Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 31
Found at i:3336698 original size:19 final size:19
Alignment explanation
Indices: 3336674--3336726 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
3336664 ACATTGCGAT
3336674 TTTCACGTTGCGATTTTTA
1 TTTCACGTTGCGATTTTTA
*
3336693 TTTCACGTTGCAATTTTTA
1 TTTCACGTTGCGATTTTTA
* *
3336712 TTTCGCATTGCGATT
1 TTTCACGTTGCGATT
3336727 ATCCCGTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (19 bp):
TTTCACGTTGCGATTTTTA
Found at i:3336756 original size:20 final size:20
Alignment explanation
Indices: 3336731--3336775 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3336721 GCGATTATCC
3336731 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3336751 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3336771 CGTTG
1 CGTTG
3336776 TGATTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3338703 original size:20 final size:20
Alignment explanation
Indices: 3338680--3338720 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3338670 TCTGAAACTT
3338680 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
3338700 AAAATCACAACACGGAAATG
1 AAAATCACAACACGAAAATG
3338720 A
1 A
3338721 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:3338730 original size:20 final size:20
Alignment explanation
Indices: 3338687--3338759 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 20
3338677 CTTAAAATCA
* ** *
3338687 CAACACGAAAATGAAAATCA
1 CAACACGGAAATGACTATCG
3338707 CAACACGGAAATGACTATCG
1 CAACACGGAAATGACTATCG
*
3338727 C-A-ACGCAAATTTGACTATCG
1 CAACACGGAAA--TGACTATCG
*
3338747 CAACTC-GAAATGA
1 CAACACGGAAATGA
3338760 AAATTGCAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 6 0.14
19 4 0.10
20 27 0.64
21 4 0.10
22 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.16
Consensus pattern (20 bp):
CAACACGGAAATGACTATCG
Found at i:3339214 original size:22 final size:22
Alignment explanation
Indices: 3339187--3339237 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3339177 GATGGAGATA
*
3339187 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3339209 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3339231 GACGGAT
1 GACGGAT
3339238 GTCGTCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3339242 original size:22 final size:22
Alignment explanation
Indices: 3339199--3339244 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3339189 CGGATTTTGC
*
3339199 CGGAGATGGGGACGGATTTCGT
1 CGGAGATGGGGACGGATGTCGT
3339221 CGGAGATGGGGACGGATGTCGT
1 CGGAGATGGGGACGGATGTCGT
3339243 CG
1 CG
3339245 TAGAGAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.20
Consensus pattern (22 bp):
CGGAGATGGGGACGGATGTCGT
Found at i:3339438 original size:20 final size:20
Alignment explanation
Indices: 3339412--3339493 Score: 103
Period size: 20 Copynumber: 4.0 Consensus size: 20
3339402 TTATCGCAAC
*
3339412 GCGATAGTCAGAATCACGTT
1 GCGATAGTCAGAATCGCGTT
*
3339432 ACGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
3339452 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
3339473 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
3339493 G
1 G
3339494 GGATTTACAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 33 0.63
21 15 0.29
22 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:3340066 original size:45 final size:45
Alignment explanation
Indices: 3340002--3340105 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
3339992 AATGAAAAAA
* * *
3340002 AAATGCATATGAGTGCATTATCGGTATGAAATGATGCCATAACTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAACTG
*
3340047 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAACTG
3340092 AAATGCATATGGGT
1 AAATGCATATGGGT
3340106 AGGGTTGTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAACTG
Found at i:3340412 original size:16 final size:16
Alignment explanation
Indices: 3340391--3340444 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
3340381 GTATTACCCG
3340391 ACCTGTTTTCAACCTA
1 ACCTGTTTTCAACCTA
** * *
3340407 ACCTGTAATGAACCTG
1 ACCTGTTTTCAACCTA
* *
3340423 ACCTGTTTTTAACCGA
1 ACCTGTTTTCAACCTA
3340439 ACCTGT
1 ACCTGT
3340445 AAATTATCTG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (16 bp):
ACCTGTTTTCAACCTA
Found at i:3340497 original size:16 final size:15
Alignment explanation
Indices: 3340476--3340516 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
3340466 ACTTGATCTA
*
3340476 ATATTTATCTGACTT
1 ATATTTACCTGACTT
3340491 GATATTTACCTGACTT
1 -ATATTTACCTGACTT
3340507 ATATATTACC
1 ATAT-TTACC
3340517 ATGGATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (15 bp):
ATATTTACCTGACTT
Found at i:3340704 original size:24 final size:22
Alignment explanation
Indices: 3340650--3340706 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
3340640 AAATAGACCT
*
3340650 ATTATATAAAATTATTTAATAAA
1 ATTA-ATAAAATTATTTAAAAAA
3340673 ATTAATAAAA-TATTTAAAAGTAA
1 ATTAATAAAATTATTTAAAA--AA
3340696 ATTAGATAAAA
1 ATTA-ATAAAA
3340707 CATGATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.27
22 6 0.20
23 10 0.33
24 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTAATAAAATTATTTAAAAAA
Found at i:3340919 original size:20 final size:20
Alignment explanation
Indices: 3340891--3340928 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3340881 CCCAAAAATA
*
3340891 AGTCAATTTGCATTAGTTCT
1 AGTCAATTTACATTAGTTCT
*
3340911 AGTCCATTTACATTAGTT
1 AGTCAATTTACATTAGTT
3340929 TACATAGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (20 bp):
AGTCAATTTACATTAGTTCT
Found at i:3341527 original size:14 final size:14
Alignment explanation
Indices: 3341508--3341565 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
3341498 TCAATTTACA
3341508 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
3341522 TTAGGG-TTATAGT
1 TTAGGGTTTATGGT
*
3341535 TTAGGGTTTATGGA
1 TTAGGGTTTATGGT
*
3341549 TTAGGGTTTAGGGT
1 TTAGGGTTTATGGT
3341563 TTA
1 TTA
3341566 TATAAACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
13 12 0.32
14 26 0.68
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:3341539 original size:508 final size:528
Alignment explanation
Indices: 3340649--3342084 Score: 1950
Period size: 508 Copynumber: 2.7 Consensus size: 528
3340639 TAAATAGACC
* * * *
3340649 TATTATATAAAATTATTTAATAAAATTAATAAAAT-ATTTAAAAGTAAATTAGATAAAACATGAT
1 TATTATATAAACTTATTTAATAAATTTAAAAAAATAATTTAAATGTAAATTAG-T---A-ATGA-
*
3340713 TAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACAT
60 TAATTAGGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACAT
3340778 GTCATATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAG
125 GTCATATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTTAA-TCACATTAATAG
*
3340843 CCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCAATTTGCATTAGT
189 CCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATTAGT
* *
3340908 TCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCAACTCTTTTATTACAAATATA
254 GCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATA
* *
3340973 TATGCATTAGTGCTAGTTCATTTATATTAAGGTTTGTGGTTT-GTGGTTTAGGGTTTAGGG-TT-
319 TATGCATTAGTGCTAG-TCATTTATATTAGGGTTTATGGTTTAG-GGTTTA-GGTTTAGGGTTTA
*
3341035 T-CTA-T-G-AACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATA
381 TGCTAGTGGTAACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATA
* *
3341096 T-A-AG-TA-AT-T-TA-CCT-T-T-TA-TA-G-TATATATATATATATAGGTTATATATATTAT
446 TAAGAGTTACATATATATCATATATATATTAGGTTATATATATATATATAGGTTATATATACTAT
3341148 ACATGGTTTATACATACA
511 ACATGGTTTATACATACA
3341166 TATTATATACAA-TTATTTAATAAATTTAAAAAAATAATTTAAATGTAAATTA-T-AT-A-AATT
1 TATTATATA-AACTTATTTAATAAATTTAAAAAAATAATTTAAATGTAAATTAGTAATGATAATT
3341226 AGGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
65 AGGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
*
3341291 ATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAAATCACATTAATAGCCCAT
130 ATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTT-AATCACATTAATAGCCCAT
*
3341356 TTATTTTTTTGTTATGAATAAGTAATAA-AAAACCCAAAAATAAGTCCATTTGCATTAGTGCTAG
194 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTAG
3341420 TCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATAT
259 TCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTAC-AA-ATATATAT
* *
3341485 GCATTAGTACTAGTCAATTTACATTAGGGTTTATGGTTTAGGGTTATA-GTTTAGGGTTTATGGA
322 GCATTAGTGCTAGTC-ATTTATATTAGGGTTTATGGTTTAGGGTT-TAGGTTTAGGGTTTAT-G-
*
3341549 TTAGGGTTTAGGGTTTATATAAACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTC
383 CTA--G--T--GG------T-AACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTC
3341614 TATAAACTATATAAGTAGTTTACCATATATAGTTCATATATATATTAGGTTATATATATATATAT
435 TATAAACTATATAAG-AG-TTA-CATATATA--TCATATATATATTAGG-T-TATATATATATAT
*
3341679 ATAGTTTATATATACTATACATGGTTTATACATACA
493 ATAGGTTATATATACTATACATGGTTTATACATACA
*
3341715 TATTATATAAACTTATTTAATAAATTTTAAAAAATAATTTAAATGTAAATTATGTAAAACATGAT
1 TATTATATAAACTTATTTAATAAATTTAAAAAAATAATTTAAATGTAAATTA-GT---A-ATGA-
*
3341780 TAATTAGGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTTATAAATAGTAGTACAT
60 TAATTAGGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACAT
* *
3341845 TTAATATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGG-T--T---ATTAATAGC
125 GTCATATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTTAATCACATTAATAGC
*
3341904 CCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAATAAGTCCATTTGCATTAAT
190 CCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCC-AAAAATAAGTCCATTTGCATTAGT
* * *
3341969 GCTAGTCTATTTACATTAGTTTACATAAGCCCAATACATAAGCCCACTCTTTCATTACAAATATA
254 GCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATA
* * *
3342034 TATGCATTAGTGCTAGACTATTTATATTAGGGTTTATGATTTAGGGCTTAG
319 TATGCATTAGTGCTAGTC-ATTTATATTAGGGTTTATGGTTTAGGGTTTAG
