Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006553.1 Corchorus capsularis cultivar CVL-1 contig06574, 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: 1713
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Found at i:652 original size:335 final size:331
Alignment explanation
Indices: 1--1713 Score: 2121
Period size: 335 Copynumber: 5.1 Consensus size: 331
* * * *
1 TCGGCTCTGTTTTCCATGATTTTTTGTGCCAATACTCATTAAAATATCTATATTCATCTAACTAA
1 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACTAA
* * * * * *
66 ATCTCAGGCAAAATACCTTTAAAGATTTGTTTTTACGACCATCTCAATCCGGCTTCGATTTAATT
66 ATCTCAGCCACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATT
* * * *
131 AAAAATTAATTTGGAAAAAATAGGAAAAACGATATTAAAAATTTGAGAAGCCCTTCAATTTTTTT
131 AGAAATTAATTTGAAAAAAATAGGAAAAACGATATTAGAAATGTGAGAAGCCCTTCAATTTTTTT
* *
196 GGCGTTGAGTTACATATTTTTTTCGAGTATTGTGGCAAAAAATTGAGGGATAATTTTTCGGGTCA
196 GGCGTTGAGTTATATATTTTTTT-GAGTATTGTGGCCAAAAATTGAGGGA-AATTTTTCGGGTCA
*
261 ATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGACTAAAAACGCGTT
259 ATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTT
326 CTAGGGCC
324 CTAGGGCC
*
334 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGAGTCATTGAAATATCTATATTCATCTAACTAA
1 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACTAA
* *
399 ATCTCAGCCACAAGGCCTTTAAGGATTTGTTTTTACGAGTATCTCAATCCGGTTTCGATTTAATT
66 ATCTCAGCCACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATT
* * *
464 AGAAATTAATTCTGAAAAAAATAAGAAAAACAATATTAGAAATGTAGAGAAACCCTTCAATTTTT
131 AGAAATTAATT-TGAAAAAAATAGGAAAAACGATATTAGAAATGT-GAGAAGCCCTTCAATTTTT
* *
529 TTGGCATTGAGTTATATACTTTTTTTGAGTATTGTGGCAAAAAATTGAGGGAAATTTTTTCGGGT
194 TTGGCGTTGAGTTATATA-TTTTTTTGAGTATTGTGGCCAAAAATTGAGGGAAA-TTTTTCGGGT
*
594 CAATTTTTTGCAAAATTTTAGCCGAAATCGGGTACTAACCATCACGGTTTTTGACTAAAAACGCG
257 CAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCG
*
659 TTCCAGGGCC
322 TTCTAGGGCC
* * * * * *
669 CCGGCTCTGTTTTGCATGATTTTTTGTGTCAAGACTCATTGAAAAATATATATTCATCGAACTAA
1 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACTAA
*
734 ATCTCAGCCAAAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATT
66 ATCTCAGCCACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATT
* *
799 AGAAATTAATTTGGAAAAAAAAAAGAAAAAGCGATATTAGAAATGTGAGAAGCCCTTCAAATTTT
131 AGAAATTAATTT-GAAAAAAATAGGAAAAA-CGATATTAGAAATGTGAGAAGCCCTTC-AATTTT
* * *
864 TTTTGCGTTGAGTTATACATTTTTTTCGAGTATTGTGGCCAAAAATTTAGGGGAAATTTTTCGGG
193 TTTGGCGTTGAGTTATATATTTTTTT-GAGTATTGTGGCCAAAAATTGA-GGGAAATTTTTCGGG
* * * *
929 TTAATTTTTTTGCAAAATGTTAGCCGAAATCATGTACGT---TATCACGGTTTTTGACTAAAAAC
256 TCAA-TTTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGACTAAAAAC
*
991 ACGTT-TCAGGGTCC
319 GCGTTCT-AGGG-CC
* * * *
1005 T-TGCTCTGTTTTACATGATTTTTTGCGCCAAGACTCATTGAAATA-CATATATTCATCTACCGA
1 TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATC-TATATTCATCTAACTA
* * * *
1068 AATCTCAGCAACATTGCCTTTAAGGTTTTGATTTTACGAGCATCTCAATCCGGTTTCGATTTAAT
65 AATCTCAGCCACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAAT
* *
1133 TAGAAATTAATTTGGAAAAAATAGGAAAAACGGTATTAGAAATGTGAGAAGCCCTTCAATTTTTT
130 TAGAAATTAATTTGAAAAAAATAGGAAAAACGATATTAGAAATGTGAGAAGCCCTTCAA-TTTTT
* * * * * **
1198 TTTGCGTTGAGTTATAT-TATTATT-ATTATTATTACCAAAAATTGAGGGGAAATTTTT-GGGTC
194 TTGGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCAAAAATTGA-GGGAAATTTTTCGGGTC
* * * *
1260 AGTTTTTTGAAAAATTTTAGCTGAAATCGTGTAATAACCATCACGGTTTTTGACTAAAAACGCGT
258 AATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGT
1325 TAC-AGGG-C
323 T-CTAGGGCC
* * * * *
1333 TCCGGCTCTGTTTTGCATGATTTTTGGCACCAAGTCTCATTGAAATATCTATATCCATCTAACCA
1 T-CGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACTA
* * ** * **
1398 AAACTCA-CTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAA
65 AATCTCAGC-CACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAA
* * * ** * *
1462 TTATAAAGTAATTCAGAAAAAAATAGGAAAATA-GATATTAGAGGTGTGAAAAGCCTTTC-ATTA
129 TTAGAAATTAATT-TGAAAAAAATAGGAAAA-ACGATATTAGAAATGTGAGAAGCCCTTCAATT-
* * * * ** * * *
1525 TTTTTGGTGTTGAATTATATTTTTTTTTTTAGT-TCCATGGCCAAAAATTTAGGAAAAAATCTTT
191 TTTTTGGCGTTGAGTTATA-TATTTTTTTGAGTAT-TGTGGCCAAAAATTGAGG--GAAATTTTT
* * *
1589 CGGGT-AATTTTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAA
252 CGGGTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAA
1653 ACGCGTT-TCAGGGTCC
317 ACGCGTTCT-AGGG-CC
* * *
1669 CCGGCTCAGTTTTGCATGATTTTTTG-GCACTAAGACTGATTGAAA
1 TCGGCTCTGTTTTGCATGATTTTTTGCGC-C-AAGACTCATTGAAA
Statistics
Matches: 1204, Mismatches: 136, Indels: 77
0.85 0.10 0.05
Matches are distributed among these distances:
327 1 0.00
328 29 0.02
329 8 0.01
330 191 0.16
331 38 0.03
332 16 0.01
333 188 0.16
334 117 0.10
335 490 0.41
336 90 0.07
337 35 0.03
338 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (331 bp):
TCGGCTCTGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTAACTAA
ATCTCAGCCACAATGCCTTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATT
AGAAATTAATTTGAAAAAAATAGGAAAAACGATATTAGAAATGTGAGAAGCCCTTCAATTTTTTT
GGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCAAAAATTGAGGGAAATTTTTCGGGTCAAT
TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCT
AGGGCC
Done.