Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006763.1 Corchorus capsularis cultivar CVL-1 contig06784, 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: 86924
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:94 original size:40 final size:41
Alignment explanation
Indices: 38--125 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 41
28 AACTCTCTCA
* *
38 AAAGTCCTCAAGCACATTTATAACA-AGAGACATCAATATT
1 AAAGTCCTCAAACACATTTATAACACAGAGACATCAATATC
* *
78 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGACATCAATATC
119 AAAGTCC
1 AAAGTCC
126 CTAAGCACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 24 0.56
41 19 0.44
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTATAACACAGAGACATCAATATC
Found at i:135 original size:41 final size:41
Alignment explanation
Indices: 7--135 Score: 154
Period size: 41 Copynumber: 3.1 Consensus size: 41
1 CCCCAG
* * * *
7 GCACATTTATAACACAGGGGCAACTCTCTCAAAAGTCCTCAA
1 GCACATTTATAACACAGAGGCATCTATATC-AAAGTCCTCAA
* * *
49 GCACATTTATAACA-AGAGACATCAATATTAAAGTCCTCAA
1 GCACATTTATAACACAGAGGCATCTATATCAAAGTCCTCAA
*
89 ACACATTTATAACACAGAGGCATCTATATCAAAGTCC-CTAA
1 GCACATTTATAACACAGAGGCATCTATATCAAAGTCCTC-AA
130 GCACAT
1 GCACAT
136 GTAACACAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
40 25 0.34
41 34 0.47
42 14 0.19
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (41 bp):
GCACATTTATAACACAGAGGCATCTATATCAAAGTCCTCAA
Found at i:5113 original size:30 final size:30
Alignment explanation
Indices: 5073--5131 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5063 TGTCTTCAAG
5073 TCCATAATAAGTCCTT-GGCACATCATTCCT
1 TCCATAATAAG-CCTTGGGCACATCATTCCT
* *
5103 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCACATCATTCC
5132 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCACATCATTCCT
Found at i:5577 original size:33 final size:33
Alignment explanation
Indices: 5512--5648 Score: 208
Period size: 33 Copynumber: 4.2 Consensus size: 33
5502 CTCGTCACCA
* *
5512 AAAACAGATTTATTTTCAATGC--T-ATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
*
5542 AAAACAGGATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
* *
5575 AAAACAAAATTATTTGCAATGCTATGATCAACT
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
5608 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
5641 AAAACAGA
1 AAAACAGA
5649 TTTGTTTTCA
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.20
32 1 0.01
33 76 0.79
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.28
Consensus pattern (33 bp):
AAAACAGAATTATTTGCAATGCTATGATCAACC
Found at i:5678 original size:66 final size:66
Alignment explanation
Indices: 5537--5681 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
5527 TCAATGCTAT
* * *
5537 CAACCAAAACAGGATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATGCTATGA
1 CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATACAATGA
*
5602 T
66 G
* * * * * *
5603 CAACTAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATT
1 CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAAT-ACAATG
5667 AG
65 AG
*
5669 CATCCAAAACAGA
1 CAACCAAAACAGA
5682 TTTAGTATCA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 2 0.03
66 64 0.97
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (66 bp):
CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATACAATGA
G
Found at i:5711 original size:33 final size:33
Alignment explanation
Indices: 5674--5778 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
5664 ATTAGCATCC
*
5674 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
5707 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
5740 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
5773 AAAACA
1 AAAACA
5779 CTCTCTTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:7959 original size:539 final size:540
Alignment explanation
Indices: 6783--8272 Score: 2741
Period size: 539 Copynumber: 2.8 Consensus size: 540
6773 AGCAAACAAA
6783 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
1 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
*
6848 GAAGTTAGTATATAGGTTGCTGGACTAATAAAACTTGACTCAGATTATGTTGAAAAGCAAAACGG
