Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009602.1 Corchorus olitorius cultivar O-4 contig09634, 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: 10064
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:5309 original size:2 final size:2
Alignment explanation
Indices: 5302--5332 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5292 TTTATTGCAA
5302 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5333 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5337 original size:2 final size:2
Alignment explanation
Indices: 5332--5395 Score: 57
Period size: 2 Copynumber: 33.5 Consensus size: 2
5322 TCTCTCTCTC
*
5332 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA T- TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5370 AA TA -A GTGA TA TA TA TA TA TA TA TA T
1 TA TA TA -T-A TA TA TA TA TA TA TA TA T
5396 TATTAAGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
1 5 0.09
2 46 0.87
3 1 0.02
4 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5427 original size:39 final size:35
Alignment explanation
Indices: 5343--5412 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
5333 ATATATATAT
5343 ATATATATATATATTATATTATTAAGAAATAAGTG
1 ATATATATATATATTATATTATTAAGAAATAAGTG
5378 ATATATATATATA-TATATTATTAAGAAATAAGTG
1 ATATATATATATATTATATTATTAAGAAATAAGTG
5412 A
1 A
5413 ATTGATAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 22 0.63
35 13 0.37
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (35 bp):
ATATATATATATATTATATTATTAAGAAATAAGTG
Found at i:9918 original size:322 final size:322
Alignment explanation
Indices: 9334--10062 Score: 750
Period size: 322 Copynumber: 2.3 Consensus size: 322
9324 TTAGTATACA
* * * * * * **
9334 ATTTCGGCT-AAATTTTACAAAAATTTAC-CTGAAAGAATTTTCCTAAATTTTTGGCATTGATAC
1 ATTTCGGATAAAATTTTGCAAAAATTGACAC-GAAAGAATTTACCTCAATTTTTGCCA-CAATAC
* * * * * * *
9397 ACATAAAAA-A-ATAATTTAACGACAAAAAGATTGAAAGGATTTTCGCGCTTCTAATATCGGTTT
64 TCATAAAAATATATAACTCAATGCCAAAAAGATTGAAAGGATTCTCACGCTTCTAATATCGGTTT
* * *
9460 TTTAATTTTTCCGAATTAATTTTTAATTAAATCGAAACATGATTCAGATACTCGTAAAAAAAAAA
129 TTTAATTTTTCAGAATTAATTTCTAATTAAATCGAAACATAATTCAGATA-TCGTAAAAAAAAAA
* * *
9525 ATCCTTAAATCCAATGTGGGTGAAATTTGGTTAGATGGATATATATTTCAATGATACTTGGCGCA
193 ATCCTTAAATCCAATGAGGCTGAAATTTGGTTAGATGAATATATATTTCAATGATACTTGGCGCA
* * * *
9590 AAAAATCATACAAAA-CAGAGCCGGGGCCCTAGAACGCATTTTTAGTC-AAACTGTG-A-TACAC
258 AAAAATCATACAAAAGCA-AGCCGGGGCCCCAGAACGCATTTTTAGCCAAAACCGTGAAGTAAAC
9651 G
322 G
* *
9652 ATTTCGGGTAAAATTTTGCAAAAATTGACACGAAA-CATTTCACCTCAATTTTTGGCCACAATAC
1 ATTTCGGATAAAATTTTGCAAAAATTGACACGAAAGAATTT-ACCTCAATTTTT-GCCACAATAC
* *
9716 TCATAAAAAATATATAACTCAATGCCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATCTC-GTT
64 TCAT-AAAAATATATAACTCAATGCCAAAAAGATTGAAAGGATTCTCACGCTTCTAATATCGGTT
* * * * * *
9780 TTTCCTATTTTTTTAGAATTGATTTCTAATTAAATTGAAACCA-AATTGAGAT-TC-TAATAAAA
128 TTT--TAATTTTTCAGAATTAATTTCTAATTAAATCGAAA-CATAATTCAGATATCGTAAAAAAA
* * ** *
9842 CAAATCCTTCAATCCAATGAGGCT-AAGATTTTTTTTAGATGAATATAGATATTTCAATGGT-CT
190 AAAATCCTTAAATCCAATGAGGCTGAA-A-TTTGGTTAGATGAATAT--ATATTTCAATGATACT
* ** * * *
9905 TGGCGCCAAAAATCATGGAAAAGTAAGCTGGGGCCCCGGAACGCATTTTTAGCCAAAAACCGTGA
251 TGGCGCAAAAAATCATACAAAAGCAAGCCGGGGCCCCAGAACGCATTTTTAGCC-AAAACCGTGA
9970 TAGTAAACG
315 -AGTAAACG
* * * *
9979 ATTTCGGATAAAATTTTGCAAAATTTGACCCGAAAGAATTTTCCTCAATTTTTGCCACGATACTC
1 ATTTCGGATAAAATTTTGCAAAAATTGACACGAAAGAATTTACCTCAATTTTTGCCACAATACTC
*
10044 ATAAAAATATATAATTCAA
66 ATAAAAATATATAACTCAA
10063 CA
Statistics
Matches: 338, Mismatches: 52, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
318 12 0.04
319 40 0.12
320 37 0.11
321 23 0.07
322 86 0.25
323 49 0.14
324 9 0.03
325 16 0.05
326 14 0.04
327 48 0.14
328 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (322 bp):
ATTTCGGATAAAATTTTGCAAAAATTGACACGAAAGAATTTACCTCAATTTTTGCCACAATACTC
ATAAAAATATATAACTCAATGCCAAAAAGATTGAAAGGATTCTCACGCTTCTAATATCGGTTTTT
TAATTTTTCAGAATTAATTTCTAATTAAATCGAAACATAATTCAGATATCGTAAAAAAAAAAATC
CTTAAATCCAATGAGGCTGAAATTTGGTTAGATGAATATATATTTCAATGATACTTGGCGCAAAA
AATCATACAAAAGCAAGCCGGGGCCCCAGAACGCATTTTTAGCCAAAACCGTGAAGTAAACG
Done.