3342085 TGATTATGAT
Statistics
Matches: 822, Mismatches: 34, Indels: 91
0.87 0.04 0.10
Matches are distributed among these distances:
507 86 0.10
508 168 0.20
509 48 0.06
510 5 0.01
511 2 0.00
513 2 0.00
516 1 0.00
517 30 0.04
518 18 0.02
521 1 0.00
529 55 0.07
530 1 0.00
532 2 0.00
534 2 0.00
536 2 0.00
537 1 0.00
538 2 0.00
541 2 0.00
542 1 0.00
543 1 0.00
544 2 0.00
545 2 0.00
546 1 0.00
548 2 0.00
549 95 0.12
551 3 0.00
552 87 0.11
553 9 0.01
554 78 0.09
555 1 0.00
556 2 0.00
557 1 0.00
558 1 0.00
559 108 0.13
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (528 bp):
TATTATATAAACTTATTTAATAAATTTAAAAAAATAATTTAAATGTAAATTAGTAATGATAATTA
GGTGTTAAATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATA
TTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTTAATCACATTAATAGCCCATTT
ATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTAGTC
CATTTACATTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCAT
TAGTGCTAGTCATTTATATTAGGGTTTATGGTTTAGGGTTTAGGTTTAGGGTTTATGCTAGTGGT
AACTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGAGTTAC
ATATATATCATATATATATTAGGTTATATATATATATATAGGTTATATATACTATACATGGTTTA
TACATACA
Found at i:3341655 original size:529 final size:529
Alignment explanation
Indices: 3341010--3342079 Score: 1534
Period size: 529 Copynumber: 2.0 Consensus size: 529
3341000 TAAGGTTTGT
* * * * *
3341010 GGTTTGTGGTTTAGGGTTTAGGGTTTCTATGAACTATATATTTTATTACTTTATATAGTTTATGC
1 GGTTTATGGATTAGGGTTTAGGGTTTATATAAACTATATAATTTATTACTTTATATAGTTTATGC
* *
3341075 ATAGTGTTTCTATAAACTATATAAGTAATTTACCTTTTATAGTATATATATATATATAGG-T-TA
66 ATAGTGTTTCTATAAACTATATAAGTAATTTACCATATATAGTATATATATATAT-TAGGTTATA
3341138 -TATATAT-TATACATGGTTTATACATACATATTATATACAA-TTATTTAATAAATTTAAAAAAA
130 TTATATATATATACATGGTTTATACATACATATTATATA-AACTTATTTAATAAATTTAAAAAAA
3341200 TAATTTAAATGTAAATTA-T-AT-A-AATTAGGTGTTAAATAATTAGTATGCCACATTGCATATT
194 TAATTTAAATGTAAATTAGTAATGATAATTAGGTGTTAAATAATTAGTATGCCACATTGCATATT
*
3341261 ATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGC
259 ATATGGTTCATAAATAGTAGTACATGTAATATTAATTTCATTTGCATAATTAGTATTTTAGTTGC
*
3341326 ATGTTAGGTTAAATCACATTAATAGCCCATTTATTTTTTTGTTATGAATAAGTAATAA-AAAACC
324 ATGTTAGG-T---T---ATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACC
* *
3341390 C-AAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACAT
382 CAAAAAATAAGTCCATTTGCATTAATGCTAGTCCATTTACATTAGTTTACATAAGCCCAATACAT
* *
3341454 AAGCCCACTCTTTTATTACAAATATATATATGCATTAGTACTAGTCAATTTACATTAGGGTTTAT
447 AAGCCCACTCTTTCATTAC-AA-ATATATATGCATTAGTACTAGACAATTTACATTAGGGTTTAT
*
3341519 GGTTTAGGGTTATAGTTTAG
510 GATTTAGGGTTATAGTTTAG
3341539 GGTTTATGGATTAGGGTTTAGGGTTTATATAAACTATATAATTTATTACTTTATATAGTTTATGC
1 GGTTTATGGATTAGGGTTTAGGGTTTATATAAACTATATAATTTATTACTTTATATAGTTTATGC
*
3341604 ATAGTGTTTCTATAAACTATATAAGTAGTTTACCATATATAGT-TCATATATATATTAGGTTATA
66 ATAGTGTTTCTATAAACTATATAAGTAATTTACCATATATAGTAT-ATATATATATTAGG-----
3341668 TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAACTTATTT
125 --------T-TATA--TTATATATA-TATACATGGTTTATACATACATATTATATAAACTTATTT
*
3341733 AATAAATTTTAAAAAATAATTTAAATGTAAATTATGTAAAACATGATTAATTAGGTGTTAAATAA
178 AATAAATTTAAAAAAATAATTTAAATGTAAATTA-GT---A-ATGA-TAATTAGGTGTTAAATAA
* *
3341798 TTAGTATGCCACATTGCATATTATATGGTTTATAAATAGTAGTACATTTAATATTAATTTCATTT
237 TTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTAATATTAATTTCATTT
*
3341863 GTATAATTAGTATTTTAGTTGCATGTTAGGTTATTAATAGCCCATTTATTTTGTTGTTATGAATA
302 GCATAATTAGTATTTTAGTTGCATGTTAGGTTATTAATAGCCCATTTATTTTGTTGTTATGAATA
*
3341928 AGTAATAATAAAACCCAAAAAATAAGTCCATTTGCATTAATGCTAGTCTATTTACATTAGTTTAC
367 AGTAATAATAAAACCCAAAAAATAAGTCCATTTGCATTAATGCTAGTCCATTTACATTAGTTTAC
* *
3341993 ATAAGCCCAATACATAAGCCCACTCTTTCATTACAAATATATATGCATTAGTGCTAGACTATTTA
432 ATAAGCCCAATACATAAGCCCACTCTTTCATTACAAATATATATGCATTAGTACTAGACAATTTA
*
3342058 TATTAGGGTTTATGATTTAGGG
497 CATTAGGGTTTATGATTTAGGG
3342080 CTTAGTGATT
Statistics
Matches: 483, Mismatches: 23, Indels: 47
0.87 0.04 0.08
Matches are distributed among these distances:
528 5 0.01
529 110 0.23
543 1 0.00
544 2 0.00
547 7 0.01
548 2 0.00
549 69 0.14
551 1 0.00
552 86 0.18
553 9 0.02
554 78 0.16
555 1 0.00
556 2 0.00
557 1 0.00
558 1 0.00
559 108 0.22
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (529 bp):
GGTTTATGGATTAGGGTTTAGGGTTTATATAAACTATATAATTTATTACTTTATATAGTTTATGC
ATAGTGTTTCTATAAACTATATAAGTAATTTACCATATATAGTATATATATATATTAGGTTATAT
TATATATATATACATGGTTTATACATACATATTATATAAACTTATTTAATAAATTTAAAAAAATA
ATTTAAATGTAAATTAGTAATGATAATTAGGTGTTAAATAATTAGTATGCCACATTGCATATTAT
ATGGTTCATAAATAGTAGTACATGTAATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCAT
GTTAGGTTATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAATA
AGTCCATTTGCATTAATGCTAGTCCATTTACATTAGTTTACATAAGCCCAATACATAAGCCCACT
CTTTCATTACAAATATATATGCATTAGTACTAGACAATTTACATTAGGGTTTATGATTTAGGGTT
ATAGTTTAG
Found at i:3341674 original size:20 final size:21
Alignment explanation
Indices: 3341649--3341697 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3341639 TATATAGTTC
3341649 ATATATATAT-TAGGTTATAT
1 ATATATATATATAGGTTATAT
*
3341669 ATATATATATATAGTTTATAT
1 ATATATATATATAGGTTATAT
3341690 ATACTATA
1 ATA-TATA
3341698 CATGGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
ATATATATATATAGGTTATAT
Found at i:3341705 original size:20 final size:20
Alignment explanation
Indices: 3341661--3341713 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3341651 ATATATATTA
*
3341661 GGTTATATATATA-TATATAT
1 GGTT-TATATATACTATACAT
*
3341681 AGTTTATATATACTATACAT
1 GGTTTATATATACTATACAT
*
3341701 GGTTTATACATAC
1 GGTTTATATATAC
3341714 ATATTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (20 bp):
GGTTTATATATACTATACAT
Found at i:3342008 original size:13 final size:13
Alignment explanation
Indices: 3341990--3342014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3341980 TACATTAGTT
3341990 TACATAAGCCCAA
1 TACATAAGCCCAA
3342003 TACATAAGCCCA
1 TACATAAGCCCA
3342015 CTCTTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (13 bp):
TACATAAGCCCAA
Found at i:3342173 original size:2 final size:2
Alignment explanation
Indices: 3342168--3342213 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3342158 TTATATAGTT
** * *
3342168 TA TA TA TA TA TA GG TG TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3342210 TA TA
1 TA TA
3342214 CATGTACTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3342189 original size:16 final size:15
Alignment explanation
Indices: 3342159--3342209 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
3342149 TAATTTACTT
*
3342159 TATATAGTTTATATA
1 TATATAGTGTATATA
3342174 TATATAGGTGTATATA
1 TATATA-GTGTATATA
*
3342190 TATATA-TATATATA
1 TATATAGTGTATATA
*
3342204 TTTATA
1 TATATA
3342210 TATACATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.38
15 6 0.19
16 14 0.44
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (15 bp):
TATATAGTGTATATA
Found at i:3342203 original size:559 final size:539
Alignment explanation
Indices: 3341117--3342179 Score: 1476
Period size: 559 Copynumber: 1.9 Consensus size: 539
3341107 CCTTTTATAG
*
3341117 TATATATATATATATAGGTTATATATATTATACATGGTTTATACATACATATTATATACAATTAT
1 TATATATATATATATAGGTTATATATACTATACATGGTTTATACATACATATTATATACAATTAT
3341182 TTAATAAATTTAAAAAAATAATTTAAATGTAAATTATATAAATTAGGTGTTAAATAATTAGTATG
66 TTAATAAATTTAAAAAAATAATTTAAATGTAAATTATATAAATTAGGTGTTAAATAATTAGTATG
*
3341247 CCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATT
131 CCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTAATATTAATTTCATTTGCATAATT
*
3341312 AGTATTTTAGTTGCATGTTAGGTTAAATCACATTAATAGCCCATTTATTTTTTTGTTATGAATAA
196 AGTATTTTAGTTGCATGTTAGGTT--AT--CATTAATAGCCCATTTATTTTGTTGTTATGAATAA
*
3341377 GTAATAAAAAACCCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATA
257 GTAATAAAAAACCCAAAAATAAGTCCATTTGCATTAATGCTAGTCCATTTACATTAGTTTACATA
* * *
3341442 GGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATATGCATTAGTACTAGTCAATTTAC
322 AGCCCAATACATAAGCCCACTCTTTCATTACAAATATATATATGCATTAGTACTAGACAATTTAC
* * *
3341507 ATTAGGGTTTATGGTTTAGGGTTATAGTTTAGGGTTTATGGATTAGGGTTTAGGGTTTATATAAA
387 ATTAGGGTTTATGATTTAGGGTTATAGTTTAGGGTTTAGGGATTAGGATTTAGGGTTTATATAAA
* * * *
3341572 CTATATAATTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAGTTTAC
452 CTATATAAGTAATTACTTTATATAGTTTAT-CATA----TTATATAAACTATATAAGTAGTATAC
3341637 CATATATAGTTCATATATATATTAGGTTA
512 CATATATA-TTCATATATATATTAGGTTA
*
3341666 TATATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATA-AACTTA
1 TATATATATATATATAGGTTATATATACTATACATGGTTTATACATACATATTATATACAA-TTA
*
3341730 TTTAATAAATTTTAAAAAATAATTTAAATGTAAATTATGTAAAACATGATTAATTAGGTGTTAAA
65 TTTAATAAATTTAAAAAAATAATTTAAATGTAAATTA--T-----AT-A--AATTAGGTGTTAAA
* *
3341795 TAATTAGTATGCCACATTGCATATTATATGGTTTATAAATAGTAGTACATTTAATATTAATTTCA
120 TAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTAATATTAATTTCA
*
3341860 TTTGTATAATTAGTATTTTAGTTGCATGTTAGG-T-T-ATTAATAGCCCATTTATTTTGTTGTTA
185 TTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTATCATTAATAGCCCATTTATTTTGTTGTTA
*
3341922 TGAATAAGTAATAATAAAACCCAAAAAATAAGTCCATTTGCATTAATGCTAGTCTATTTACATTA
250 TGAATAAGTAATAA-AAAACCC-AAAAATAAGTCCATTTGCATTAATGCTAGTCCATTTACATTA
*
3341987 GTTTACATAAGCCCAATACATAAGCCCACTCTTTCATTAC-AA-ATATATATGCATTAGTGCTAG
313 GTTTACATAAGCCCAATACATAAGCCCACTCTTTCATTACAAATATATATATGCATTAGTACTAG
* *
3342050 ACTATTTATATTAGGGTTTATGATTTAGGGCTTAGTGATTATGATTTTAAAGTTTAGGGTTTAGG
378 ACAATTTACATTAGGGTTTATGATTTA--G----G-G--T-T-A---T--AGTTTAGGGTTTAGG
* * *
3342115 GTTTATGATTTAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT-ATA-TATA
427 GATTAGGATTTAGGGTTTATATAAACTATATAAGTAA-TTACTTTATATAGTTTATCATATTATA
3342178 TA