66 GAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGG
*
6913 CTACGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCTAGTCCAATGCAAA
131 CTACGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAA
*
6978 ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAAGGCATTTGCATGTATGGA
196 ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
*
7043 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAAACG
261 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
7108 CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
326 CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
* *
7173 AGGCTAATTCATCCGAGAGGCGGCAAAAAGCATCTAATAAATCAAACAAGAAGCAATGACAATGT
391 AGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAAGCAATGACAATGT
* *
7238 ATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAACGGCTATG
456 ATATGGCAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAACGGCTATG
7303 TACCTGCACAAATTAAGTAG
521 TACCTGCACAAATTAAGTAG
7323 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
1 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
7388 GAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGG
66 GAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGG
* * *
7453 CTACGTACCTGCACTAATAAAGGCCTTTGCATTCTACATTGCTTTCGATTCCAGTCCAATGCAAA
131 CTACGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAA
* *
7518 ACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
196 ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
7583 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
261 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
7648 CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATT-AAGAGCAAAATTTCAGCAGGCACTGAG
326 CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
*
7712 AGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATGACAATGT
391 AGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAAGCAATGACAATGT
*
7777 ATATGGCAACAATGAAAGTAGCAATTTGGCACATGGTCAGTAGAAAAAGAAGCAAAACGGCTACT
456 ATATGGCAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAACGGCTA-T
7842 -TACCTGCACAAATTAAGTAG
520 GTACCTGCACAAATTAAGTAG
7862 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
1 CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
* * *
7927 GAAGTTAGTATATAGGTTGCTAGACCAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAAGGG
66 GAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGG
* * *
7992 GTATGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGAAAA
131 CTACGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAA
8057 ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
196 ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
8122 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
261 CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
*
8187 CATTGTGTGTTCACCATTCAGACTAAAATTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
326 CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
* *
8252 AGGCTAGTTCAGCCAAGAGGC
391 AGGCTAATTCATCCAAGAGGC
8273 AATGACAATG
Statistics
Matches: 919, Mismatches: 29, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
539 519 0.56
540 400 0.44
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (540 bp):
CAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAG
GAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGG
CTACGTACCTGCACAAATTAAGGCCTTTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAA
ACAATCCTTTTCACGTCAAACACTTCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGA
CATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCG
CATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAG
AGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAAGCAATGACAATGT
ATATGGCAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAACGGCTATG
TACCTGCACAAATTAAGTAG
Found at i:8711 original size:507 final size:506
Alignment explanation
Indices: 7219--8721 Score: 1238
Period size: 539 Copynumber: 2.9 Consensus size: 506
7209 ATAAATCAAA
* * *
7219 CAAGAAGCAATGACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAA
1 CAAGAGGCAATGACAATGTATATGGAAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAA
