Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022649.1 Corchorus olitorius cultivar O-4 contig22682, 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: 32730
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1229 original size:13 final size:13
Alignment explanation
Indices: 1213--1242 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1203 TCTACAACTA
*
1213 TTTTCAAAAGCAG
1 TTTTCAAAAGCAC
1226 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
1239 TTTT
1 TTTT
1243 TGCAAACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:2922 original size:218 final size:218
Alignment explanation
Indices: 2481--3462 Score: 1493
Period size: 218 Copynumber: 4.5 Consensus size: 218
2471 AAATAAGTAC
* *
2481 AAAAAATGTCAATCTCGAAAGAATTTGGGGAAGGTGCATATGATTATGTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
* * *
2546 GATTTGGGTATAAAGTATATCAGTTTGGAGATACTGAATTTTTCATTTTTTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* *
2611 GCACAAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAATATAGATTAAAACACGT
131 ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAATATAGATTAAAACACGT
* *
2676 TTAAACCCAATTTTGGGTGTATA
196 TTAAAGCCAATTTTGGGTATATA
* * *
2699 AAAAAATGCCAATCCCTAAAGAATTTGGGGATGGTGCATATAATTATGTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
* *
2764 GATTTGGGTATAAAGTATATCACTTTGGGGATACTGAATTTTGCATGTTGTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* * * * *
2829 GCACTAAATTCATTTAGACTGGG-TTATTCAATTAATTAGGAGGAAAATATGGATTAAAACACGT
131 ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAATATAGATTAAAACACGT
2893 TTAAAGCCAATTTTGGGTATATAA
196 TTAAAGCCAATTTTGGGTATAT-A
* * * *
2917 AAAAAATGGCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
* * * *
2982 GAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAACTATTAAATG
66 GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* * *
3047 ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAAGATAAAAATATAAATTAAAACACGT
131 ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAATATAGATTAAAACACGT
* *
3112 TTAAAGTCAATTTTGGGCATATA
196 TTAAAGCCAATTTTGGGTATATA
* *
3135 AAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGCTGAGAAAT
1 AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
3200 GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
66 GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
* * * *
3265 ACACTAAATTCATATAGACGGGGTTTATTCAATTAA-TATGGATGAAAATATGGATCAAAGCACG
131 ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTA-GGATGAAAATATAGATTAAAACACG
3329 TTTAAAGCCAATTTTGGGTATATA
195 TTTAAAGCCAATTTTGGGTATATA
* * * * *
3353 AGATAAGATGTCAATCTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGAATGATGAG-A
1 A-A-AAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAA
* * *
3417 ATGATTTGGGTATAGAGTATATCACTTTGGGGATGCTGAATTTTGC
64 ATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGC
3463 GCATGTCTCA
Statistics
Matches: 691, Mismatches: 68, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
217 61 0.09
218 477 0.69
219 101 0.15
220 52 0.08
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (218 bp):
AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGAGAAAT
GATTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATG
ACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAATATAGATTAAAACACGT
TTAAAGCCAATTTTGGGTATATA
Found at i:4331 original size:220 final size:218
Alignment explanation
Indices: 3948--5685 Score: 2341
Period size: 211 Copynumber: 8.0 Consensus size: 218
3938 CTTGATATTA
* * *
3948 CTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGATATTGGCATTTTTTCTTA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACA-TTTTT-TTA
4013 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
64 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
* * * * * * *
4078 CCGTCTAAATGAATTTAGTGCCATCTAATAATTAAACAACATGCAGA-ATTTAGTATTCCCAAAG
129 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCA-ATATTCAGTATCCCCAAAC
4142 TGATATACTTTATACCCAAATCATTT
193 TGATATACTTTATACCCAAATCATTT
* * * * *
4168 TTCATCATCCCCACATAATCATATGCACCATCCCGAAATTCTTTAGAGATTGACATTTTTTTTTA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACA--TTTTTTTA