491 TA
3342180 GGTGTATATA
Statistics
Matches: 459, Mismatches: 25, Indels: 47
0.86 0.05 0.09
Matches are distributed among these distances:
548 2 0.00
549 95 0.21
551 1 0.00
552 83 0.18
553 9 0.02
554 79 0.17
555 1 0.00
556 2 0.00
557 1 0.00
558 2 0.00
559 109 0.24
561 1 0.00
562 6 0.01
563 1 0.00
566 1 0.00
567 3 0.01
568 45 0.10
569 18 0.04
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (539 bp):
TATATATATATATATAGGTTATATATACTATACATGGTTTATACATACATATTATATACAATTAT
TTAATAAATTTAAAAAAATAATTTAAATGTAAATTATATAAATTAGGTGTTAAATAATTAGTATG
CCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTAATATTAATTTCATTTGCATAATT
AGTATTTTAGTTGCATGTTAGGTTATCATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAA
TAAAAAACCCAAAAATAAGTCCATTTGCATTAATGCTAGTCCATTTACATTAGTTTACATAAGCC
CAATACATAAGCCCACTCTTTCATTACAAATATATATATGCATTAGTACTAGACAATTTACATTA
GGGTTTATGATTTAGGGTTATAGTTTAGGGTTTAGGGATTAGGATTTAGGGTTTATATAAACTAT
ATAAGTAATTACTTTATATAGTTTATCATATTATATAAACTATATAAGTAGTATACCATATATAT
TCATATATATATTAGGTTA
Found at i:3342355 original size:2 final size:2
Alignment explanation
Indices: 3342348--3342496 Score: 150
Period size: 2 Copynumber: 76.0 Consensus size: 2
3342338 TTCTATAAAC
*
3342348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3342388 TA TA TA TA TA TA TA TA TA TA TA CTA TA T- TA TA TA CTA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* * * * *
3342430 TA TA T- TA AA CTA -A TA T- TT TA TA TA GTT TA TA CA TA TA TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
3342471 TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3342497 ATTAAAAGTA
Statistics
Matches: 124, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
1 7 0.06
2 111 0.90
3 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3342867 original size:14 final size:14
Alignment explanation
Indices: 3342837--3342879 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3342827 ACTTTGAAGA
3342837 ATATATATATAAA-T
1 ATATATATA-AAATT
*
3342851 ATATACATAAAATT
1 ATATATATAAAATT
*
3342865 ATATATATATAATT
1 ATATATATAAAATT
3342879 A
1 A
3342880 AACATAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATAAAATT
Found at i:3343305 original size:2 final size:2
Alignment explanation
Indices: 3343298--3343325 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3343288 ACTCATGTGA
3343298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3343326 TAGCCAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3343521 original size:2 final size:2
Alignment explanation
Indices: 3343514--3343543 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3343504 TGTGTACCAA
3343514 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3343544 GTTTATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3343557 original size:23 final size:22
Alignment explanation
Indices: 3343531--3343581 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
3343521 TATATATATA
3343531 TATATAATATATAGTTTATAAAC
1 TATATAATATATAGTTTAT-AAC
** * *
3343554 TATATTTTTTATAGTTTATACC
1 TATATAATATATAGTTTATAAC
3343576 TATATA
1 TATATA
3343582 GTTTACATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (22 bp):
TATATAATATATAGTTTATAAC
Found at i:3343601 original size:22 final size:22
Alignment explanation
Indices: 3343541--3343601 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
3343531 TATATAATAT
* * **
3343541 ATAGTTTATAAACTATATTTTTT
1 ATAGTTTATATA-TATAGTTTAC
3343564 ATAGTTTATACCTATATAGTTTAC
1 ATAGTTTATA--TATATAGTTTAC
3343588 ATAGTTTATATATA
1 ATAGTTTATATATA
3343602 GTTCATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 4 0.12
23 10 0.31
24 17 0.53
25 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (22 bp):
ATAGTTTATATATATAGTTTAC
Found at i:3343644 original size:18 final size:18
Alignment explanation
Indices: 3343623--3343675 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
3343613 CATAATTTTA
*
3343623 TATATAGCTTATAATAAT
1 TATATAGTTTATAATAAT
3343641 TATATAGTTTATAAT-AT
1 TATATAGTTTATAATAAT
*
3343658 AATATAGTTTATATATAA
1 TATATAGTTTATA-ATAA
3343676 ACTTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 14 0.45
18 16 0.52
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATAGTTTATAATAAT
Found at i:3343664 original size:17 final size:17
Alignment explanation
Indices: 3343624--3343675 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3343614 ATAATTTTAT
* *
3343624 ATATAGCTTATAATAATT
1 ATATAGTTTATAAT-ATA
3343642 ATATAGTTTATAATATA
1 ATATAGTTTATAATATA
3343659 ATATAGTTTAT-ATATA
1 ATATAGTTTATAATATA
3343675 A
1 A
3343676 ACTTATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.19
17 13 0.41
18 13 0.41
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATAGTTTATAATATA
Found at i:3345792 original size:60 final size:60
Alignment explanation
Indices: 3345650--3345793 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 60
3345640 GTTTGGGGAC
* * * * * *
3345650 TAATTTAGAATGAAG-GTTATAGTTTAGGGATGAAATTGAAATATTTAAAAAATTAAGGAA
1 TAATTTAAAAT-AAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
* * * * *
3345710 TAATTTGAAATAATAGTCATAATTTAAGGATAAAATTAAAATATTT-AAAATTTTAGAAA
1 TAATTTAAAATAAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
*
3345769 TCAATTTAAAATTAGAGTTATAATT
1 T-AATTTAAAATAAGAGTTATAATT
3345794 GAAGACGTGT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 13 0.19
60 54 0.81
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (60 bp):
TAATTTAAAATAAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
Found at i:3350127 original size:37 final size:37
Alignment explanation
Indices: 3350086--3350164 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
3350076 TGTAAAATAA
*
3350086 GACTCGTCAACTCTAATAACTCGAAAATTTTTAACTC
1 GACTCGTCAACTCTAATAACTCAAAAATTTTTAACTC
* * *
3350123 GACTCGTCAACTTTAATCACTCAAAAATTTTTAACTT
1 GACTCGTCAACTCTAATAACTCAAAAATTTTTAACTC
3350160 GACTC
1 GACTC
3350165 AACCGAACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (37 bp):
GACTCGTCAACTCTAATAACTCAAAAATTTTTAACTC
Found at i:3350909 original size:3 final size:3
Alignment explanation
Indices: 3350903--3350946 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
3350893 CATTTATTTA
3350903 TAT TAT TAT T-T ATAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
3350947 CTAATTACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3350913 original size:12 final size:12
Alignment explanation
Indices: 3350896--3350945 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
3350886 TTTTTTTCAT
3350896 TTATTTATATTA
1 TTATTTATATTA
3350908 TTA-TT-TA-TA
1 TTATTTATATTA
3350917 TTATTTATATTA
1 TTATTTATATTA
3350929 TTA-TTATTATTA
1 TTATTTA-TATTA
3350941 TTATT
1 TTATT
3350946 ACTAATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 7 0.21
12 16 0.48
13 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:3350918 original size:9 final size:9
Alignment explanation
Indices: 3350894--3350939 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
3350884 TCTTTTTTTC
3350894 ATTTAT-TT
1 ATTTATATT
*
3350902 ATAT-TATT
1 ATTTATATT
3350910 ATTTATATT
1 ATTTATATT
3350919 ATTTATATT
1 ATTTATATT
3350928 A-TTATTATT
1 ATTTA-TATT
3350937 ATT
1 ATT
3350940 ATTATTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 1 0.03
8 11 0.34
9 19 0.59
10 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTATATT
Found at i:3350920 original size:21 final size:21
Alignment explanation
Indices: 3350896--3350942 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
3350886 TTTTTTTCAT
3350896 TTATTTATATTATTATT-TATA
1 TTATTTATATTATTATTAT-TA
3350917 TTATTTATATTATTATTATTA
1 TTATTTATATTATTATTATTA
3350938 TTATT
1 TTATT
3350943 ATTACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATATTATTATTATTA
Found at i:3352768 original size:25 final size:24
Alignment explanation
Indices: 3352740--3352787 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3352730 TGTTTAACTT
3352740 TATATGTTATAAATATTTTGTTTCG
1 TATATGTTATAAATA-TTTGTTTCG
* **
3352765 TATATTTTATTTATATTTGTTTC
1 TATATGTTATAAATATTTGTTTC
3352788 CATTGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (24 bp):
TATATGTTATAAATATTTGTTTCG
Found at i:3356548 original size:10 final size:10
Alignment explanation
Indices: 3356533--3356571 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
3356523 AAGAGAAAAG
3356533 AAACAAAGAA
1 AAACAAAGAA
3356543 AAACAAAGAAA
1 AAACAAAG-AA
*
3356554 AAATAAATGAA
1 AAACAAA-GAA
3356565 AAACAAA
1 AAACAAA
3356572 AACAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.32
11 16 0.64
12 1 0.04
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.05
Consensus pattern (10 bp):
AAACAAAGAA
Found at i:3356587 original size:22 final size:22
Alignment explanation
Indices: 3356537--3356588 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3356527 GAAAAGAAAC
3356537 AAAGAAAAACAAAGAAAAAATA
1 AAAGAAAAACAAAGAAAAAATA
*
3356559 AATGAAAAACAAA-AACAATAA-A
1 AAAGAAAAACAAAGAA-AA-AATA
3356581 AAAGAAAA
1 AAAGAAAA
3356589 GAAAAGAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.81, C:0.06, G:0.08, T:0.06
Consensus pattern (22 bp):
AAAGAAAAACAAAGAAAAAATA
Found at i:3357294 original size:21 final size:23
Alignment explanation
Indices: 3357253--3357295 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3357243 AGAATCGAAG
*
3357253 TTGGGGCAAGAGAAGCTAAATTT
1 TTGGGGCAAGAGAAACTAAATTT
3357276 TTGGGGCAAGA-AAAC-AAATT
1 TTGGGGCAAGAGAAACTAAATT
3357296 GTCTCAGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (23 bp):
TTGGGGCAAGAGAAACTAAATTT
Found at i:3357415 original size:4 final size:4
Alignment explanation
Indices: 3357406--3358495 Score: 2040
Period size: 4 Copynumber: 273.0 Consensus size: 4
3357396 ATTGAGAAAA