* * ** *
7284 AAGAAGCAAAACGGCTATGTACCTGCACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTC
66 GAGAAGCAAAACAGCTACATACCTGCACAAATTAAATAGCAATGAAAGTAGCAATTTTACCTTTC
* * * *
7349 CTTATTGATCTAGGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACT
131 CTAATTGATCTAGGTTTAATCTGCTAATAGGAAAAGAAGGAAGTTAGTATATAGGTTACTGGACT
* *
7414 AATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGGCTACGTACCTGCACTAATAAAGGCCT
196 AATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGGCTACGTACCTGCACAAATTAAGGCCT
* *
7479 TTGCATTCTACATTGCTTTCGATTCCAGTCCAATGCAAAACAGTCCTTTTCACGTCAAACAATTC
261 TTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAAACAATCCTTTTCACGTCAAACAATTC
7544 ACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGTAA
326 ACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGTAA
7609 TTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACTAA
391 TTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACTAA
*
7674 AAGTGCACATTAAGAGCAAAATTTCAGCAGGCACTGAGAGGCTAATTCATC
456 AAGTGCACATTAAGAGCAAAATTTCAGCAGGCACTGAGAGGCTAATTCAGC
* * * * * * * *
7725 CAAGAGGC--GGCAAAAAGCATCTAAGAAATCAA--ACAAG-AGGCAA--TGACA-AT-GTATAT
1 CAAGAGGCAATG-ACAATGTATAT-GGAAA-CAATGA-AAGTA-GCAATTTGGCACATGGT-CA-
* **** ** * * * *
7781 GGCA-ACAATGAAAGTAGCAATTTGGC-ACATGGTCAGTAGAAA--AAGA-AGCAA--AACG--G
59 -GCAGA-AA-G--AGAAGCAAAACAGCTACAT-ACCTGCACAAATTAA-ATAGCAATGAAAGTAG
* * * * ** * * * *** ****** *
7837 CTA-CTTACC-TGCACAAATT-AAGTA-G--CAA--TG-AAAGTAGCAATTTTACCTTTCCTTAT
117 CAATTTTACCTTTC-CTAATTGATCTAGGTTTAATCTGCTAA-TAGGAA-AAGA-AGGAAGTTAG
* * *** * * * * * *
7893 TGATCTAGGTTTAATCTGCAAAC-AGGA-AAAGAAGGAAGTTAGTATATAGGTTGCTAGACCAAT
178 T-ATATAGG-TT-A-CTG--GACTA--ATAAAGCTTG-ACTCAG-AT-TATGTTG-AAAAGCAA-
* ** ** ** * * *
7956 AA-AGCTTGACTCAGATTATGTTG-A-AAAGCAAAAGGGGTATGTACCTGC-ACAAATTAAGGCC
230 AACGGC-T-A--C-G--TA-CCTGCACAAA--TTAAGGCCT-T-TGCGTTCTAC--ATT---G-C
* * * ** ****** *
8017 TTTGCG-TTCTACATTGCTTTCGATTCCAGTCCAATGAAAAACAATCCTTTTCACGTCAAACACT
277 TTT-CGATTC--CA--G---TCCAAT---G-CAAAACAATCCTTTT------CACGTCAAACAAT
8081 TCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGT
324 TCACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGT
8146 AATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACT
389 AATTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACT
* *
8211 AAAATTGCACATTCAAGAGCAAAATTTCAGCAGGCACTGAGAGGCTAGTTCAGC
454 AAAAGTGCACATT-AAGAGCAAAATTTCAGCAGGCACTGAGAGGCTAATTCAGC
*
8265 CAAGAGGCAATGACAATGTATATGGCAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAA
1 CAAGAGGCAATGACAATGTATATGGAAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAA
8330 GAGAAGCAAAACAGCTACATACCTGCACAAATTAAATAGCAATGAAAGTAGCAATTTTACCTTTC
66 GAGAAGCAAAACAGCTACATACCTGCACAAATTAAATAGCAATGAAAGTAGCAATTTTACCTTTC
8395 CTAATTGATCTAGGTTTAATCTGCTAATAGGAAAAGAAGGAAGTTAGTATATAGGTTACTGGACT
131 CTAATTGATCTAGGTTTAATCTGCTAATAGGAAAAGAAGGAAGTTAGTATATAGGTTACTGGACT
*
8460 AATAAAGCTTGACTCAGATTATGTTGAAAAGTAAAACGGCTACGTACCTGCACAAATTAAGGCCT
196 AATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGGCTACGTACCTGCACAAATTAAGGCCT
* * * * *
8525 TTGTGTTGTACATTGCTTTCGATTCCAGTACAATGCAAAATATTCCTTTTCACGTCAAACAATTC
261 TTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAAACAATCCTTTTCACGTCAAACAATTC
* *
8590 ACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGAAAGGTAGTAAAGGAAGTAA
326 ACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGTAA
* * *
8655 ATTCAAAACAGAAGACAAGGCAAGGGAAAATCTTAACCGCAATGTGTGTTCACCATTCAGACTAA
391 TTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACTAA
8720 AA
456 AA
8722 CATTTTAGCA
Statistics
Matches: 730, Mismatches: 165, Indels: 203
0.66 0.15 0.18
Matches are distributed among these distances:
494 3 0.00
495 6 0.01
496 1 0.00
497 6 0.01
498 6 0.01
499 3 0.00
500 5 0.01
501 12 0.02
502 6 0.01
503 10 0.01
504 14 0.02
505 16 0.02
506 29 0.04
507 153 0.21
508 19 0.03
509 1 0.00
511 1 0.00
512 1 0.00
513 7 0.01
514 4 0.01
515 8 0.01
516 3 0.00
517 7 0.01
518 3 0.00
520 1 0.00
521 1 0.00
522 9 0.01
523 4 0.01
524 9 0.01
525 1 0.00
526 1 0.00
528 3 0.00
529 6 0.01
530 3 0.00
531 7 0.01
