanation
Indices: 412712--412787 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
412702 CCGTTGACCC
412712 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
412725 TACCCGACCCATT
1 GACCCGACCCGTT
412738 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
412756 GACCCGACCCGTT
1 GACCCGACCCGTT
*
412769 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
412784 GACC
1 GACC
412788 GTTGACCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:412713 original size:18 final size:18
Alignment explanation
Indices: 412690--412766 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
412680 ACCGGTCACA
412690 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
412708 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
412726 ACCCGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
412739 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
412757 ACCCGACCCG
1 ACCCGACCCG
412767 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.18, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:412733 original size:31 final size:31
Alignment explanation
Indices: 412694--412772 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
412684 GTCACAACCC
412694 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
412725 TACCCGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
412756 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
412773 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:412759 original size:8 final size:8
Alignment explanation
Indices: 412748--412794 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
412738 GACCCGACCC
412748 GACCCGTT
1 GACCCGTT
412756 GACCC---
1 GACCCGTT
412761 GACCCGTT
1 GACCCGTT
412769 GA-CCGTT
1 GACCCGTT
412776 GACCCGTT
1 GACCCGTT
412784 GA-CCGTT
1 GACCCGTT
412791 GACC
1 GACC
412795 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:412776 original size:7 final size:7
Alignment explanation
Indices: 412764--412795 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
412754 TTGACCCGAC
412764 CCGTTGA
1 CCGTTGA
412771 CCGTTGA
1 CCGTTGA
412778 CCCGTTGA
1 -CCGTTGA
412786 CCGTTGA
1 CCGTTGA
412793 CCG
1 CCG
412796 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:412781 original size:15 final size:15
Alignment explanation
Indices: 412748--412794 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
412738 GACCCGACCC
*
412748 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
412761 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
412776 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
412791 GACC
1 GACC
412795 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:414132 original size:18 final size:18
Alignment explanation
Indices: 414106--414141 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
414096 TCGAAAGGAC
*
414106 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
414124 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
414142 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:415304 original size:24 final size:24
Alignment explanation
Indices: 415210--415309 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
415200 ATATTTTATC
* *
415210 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
415234 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
415258 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
415282 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
415306 TGAT
1 TGAT
415310 TTTTGATATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:422769 original size:75 final size:75
Alignment explanation
Indices: 422649--422843 Score: 203
Period size: 75 Copynumber: 2.6 Consensus size: 75
422639 TATGAATAAA
* * * * * * * * *
422649 GTCAAATATAAAGACTCAAACAACAATATTAAGTTTAGAACAATAAAATCCATAA-ACAAACTAC
1 GTCAAATTTCAAGACTCAAACCATAATAGTAACTCTAAAAAAATAAAATCCATAATA-AAACTAC
422713 AATATTAAAAT
65 AATATTAAAAT
* * * * *
422724 GTCAAATTTCAAGATTCAAACCATAATAGTAACTCTAAAATAATAAAATTCATAATAAAATTATA
1 GTCAAATTTCAAGACTCAAACCATAATAGTAACTCTAAAAAAATAAAATCCATAATAAAACTACA
*
422789 ATATTAAAGT
66 ATATTAAAAT
* * * *
422799 GTTAAATTTTAAGACTCAAACCATAATATTAAGTCTAAAAAAATA
1 GTCAAATTTCAAGACTCAAACCATAATAGTAACTCTAAAAAAATA
422844 TTAAACCCAA
Statistics
Matches: 99, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
75 98 0.99
76 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (75 bp):
GTCAAATTTCAAGACTCAAACCATAATAGTAACTCTAAAAAAATAAAATCCATAATAAAACTACA
ATATTAAAAT
Found at i:424404 original size:3 final size:3
Alignment explanation
Indices: 424396--424457 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
424386 TTTACTTAAT
** * *
424396 TTA TTA TTA TTA AAA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
424444 TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA
424458 AATAATAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:424416 original size:15 final size:16
Alignment explanation
Indices: 424396--424460 Score: 82
Period size: 15 Copynumber: 4.1 Consensus size: 16
424386 TTTACTTAAT
424396 TTATTATTATTA-AAA
1 TTATTATTATTATAAA
424411 TTATTATTATTATAAA
1 TTATTATTATTATAAA
424427 -TATTATTATTATATATA
1 TTATTATTATTATA-A-A
424444 TTA-TATTATTATTAAA
1 TTATTATTATTA-TAAA
424460 T
1 T
424461 AATAATTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
15 25 0.56
16 6 0.13
17 10 0.22
18 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTATTATTATAAA
Found at i:426250 original size:46 final size:45
Alignment explanation
Indices: 426166--426253 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
426156 TATAAATATA
* *
426166 TATAAATTAATATTTTTCATAATTATAATTTTGAAATAATAGGAT
1 TATAAATTAATATTTTTCATAATTATAAATTTCAAATAATAGGAT
* * *
426211 TATAAATTAAATATATTTTGA-AATTTTAAATTTCCAATAATAG
1 TATAAATT-AATAT-TTTTCATAATTATAAATTTCAAATAATAG
426254 AGACAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 8 0.22
46 23 0.64
47 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (45 bp):
TATAAATTAATATTTTTCATAATTATAAATTTCAAATAATAGGAT
Found at i:431184 original size:13 final size:13
Alignment explanation
Indices: 431158--431209 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
431148 TCCAGCAAAG
* *
431158 AAAGAAGAAGGAA
1 AAAGAAAAAAGAA
431171 AAAGAAAAAAG-A
1 AAAGAAAAAAGAA
431183 AAAG-AAAAA-AA
1 AAAGAAAAAAGAA
*
431194 AAAGAAACAAGAA
1 AAAGAAAAAAGAA
431207 AAA
1 AAA
431210 AAAGAGGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.30
12 9 0.27
13 14 0.42
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:431187 original size:12 final size:12
Alignment explanation
Indices: 431170--431212 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
431160 AGAAGAAGGA
431170 AAAAGAAAAAAG
1 AAAAGAAAAAAG
431182 AAAAGAAAAAA-
1 AAAAGAAAAAAG
*
431193 AAAAGAAACAAG
1 AAAAGAAAAAAG
431205 AAAA-AAAA
1 AAAAGAAAA
431213 GAGGAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 13 0.46
12 15 0.54
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Done.