Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019202.1 Corchorus olitorius cultivar O-4 contig19235, 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: 7404
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:714 original size:335 final size:332
Alignment explanation
Indices: 46--1390 Score: 1564
Period size: 333 Copynumber: 4.1 Consensus size: 332
36 GCATTTCGGA
* * * * *
46 GCCCCAGCTCAGTTTTGCTTGACTTTAGGCGTCAAAGATCCTTGAAATATCTATCTTTATCTACC
1 GCCCCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGAAATATCCATATTCATCTACC
* * *
111 CAAAT-TTCAGCC-AAAGTAGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGTTT
66 CAAATCTT-AGCCAAAAG--GATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATT
*
174 TAAATATAAATTAATTA-GAAAATAAATTGGAAAAAATGATATTAGAGAGGTTAGAAGCCCTTCA
128 TAAATAGAAATTAATTAGGAAAA-AAATTGGAAAAAATGATATTAGA-AGGTTAGAAGCCCTTCA
* *
238 ATC-TTTTTGCGTTGAATTATATACTTTTTATCG-GAATTTTGGCCAAAAATTGAGGAAAACTTT
191 ATCTTTTTTGCGTTGAATTATATATTTTTTAT-GAGTATTTTGGCCAAAAATTGAGGAAAACTTT
* * * *
301 TTCGGGTCAGTTTTTGCAAAATCTTAG-CTGAAATCGTGTACTAACCATCACGGTTTTTAGCTAA
255 TTCGAGTCAGTTTTTGCAAAATTTTAGTC-GAAATCGTGGACTAACCATCACGGTTTTTAGCGAA
*
365 ACCCGCGTTTCCGG
319 AACCGCGTTTCCGG
* * * * **
379 GCTCCGGTTTAGTTTTGCTTGACTTTTGGCTTC-GGGACTCCTTGAAATATCCATATTCATCTAC
1 GCCCCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGA-TCCTTGAAATATCCATATTCATCTAC
*
443 CCAAATCTTAG-CAACAATGGATTTAAGGATATTTTTTTACGAGCATCAGAATCTTGTTTCGATT
65 CCAAATCTTAGCCAA-AA-GGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATT
* * * * * *
507 T-AATCAGAAATTGATTAGGACAAAAATTTGG-AAAAGTGATATTAGAAGCATTGGAAGCCTTTC
128 TAAAT-AGAAATTAATTAGGA-AAAAAATTGGAAAAAATGATATTAGAAG-GTTAGAAGCCCTTC
* * *
570 AATCTTTTTTGCGTTGAAATCATATATTTTTTATGAGTATTTTGGCCAAAATTTGAGGAAAAATT
190 AATCTTTTTTGCGTTG-AATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAACTT
* * *
635 TTTCG-GATCAGTTTTTGCAAATTTTTAGTCGAAATCGTGGATTAACCATCACGGTTTTAAGCGA
254 TTTCGAG-TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGGACTAACCATCACGGTTTTTAGCGA
699 AAACCGCGTTTCCGG
318 AAACCGCGTTTCCGG
* * * * *
714 GCCCCAGCTCAGTTTTG-TAT-AATTTTCGGCATC-AGGACTTCTTGAAATATCCATATTCATCT
1 GCCCCGGCTCAGTTTTGCT-TGACTTTT-GGCGTCAAAGA-TCCTTGAAATATCCATATTCATCT
* *
776 ACCCAAATC-T---C---AGCATTTAAGGATATGTTTTTACGAGCATCAAAATCTTGTTTCGATT
63 ACCCAAATCTTAGCCAAAAGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATT
834 T-AATCAGAAATTAATTAGGAAAAAAATTGG-AAAAATGATATTAGAAGCGTTAGAAGCCCTTCA
128 TAAAT-AGAAATTAATTAGGAAAAAAATTGGAAAAAATGATATTAGAAG-GTTAGAAGCCCTTCA
* * * * *
897 ATCTTTTTTGCGTTTAATTATATATTTTCTATGAGTATTTTTGCCCAAAATTAAGGAAAACTTTT
191 ATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAACTTTT
* * *
962 TCGAGTCAGTTTTTGCAAAATTTTATTCGAAATCGT-G--TACCCATCACGGTTTTTGGCGAAAA
256 TCGAGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGGACTAACCATCACGGTTTTTAGCGAAAA
* *
1024 ACGCATTT-CGG
321 CCGCGTTTCCGG
* *
1035 AGCCCCGGCTCAGTTTTGCTTAACTTTTGGCGTCAAAGATCCTTGAAATATCTATATTCATCTAC