532 4 0.01
533 8 0.01
534 1 0.00
535 1 0.00
537 1 0.00
538 18 0.02
539 168 0.23
540 70 0.10
541 16 0.02
542 14 0.02
543 10 0.01
544 6 0.01
545 13 0.02
546 6 0.01
547 3 0.00
548 6 0.01
549 6 0.01
550 1 0.00
551 7 0.01
552 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (506 bp):
CAAGAGGCAATGACAATGTATATGGAAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAA
GAGAAGCAAAACAGCTACATACCTGCACAAATTAAATAGCAATGAAAGTAGCAATTTTACCTTTC
CTAATTGATCTAGGTTTAATCTGCTAATAGGAAAAGAAGGAAGTTAGTATATAGGTTACTGGACT
AATAAAGCTTGACTCAGATTATGTTGAAAAGCAAAACGGCTACGTACCTGCACAAATTAAGGCCT
TTGCGTTCTACATTGCTTTCGATTCCAGTCCAATGCAAAACAATCCTTTTCACGTCAAACAATTC
ACCGGAAGTCTCATAGAACAGGGCATTTGCATGTATGGACATAAGCAAGGCAGTAAAGGAAGTAA
TTTCAAAACAGAAGACAAGGCGAGGGAAAATCTTAACCGCATTGTGTGTTCACCATTCAGACTAA
AAGTGCACATTAAGAGCAAAATTTCAGCAGGCACTGAGAGGCTAATTCAGC
Found at i:9883 original size:540 final size:540
Alignment explanation
Indices: 8859--12997 Score: 6696
Period size: 540 Copynumber: 7.7 Consensus size: 540
8849 AAAAAGAAAT
**
8859 AAAACGGCTATTTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* * * *
8924 ATGCAAAACTGTCCTTTTCACGTCAAACAATTCACCAGAAGTCTCATAAAACAGGGCACTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
*
8989 GTATGGACATAAGCAAGGCAGTAAACGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
* *
9054 TTAACCGCATTGTGTGTTCACCATTCAGAATAAAAGTGCACATTCAAGAGGAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
* * * * *
9119 CATTGAGAGGCTAATTCATCCGAGAAGCGGCAAAAAGCATCTAATAAATCAAATAAGAGGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
* *
9184 ACAATGTATATGGTAACAATGATAGTAACAATTTGGCACATGGTCAGCAGAAAAAGAAGGAAAAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
*
9249 GGCTACGTACCTACACATATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
* *
9314 GGTTTAATCTGCAATCAGGAAATGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
9379 CTCAGATTATGTTGAAAAGC
521 CTCAGATTATGTTGAAAAGC
* * ** * *
9399 AAAACGGCTATGTACCTGCACAAATAAAGGCCTTTGAATTCTACATTGCTTTTGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
*
9464 ATGCAAAACAGTCCTTTTAACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* * *
9529 GTATGGACATAAGCAAGGCAGTAGAGGAAGTAATTTCAAAACAGAGGGCAAGGCGAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
*
9594 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCGAGAGCAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
* * * *
9659 CA-TAGATAGGCTAATTCATCCGAGAGGCGGCAAAAAGCATCTAAGAAGTCAAACAAGAAGCAAT
261 CACT-GAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAAT
9723 GACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAA
325 GACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAA
* *
9788 CGGCTACGTACCTATACAAATTAAGTAGCAATGAAAGTAGCAATTTGACCTTTCCTTATTGATCT
390 CGGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCT
* * *
9853 ATGTTTAATCTACAAATAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTG
455 AGGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTG
*
9918 ACTCAAATTATGTTGAAAAGC
520 ACTCAGATTATGTTGAAAAGC
* * *
9939 AAAACGGCTACGTACCTGCACAAATTAAAGCCTTTGCATTCTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* *
10004 ATGCAAAACAGTCCTTTTCACGTCAAATAATTCACTGGAAGTCTCATAGAACAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* * * *
10069 GTATGGACATAAGCAAGGCAGTAAAGGAACTAAGTTCAAAACAGAAGGCAAGGCTAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
* * *
10134 ATAACCGCATTGTGTGTTTAACATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
* * * *
10199 CATTGAGAGGCTAATTCATCCGAGAGGCGGCAAAAAGCATCTAATAAATCAAACAAGAAGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
* * * * *
10264 ACAAGGTATATAGTAACAATGATAGTAGCCATTTGGCACATAGTCAGCAGAAAAAGAAGTAAAAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
* * *
10329 GGCAACGTTCCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTAACCTTTCCTTATTGATCTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
*
10394 GGTTTAATTTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
* *
10459 CACAGATTATGTTGAATAGC
521 CTCAGATTATGTTGAAAAGC
**
10479 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTATGTTGTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* * *