* * * *
4233 TATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTTATTGAATAAGCC
64 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
** * **
4298 ATGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAA-ATTTCAGTATCTTCAAAC
129 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATA-TTCAGTATCCCCAAAC
4362 TGATATACTTTATACCCAAATCATTT
193 TGATATACTTTATACCCAAATCATTT
* * * * *
4388 CTCATAATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTTATA
* *
4453 TACCTAAAATTCGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* *
4518 GTCCATATAAATTTTGTGACATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
131 GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
4583 TATACTTTATACCCAAATCATTT
196 TATACTTTATACCCAAATCATTT
* * *
4606 CTCATCATCCCCAAATAATTATAAACACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTT
1 CTCATCATCCCCAAATAATCATAAGCACCAT-CCCAAAATTCATTAGAGATTGACA-TTTTT-TT
* * * *
4671 ATATACCCAAAGTTGGTTTTAAAAAGTGCTTTAATCCATATTTTCATCCTAATTTATTGAATAAA
63 ATATACCCAAAATTGGCTTT-AAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAA
*** * * *
4736 CTATGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCTCCAAA
127 CCCCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAA
4801 CTGATATACTTTATACCCAAATCATTT
192 CTGATATACTTTATACCCAAATCATTT
* * * * *
4828 CTCATAATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTTATA
* * * *
4893 TACCTAAAGTTGGC-TTAAACGTGCTTTAATTCATATTTTCATCATAATTAATTGAATAAACCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* * *
4957 GTCCATATGAATTTTGTGCCATCTAATAAGTAAACAAAATGCAATATTCTGTATCCTCAAACTGA
131 GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
*
5022 TATACTTTATACACAAATCATTT
196 TATACTTTATACCCAAATCATTT
* *
5045 CTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGA-A------TA-
1 CTCATCATCCCCAAATAATCATAAGCACCAT-CCCAAAATTCATTAGAGATTGACATTTTTTTAT
* *
5102 AAACCCAAAATTGGCTTTAAACGTGCTTTAGTCCATATTTTCATCCTAATTAATTGAATAAACCC
65 ATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
*
5167 CGTCCATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTG
130 CGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTG
*
5232 ATATACTTTATACCTAAATCATTT
195 ATATACTTTATACCCAAATCATTT
* * * *
5256 CTCATCATCCCCAAATAGTTATAAGCACCGTACCCAAAATTCATTAGACATTGA-A------TA-
1 CTCATCATCCCCAAATAATCATAAGCACCAT-CCCAAAATTCATTAGAGATTGACATTTTTTTAT
5313 A-ACCCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
65 ATA-CCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
*
5377 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCATTATCCCCAAACT
129 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACT
*
5442 GATATACTTTATACCCAAATTATTT
194 GATATACTTTATACCCAAATCATTT
* *
5467 CTCATCATCCCCAAATAATTATAAGCACCGTAT-CTAAAATTCATTAGAGATTGACATTTTTTTC
1 CTCATCATCCCCAAATAATCATAAGCACC--ATCCCAAAATTCATTAGAGATTGACA--TTTTT-
* * * *
5531 TTATATACCCAAAGTTGGTTTTAAAAAGTGCTTTAATCCATATTTTCATCCTAATTTATTGAATA
61 TTATATACCCAAAATTGGCTTT-AAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATA
* ** * * * * * * * *
5596 AACCCCATATATATTAGTTTAT-TGTCATCTAATAATGAAACAAAACGCAAAATTTATTATCCCC
125 AACCCCGTCCATATGAATTT-TGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCC
*
5660 AAACTGATATACTGTATACCCAAATC
189 AAACTGATATACTTTATACCCAAATC
5686 TTGTGATGCC
Statistics
Matches: 1363, Mismatches: 129, Indels: 49
0.88 0.08 0.03
Matches are distributed among these distances:
210 13 0.01
211 380 0.28
212 1 0.00
213 1 0.00
217 149 0.11
218 195 0.14
219 42 0.03
220 251 0.18
221 48 0.04
222 165 0.12
223 117 0.09
224 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (218 bp):
CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTTATA
TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
TATACTTTATACCCAAATCATTT
Found at i:4782 original size:440 final size:439
Alignment explanation
Indices: 3948--5685 Score: 2491
Period size: 440 Copynumber: 4.0 Consensus size: 439
3938 CTTGATATTA
* * *
3948 CTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGATATTGGCATTTTTTCTTA
1 CTCATAATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGAGATTGACA-TTTTT-TTA
4013 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