3357406 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357454 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357502 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357550 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357598 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357646 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357694 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357742 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
3357790 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * *
3357838 ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT GCAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357886 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357934 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3357982 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358030 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358078 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358126 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358174 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358220 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358268 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358316 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358364 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358412 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
3358460 ACAT ACGT ACGT ACGT ACGT ACGT ACGT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3358496 GACACATAAA
Statistics
Matches: 1070, Mismatches: 14, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
2 2 0.00
4 1068 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:3358890 original size:35 final size:37
Alignment explanation
Indices: 3358822--3358965 Score: 177
Period size: 38 Copynumber: 3.9 Consensus size: 37
3358812 AAATGTCGTT
* *
3358822 TCGCTAGAGACAATTTCTTTTGAAAAACAAATTTTGTC
1 TCGCTTGAGACAATTT-TCTTGAAAAACAAATTTTGTC
3358860 TCGCTTGAGACAATTTTC-T-AAAAACAAATTTTGTC
1 TCGCTTGAGACAATTTTCTTGAAAAACAAATTTTGTC
*
3358895 TCGTTTGAGACAA-TTTCTTGAAAAACAAATTTTGTC
1 TCGCTTGAGACAATTTTCTTGAAAAACAAATTTTGTC
* * * * *
3358931 TAGCTAGAGACATTTTTCCTTGAGATACAAATTTT
1 TCGCTTGAGACAATTTT-CTTGAAAAACAAATTTT
3358966 TGAATTTGTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
34 4 0.04
35 29 0.31
36 26 0.28
37 4 0.04
38 30 0.32
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (37 bp):
TCGCTTGAGACAATTTTCTTGAAAAACAAATTTTGTC
Found at i:3358926 original size:36 final size:36
Alignment explanation
Indices: 3358822--3358965 Score: 166
Period size: 35 Copynumber: 3.9 Consensus size: 36
3358812 AAATGTCGTT
*
3358822 TCGCTAGAGACAATTTCTTTTGAAAAACAAATTTTGTC
1 TCGCTTGAGACAATTTC--TTGAAAAACAAATTTTGTC
3358860 TCGCTTGAGACAATTT-TCT-AAAAACAAATTTTGTC
1 TCGCTTGAGACAATTTCT-TGAAAAACAAATTTTGTC
*
3358895 TCGTTTGAGACAATTTCTTGAAAAACAAATTTTGTC
1 TCGCTTGAGACAATTTCTTGAAAAACAAATTTTGTC
* * * * *
3358931 TAGCTAGAGACATTTTTCCTTGAGATACAAATTTT
1 TCGCTTGAGACA-ATTT-CTTGAAAAACAAATTTT
3358966 TGAATTTGTT
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
35 33 0.35
36 27 0.29
37 3 0.03
38 30 0.32
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (36 bp):
TCGCTTGAGACAATTTCTTGAAAAACAAATTTTGTC
Found at i:3359600 original size:33 final size:33
Alignment explanation
Indices: 3359556--3359620 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3359546 ACAACATTTA
3359556 CCATCTATGAGTCTGTTTCCCTTGAAACAAAGC
1 CCATCTATGAGTCTGTTTCCCTTGAAACAAAGC
* * * **
3359589 CCATCTTTGAGTGTTTTTCTTTTGAAACAAAG
1 CCATCTATGAGTCTGTTTCCCTTGAAACAAAG
3359621 TTTTGTCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (33 bp):
CCATCTATGAGTCTGTTTCCCTTGAAACAAAGC
Found at i:3359776 original size:65 final size:63
Alignment explanation
Indices: 3359678--3359839 Score: 166
Period size: 63 Copynumber: 2.5 Consensus size: 63
3359668 TTTCTATAAG
* * * *
3359678 AACAAAAATCTTTGACTCTGTTTC-TCTGAAAACAAATTTTTTGTCTCTTGAGACAATTTCTGTG
1 AACAAAAATCTTTGAGTTTGTTTCTTTTG-AAACAAA-ATTTTGTCTC--GAGACAATTTCTGTG
3359742 GA
62 GA
* * *
3359744 AA-AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCGAGATAATTTCTTTTGA
1 AACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCGAGACAATTTCTGTGGA
*** * *
3359806 AACACCTATCTTTGAGTTAGTTTCTCTTGAAACA
1 AACAAAAATCTTTGAGTTTGTTTCTTTTGAAACA
3359840 CCCACCTTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
62 16 0.20
63 26 0.32
64 9 0.11
65 26 0.32
66 5 0.06
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (63 bp):
AACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCGAGACAATTTCTGTGGA
Found at i:3359836 original size:30 final size:30
Alignment explanation
Indices: 3359789--3359869 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
3359779 ATTTTGTCTC
* * * *
3359789 GAGATAATTTCTTTTGAAACACCTATCTTT
1 GAGATAGTTTCTATTGAAACACCCACCTTT
* *
3359819 GAGTTAGTTTCTCTTGAAACACCCACCTTT
1 GAGATAGTTTCTATTGAAACACCCACCTTT
* *
3359849 GAGATCGTTTCTATTAAAACA
1 GAGATAGTTTCTATTGAAACA
3359870 ATTTTGTTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (30 bp):
GAGATAGTTTCTATTGAAACACCCACCTTT
Found at i:3360510 original size:28 final size:31
Alignment explanation
Indices: 3360447--3360524 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 31
3360437 TTTTCGAGAC
*
3360447 AGTTGCTTTTGAAACACATTATCTTTGAGTCT
1 AGTTTCTTTTGAAACACA-TATCTTTGAGTCT
3360479 -GTTTCTTTTGAAACA-A-ATCTTTGAGT-T
1 AGTTTCTTTTGAAACACATATCTTTGAGTCT
* *
3360506 AGTTTATCTTGAAAC-CATA
1 AGTTTCTTTTGAAACACATA
3360525 ATCCTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 1 0.03
28 23 0.57
29 1 0.03
30 1 0.03
31 14 0.35
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
AGTTTCTTTTGAAACACATATCTTTGAGTCT
Found at i:3360635 original size:42 final size:40
Alignment explanation
Indices: 3360545--3360644 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
3360535 ATGGCCAGCA
* *
3360545 GTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGAC
1 GTCCTCATCACGTAGGAACCGTGTCATACCCTGACCAGAC
* * *
3360585 CTCCTCATCACGTAGGAGCCGTGTCA-ACCTTGATAACCAGAC
1 GTCCTCATCACGTAGGAACCGTGTCATACCCTG---ACCAGAC
*
3360627 GTCCTCATCATGTAGGAA
1 GTCCTCATCACGTAGGAA
3360645 TCGAGTTATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 4 0.08
40 23 0.47
42 22 0.45
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (40 bp):
GTCCTCATCACGTAGGAACCGTGTCATACCCTGACCAGAC
Found at i:3360744 original size:94 final size:93
Alignment explanation
Indices: 3360577--3360750 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 93
3360567 GTCATCCCCT
* * *
3360577 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTGATAACCAGACGTCCTCATCATGTAG
1 GACCAGACCTCCTCATCAAGTAGGAGCCGTGTCAACCTAGATAACCAGACGTCCTCATCACGTAG
*
3360642 GAATCGAGTTATCACATTTCCTTTAAAC
66 GAACCGAGTTATCACATTTCCTTTAAAC
* * * * *
3360670 GACCAGTCCTCCTCATCAAGTAGGAGCTGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTA
1 GACCAGACCTCCTCATCAAGTAGGAGCCGTGTCA-ACCTAGATAACCAGACGTCCTCATCACGTA
3360735 GGAACCGAGTTATCAC
65 GGAACCGAGTTATCAC
3360751 CCTTCCTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 31 0.44
94 40 0.56
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (93 bp):
GACCAGACCTCCTCATCAAGTAGGAGCCGTGTCAACCTAGATAACCAGACGTCCTCATCACGTAG
GAACCGAGTTATCACATTTCCTTTAAAC
Found at i:3360861 original size:135 final size:134
Alignment explanation
Indices: 3360669--3360980 Score: 484
Period size: 135 Copynumber: 2.3 Consensus size: 134
3360659 TTCCTTTAAA
* *
3360669 CGACCAG-TCCTCCTCATCAAGTAGGAGCTGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
1 CGACCAGAT-CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
* *
3360733 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGATCCGTGTC
65 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCAGTGTC
3360798 ATCCC-
129 ATCCCT
* *
3360803 CTGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
1 C-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
3360868 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCA
65 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCA
3360933 TCCCT
130 TCCCT
* * * * *
3360938 CGACTATATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGA
1 CGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGA
3360981 CGACTCGAAC
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
134 68 0.42
135 93 0.57
136 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (134 bp):
CGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGT
AGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCAT
CCCT
Found at i:3361188 original size:9 final size:9
Alignment explanation
Indices: 3361174--3361214 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3361164 CTTTTTTCAT
3361174 TTATTTATA
1 TTATTTATA
3361183 TTATTTATA
1 TTATTTATA
3361192 TTA-TTAT-
1 TTATTTATA
3361199 TTATATTATTA
1 TTAT-TTA-TA
3361210 TTATT
1 TTATT
3361215 ACTAATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
7 3 0.11
8 4 0.14
9 15 0.54
10 2 0.07
11 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTTATA
Found at i:3361198 original size:12 final size:12
Alignment explanation
Indices: 3361181--3361211 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3361171 CATTTATTTA
3361181 TATTATTTATAT
1 TATTATTTATAT
3361193 TATTATTTATAT
1 TATTATTTATAT
3361205 TATTATT
1 TATTATT
3361212 ATTACTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTATTTATAT
Found at i:3363026 original size:25 final size:24
Alignment explanation
Indices: 3362998--3363045 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3362988 TGTTTAACAT
3362998 TATATGTTATAAATATTTTGTTTCA
1 TATATGTTATAAATA-TTTGTTTCA
* **
3363023 TATATTTTATTTATATTTGTTTC
1 TATATGTTATAAATATTTGTTTC
3363046 CAATGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (24 bp):