10544 ATGCAAAACATTCCTTTTCACGTCAAACAATTCACTGGAAGTCTCATAGAACTGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
*
10609 GTATGGACATAAGCAAGGCAGTAAAGGGAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
*
10674 TTAACCGCATTGTGTGTTCACCATTCAGAATAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
10739 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
*
10804 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAACAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
* *
10869 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTA-----CCTTATTAATGTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
* * * * *
10929 GGTTTAATCTGCAACCAAGAAAAGATGGAAGTTAATATATAGGTTGATGGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
* *
10994 CACAGATTATGTTGAATAGC
521 CTCAGATTATGTTGAAAAGC
* * *
11014 AAAACGGCTACGTACCTGCACAAATTAAAGCCTTTGCATTCTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* *
11079 ATGCAAAACAGTCCTTTTCACGTCAAATAATTCACTGGAAGTCTCATAGAACAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* ** *
11144 GTATGGACATAAGCAAGGCAGTAAAGGAAATAATCCCAAAACAGAAGACAAGGCAAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
* * * *
11209 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAACTGCACATTAAAGAGCAACATTTTAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
* *
11274 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAGCAAGATGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
* * *
11339 ACAATGTATATGGAAACAACGAAAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
*
11404 GGCTACGTACCTGCAC--A--AA-T-----T--AAGTAGCAATTTTACCTTTCCTTATTGATCTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
* *
11457 TGTTTAATCTACAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
* * *
11522 CTCAAATTATGTAGAATAGC
521 CTCAGATTATGTTGAAAAGC
*
11542 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGTGTTGTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
*
11607 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACTGGAAGTCTCATAGAACAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* * ** *
11672 GTATGGACATAAGTAAGGCAGTAAAGGGAGTAATTTCAAAACAGAAGACAAGGATAAGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
** * *
11737 TTAAAAGCATTGTGTGTTCACCATTCAGAATAAAAGTGCACATTCAGGAGCAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
*
11802 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATGTAAGAAATCAAACAAGAGGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
11867 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
*
11932 GGCTACGTACCTGCACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
*
11997 GGTTTAATCTGCAAACAAGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
12062 CTCAGATTATGTTGAAAAGC
521 CTCAGATTATGTTGAAAAGC
12082 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* * *
12147 ATGCAAAACAGTCCTTCTCACGTCAAGCAATTCACCGGAAGACTCATAGAACAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* *
12212 GTATGGACATAAGCAAGGTAGTAAAGGAAGTAATTTCAAAATAGAAGACAAGGCGAGGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
* ** *
12277 TTAACCGCATTGTGTGTTCACCATTTAGACTAAAAGTGCACATTCAAGAGCTTAATTGCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
*
12342 CACTGAGAGGCTAATTCATCCAAGTGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
* * *
12407 ACAATGAATATGGTAACAATGAAAGTAGCAATTTGGCACATGGTCAGCAGAAGAAGAAGCAAAAC
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
* *
12472 GGCTAAGTACCTGCACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
391 GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
* * * * * *
12537 TGTTTAATATGCAAACAAGAAAAGAA-GTAGTTAGTACATAGGTTGCTAGACTAATAAAGCTTGA
456 GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
*
12601 CTTAGATTATGTTGAAAAGC
521 CTCAGATTATGTTGAAAAGC
*
12621 AAAACAGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
1 AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
* * *
12686 ATGCAAAACAGTCCTTTTCATGTCAAACAATTCACCAGAAGTCTCATAGAATAGGGCATTTGCAT
66 ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
* *
12751 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAATAGAAGACAAGGCGAAGGAAAATC