64 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
* * * * * * *
4078 CCGTCTAAATGAATTTAGTGCCATCTAATAATTAAACAACATGCAGA-ATTTAGTATTCCCAAAG
129 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCA-ATATTCAGTATCCCCAAAC
* * * * * *
4142 TGATATACTTTATACCCAAATCATTTTTCATCATCCCCACATAATCATATGCACCAT-CCCGAAA
193 TGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAA
* * * * *
4206 TTCTTTAGAGATTGACATTTTTTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATA
258 TTCATTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGTTTTAAAAGTGCTTTAATCCATA
* *
4271 TTTTCATCCTAATTTATTGAATAAGCCATGTCTATATGAATTTTGTGCCATCTAATAATTAAACA
323 TTTTCATCCTAATTTATTGAATAAACCACGTCTATATGAATTTTGTGCCATCTAATAATTAAACA
**
4336 AAATGCAAATTTCAGTATCTTCAAACTGATATACTTTATACCCAAATCATTT
388 AAATGCAAATTTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTT
* * *
4388 CTCATAATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
1 CTCATAATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGAGATTGACATTTTTTTATA
* *
4453 TACCTAAAATTCGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* *
4518 GTCCATATAAATTTTGTGACATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
131 GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
*
4583 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAACACCGTACCCAAAATTC
196 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTC
*
4648 ATTAGAGATTGACATTTTTTCTTATATACCCAAAGTTGGTTTTAAAAAGTGCTTTAATCCATATT
261 ATTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGTTTT-AAAAGTGCTTTAATCCATATT
* *
4713 TTCATCCTAATTTATTGAATAAACTATGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAA
325 TTCATCCTAATTTATTGAATAAACCACGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAA
* *
4778 ATGCAAAATTCAGTATCTCCAAACTGATATACTTTATACCCAAATCATTT
390 ATGCAAATTTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTT
* * *
4828 CTCATAATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
1 CTCATAATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGAGATTGACATTTTTTTATA
* * * *
4893 TACCTAAAGTTGGC-TTAAACGTGCTTTAATTCATATTTTCATCATAATTAATTGAATAAACCCC
66 TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* * *
4957 GTCCATATGAATTTTGTGCCATCTAATAAGTAAACAAAATGCAATATTCTGTATCCTCAAACTGA
131 GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
*
5022 TATACTTTATACACAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTC
196 TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTC
* * * *
5087 ATTAGAGATTGA-A--------TA-AAACCCAAAATTGGCTTTAAACGTGCTTTAGTCCATATTT
261 ATTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGTTTTAAAAGTGCTTTAATCCATATTT
* * * *
5142 TCATCCTAATTAATTGAATAAACCCCGTCCATATGAATTTTGTGTCATCTAATAATTAAACAAAA
326 TCATCCTAATTTATTGAATAAACCACGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAA
*
5207 TGC-AATATTCAGTATCCCCAAACTGATATACTTTATACCTAAATCATTT
391 TGCAAAT-TTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTT
* * * * * *
5256 CTCATCATCCCCAAATAGTTATAAGCACCGTACCCAAAATTCATTAGACATTGA-A------TA-
1 CTCATAATCCCCAAATAATCATAAGCACCAT-CCCCAAATTCATTAGAGATTGACATTTTTTTAT
5313 A-ACCCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
65 ATA-CCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
*
5377 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCATTATCCCCAAACT
129 CCGTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACT
* * *
5442 GATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATAATTATAAGCACCGTATCTAAAAT
194 GATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAAT
*
5507 TCATTAGAGATTGACATTTTTTTCTTATATACCCAAAGTTGGTTTTAAAAAGTGCTTTAATCCAT
259 TCATTAGAGATTGACA-TTTTTTCTTATATACCCAAAATTGGTTTT-AAAAGTGCTTTAATCCAT
* * * * * * *
5572 ATTTTCATCCTAATTTATTGAATAAACCCCATATATATTAGTTTAT-TGTCATCTAATAATGAAA
322 ATTTTCATCCTAATTTATTGAATAAACCACGTCTATATGAATTT-TGTGCCATCTAATAATTAAA
* * *
5636 CAAAACGCAAAATTT-ATTATCCCCAAACTGATATACTGTATACCCAAATC
386 CAAAATGC-AAATTTCAGTATCCCCAAACTGATATACTTTATACCCAAATC
5686 TTGTGATGCC
Statistics
Matches: 1180, Mismatches: 96, Indels: 50
0.89 0.07 0.04
Matches are distributed among these distances:
420 1 0.00
421 11 0.01
422 184 0.16
423 1 0.00
427 2 0.00
428 148 0.13