TATATGTTATAAATATTTGTTTCA
Found at i:3366680 original size:17 final size:17
Alignment explanation
Indices: 3366654--3366687 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3366644 TTGGTATGTC
*
3366654 ATTGTGGAAATTATATT
1 ATTGTGGAAAGTATATT
*
3366671 ATTGTTGAAAGTATATT
1 ATTGTGGAAAGTATATT
3366688 CTGGACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
ATTGTGGAAAGTATATT
Found at i:3368302 original size:26 final size:24
Alignment explanation
Indices: 3368273--3368325 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3368263 TATTATTAAA
3368273 ATAAAAATATAATATCATATATTATT
1 ATAAAAATA-AATAT-ATATATTATT
* *
3368299 AT-AAAATAATTATATATGTTATT
1 ATAAAAATAAATATATATATTATT
3368322 ATAA
1 ATAA
3368326 CACTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 11 0.46
24 5 0.21
25 6 0.25
26 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAAAAATAAATATATATATTATT
Found at i:3368315 original size:23 final size:23
Alignment explanation
Indices: 3368281--3368325 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3368271 AAATAAAAAT
3368281 ATAATATCATATATTATTATAAA
1 ATAATATCATATATTATTATAAA
*
3368304 ATAATTAT-ATATGTTATTATAA
1 ATAA-TATCATATATTATTATAA
3368326 CACTGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATATCATATATTATTATAAA
Found at i:3368404 original size:19 final size:19
Alignment explanation
Indices: 3368388--3368430 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3368378 ATTAAAATCG
3368388 TATTAAAATA-ATAAAATAA
1 TATT-AAATACATAAAATAA
3368407 TATTAAATACATAAAATAA
1 TATTAAATACATAAAATAA
3368426 TATTA
1 TATTA
3368431 TTTTGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TATTAAATACATAAAATAA
Found at i:3370790 original size:19 final size:20
Alignment explanation
Indices: 3370766--3370813 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3370756 AATGATTTTC
* * *
3370766 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
3370785 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
3370805 TTTTGAAAA
1 TTTTGAAAA
3370814 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:3372226 original size:40 final size:40
Alignment explanation
Indices: 3372161--3372254 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
3372151 GGACAAGCAA
* * *
3372161 TACCAATATTGTTCTTACAATATCGATACCTCATGAATAG
1 TACCGATACTGTTCTTACAACATCGATACCTCATGAATAG
*
3372201 TACCGATACTGTTCTTACAGCATCGATACCTCATGAATAG
1 TACCGATACTGTTCTTACAACATCGATACCTCATGAATAG
*
3372241 TACAGATACTGTTC
1 TACCGATACTGTTC
3372255 ATATGGTACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (40 bp):
TACCGATACTGTTCTTACAACATCGATACCTCATGAATAG
Found at i:3372413 original size:20 final size:21
Alignment explanation
Indices: 3372388--3372428 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3372378 ACTTTGTATA
3372388 ATAGTATCAATACCAT-AGGC
1 ATAGTATCAATACCATCAGGC
*
3372408 ATAGTATCGATACCATCAGGC
1 ATAGTATCAATACCATCAGGC
3372429 CCCAACAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (21 bp):
ATAGTATCAATACCATCAGGC
Found at i:3373353 original size:26 final size:27
Alignment explanation
Indices: 3373288--3373353 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 27
3373278 ATTGAATAAC
** *
3373288 ATTATAATGTTAAAATAATATATATAT
1 ATTATAATAATAAAATAATATAAATAT
3373315 ATATATAGTATAATAAAATAATATAAATA-
1 AT-TATA--ATAATAAAATAATATAAATAT
3373344 ATTATAATAA
1 ATTATAATAA
3373354 CTCGAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 8 0.24
29 2 0.06
30 17 0.52
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
ATTATAATAATAAAATAATATAAATAT
Found at i:3374800 original size:20 final size:20
Alignment explanation
Indices: 3374777--3374828 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3374767 AACGCGATCC
3374777 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3374797 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3374817 CCAAAATCGCAA
1 CCAGAATCGCAA
3374829 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:3374909 original size:20 final size:20
Alignment explanation
Indices: 3374884--3375077 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
3374874 GATTTTCCAT
* *
3374884 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
3374904 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
3374924 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3374944 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
3374964 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
3374984 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3375004 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
3375024 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
3375045 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
3375065 AATCGCAACGCGA
1 AATCGCAACGCGA
3375078 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:3374929 original size:40 final size:39
Alignment explanation
Indices: 3374880--3375077 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
3374870 TTGCGATTTT
* ** *
3374880 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
3374918 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
3374959 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
3374999 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
3375038 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
3375078 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:3374967 original size:60 final size:60
Alignment explanation
Indices: 3374884--3375076 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3374874 GATTTTCCAT
* ** * *
3374884 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
3374944 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
3375004 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
3375065 AATCGCAACGCG
1 AATCGCAACGCG
3375077 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:3375494 original size:33 final size:33
Alignment explanation
Indices: 3375455--3375525 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3375445 TTCACTTAGA
*
3375455 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3375488 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3375521 TTTCA
1 TTTCA
3375526 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3375665 original size:14 final size:14
Alignment explanation
Indices: 3375646--3375700 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3375636 AGAATGACTG
3375646 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3375660 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
3375679 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3375693 TCGCAACG
1 TCGCAACG
3375701 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3375683 original size:33 final size:33
Alignment explanation
Indices: 3375646--3375716 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3375636 AGAATGACTG
**
3375646 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3375679 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3375712 TCGCA
1 TCGCA
3375717 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3375734 original size:19 final size:19
Alignment explanation
Indices: 3375712--3375809 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3375702 GAAACCAAAA
*
3375712 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3375731 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3375745 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3375764 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3375778 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3375797 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3375810 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3375753 original size:14 final size:14
Alignment explanation
Indices: 3375734--3375823 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3375724 TTTCATTTCG
3375734 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3375748 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3375767 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3375781 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3375798 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3375814 CGTTGCGATT
1 CGTTGCGATT
3375824 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3375759 original size:33 final size:33
Alignment explanation
Indices: 3375717--3375831 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3375707 CAAAATCGCA
3375717 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3375750 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3375783 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3375816 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3375832 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3377748 original size:184 final size:185
Alignment explanation
Indices: 3377514--3378075 Score: 1067
Period size: 184 Copynumber: 3.0 Consensus size: 185
3377504 TAGATTGCTT
*
3377514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3377579 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
3377644 GTATATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3377699 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3377763 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
3377828 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3377883 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3377947 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
3378012 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3378067 AGTAAATTT
1 AGTAAATTT
3378076 ATCCATTCAA
Statistics
Matches: 371, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
183 91 0.25
184 226 0.61
185 54 0.15
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3377899 original size:93 final size:92