131 GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
* *
12816 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGGGAAAAATTTCAGCAGG
196 TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
** *
12881 CACTGAGAGGCTAATTCATAAAAGAGGCGGCAAAAATCATCTAAGAAATCAAACAAGAGGCAATG
261 CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
* * * * *
12946 ACAATGTATATGGCAATAATAAAAGTAGCAGTTTGGCACATGGTCAGCAGAA
326 ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAA
12998 TCAATTTCAG
Statistics
Matches: 3345, Mismatches: 235, Indels: 39
0.92 0.06 0.01
Matches are distributed among these distances:
523 14 0.00
525 1 0.00
528 465 0.14
530 2 0.00
531 2 0.00
532 2 0.00
533 2 0.00
535 471 0.14
538 1 0.00
539 408 0.12
540 1976 0.59
541 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (540 bp):
AAAACGGCTACGTACCTGCACAAATTAAGGCCTTTGCGTTGTACATTGCTTTCGATTCCAGTCCA
ATGCAAAACAGTCCTTTTCACGTCAAACAATTCACCGGAAGTCTCATAGAACAGGGCATTTGCAT
GTATGGACATAAGCAAGGCAGTAAAGGAAGTAATTTCAAAACAGAAGACAAGGCGAGGGAAAATC
TTAACCGCATTGTGTGTTCACCATTCAGACTAAAAGTGCACATTCAAGAGCAAAATTTCAGCAGG
CACTGAGAGGCTAATTCATCCAAGAGGCGGCAAAAAGCATCTAAGAAATCAAACAAGAGGCAATG
ACAATGTATATGGTAACAATGATAGTAGCAATTTGGCACATGGTCAGCAGAAAAAGAAGCAAAAC
GGCTACGTACCTACACAAATTAAGTAGCAATGAAAGTAGCAATTTTACCTTTCCTTATTGATCTA
GGTTTAATCTGCAAACAGGAAAAGAAGGAAGTTAGTATATAGGTTGCTGGACTAATAAAGCTTGA
CTCAGATTATGTTGAAAAGC
Found at i:20672 original size:20 final size:21
Alignment explanation
Indices: 20647--20717 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
20637 TGGTTGTGTG
20647 TTTATGTTTCCTCTA-TTGTT
1 TTTATGTTTCCTCTAGTTGTT
*
20667 TTTATGTTT-TTCTAGTTGTT
1 TTTATGTTTCCTCTAGTTGTT
*
20687 TTTAATTGTTTCCTCAAGTTGTT
1 TTT-A-TGTTTCCTCTAGTTGTT
20710 TTTA-GTTT
1 TTTATGTTT
20718 TCTTCAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.09
20 21 0.48
21 1 0.02
22 6 0.14
23 12 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (21 bp):
TTTATGTTTCCTCTAGTTGTT
Found at i:23024 original size:50 final size:51
Alignment explanation
Indices: 22965--23065 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 51
22955 CTGTGACAAG
22965 ATTGGTCACCTAGCCAAATCCTGCCGTAAGGGG-AAATTTTTTTTTCCTCC
1 ATTGGTCACCTAGCCAAATCCTGCCGTAAGGGGAAAATTTTTTTTTCCTCC
23015 ATTGGTCACCTAGCCAAATCCTGCCGTAAGGGGAAAATTTTTTTTTCCTCC
1 ATTGGTCACCTAGCCAAATCCTGCCGTAAGGGGAAAATTTTTTTTTCCTCC
23066 TCACCTCGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 33 0.66
51 17 0.34
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (51 bp):
ATTGGTCACCTAGCCAAATCCTGCCGTAAGGGGAAAATTTTTTTTTCCTCC
Found at i:28057 original size:22 final size:23
Alignment explanation
Indices: 28032--28088 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
28022 CTTACCTTTA
*
28032 TCTTTTTATTTTTCG-TTATTTT
1 TCTTTTTATTTTTAGTTTATTTT
**
28054 TCTTTTT-CGTTTAGTTTATTTT
1 TCTTTTTATTTTTAGTTTATTTT
28076 TACTTTTTATTTT
1 T-CTTTTTATTTT
28089 CTTTGGTACT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.15
22 15 0.56
23 6 0.22
24 2 0.07
ACGTcount: A:0.11, C:0.09, G:0.05, T:0.75
Consensus pattern (23 bp):
TCTTTTTATTTTTAGTTTATTTT
Found at i:28059 original size:16 final size:16
Alignment explanation
Indices: 28034--28064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28024 TACCTTTATC
28034 TTTTTATTTTTCGTTA
1 TTTTTATTTTTCGTTA
*
28050 TTTTTCTTTTTCGTT
1 TTTTTATTTTTCGTT
28065 TAGTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTCGTTA
Found at i:29251 original size:21 final size:21
Alignment explanation
Indices: 29212--29260 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29202 TCAATGCTTT
**
29212 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
29234 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
29255 A-GAAGC
1 AGGAAGC
29261 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:36793 original size:10 final size:10
Alignment explanation
Indices: 36769--36815 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
36759 AAAAGAAATT
*
36769 GTATGTG-AT
1 GTATGTGAAG
36778 GTATGTGAAG
1 GTATGTGAAG
36788 GTATGTGAAG
1 GTATGTGAAG
*
36798 GTATATGAAG
1 GTATGTGAAG
36808 GTATGTGA
1 GTATGTGA