1 -GCCCCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGAAATATCCATATTCATCTAC
* * * *
1100 CCAAATCTCAGCCAAAGAGGATTTAGGGATATATTTTTACGAGCATCTGAAT-TTAGTTTCGATT
65 CCAAATCTTAGCCAAA-AGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTT-GTTTCGATT
* * * *
1164 TAAATAGAAAATAAATTAGGAAAAAAGTTGGAAAAATTG-TATTAGAAAGGTTAGAAGCCCCTCA
128 TAAATAG-AAATTAATTAGGAAAAAAATTGGAAAAAATGATATTAG-AAGGTTAGAAGCCCTTCA
* ** *
1228 ATCTTTTTTGCGTTGTATTATATATTTTTTATGTTTATTTTGGCCAAAAATTGAGG-AAAGTTTT
191 ATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAACTTTT
* * * * *
1292 TCGAGTCAGTTTTTGTAAAATTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTTGGCGAAAA
256 TCGAGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGGACTAACCATCACGGTTTTTAGCGAAAA
* * *
1357 ACACATTT-CGG
321 CCGCGTTTCCGG
*
1368 AGCCCCGACTCAGTTTTGCTTGA
1 -GCCCCGGCTCAGTTTTGCTTGA
1391 ATTATATGGA
Statistics
Matches: 875, Mismatches: 100, Indels: 74
0.83 0.10 0.07
Matches are distributed among these distances:
321 3 0.00
322 81 0.09
323 9 0.01
324 1 0.00
325 75 0.09
326 54 0.06
327 62 0.07
328 1 0.00
329 2 0.00
330 83 0.09
331 92 0.11
332 18 0.02
333 193 0.22
334 32 0.04
335 168 0.19
336 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (332 bp):
GCCCCGGCTCAGTTTTGCTTGACTTTTGGCGTCAAAGATCCTTGAAATATCCATATTCATCTACC
CAAATCTTAGCCAAAAGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAA
ATAGAAATTAATTAGGAAAAAAATTGGAAAAAATGATATTAGAAGGTTAGAAGCCCTTCAATCTT
TTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAACTTTTTCGAG
TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGGACTAACCATCACGGTTTTTAGCGAAAACCGCG
TTTCCGG
Found at i:1542 original size:2 final size:2
Alignment explanation
Indices: 1535--1566 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1525 GTGATTTTAT
1535 TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1567 GTAGTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4822 original size:2 final size:2
Alignment explanation
Indices: 4815--4839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4805 TAGGGTTTGA
4815 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4840 AACCTGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5415 original size:23 final size:23
Alignment explanation
Indices: 5365--5409 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5355 GTATCCTCAC
**
5365 ATTTTATTGACTTTTTTTTAAAA
1 ATTTTATTGACTTGATTTTAAAA
5388 ATTTTATTGACTTGATTTTAAA
1 ATTTTATTGACTTGATTTTAAA
5410 TCTTTTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTTATTGACTTGATTTTAAAA
Found at i:7281 original size:24 final size:24
Alignment explanation
Indices: 7236--7283 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7226 TTATTTTATT
*
7236 TTCTTCAAACTTCAAAATTTTCAA
1 TTCTTCAAACTTCAAAACTTTCAA
*
7260 TTCTCTCAACCTTC-AAACTTTCAA
1 TTCT-TCAAACTTCAAAACTTTCAA
7284 AACTCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (24 bp):
TTCTTCAAACTTCAAAACTTTCAA
Done.