Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011916.1 Corchorus olitorius cultivar O-4 contig11949, 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: 2128
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:788 original size:330 final size:332
Alignment explanation
Indices: 4--2127 Score: 2991
Period size: 330 Copynumber: 6.4 Consensus size: 332
1 TCT
* * * *
4 GATTTCCATTTAATTAGATATTAATTTGGAAAAGATTGTAAAAAACGATAATTAGAAAGCGAGAA
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAG-GAAAAACGAT-ATTAG-AAGCGAGAA
*
69 AAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCGAAAATTGAG
63 AAGCCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAG
* * * * *
134 AAAAAATTTGTCGGGTCAGTTTTCACAGAATTTGAGCCGAATTCATGTACTAACCATCACGGTTT
128 AAAAAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGG-TT
* * * *
199 TTA-GCTAAAAACGCGTTCCGGGGCCCCGGCTCTGTTTTTCATGATTTTTGGTGCCTAGACTCAT
192 TTAGGCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCAT
* *
263 TGCAATATCTATA-ATCTTCTAAACAAATCTT-AGCCACATTGGATTTATAGATTTGTTTTTATG
257 TGCAATATCTATATA-CTTCTAAACAAAT-TTCAGCCAAATTGGATTTATAGATTTGTTTTTACG
326 AGAATCAAAATCC
320 AGAATCAAAATCC
*
339 GATTTCCATTTAATTAGATATTAATTCAGAAAAAATAGGAAAAACGATATTAGACA-CGAGAAAA
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGA-AGCGAGAAAA
* * * * *
403 TCCTTTCCATCATTTTGGCGTTGAATTATATAATTTT-AATGACTATTGTGGCCAAAAATTGAGA
65 GCCCTTCAATCATTTTGGCGTTGAATTATAT-ATTTTCTATGAGTATTGTGGCCAAAAATTGAGA
* *
467 AAAAGTTTGTCGGGCCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTT
129 AAAAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTT
* * * *
532 AGGCTAAAAACGTGTTCCGAGGTCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGTCTCATTG
194 AGGCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTG
597 C-ATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTAT-GATTTGTTTTTACGAGAA
259 CAATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTATAGATTTGTTTTTACGAGAA
*
660 TCTAAATCC
324 TCAAAATCC
* * * * * *
669 GATTTCCATTTAATTAGATATTAATTTGGAAAAGATTGTAAAAATGAAATTAGAAGCGAGAAAAG
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGAGAAAAG
734 CCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAAA
66 CCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAAA
799 AAGTTTGTCGGGTCAGTTTTCGCAGAAA-TTTAGCCG-AATGCATGTACTAACCATCACGGTTTT
131 AAGTTTGTCGGGTCAGTTTTCGCA-AAATTTTAGCCGAAAT-CATGTACTAACCATCACGGTTTT
* * *
862 AGGCTAAAAACGCGTTTCGGGGTCCCGTCTCTATTTTGCATGATTTTTGGTGCCTAGACTCATTG
194 AGGCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTG
* * *
927 C-ATATCTATATACTTCTAAACAAATCTCAGCCACATTGGATTTAT-GTATTTGTTTTTACGATA
259 CAATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTATAG-ATTTGTTTTTACGAGA
990 ATCAAAATCC
323 ATCAAAATCC
* *
1000 GATTTCCA-TTATTTAGTTATTAATTCGGAAAAAATAGGAAAAACGATATTAGACA-CGAGAAAA
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGA-AGCGAGAAAA
* * * * **
1063 GACCTTCAATCATTTTGGCTTTGAATAATATATTTTCAATGAGTATTGTGGCTGAAAATTGAGAA
65 GCCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAA
* * ** * * *