36816 TTTGTGTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 7 0.21
10 27 0.79
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (10 bp):
GTATGTGAAG
Found at i:41998 original size:21 final size:22
Alignment explanation
Indices: 41966--42009 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41956 TGTAATGATG
41966 AAGTAGTGGAA-TTGAAAATTA
1 AAGTAGTGGAATTTGAAAATTA
*
41987 AAGTGAGT-GAATTTGAGAATTA
1 AAGT-AGTGGAATTTGAAAATTA
42009 A
1 A
42010 GGTAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (22 bp):
AAGTAGTGGAATTTGAAAATTA
Found at i:45687 original size:21 final size:22
Alignment explanation
Indices: 45655--45698 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
45645 GTAAGTGATG
45655 AAGTAGTGGAA-TTGAAAATTA
1 AAGTAGTGGAATTTGAAAATTA
*
45676 AAGTGAGT-GAATTTGAGAATTA
1 AAGT-AGTGGAATTTGAAAATTA
45698 A
1 A
45699 GGTAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (22 bp):
AAGTAGTGGAATTTGAAAATTA
Found at i:48203 original size:21 final size:21
Alignment explanation
Indices: 48170--48218 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
48160 AAGAATTGTA
**
48170 GCTT-CTTAGAAATGGCTCTT
1 GCTTCCTTAGAAATCCCTCTT
*
48190 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTAGAAATCCCTCTT
48211 GCATTCCT
1 GC-TTCCT
48219 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.16, C:0.29, G:0.14, T:0.41
Consensus pattern (21 bp):
GCTTCCTTAGAAATCCCTCTT
Found at i:51252 original size:19 final size:19
Alignment explanation
Indices: 51219--51255 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51209 TTGAAATAAT
*
51219 TCTTCAAATGGTCTTCAAA
1 TCTTCAAATGATCTTCAAA
*
51238 TCTTCAAATTATCTTCAA
1 TCTTCAAATGATCTTCAA
51256 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (19 bp):
TCTTCAAATGATCTTCAAA
Found at i:58054 original size:29 final size:29
Alignment explanation
Indices: 58008--58063 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
57998 ATAAATAATT
*
58008 GCAATTCAATCAATCAATAGCAAGATATA
1 GCAATTCAATCAATCAATAGAAAGATATA
*
58037 GCAATTCAAATCAA-CAATTGAAAGATA
1 GCAATTC-AATCAATCAATAGAAAGATA
58064 GAATAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (29 bp):
GCAATTCAATCAATCAATAGAAAGATATA
Found at i:63501 original size:14 final size:16
Alignment explanation
Indices: 63476--63509 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
63466 AACAACTAAG
63476 AAAGCAAACAGATTA-
1 AAAGCAAACAGATTAT
63491 AAAGC-AACAGATTAT
1 AAAGCAAACAGATTAT
63506 AAAG
1 AAAG
63510 AAAGCAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAGCAAACAGATTAT
Found at i:67035 original size:21 final size:21
Alignment explanation
Indices: 67011--67053 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
67001 CACTTGAGCG
67011 TAAGAAGGATAAGGATGAGGT
1 TAAGAAGGATAAGGATGAGGT
*
67032 TAAGAATGATAAGGATGAGGT
1 TAAGAAGGATAAGGATGAGGT
67053 T
1 T
67054 GCTTGAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (21 bp):
TAAGAAGGATAAGGATGAGGT
Found at i:71012 original size:73 final size:75
Alignment explanation
Indices: 70880--71026 Score: 194
Period size: 73 Copynumber: 2.0 Consensus size: 75
70870 GGGGCCATGG
***
70880 CCCCCCAAACTTCCAAGAAATCTTTCATATATATGCACTTCAAATGAAAAAATTTTGAAAA-TTT
1 CCCCCCAAACTTCCAAGAAATCTTTCATATATATGCACTTCAAATGAAAAAAAAATGAAAAGTTT
70944 ATAATTTGGC
66 ATAATTTGGC
* *
70954 CCCCCCAAA-TTGCCAA-AAAT-TCTTCATATATATGCATTTCAATTGAAAAAAAAATGAAAAGT
1 CCCCCCAAACTT-CCAAGAAATCT-TTCATATATATGCACTTCAAATGAAAAAAAAATGAAAAGT
*
71016 TTTTAATTTGG
64 TTATAATTTGG
71027 TCCCTAAAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
72 1 0.02
73 39 0.61
74 24 0.38
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (75 bp):
CCCCCCAAACTTCCAAGAAATCTTTCATATATATGCACTTCAAATGAAAAAAAAATGAAAAGTTT
ATAATTTGGC
Found at i:71233 original size:30 final size:30
Alignment explanation
Indices: 71198--71256 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
71188 TTTCATTGAA
*
71198 TTTTTTCTTTTT-GACTCCTTAAAATAATTC
1 TTTTTTCTTTTTAG-CTCCTGAAAATAATTC
*
71228 TTTTTTCTTTTTAGCTTCTGAAAATAATT
1 TTTTTTCTTTTTAGCTCCTGAAAATAATT
71257 TATCTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.58
Consensus pattern (30 bp):
