Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005903.1 Corchorus capsularis cultivar CVL-1 contig05921, 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: 1894
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:686 original size:332 final size:330
Alignment explanation
Indices: 21--1894 Score: 2073
Period size: 332 Copynumber: 5.6 Consensus size: 330
11 TCTTACATTT
* * * *
21 GATTTAAGGATTTGGTTTTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTTGG-
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCGGA
* * * * * * *
85 AAAATAGGAAAACCGATATTACAAGCGTGAATAGCCTTTCAATATTTTAGGTGTTGAATTATATA
66 AAAATAGAAAAACCAATATTAGAAGCGTGAATAGCCCTTCAATCTTTTAGGCGTTGAAATATATA
* * * *
150 TTTTCTATGATTATCGTGGCCAAAAATTGAGGAAAATTATTTCCAGTCAATTTTTACAAAATTTT
131 TTTTCTATGAATATCGTGGCCAAAAATTGAGGAAAATT-TCTCGAGTCAATTTTGACAAAATTTT
* * *
215 AGCCGAAATCGTG---T-ACCATTACGGTTTTTTGGCTACAAACGCGTTCCGGGGCCCCGACCCA
195 AGCCGAAATCGTGCACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCA
* * * * *
276 GTTTCGCATGATTTTT-GACGTCAAGACTCATTGAAATTTCTATATTTATCTAACGAAATCTCTG
259 GTTTTGCATGATTTTTAG-CGCCAAGACTCATTGAAATATCTATATCTATCTAACGAAATCTCTC
340 CCAAATTG
323 CCAAATTG
* * * **
348 GATTTAAGGATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGA
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCGGA
* *
413 AAAATAGAAAAAATCAATATTAGAAGCGTGAGA-AGCCCTTCAATCTTTTTGGCGTTGAAATATA
66 AAAATAG-AAAAACCAATATTAGAAGCGTGA-ATAGCCCTTCAATCTTTTAGGCGTTGAAATATA
* * ** * *
477 TATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAATTTCTCG-GATTAATTTTGGCAAAAT
129 TATTTTCTATGAATATCGTGGCCAAAAATTGAGGA-AAATTTCTCGAG-TCAATTTTGACAAAAT
* * * *
541 TTTAGCTGAAATCGTGCACTAACCATCACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACT
192 TTTAGCCGAAATCGTGCACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACT
* * * * *
606 CAGTTTTGCACGATTTTTAGCGCCTAGTCTCATTGAAATATCTATATCCATCTAAAC-AAATCTT
257 CAGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTATATCTATCT-AACGAAATCTC
* *
670 TCCCACATTT
321 TCCCAAATTG
* *
680 GATTTAAGGATTTGTTTTTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGG-
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCGGA
* * * * *
744 AAAATAGGAAAACCGATATTAGAAGCGTGAATAGCCTTTCAATCTTTTAGGTGTTGAATTATATA
66 AAAATAGAAAAACCAATATTAGAAGCGTGAATAGCCCTTCAATCTTTTAGGCGTTGAAATATATA
* * *
809 TTTTCTATGATTATCGTGGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTTACAAAATTTT
131 TTTTCTATGAATATCGTGGCCAAAAATTGAGGAAAATT-TCTCGAGTCAATTTTGACAAAATTTT
*
874 AGCCGAAATCGTGTACTAACCATCACGGTGTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCA
195 AGCCGAAATCGTGCACTAACCATCACGGT-TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCA
* * * * * * *
939 GTTTCGCATGATTTTTGGCGTCAAGACTCATTGAAATCTCTCTATTTATCTAACGAAATCTCTGC
259 GTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTATATCTATCTAACGAAATCTCTCC
*
1004 AAAATTG
324 CAAATTG
* * * * *
