Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002685.1 Corchorus olitorius cultivar O-4 contig02687, 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: 2902
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Found at i:2195 original size:333 final size:330
Alignment explanation
Indices: 1366--2898 Score: 1487
Period size: 333 Copynumber: 4.6 Consensus size: 330
1356 ATACTTTACA
* * * * * *
1366 TCATCTAATCAAATTTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGCATATGAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTAGATTCAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
1431 TTCAATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACAATATTAAAAGCGTAAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCAAAAGCCC
1496 TCCAATC-TTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAA
131 TCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGG--AAAA
* * * *
1560 ATCTTTCGTGTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTATTAAACAAACTATCACGGTTT
194 ATCTTTCGGGTCATTTTTTACAAAATTTTAGCCGAAATCGTGTAAT-AAC---C-ATCACGGTTT
* * * * * * *
1625 TTAGCTAAAAACA-CGTTCCGGGGATCCGGCTCAATTTTGCATGATTTCTGGCTCCGAGACTACT
254 TTGGCTAAAAA-AGCGTTCCGGGG-CCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCCT
1689 TGAAATATCTATAT
317 TGAAATATCTATAT
* * * * * * *
1703 TTATCTAACCAAATCTCACCCACATTAGATTTAAAGAATTTATTTTTACGAGCATCTGAATTTTG
1 TCATCTAATCAAATCTCAGCTACATTAGATTCAAA-AATTTGTTTTTACGAGCATCTGAATCTTG
* ** *
1768 TTTCGATTTAATTAGAAATTAATTTGGAAAAAATATGAAAAATGATATTAGAAA-TGTCAAAAGC
65 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTA-AAAGCGTCAAAAGC
* *
1832 CC-CTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAATATTTTAGCCAAAAATTGAGGAA
129 CCTC-CAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * * *
1896 ATATCTTTCGGGTCAATGTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTG
192 AAATCTTTCGGGTCATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTG
* *** * * *
1961 GATAAAAAAGCGTTCTATGGCCCTGACTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGAG
257 GCTAAAAAAGCGTTCCGGGGCCC-GACTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
2026 ATATCTATAT
321 ATATCTATAT
* * *
2036 TCATCTAATCAAATCTCAGCTACATTGGATTCAAAAATTTGTTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTAGATTCAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
* ** * * *
2101 TTCGATTTAATTAAAAATTAATACAG-AAAAATATGAAAAACAATATTAAAAGTGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCAAAAGCCC
* * * * *
2165 TCCAATATTTTTGCCGTTAAATTATATATATATTTAGGAGTATTTTATCCAAAAATTGAGGAAAA
131 TCCAATCTTTTTGGCGTTGAATTATATAT-T-TTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * * *
2230 ATTTTTTGAGTCATTTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGG
194 ATCTTTCGGGTCA-TTTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGG
* * * *
2295 CTAAAAACGCGTTTCGGGGCACC-AGCTCAATTTTGCATGATTTTTTTTGGC-TCAGACACTCCT
258 CTAAAAAAGCGTTCCGGGGC-CCGA-CTCAATTTTGCATGA---TTTTTGGCGCCA-AGACTCCT
*
2358 TGAAATAACTATAT
317 TGAAATATCTATAT
* * * ****
2372 TCATCTAATAAAATCTTTGCCAACTTATATTTAAGATTC-TTTTTTTGTTTTTAACGAGTCATCT
1 TCATCTAATCAAATC--T--CAGC-TACA-TT-AGATTCAAAAATTTGTTTTT-ACGAG-CATCT
* * * *
2436 GAATCATATTTCGATTTAATTAGAAATTAATTTAG-AAAAATATGAAAGACGATATTAAAAGCGT
57 GAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGT
* * * * *
2500 CAAAAGCCCTTCAATCTTTTTGGAGTTGGATTATATATTTTTTATGAGTATTAT-GTCAAAAATT
122 CAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATT
* * ** * *
2564 GAGCAAATATCTTTCGGGTCATTTTTTTGAAAATTTTAGTCGAAATCGTGTAATAATCATCACGG
186 GAGGAAAAATCTTTCGGGTCATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG
* * * * *
2629 TTTTTGGCTAAAAACGCGTTCCGGGGCCC-ATTTCAGTTTTGAATGATTTTTGGCGCCGAGACTC
251 TTTTTGGCTAAAAAAGCGTTCCGGGGCCCGA-CTCAATTTTGCATGATTTTTGGCGCCAAGACTC
*
2693 CTTGAAATACCTATAT
315 CTTGAAATATCTATAT
* * * *
2709 TCATCTAATCAAATCCCAGC--CATT-G----------TT-TTTATA--AGTATCTGAATCATGT
1 TCATCTAATCAAATCTCAGCTACATTAGATTCAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * *
2758 TTCGTTTTAATTAAAAATTAA-TTCGGAAAAATAGGAAAAAC-----TAGAAGCGTGAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCAAAAGCCC
* * * *
2817 TTCAATCTTTTTGGTGTTGAATTATATATTTTTATGAGTATTGT-GACTAAAAATTGAGGAAAAA
131 TCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAG-CCAAAAATTGAGGAAAAA
* *
2881 TATTTCAGGTCATTTTTT
195 TCTTTCGGGTCATTTTTT
2899 TGCA
Statistics
Matches: 1005, Mismatches: 160, Indels: 91
0.80 0.13 0.07
Matches are distributed among these distances:
307 16 0.02
308 72 0.07
312 3 0.00
313 44 0.04
314 2 0.00
316 1 0.00
317 4 0.00
318 2 0.00
327 1 0.00
329 2 0.00
330 5 0.00
331 53 0.05
332 92 0.09
333 174 0.17
334 3 0.00
335 2 0.00
336 40 0.04
337 74 0.07
338 131 0.13
339 22 0.02
340 48 0.05
341 67 0.07
342 35 0.03
343 21 0.02
344 90 0.09
345 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (330 bp):
TCATCTAATCAAATCTCAGCTACATTAGATTCAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCAAAAGCCC
TCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAT
CTTTCGGGTCATTTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTA
AAAAAGCGTTCCGGGGCCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
TATAT
Done.