429 34 0.03
430 2 0.00
432 2 0.00
433 15 0.01
434 110 0.09
435 3 0.00
436 3 0.00
437 1 0.00
438 171 0.14
439 236 0.20
440 256 0.22
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (439 bp):
CTCATAATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGAGATTGACATTTTTTTATA
TACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
GTCCATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACTGA
TATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTC
ATTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGTTTTAAAAGTGCTTTAATCCATATTT
TCATCCTAATTTATTGAATAAACCACGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAA
TGCAAATTTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTT
Found at i:12886 original size:2 final size:2
Alignment explanation
Indices: 12879--12912 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12869 AAACTATTTC
12879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12913 CAAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13482 original size:32 final size:34
Alignment explanation
Indices: 13431--13494 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
13421 GATATCAACT
*
13431 ACTTTTTTTACTTGATTTATTATTTTTTTCTCTA
1 ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA
* *
13465 ACTTTTTTTA-TT-TTTTATTCTTTTCTTCTC
1 ACTTTTTTTACTTGATTTATTATTTTCTTCTC
13495 CGTTGATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
33 2 0.07
34 10 0.37
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (34 bp):
ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA
Found at i:13927 original size:28 final size:28
Alignment explanation
Indices: 13876--13929 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13866 TCATGAATTT
* * * *
13876 ATAAGATTATAATCTTTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTATTTGAAAA
13904 ATAAGACTATAATCATTCTATTTGAA
1 ATAAGACTATAATCATTCTATTTGAA
13930 CATGAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
ATAAGACTATAATCATTCTATTTGAAAA
Found at i:14775 original size:13 final size:13
Alignment explanation
Indices: 14733--14775 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
14723 GAAGAAAAGG
14733 AAAAGAAATA-AA
1 AAAAGAAATAGAA
**
14745 AAAAGGAAATAGGG
1 AAAA-GAAATAGAA
14759 AAAAGAAATAGAA
1 AAAAGAAATAGAA
14772 AAAA
1 AAAA
14776 CGTAGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (13 bp):
AAAAGAAATAGAA
Found at i:17095 original size:27 final size:27
Alignment explanation
Indices: 17055--17109 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
17045 TTGATATAAT
17055 TAATTGTTTATGACAATCACACTGCCA
1 TAATTGTTTATGACAATCACACTGCCA
* * *
17082 TAATTGTTTTTGACGATGACACTGCCA
1 TAATTGTTTATGACAATCACACTGCCA
17109 T
1 T
17110 TTCCATGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (27 bp):
TAATTGTTTATGACAATCACACTGCCA
Found at i:20204 original size:1 final size:1
Alignment explanation
Indices: 20198--20232 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
20188 GTCTCTCTTG
20198 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20233 CCTTACCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31615 original size:6 final size:6
Alignment explanation
Indices: 31600--31636 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
31590 CCTCTCATCG
* *
31600 TTTTCA TTTTCG TTTTCA TTTTCA TCTTCA TTTTCA T
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA T
31637 GGTCCAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.65
Consensus pattern (6 bp):
TTTTCA
Found at i:31716 original size:6 final size:6
Alignment explanation
Indices: 31701--31735 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
31691 AGCTGGCATT
* *
31701 TATCCA TATCCG TATCCG TATCCA TATCCG TATCC
1 TATCCG TATCCG TATCCG TATCCG TATCCG TATCC
31736 ACTGGTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (6 bp):
TATCCG
Found at i:31724 original size:18 final size:18
Alignment explanation
Indices: 31701--31735 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31691 AGCTGGCATT
31701 TATCCATATCCGTATCCG
1 TATCCATATCCGTATCCG
31719 TATCCATATCCGTATCC
1 TATCCATATCCGTATCC
31736 ACTGGTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (18 bp):
TATCCATATCCGTATCCG
Done.