Alignment explanation
Indices: 3377514--3378075 Score: 1056
Period size: 93 Copynumber: 6.1 Consensus size: 92
3377504 TAGATTGCTT
*
3377514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3377579 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3377607 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3377672 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3377699 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3377763 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3377790 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3377855 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3377883 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3377947 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3377974 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3378039 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3378067 AGTAAATTT
1 AGTAAATTT
3378076 ATCCATTCAA
Statistics
Matches: 462, Mismatches: 3, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
91 178 0.39
92 98 0.21
93 186 0.40
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3378007 original size:276 final size:277
Alignment explanation
Indices: 3377514--3378077 Score: 1078
Period size: 276 Copynumber: 2.0 Consensus size: 277
3377504 TAGATTGCTT
3377514 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3377579 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3377644 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
3377709 TTCGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TATTTGTCTTTGT
196 TTCGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
3377773 TTTGTCTTTTGGTTGAA
261 TTTGTCTTTTGGTTGAA
*
3377790 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3377855 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
3377920 GTGTATTCTTTAACACTGTG-AATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
*
3377984 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTC-GTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
3378049 TTTTGTCTTTTGGTTGAA
260 TTTTGTCTTTTGGTTGAA
3378067 AGTAAATTTAT
1 AGTAAATTTAT
3378078 CCATTCAAGT
Statistics
Matches: 282, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
275 47 0.17
276 195 0.69
277 40 0.14
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.47
Consensus pattern (277 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
TTTGTCTTTTGGTTGAA
Found at i:3378220 original size:19 final size:19
Alignment explanation
Indices: 3378119--3378214 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
3378109 TAGTTTACTT
* *
3378119 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3378139 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3378158 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3378177 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3378191 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3378210 TCGCA
1 TCGCA
3378215 TTGCGATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 36 0.56
20 13 0.20
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3378232 original size:19 final size:19
Alignment explanation
Indices: 3378210--3378344 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3378200 GAAACCAAAA
*
3378210 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3378229 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3378245 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3378262 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3378278 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3378295 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3378314 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3378334 TCGTGTTGCGA
1 TCGCGTTGCGA
3378345 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3378251 original size:14 final size:14
Alignment explanation
Indices: 3378232--3378288 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3378222 TTTCATTTCG
3378232 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3378246 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3378263 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3378279 CGTTGCGATT
1 CGTTGCGATT
3378289 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3378257 original size:33 final size:33
Alignment explanation
Indices: 3378215--3378307 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3378205 CAAAATCGCA
*
3378215 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3378248 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3378281 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3378308 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3380266 original size:14 final size:14
Alignment explanation
Indices: 3380247--3380282 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3380237 ATTGTTTAAT
3380247 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3380261 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3380275 TGATTTGT
1 TGATTTGT
3380283 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3380405 original size:19 final size:19
Alignment explanation
Indices: 3380389--3380490 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3380379 AAAAATGACT
3380389 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3380408 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3380427 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3380441 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3380460 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3380480 ATCGCAATGCG
1 ATCGCAATGCG
3380491 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3380543 original size:19 final size:19
Alignment explanation
Indices: 3380519--3380811 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
3380509 GATTATCTCG
3380519 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380538 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380557 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3380571 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380590 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380609 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380628 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380647 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3380666 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3380685 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
3380699 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3380718 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3380737 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
3380751 TTGCAATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3380771 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3380785 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3380804 TTGCGATT
1 TTGCGATT
3380812 GTATTTTCCG
Statistics
Matches: 243, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 28 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.65
20 11 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3380559 original size:52 final size:52
Alignment explanation
Indices: 3380497--3380811 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
3380487 TGCGTTTATA
*
3380497 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3380549 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
3380601 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
3380658 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3380710 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCAATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3380762 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
3380812 GTATTTTCCG
Statistics
Matches: 239, Mismatches: 11, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 128 0.54
53 17 0.07
54 6 0.03
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3383111 original size:12 final size:12
Alignment explanation
Indices: 3383094--3383118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3383084 TCTTCGGGGA
3383094 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3383106 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3383118 C
1 C
3383119 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3383327 original size:24 final size:24
Alignment explanation
Indices: 3383293--3383339 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3383283 CTGAAACATC
3383293 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3383317 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3383340 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3384050 original size:20 final size:20
Alignment explanation
Indices: 3384022--3384390 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
3384012 AAATTTAAGT
* * * *
3384022 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3384042 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3384062 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3384082 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3384102 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3384122 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
3384142 GTTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3384162 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3384182 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3384202 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3384222 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
3384242 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3384262 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3384282 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3384302 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3384322 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3384342 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3384362 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3384382 GTTGCGATT