1011 GATTTAAGGATTAGTTTTTACGATCATCTCCATC-TAGTTTCGATTTAATTAGAAATTATTTCGG
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCAT-GTTTCGATTTAATTAGAAATTAATTCGG
* * * *
1075 AAAAATAGAAAAAAAAAAAACACTATTAGAAGCGTGAGA-AGCCCTTCAATTTTTTTGGCGTTGA
65 AAAAATAG------AAAAACCAATATTAGAAGCGTGA-ATAGCCCTTCAATCTTTTAGGCGTTGA
* * ** * *
1139 AATATATATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAATTTCTCG-GATTAATTTTGG
123 AATATATATTTTCTATGAATATCGTGGCCAAAAATTGAGGA-AAATTTCTCGAG-TCAATTTTGA
* * * * * * * * * *
1203 CAAAATTTCATCTGAAATTGTGCACTAATCATCACTGTTTTTGACTAAAAAGGCGTTCTGGAGCC
186 CAAAATTTTAGCCGAAATCGTGCACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC
* * * *
1268 CCGACTTCAGTTTTGCACGATTTTTAGCGCCTAGTCTCATTGAAATATCTATATCCATCTAAAC-
251 CCGAC-TCAGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTATATCTATCT-AACG
* * *
1332 AAATCTTTCCCACATTT
314 AAATCTCTCCCAAATTG
* * *
1349 GATTTAAGGATTTATTTTTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGA
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCGGA
* * * * *
1414 AAAATAGGAAAACCGATATTAGAAGCGTGAATAGCCTTTCAATCTTTTAGGTGTTGAATTATATA
66 AAAATAGAAAAACCAATATTAGAAGCGTGAATAGCCCTTCAATCTTTTAGGCGTTGAAATATATA
* * *
1479 TTTTCTATGATTATCGTGGCCAAAAATTGAGGAAAATTATTTTCGAGTCAATTTTTACAAAATTT
131 TTTTCTATGAATATCGTGGCCAAAAATTGAGGAAAA-T-TTCTCGAGTCAATTTTGACAAAATTT
* *
1544 TAGCCGAAATCGTGTACAAACCATCACGGTTTTTTTGGCTAAAAAACGCGTTCCGGGGCCCCGAC
194 TAGCCGAAATCGTGCACTAACCATCACGG--TTTTTGGCT-AAAAACGCGTTCCGGGGCCCCGAC
* * *
1609 CCAGTTTTGCATGATTTTTGGCGCCAAGACTCGTTGAAAT-TACTATA-CTTATCTAACGAAATC
256 TCAGTTTTGCATGATTTTTAGCGCCAAGACTCATTGAAATAT-CTATATC-TATCTAACGAAATC
**
1672 TCAACCAAATTG
319 TCTCCCAAATTG
* * * * ** * *
1684 GATATAAGGA-TTG-TTTTACGATCATCTCCATCCGGTTTTGATTTAATTAGAAATTAATTCGAA
1 GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCG-G
* **
1747 AAAAATAGAAAATAACAATATTAGAAGCGTGAGA-AGCCCTTCAATCTTTTTTGCGTTGAAATAT
65 AAAAATAGAAAA-ACCAATATTAGAAGCGTGA-ATAGCCCTTCAATCTTTTAGGCGTTGAAATAT
* * * ** * *
1811 ATATTTTTTACGAATATGGTGGCCGGACATTGAGGAGAAATTTCTCG-GAT-AA-TTTGGCAAAA
128 ATATTTTCTATGAATATCGTGGCCAAAAATTGAGGA-AAATTTCTCGAG-TCAATTTTGACAAAA
*
1873 TTTTAGCTGAAATCGTGCACTA
191 TTTTAGCCGAAATCGTGCACTA
Statistics
Matches: 1279, Mismatches: 223, Indels: 85
0.81 0.14 0.05
Matches are distributed among these distances:
327 55 0.04
328 8 0.01
329 112 0.09
330 134 0.10
331 152 0.12
332 253 0.20
333 97 0.08
334 25 0.02
335 144 0.11
336 25 0.02
337 29 0.02
338 235 0.18
339 10 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (330 bp):
GATTTAAGGATTTGTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGAAATTAATTCGGA
AAAATAGAAAAACCAATATTAGAAGCGTGAATAGCCCTTCAATCTTTTAGGCGTTGAAATATATA
TTTTCTATGAATATCGTGGCCAAAAATTGAGGAAAATTTCTCGAGTCAATTTTGACAAAATTTTA
GCCGAAATCGTGCACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGT
TTTGCATGATTTTTAGCGCCAAGACTCATTGAAATATCTATATCTATCTAACGAAATCTCTCCCA
AATTG
Done.