TTTTTTCTTTTTAGCTCCTGAAAATAATTC
Found at i:73430 original size:16 final size:16
Alignment explanation
Indices: 73409--73439 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73399 TGTAGCATCA
*
73409 ATTTTTTGTTTCCCAC
1 ATTTTTTGTTCCCCAC
73425 ATTTTTTGTTCCCCA
1 ATTTTTTGTTCCCCA
73440 ACACATCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTTTTGTTCCCCAC
Found at i:73922 original size:21 final size:21
Alignment explanation
Indices: 73877--73927 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
73867 TTGAATGTGG
* *
73877 TTTGACAATCAAAATTTGGGA
1 TTTGACCATCAAAATTTGAGA
73898 TTTGACCATCAAAATTT-AGA
1 TTTGACCATCAAAATTTGAGA
73918 CTTTGACCAT
1 -TTTGACCAT
73928 GGATGTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTGACCATCAAAATTTGAGA
Found at i:74453 original size:21 final size:22
Alignment explanation
Indices: 74424--74469 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
74414 TGAAATGTTT
* *
74424 TTTGTGGTTTTACAAT-CAAAA
1 TTTGGGGTTTGACAATGCAAAA
*
74445 TTTGGGGTTTGACCATGCAAAA
1 TTTGGGGTTTGACAATGCAAAA
74467 TTT
1 TTT
74470 ATAATTCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTGGGGTTTGACAATGCAAAA
Found at i:75078 original size:21 final size:21
Alignment explanation
Indices: 75054--75156 Score: 129
Period size: 21 Copynumber: 4.9 Consensus size: 21
75044 TCAATCACAT
75054 AAATTTTGATAGTCAAATCCC
1 AAATTTTGATAGTCAAATCCC
75075 AAATTTTGA-AGGTCAAATCCC
1 AAATTTTGATA-GTCAAATCCC
* *
75096 AAAGTTTGATAGTCAAACCCC
1 AAATTTTGATAGTCAAATCCC
*
75117 AAATTTTGATTGTCAAA-CCTC
1 AAATTTTGATAGTCAAATCC-C
* *
75138 AAAGTTTGATAGTTAAATC
1 AAATTTTGATAGTCAAATC
75157 ATGTTAAACC
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.04
21 66 0.93
22 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (21 bp):
AAATTTTGATAGTCAAATCCC
Found at i:75118 original size:42 final size:42
Alignment explanation
Indices: 75058--75150 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
75048 TCACATAAAT
*
75058 TTTGATAGTCAAATCCCAAATTTTGAAGGTCAAATCC-CAAAG
1 TTTGATAGTCAAACCCCAAATTTTGAAGGTCAAA-CCTCAAAG
**
75100 TTTGATAGTCAAACCCCAAATTTTGATTGTCAAACCTCAAAG
1 TTTGATAGTCAAACCCCAAATTTTGAAGGTCAAACCTCAAAG
75142 TTTGATAGT
1 TTTGATAGT
75151 TAAATCATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 2 0.04
42 45 0.96
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (42 bp):
TTTGATAGTCAAACCCCAAATTTTGAAGGTCAAACCTCAAAG
Found at i:75270 original size:16 final size:16
Alignment explanation
Indices: 75249--75279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
75239 AAGGTCTATT
*
75249 AATAAATTAATGTCCA
1 AATAAATCAATGTCCA
75265 AATAAATCAATGTCC
1 AATAAATCAATGTCC
75280 GGTGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (16 bp):
AATAAATCAATGTCCA
Found at i:76745 original size:21 final size:21
Alignment explanation
Indices: 76719--76760 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
76709 CAGAAATCAA
76719 AACGAGTCTGCTCAATACTCG
1 AACGAGTCTGCTCAATACTCG
*
76740 AACGAGTCTGCTCATTACTCG
1 AACGAGTCTGCTCAATACTCG
76761 CGTCGATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (21 bp):
AACGAGTCTGCTCAATACTCG
Found at i:81612 original size:1 final size:1
Alignment explanation
Indices: 81608--81633 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
81598 TGAATAAAGG
81608 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
81634 GCTACTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:82968 original size:18 final size:18
Alignment explanation
Indices: 82945--82980 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
82935 AATATGAATC
82945 TATTGTTGTTTGTTTGTT
1 TATTGTTGTTTGTTTGTT
82963 TATTGTTGTTTGTTTGTT
1 TATTGTTGTTTGTTTGTT
82981 CATGAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.00, G:0.22, T:0.72
Consensus pattern (18 bp):
TATTGTTGTTTGTTTGTT
Found at i:83663 original size:14 final size:14
Alignment explanation
Indices: 83644--83672 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
83634 GCATCGTGAC
83644 TCAATATATTTAAA
1 TCAATATATTTAAA
83658 TCAATATATTTAAA
1 TCAATATATTTAAA
83672 T
1 T
83673 TAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TCAATATATTTAAA
Done.