Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024479.1 Corchorus olitorius cultivar O-4 contig24512, 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: 14253
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6586 original size:440 final size:437
Alignment explanation
Indices: 5456--6620 Score: 1379
Period size: 440 Copynumber: 2.7 Consensus size: 437
5446 TGGATCTTTG
* * * * * **
5456 TTAATCAGACATCTGGAT-AAAAATTATATGATATTAAATAGACCGTCAATTGAAACCATAAAAT
1 TTAATCGGACATGTGGATCGAAAATTATATGATATTAAATAGACCGGCAATCGAAACCACCAAAT
* * * * *
5520 TTCAGAAACATTTTTTTAAAATTGAAATATAAAAATTAGCTTTTGAA-TCTTTCATGAAAGTTGC
66 TTC-GGAAGATTTTTTT-AAATTGAAACATAAAAATTA-CTTTT-AAGTCATTCATGAAAGTTGT
* * * * * * *
5584 AAATCATGAAATTACCTTTTAATAGACAGCTAAATTATCTTAATTAGACAAATTG---G---AAA
127 AGATCATGAAATTATCTTTTAATAGACACCTGAATCATCTTAATTGGACAAATAGAAAGAAAAAA
* * * *
5643 AAGAA-AAAGCTTAAGCGTAAAATCGAGTAAGATAGGATTTGTAAAGGACTAAGTAGTATAAAGT
192 AAAAATAAAGCTGAAGCGTAAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGT
* * *
5707 AGATAAATATGAGGGTCATTTGATAAATAACCCTAATAAGAAAATGTTTGTTGATGAAGATCTTG
257 AGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGAAGATCTTG
* * *
5772 AAACATAAAAATTCCTTTTTGAACCTTTTATGAACCCGTAGATCAAATTTAGCTTTCAGGTTCTT
322 AAACATAAAAATTCCCTTTTGAACCCTTAATGAACCCGTAGATCAAATTTAGCTTTCAGGTTCTT
* **
5837 AATGAAATTCGTACATCATGCAATAACCTTTTAGTCGACACTTGAATAACT
387 AATGAAAGTCGTACATCATGCAATAACCTTTTAACCGACACTTGAATAACT
* * * *
5888 TCAATCGGACATGTGGATCGAAAATTATATGGTATTAAATAGATCGGCAATCAAAACCACCAAAT
1 TTAATCGGACATGTGGATCGAAAATTATATGATATTAAATAGACCGGCAATCGAAACCACCAAAT
* * * * *
5953 TTGGGAAGCAATTTTTTTTAATTGAAACAT-AAATTTCACTTTTAAGTTATTTATGAAAGTTGTA
66 TTCGGAAG--ATTTTTTTAAATTGAAACATAAAAATT-ACTTTTAAGTCATTCATGAAAGTTGTA
* * * * * * * *
6017 GAACATGAAATTGTCTTTTAATAGGCACATGAATCACCTTAATCAGG-CAAATAAAACAAAAAAT
128 GATCATGAAATTATCTTTTAATAGACACCTGAATCATCTTAAT-TGGACAAATAGAA-AGAAAA-
* * * * * *
6081 AAAAAAATAGAGCTGAAG-ATAAAATCGGTTAAGGTAAAATTAGTAAAGGACTAAGTAGTATAAA
190 AAAAAAATAAAGCTGAAGCGTAAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAA
*
6145 GTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCT
255 GTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGAAGATCT
* * * **
6210 TGAAACATAGAAATTCCCTTTTGAACCCTTAATGAAACTCC-TATATCAGATTTAGCTTTCTTG-
320 TGAAACATAAAAATTCCCTTTTGAACCCTTAATG-AAC-CCGTAGATCAAATTTAGCTTTCAGGT
* *
6273 TCATTCATGAAAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTGAATAACT
383 TC-TTAATGAAAGTCGTACATCATGCAATAACCTTTTAACCGACACTTGAATAACT
*
6329 TTAATCGGACATGTGGATCGAAAATTATATGATATCAAATAGACCGGCAATCGAAACCACCAAAT
1 TTAATCGGACATGTGGATCGAAAATTATATGATATTAAATAGACCGGCAATCGAAACCACCAAAT
** *
6394 TTCGGAAGATTTTTTTGCATTGAAACATAAAAATTGACTTTTAAGTCCTTCATGAAAGTTGTAGA
66 TTCGGAAGATTTTTTTAAATTGAAACATAAAAATT-ACTTTTAAGTCATTCATGAAAGTTGTAGA
6459 TCATGAAATTATCTTTTAATAGACACCTGAATCATCTTAATTGGACAAATAGAAAGAAATAAAAA
130 TCATGAAATTATCTTTTAATAGACACCTGAATCATCTTAATTGGACAAATAGAAAGAAA-AAAAA
* * * * * * *
6524 AAATAAAGATGAAGCGTTAAATCGATTAAGATAGAATTTTTAGAGGATTAAATAGCATAAAGTAG
194 AAATAAAGCTGAAGCGTAAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAG
** * **
6589 AAACGTATG-GGGTGAAATGATAAATAATCCAA
259 AAAAATATGAGGGTCATTTGATAAATAATCCAA
6621 GCAAGAAAGT
Statistics
Matches: 609, Mismatches: 102, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
431 2 0.00
432 80 0.13
433 52 0.09
434 8 0.01
439 61 0.10
440 260 0.43
441 144 0.24
442 2 0.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (437 bp):
TTAATCGGACATGTGGATCGAAAATTATATGATATTAAATAGACCGGCAATCGAAACCACCAAAT
TTCGGAAGATTTTTTTAAATTGAAACATAAAAATTACTTTTAAGTCATTCATGAAAGTTGTAGAT
CATGAAATTATCTTTTAATAGACACCTGAATCATCTTAATTGGACAAATAGAAAGAAAAAAAAAA
ATAAAGCTGAAGCGTAAAATCGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAA
AAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGAAGATCTTGAAAC
ATAAAAATTCCCTTTTGAACCCTTAATGAACCCGTAGATCAAATTTAGCTTTCAGGTTCTTAATG
AAAGTCGTACATCATGCAATAACCTTTTAACCGACACTTGAATAACT
Found at i:6886 original size:17 final size:17
Alignment explanation
Indices: 6864--6901 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
6854 TTTTTTGGTC
6864 ATTTCACTTCTTACTGA
1 ATTTCACTTCTTACTGA
6881 ATTTCACTTCTTACTGA
1 ATTTCACTTCTTACTGA
6898 ATTT
1 ATTT
6902 GTATAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTCACTTCTTACTGA
Done.