1128 AAA-ATTGTCGGGTCAATTTTCATAGAA-TTTAGCCGAATTCATGTACTAACCATCACGGTTTTT
130 AAAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTA
1191 GGCTAAAAACGCGTTCCGGGGCCCCAG-CTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTG
195 GGCTAAAAACGCGTTCCGGGGCCCC-GTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTG
* *
1255 CAATATCTATA-ATCTTCTAAACAAATCTT-AGCCACATAGGATTTATAGATTTGTTTTTACGAG
259 CAATATCTATATA-CTTCTAAACAAAT-TTCAGCCAAATTGGATTTATAGATTTGTTTTTACGAG
1318 AATCAAAATCC
322 AATCAAAATCC
* * * *
1329 GATATCCATTTAATAAGATATTAATTCGG-AAAAATAGGAAAAACGATATTAGAAGCGTGAAAAT
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGAGAAAAG
* * *
1393 CCTTTCCATCATTTTGGCGTTGAATTATATAATTTTC-ATGACTATTGTGGCCAAAAATTGAGAA
66 CCCTTCAATCATTTTGGCGTTGAATTATAT-ATTTTCTATGAGTATTGTGGCCAAAAATTGAGAA
* *
1457 AAAGTTTGTCGGGCCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTA
130 AAAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTA
* * * * * * *
1522 GGGTAAAAACGCATTCTGGGGTCCCATCTCTATTTTGCATGATTTTTGGTGCCCATACTCACTGC
195 GGCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTGC
*
1587 AATATCTATATACTTCTAAACAAATTTCAGCCAAAATGGATTTAT-GATTTGTTTTTACGAGAAT
260 AATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTATAGATTTGTTTTTACGAGAAT
*
1651 CTAAATCC
325 CAAAATCC
* *
1659 GATTTCCATTTTATTAGTTATTAATTCGGAAAAAATAGGAAAAACGATATTAGACA-CGAGAAAA
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGA-AGCGAGAAAA
* **
1723 GCCCTTCAATCATTTTGGCTTTGAATTATATATTTTCTATGAGTATTGTGGCTGAAAATTGAGAA
65 GCCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAA
* * * *
1788 AAAATTTGTCGGGTCTGTTTTCACAGAATTTTAGCCG-AATGCATGTACTAACCATCACGGTTTT
130 AAAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAAT-CATGTACTAACCATCACGGTTTT
* * * *
1852 TGGCTAAAAACGCGTTCCAGGGCCCCGGCTCTGTTTTGCATGATTTTTTGG-GCCCAGACTCATT
194 AGGCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGA-TTTTTGGTGCCCAGACTCATT
* * * *
1916 GCAATATCTACATACTTCTAAACAAATCTCAGCCAAATTGGATTTATGGATTTGTTTTTATGAGA
258 GCAATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTATAGATTTGTTTTTACGAGA
**
1981 ATCTGAATCC
323 ATCAAAATCC
* * * * * *
1991 GATTTCCATTTTATTAGATATTAATTTGGAAAAGATTGTAAAAACGATATTAGAAGCGAGAAAAT
1 GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGAGAAAAG
2056 CCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAAA
66 CCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAG-AA
2121 AAAGTTT
130 AAAGTTT
2128 T
Statistics
Matches: 1599, Mismatches: 157, Indels: 68
0.88 0.09 0.04
Matches are distributed among these distances:
328 95 0.06
329 182 0.11
330 505 0.32
331 433 0.27
332 322 0.20
333 19 0.01
334 9 0.01
335 34 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (332 bp):
GATTTCCATTTAATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGAGAAAAG
CCCTTCAATCATTTTGGCGTTGAATTATATATTTTCTATGAGTATTGTGGCCAAAAATTGAGAAA
AAGTTTGTCGGGTCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTAG
GCTAAAAACGCGTTCCGGGGCCCCGTCTCTATTTTGCATGATTTTTGGTGCCCAGACTCATTGCA
ATATCTATATACTTCTAAACAAATTTCAGCCAAATTGGATTTATAGATTTGTTTTTACGAGAATC
AAAATCC
Done.