1 GTTGCGATT
3384391 ATGTAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 295 0.96
21 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3384782 original size:22 final size:20
Alignment explanation
Indices: 3384748--3384790 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3384738 ATAATTATTT
*
3384748 AAAAAATTAAATACAAATATA
1 AAAAAATTAAATA-AAAAATA
*
3384769 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
3384790 A
1 A
3384791 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATA
Found at i:3385922 original size:5 final size:5
Alignment explanation
Indices: 3385912--3385939 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3385902 ATAATTACTC
3385912 AATAA AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AAT
3385940 GTAGGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:3400221 original size:11 final size:11
Alignment explanation
Indices: 3400205--3400235 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3400195 AAGCCACCCA
3400205 CTTTCTTCTCT
1 CTTTCTTCTCT
3400216 CTTTCTTCTCT
1 CTTTCTTCTCT
3400227 CTTTCTTCT
1 CTTTCTTCT
3400236 TTACTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
CTTTCTTCTCT
Found at i:3400242 original size:19 final size:19
Alignment explanation
Indices: 3400210--3400270 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3400200 ACCCACTTTC
3400210 TTCTCTCTTTCTTCTCTCT
1 TTCTCTCTTTCTTCTCTCT
*
3400229 TTCT-TCTTTACTTCTCTTT
1 TTCTCTCTTT-CTTCTCTCT
* * * *
3400248 TTCACTCTTACTTTTCCCT
1 TTCTCTCTTTCTTCTCTCT
3400267 TTCT
1 TTCT
3400271 TTTTTTATCT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.15
19 24 0.73
20 4 0.12
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCTCTCTTTCTTCTCTCT
Found at i:3410976 original size:45 final size:45
Alignment explanation
Indices: 3410909--3410998 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
3410899 GAGAGAAGTC
* *
3410909 TTAGGGAATAAGTTGGGAAATGCGGGTAATAGCTCCAACATAGTG
1 TTAGGGAATAAGTTGGGAAATGCCGATAATAGCTCCAACATAGTG
* *
3410954 TTAGGGAATAAGTTGGGTAATGCCGATAATAGCTCCGACATAGTG
1 TTAGGGAATAAGTTGGGAAATGCCGATAATAGCTCCAACATAGTG
3410999 AAAGAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (45 bp):
TTAGGGAATAAGTTGGGAAATGCCGATAATAGCTCCAACATAGTG
Found at i:3428243 original size:40 final size:40
Alignment explanation
Indices: 3428199--3428278 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
3428189 ATGGTGTATA
* * *
3428199 AGGTGGGCAAGGCCCGACCTCAGCACTACGGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAGCACTACGATGCAATATT
* *
3428239 AGGTGAGCAAGGCTCGACCTCAGTACTACGATGCAATATT
1 AGGTGAGCAAGGCCCGACCTCAGCACTACGATGCAATATT
3428279 TGACTCTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (40 bp):
AGGTGAGCAAGGCCCGACCTCAGCACTACGATGCAATATT
Found at i:3430990 original size:20 final size:20
Alignment explanation
Indices: 3430947--3430990 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3430937 TAGTTAGTAG
**
3430947 GTATTGATACCAAAAGGTGG
1 GTATTGATACCAAAAGGTCA
* *
3430967 GTATTGATACTAAAGGGTCA
1 GTATTGATACCAAAAGGTCA
3430987 GTAT
1 GTAT
3430991 CGGTACCAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (20 bp):
GTATTGATACCAAAAGGTCA
Found at i:3432072 original size:20 final size:19
Alignment explanation
Indices: 3432026--3432076 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3432016 ACCGATTCAA
3432026 GTGGTATCGATACCAAGAG
1 GTGGTATCGATACCAAGAG
* * *
3432045 GGGAGTATCGATACTATGAG
1 GTG-GTATCGATACCAAGAG
3432065 GATGGTATCGAT
1 G-TGGTATCGAT
3432077 TCCATTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.25
Consensus pattern (19 bp):
GTGGTATCGATACCAAGAG
Found at i:3432559 original size:12 final size:12
Alignment explanation
Indices: 3432542--3432569 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3432532 CATAATAAGT
3432542 TATGAATTTCCG
1 TATGAATTTCCG
3432554 TATGAATTTCCG
1 TATGAATTTCCG
3432566 TATG
1 TATG
3432570 GACAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (12 bp):
TATGAATTTCCG
Found at i:3435354 original size:78 final size:77
Alignment explanation
Indices: 3435249--3435393 Score: 177
Period size: 77 Copynumber: 1.9 Consensus size: 77
3435239 TAAACATTAT
* *
3435249 AAGAATGTAATTCTGATTATGACTCTTTTAATGGATATTTAACTCGGAA-TAATTAAATAACAAT
1 AAGAATGTAATTCTGATTATAACTC-TTTAATGAATATTTAA-TCGGAATTAATTAAATAACAAT
3435313 TTAAATAAATGTTA
64 TTAAATAAATGTTA
* * ** * *
3435327 AAGAGTGTAATT-TGGATTATAAGTCTTTAATGAATATTTAATTTGAATTCATTAAATAAGAATT
1 AAGAATGTAATTCT-GATTATAACTCTTTAATGAATATTTAATCGGAATTAATTAAATAACAATT
3435391 TAA
65 TAA
3435394 TTAATTCGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
76 4 0.07
77 33 0.58
78 20 0.35
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (77 bp):
AAGAATGTAATTCTGATTATAACTCTTTAATGAATATTTAATCGGAATTAATTAAATAACAATTT
AAATAAATGTTA
Found at i:3436093 original size:11 final size:11
Alignment explanation
Indices: 3436077--3436108 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3436067 ACAATGACCT
3436077 AATAAAAGTTA
1 AATAAAAGTTA
3436088 AATAAAAGTTA
1 AATAAAAGTTA
*
3436099 ATTAAAAGTT
1 AATAAAAGTT
3436109 TAATGATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (11 bp):
AATAAAAGTTA
Found at i:3436797 original size:18 final size:18
Alignment explanation
Indices: 3436771--3436816 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3436761 ATATATATTT
*
3436771 TTAATTTAAATTCAAATA
1 TTAAATTAAATTCAAATA
* *
3436789 TTAAATTAAATTTACATA
1 TTAAATTAAATTCAAATA
*
3436807 TTAACTTAAA
1 TTAAATTAAA
3436817 AAATATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTCAAATA
Found at i:3436841 original size:17 final size:18
Alignment explanation
Indices: 3436816--3436850 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3436806 ATTAACTTAA
*
3436816 AAAATATATTTTTTATTT
1 AAAATATATATTTTATTT
3436834 AAAA-ATATATTTTATTT
1 AAAATATATATTTTATTT
3436851 TCATCTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAATATATATTTTATTT
Found at i:3436895 original size:30 final size:29
Alignment explanation
Indices: 3436832--3437068 Score: 205
Period size: 30 Copynumber: 7.9 Consensus size: 29
3436822 TATTTTTTAT
* *
3436832 TTAAAAATATATTTTATTTTCATCTTCAC
1 TTAAAAATATATTTTATTTTTATCTTAAC
3436861 TTAAAAATATATTTTATTTTTATCTTTAAC
1 TTAAAAATATATTTTATTTTTATC-TTAAC
* * *
3436891 TTAAAAATATATATTATTCTTATTTTAA-
1 TTAAAAATATATTTTATTTTTATCTTAAC
* *
3436919 TGTAAAAACA-ATTTTA-TATTATCTTAAC
1 T-TAAAAATATATTTTATTTTTATCTTAAC
3436947 TTAAACAATATA-TTTATTTTTATCTTAAC
1 TTAAA-AATATATTTTATTTTTATCTTAAC
* * * * * *
3436976 TTTTATAAATATTTTTTATCTTAATGGAGCTCAAAT
1 --TTAAAAATATATTTTAT-TT--T-TATCT-TAAC
3437012 TTAAAAATATATTTTATTTTTATCTTAGA-
1 TTAAAAATATATTTTATTTTTATCTTA-AC
*
3437041 TTATTAAATATATTTTATTTTTATCTTA
1 TTA-AAAATATATTTTATTTTTATCTTA
3437069 TTATTCTTAT
Statistics
Matches: 169, Mismatches: 23, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
27 13 0.08
28 14 0.08
29 50 0.30
30 57 0.34
31 10 0.06
32 2 0.01
33 2 0.01
34 16 0.09
35 3 0.02
36 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAAAAATATATTTTATTTTTATCTTAAC
Found at i:3436925 original size:59 final size:53
Alignment explanation
Indices: 3436832--3436966 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 53
3436822 TATTTTTTAT
* * * *
3436832 TTAAAAATATATTTTATTTTCATCTTCACTTAAAAATATATTTTATTTTTATCTTTAAC
1 TTAAAAATATA-TTTATTTT-AT-TTTAATTAAAAACA-ATTTTA-TATTATC-TTAAC
3436891 TTAAAAATATATATTATTCTTATTTTAATGTAAAAACAATTTTATATTATCTTAAC
1 TTAAAAATATAT-TTATT-TTATTTTAAT-TAAAAACAATTTTATATTATCTTAAC
3436947 TTAAACAATATATTTATTTT
1 TTAAA-AATATATTTATTTT
3436967 TATCTTAACT
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
55 2 0.03
56 15 0.22
57 13 0.19
58 11 0.16
59 25 0.37
60 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (53 bp):
TTAAAAATATATTTATTTTATTTTAATTAAAAACAATTTTATATTATCTTAAC
Found at i:3437092 original size:44 final size:44
Alignment explanation
Indices: 3437025--3437109 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
3437015 AAAATATATT
* * *
3437025 TTATTTTTATCTTAGATTATTAAATATATTTTATTTTTATCTTA
1 TTATTCTTATCTTAGATTATTAAAAATATTATATTTTTATCTTA
*
3437069 TTATTCTTATCTTA-ATTTTTTAAAAATATTATATTTTTATC
1 TTATTCTTATCTTAGA-TTATTAAAAATATTATATTTTTATC
3437110 CTAATCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (44 bp):
TTATTCTTATCTTAGATTATTAAAAATATTATATTTTTATCTTA
Found at i:3441569 original size:16 final size:16
Alignment explanation
Indices: 3441548--3441580 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3441538 CGCAACCATT
3441548 GAAGGTTGTGTAACTG
1 GAAGGTTGTGTAACTG
3441564 GAAGGTTGTGTAACTG
1 GAAGGTTGTGTAACTG
3441580 G
1 G
3441581 GTTTTTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.39, T:0.30
Consensus pattern (16 bp):
GAAGGTTGTGTAACTG
Found at i:3442079 original size:4 final size:4
Alignment explanation
Indices: 3442070--3442119 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
3442060 AATGTTAGAC
**
3442070 AATA AATA AATA AATA AATA AAT- GTTA AATA AATAA AATA AAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AATA AATA AATA
3442117 AAT
1 AAT
3442120 GAAAAGGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:3442226 original size:23 final size:26
Alignment explanation
Indices: 3442182--3442228 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
3442172 TAAAAGCAAT
*
3442182 AGAATAAAGAAAAATATGAAGAAAGA
1 AGAATAAAGAAAAATATAAAGAAAGA
3442208 AGAA-AAA-AAAAAT-TAAAGAAA
1 AGAATAAAGAAAAATATAAAGAAA
3442229 ATAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 3 0.15
26 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (26 bp):
