Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009338.1 Corchorus capsularis cultivar CVL-1 contig09359, 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: 26857
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:168 original size:2 final size:2
Alignment explanation
Indices: 161--198 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
151 CTTTAGTACA
161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
199 AAAAAGGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3538 original size:27 final size:27
Alignment explanation
Indices: 3507--3570 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 27
3497 ATTTCTGGAA
3507 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAGGGAAAGGGACAATTAAAAAGG
3534 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAGGGAAAGGGACAATTAAAAAGG
3561 AACAGAGGGA
1 AACA-AGGGA
3571 GTATCATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.55, C:0.08, G:0.31, T:0.06
Consensus pattern (27 bp):
AACAAGGGAAAGGGACAATTAAAAAGG
Found at i:4842 original size:444 final size:447
Alignment explanation
Indices: 4076--4951 Score: 1174
Period size: 444 Copynumber: 2.0 Consensus size: 447
4066 GCGTTAAATC
*
4076 GATTAAGATAGAATTTGTAAAGGACTAAGTAGCGTAAAATATAAAATAGAAAAGTATGAGGGTCA
1 GATTAAGATAGAATTTGTAAAGGACTAAG-A--GT-AAATATAAAATAGAAAAATATGAGGGTCA
* * *
4141 TTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGGATATCTTGAAACATAAAAATTCTCTT
62 TTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCTCAT
* * * *
4206 TTGAACCCTTCATGAAACTCGTAAATCAAATTAACTTTTGGGTTCTTCATGAAAGTCGTAAATCA
127 TTGAACCCTTCATGAAACTCGTAAATCAAATTAACTTTCGGATCCTTCATGAAAGTCCTAAATCA
* * * ** *
4271 TTCAATAACCTTTTAACCGACACTTGAATAACTTTAATCTGACATGTGGATCGAAAATTATATGG
192 TGCAATAACCTTTTAACCGACACTTCAATAACTTTAATCGGACATGTGGATAAAAAATTATATGA
* * * * * *
4336 TATTAAATAGACCAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTTGAATTAAAACATAA
257 TATTAAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCATATTTTTAGAATCAAAACATAA
* * *
4401 AAATTTG-CTTTTGAGTCCTCCATCAAAATTGTAGATCATGAAATGACATTTTAATAGATACATG
322 AAA-TTGACTTTTGAGTCCTCCATCAAAATGGTAGATCATGAAATGACATTTTAATAGACACATA
4465 AATCAACTTAATCGGACAAATAGAACAAAGAA-TA-AAAAATAAATCTTAAACGCTAGATGTTA
386 AATCAACTTAATCGGACAAATAGAA-AAA-AATTACAAAAATAAATCTTAAACGCTAGATGTTA
* * *
4527 GATTAAGATAGAATTTGTAAAGGACTAA-A-T-AGTATAAAGTAGAAAAATATGAGGGTTATTTG
1 GATTAAGATAGAATTTGTAAAGGACTAAGAGTAAATATAAAATAGAAAAATATGAGGGTCATTTG
* * *
4589 ATAAATAA-TCAAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAATTCTCATTTG
66 ATAAATAATTC-AAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCTCATTTG
* *
4653 AACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGATCCTTCATGAAAGTCCTAAATCATG
130 AACCCTTCATGAAACTCGTAAATCAAA-TTAACTTTCGGATCCTTCATGAAAGTCCTAAATCATG
* *
4718 CAATAACCTTTTAACCGACATTTCAATAACTTTAATCGGATATGTGGATAAAAAATTATATGATA
194 CAATAACCTTTTAACCGACACTTCAATAACTTTAATCGGACATGTGGATAAAAAATTATATGATA
** ** * * *
4783 TTAAATTTACCGGCAATTAAAACCACAAAATTTCGGAAGCA-ATTTTTAGAATCAAAACATTAAA
259 TTAAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCATATTTTTAGAATCAAAACATAAAA
* * * * * * * *
4847 ATTGACTTTTGAGTTCTGCATGAGAATGGTAGATTATGAAATTACCTTTTAATAGACACTTAAAT
324 ATTGACTTTTGAGTCCTCCATCAAAATGGTAGATCATGAAATGACATTTTAATAGACACATAAAT
*
4912 CACCTTAATCGGACAAATAGAAAAAAATTACAAAAATAAA
389 CAACTTAATCGGACAAATAGAAAAAAATTACAAAAATAAA
4952 AGGCAACGCG
Statistics
Matches: 371, Mismatches: 49, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
442 2 0.01
443 10 0.03
444 208 0.56
445 121 0.33
446 1 0.00
449 1 0.00
451 28 0.08
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (447 bp):
GATTAAGATAGAATTTGTAAAGGACTAAGAGTAAATATAAAATAGAAAAATATGAGGGTCATTTG
ATAAATAATTCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCTCATTTGA
ACCCTTCATGAAACTCGTAAATCAAATTAACTTTCGGATCCTTCATGAAAGTCCTAAATCATGCA
ATAACCTTTTAACCGACACTTCAATAACTTTAATCGGACATGTGGATAAAAAATTATATGATATT
AAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCATATTTTTAGAATCAAAACATAAAAAT
TGACTTTTGAGTCCTCCATCAAAATGGTAGATCATGAAATGACATTTTAATAGACACATAAATCA
ACTTAATCGGACAAATAGAAAAAAATTACAAAAATAAATCTTAAACGCTAGATGTTA
Found at i:19644 original size:23 final size:25
Alignment explanation
Indices: 19617--19669 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19607 CTGACTTGGG
*
19617 TTTTATTTCA-TTAAT-TTTCAGTT
1 TTTTATTTCATTTAATATTTCAGAT
*
19640 TTTTATTTCATTTTATATTTCAGAT
1 TTTTATTTCATTTAATATTTCAGAT
19665 TTTTA
1 TTTTA
19670 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 10 0.38
24 4 0.15
25 12 0.46
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTTATTTCATTTAATATTTCAGAT
Found at i:22311 original size:104 final size:104
Alignment explanation
Indices: 22131--22324 Score: 343
Period size: 104 Copynumber: 1.9 Consensus size: 104
22121 ATGTCAGAAA
*
22131 AGTATTAGTCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
1 AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
22196 CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
66 CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
* * * *
22235 AGTATTAGTTGATGAAAACTCCAGTTTTAATTTCAGTATTAATCGACTAAAGCTCCAAGTCTTCA
1 AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
22300 CTTTGAAAAAGTGGCAGTGTTGACA
66 CTTTGAAAAAGTGGCAGTGTTGACA
22325 ACCACACGAC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 85 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (104 bp):
AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
Found at i:26697 original size:11 final size:11
Alignment explanation
Indices: 26661--26699 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
26651 TAACATATAC
26661 CAATTTTGTTA
1 CAATTTTGTTA
* *
26672 CAAGATTTGTAA
1 CAA-TTTTGTTA
26684 CAATTTTGTTA
1 CAATTTTGTTA
26695 CAATT
1 CAATT
26700 CATTAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (11 bp):
CAATTTTGTTA
Done.