AGAATAAAGAAAAATATAAAGAAAGA
Found at i:3443987 original size:63 final size:64
Alignment explanation
Indices: 3443920--3444071 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 64
3443910 AGGCCAATAT
* *
3443920 CCTTCGCTGTGAAGTTGAAATTG-AC-TATGAAACT-GGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAAATTGTACGTATGAAACTGGGGAA-TT-TTTGTTGACAACCAGCGGC
3443982 C
64 C
* * * * *
3443983 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGGAATTTTTGTTGACAATCAGCGGCC
1 CCTTCGTTGTGAAGTTGAAATTGTAC-GTATGAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
*
3444048 CCTTCGTTGTGAAGTTGAACTTGT
1 CCTTCGTTGTGAAGTTGAAATTGT
3444072 GTTGTCTTGA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
63 21 0.27
64 1 0.01
65 42 0.54
66 9 0.12
67 5 0.06
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAAATTGTACGTATGAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
Found at i:3444047 original size:65 final size:66
Alignment explanation
Indices: 3443949--3444079 Score: 212
Period size: 65 Copynumber: 2.0 Consensus size: 66
3443939 ATTGACTATG
*
3443949 AAACTGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
1 AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
3444014 T
66 T
* *
3444015 AAACTGGGGAA-TT-TTTGTTGACAATCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAACT-GGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTC
3444078 TT
65 TT
3444080 GAGTCCAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
65 49 0.80
66 7 0.11
67 5 0.08
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.35
Consensus pattern (66 bp):
AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
T
Found at i:3444152 original size:106 final size:107
Alignment explanation
Indices: 3443983--3444185 Score: 286
Period size: 106 Copynumber: 1.9 Consensus size: 107
3443973 GCCAGCGGCC
* * * * *
3443983 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGGAATTTTTGTTGACAATCAGCGGCC
1 CCTTCGCTGTGAAGTTGAAATTGTGC-GTCTGAAACTGGGGAATTTTTATTGACAACCAGCGGCC
*
3444048 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
65 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTGAGTCCAATAT
* *
3444091 CCTTCGCTGTGAAGTTGAAATTG-GC-TCTGAAA-TTGGGAAGTTGTTTATTGACAGCCAGCGGC
1 CCTTCGCTGTGAAGTTGAAATTGTGCGTCTGAAACTGGGGAA-TT-TTTATTGACAACCAGCGGC
3444153 CCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTT
64 CCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTT
3444186 AAACTGGGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
104 6 0.07
105 8 0.09
106 48 0.56
107 2 0.02
108 21 0.25
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (107 bp):
CCTTCGCTGTGAAGTTGAAATTGTGCGTCTGAAACTGGGGAATTTTTATTGACAACCAGCGGCCC
CTTCGTTGTGAAGTTGAACTTGTGCTGTCTTGAGTCCAATAT
Found at i:3444220 original size:64 final size:64
Alignment explanation
Indices: 3444091--3444313 Score: 299
Period size: 64 Copynumber: 3.5 Consensus size: 64
3444081 AGTCCAATAT
* * * * * *
3444091 CCTTCGCTGTGAAGTTGAAATTG-GC--TCTGAAATTGGGAAGTTGTTTATTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAA-AT-TTTGTTGACAACCAGCGGC
3444153 C
64 C
*
3444154 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* * *
3444218 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
*
3444283 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
3444314 TGAGTTCCAA
Statistics
Matches: 145, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
63 21 0.14
64 60 0.41
65 52 0.36
66 12 0.08
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
Found at i:3444301 original size:65 final size:64
Alignment explanation
Indices: 3444145--3444313 Score: 293
Period size: 65 Copynumber: 2.6 Consensus size: 64
3444135 TTATTGACAG
* * *
3444145 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATTTTGTTGACAA
1 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTAACAA
*
3444209 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAA
1 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAA-TTTTGTTAACAA
3444274 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
3444314 TGAGTTCCAA
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
64 49 0.49
65 51 0.51
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (64 bp):
CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTAACAA
Found at i:3445673 original size:22 final size:22
Alignment explanation
Indices: 3445647--3445695 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3445637 TTGTGTTTGG
* *
3445647 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
3445669 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
3445691 TCAAA
1 TCAAA
3445696 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:3445702 original size:22 final size:22
Alignment explanation
Indices: 3445659--3445702 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3445649 AAAGGTTTGG
* * *
3445659 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
3445681 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
3445703 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:3446363 original size:23 final size:22
Alignment explanation
Indices: 3446336--3446409 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
3446326 TTTTTGTCCC
3446336 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTG-TTTTTGCTCT
* * *
3446359 TTTTTCCTTTTGTTCTTGTTTCT
1 TTTTTCTTTTTGTTTTTG-CTCT
*
3446382 CTTTTTCTTTGTTTTTTTTTGCT-T
1 -TTTTTC-TT-TTTGTTTTTGCTCT
3446406 TTTT
1 TTTT
3446410 GCTTCTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 5 0.12
23 18 0.45
24 7 0.17
25 2 0.05
26 8 0.20
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTCT
Found at i:3446368 original size:8 final size:7
Alignment explanation
Indices: 3446356--3446424 Score: 59
Period size: 8 Copynumber: 9.0 Consensus size: 7
3446346 TGATTTTTGC
3446356 TCTTTTT
1 TCTTTTT
3446363 TCCTTTTGT
1 T-CTTTT-T
*
3446372 TCTTGTT
1 TCTTTTT
3446379 TCTCTTTT
1 TCT-TTTT
3446387 TCTTTGTT
1 TCTTT-TT
3446395 T-TTTTT
1 TCTTTTT
3446401 TGCTTTTT
1 T-CTTTTT
3446409 TGCTTCTTT
1 T-CTT-TTT
3446418 TCTTTTT
1 TCTTTTT
3446425 CTGTTCTTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.06
7 13 0.25
8 31 0.58
9 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:3446369 original size:16 final size:17
Alignment explanation
Indices: 3446350--3446404 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
3446340 TCTTTTTGAT
*
3446350 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
3446366 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
3446383 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
3446398 TTTTGCT
1 TTTTGCT
3446405 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:3448519 original size:36 final size:35
Alignment explanation
Indices: 3448447--3448519 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 35
3448437 AAATGAAAAA
3448447 TCCTACCCCACATGATATCTACCCGCATGCTTTAAT
1 TCCTACCCCACATGATATCTACCCGCATGC-TTAAT
* *
3448483 TCCTACCCGGACATGATCTCTATCCCGCATGC-TAAT
1 TCCTACCC-CACATGATATCTA-CCCGCATGCTTAAT
3448519 T
1 T
3448520 TCACAAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 13 0.39
37 11 0.33
38 9 0.27
ACGTcount: A:0.23, C:0.36, G:0.11, T:0.30
Consensus pattern (35 bp):
TCCTACCCCACATGATATCTACCCGCATGCTTAAT
Found at i:3449445 original size:4 final size:4
Alignment explanation
Indices: 3449436--3449485 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
3449426 AATGTTAGAC
**
3449436 AATA AATA AATA AATA AATA AAT- GTTA AATA AATAA AATA AAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AATA AATA AATA
3449483 AAT
1 AAT
3449486 GAAAAGGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:3449598 original size:16 final size:17
Alignment explanation
Indices: 3449574--3449612 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3449564 AGAAAGAAGA
*
3449574 AAAAAAATAATTAAAG-
1 AAAAAAATAAATAAAGT
*
3449590 AAAATAATAAATAAAGT
1 AAAAAAATAAATAAAGT
3449607 AAAAAA
1 AAAAAA
3449613 CTTAGAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAAAATAAATAAAGT
Found at i:3454828 original size:25 final size:25
Alignment explanation
Indices: 3454800--3454847 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3454790 GATAAAAATT
*
3454800 GATTCCAGTATACCTTTTTCGTAGC
1 GATTCCAGTATACCATTTTCGTAGC
3454825 GATTCCAGTATACCATTTTCGTA
1 GATTCCAGTATACCATTTTCGTA
3454848 TTGATACAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (25 bp):
GATTCCAGTATACCATTTTCGTAGC
Found at i:3454860 original size:25 final size:25
Alignment explanation
Indices: 3454797--3454852 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3454787 TTTGATAAAA
*
3454797 ATTGATTCCAGTATACCTTTTTCGT
1 ATTGATTCCAGTATACCATTTTCGT
**
3454822 AGCGATTCCAGTATACCATTTTCGT
1 ATTGATTCCAGTATACCATTTTCGT
3454847 ATTGAT
1 ATTGAT
3454853 ACAAGTATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (25 bp):
ATTGATTCCAGTATACCATTTTCGT
Found at i:3460640 original size:12 final size:13
Alignment explanation
Indices: 3460623--3460651 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3460613 ATTAAAATAT
3460623 AATTATTAC-CTA
1 AATTATTACACTA
3460635 AATTATTACACTA
1 AATTATTACACTA
3460648 AATT
1 AATT
3460652 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTATTACACTA
Found at i:3460884 original size:5 final size:5
Alignment explanation
Indices: 3460865--3460924 Score: 52
Period size: 5 Copynumber: 11.2 Consensus size: 5
3460855 TAATTAAGCT
3460865 AATAA AATAA TAATAA AATAA AA-AA TAA-AA AATAA ACAGTAAA ATATAA
1 AATAA AATAA -AATAA AATAA AATAA -AATAA AATAA A-A-T-AA A-ATAA
3460914 AATAA AATAA A
1 AATAA AATAA A
3460925 CATGCATTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
4 4 0.08
5 29 0.60
6 9 0.19
7 2 0.04
8 4 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
AATAA
Done.