Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009943.1 Corchorus capsularis cultivar CVL-1 contig09964, 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: 2594
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:1590 original size:331 final size:322
Alignment explanation
Indices: 681--1608 Score: 829
Period size: 331 Copynumber: 2.8 Consensus size: 322
671 TTTAATCATG
* * * *
681 TTTCGTTTTAATCAGAAATTAATTTAGAAAAAAATTATGAAAAACGATATTATAAGCATGAAAAA
1 TTTCGATTTAATTAGAAATTAATTTAG-AAAAAA-TATGAAAAACGATATTAGAAGCGTGAAAAA
746 CCCTTCAATATTATTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGGAA
64 -CCTTCAAT-TTATTGGCGTT-AATTATAT-TTTTTATGAGTATTGTGGCCAAAAATTGA-GGAA
* * * * *
811 AATATTTATGGTCAATTTGTGCAAAA-CTTTAGTCGAAATCGTGTACTATCCATCACGGTTTTTG
124 AAAAATTAGGGTCAATTTTTGCAAAATC-TTAGCCGAAATCGTGTACTATCCATCACGGTTTTTG
* * * * * * *
875 GCTAAAAAAGTGTTTCGGAACCCT-GGCTCAATTTTG-TATAATTTTTGGCTCCA-A--CACT--
188 GCTAAAAACGCG-TTC-CAAGCCTCGGCTCAGTTTTGATAT-ATTTTTGGC-CAAGACTCATTGA
* *
933 -TA-CT-TATCCATCTAACCAAATTCCAGGCACAGTTGATTTAAAGACTTGTTTTTACGAGTATC
249 ATATCTATATCCATCTAATCAAATTCCAGGCACAGTTGATTTAAAGACTTGTTTTTACGAGCATC
995 AAAACCTTA
314 AAAACCTTA
* * ** * * *
1004 TTTCGATTTTATTAGAAATCAATTCCGGGAAAAATATGAAAAACTATATTAGAAGCGTGAAGAAG
1 TTTCGATTTAATTAGAAATTAATT-TAGAAAAAATATGAAAAACGATATTAGAAGCGTGAA-AAA
** * * * * *
1069 CC-AAAATTT-TT--CATT-A-TATATTATTTACGAGTATTGTGTCCAAAAATTGAGAAAAATAA
64 CCTTCAATTTATTGGCGTTAATTATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAA-AA
* * * * * *
1128 ATTTTGAGTCAATTTTTGCAAAATTTTAGCTGAAACCGTGTACTATCCATCACGGTTTTTGGCTG
128 A-TTAGGGTCAATTTTTGCAAAATCTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTA
* * ** * * *
1193 GAAACGCGTTACGGGACCACGGCTCAGTTTTGCATA-GTTTTTGG-CATGGAGACTCCTTGGAAT
192 AAAACGCGTTCCAAG-CCTCGGCTCAGTTTTG-ATATATTTTTGGCCA---AGACTCATT-GAAT
* * * *
1256 ATCTATATTCATTTAATCAAA-TCTCA-GCAACA-TTGGATTTAAGGATTTGTTTTTACGAGCAT
251 ATCTATATCCATCTAATCAAATTC-CAGGC-ACAGTT-GATTTAAAGACTTGTTTTTACGAGCAT
* * *
1318 CTAAATCTTT
313 CAAAACCTTA
* *
1328 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAATCT
1 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAAC-
* * ***
1393 CTTCAATCTTATTGGCGTTCAATTATGTCTTTTTATGAGTATTTTGGGTTAAAATTGAGGAAAAA
65 CTTCAAT-TTATTGGCGTT-AATTATAT-TTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAA
* * *
1458 ACATTCGGGTCAATTTTTGCAAAATCTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCT
127 A-ATTAGGGTCAATTTTTGCAAAATCTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCT
*
1523 AAAAACGCGTTCCAATGCCTCGGCTCAGTTTTGATGATCTTTTTGTGCCAAGACTCATTGAAATA
191 AAAAACGCGTTCCAA-GCCTCGGCTCAGTTTTGAT-ATATTTTTG-GCCAAGACTCATTG-AATA
1588 TCTATATCCATCTAATCAAAT
252 TCTATATCCATCTAATCAAAT
1609 ATTAGCCACA
Statistics
Matches: 474, Mismatches: 89, Indels: 75
0.74 0.14 0.12
Matches are distributed among these distances:
312 6 0.01
313 31 0.07
314 81 0.17
315 2 0.00
316 3 0.01
317 3 0.01
318 2 0.00
319 2 0.00
320 2 0.00
321 3 0.01
322 31 0.07
323 67 0.14
324 75 0.16
325 2 0.00
326 2 0.00
328 3 0.01
330 4 0.01
331 117 0.25
332 35 0.07
333 1 0.00
334 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (322 bp):
TTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAACC
TTCAATTTATTGGCGTTAATTATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAAATT
AGGGTCAATTTTTGCAAAATCTTAGCCGAAATCGTGTACTATCCATCACGGTTTTTGGCTAAAAA
CGCGTTCCAAGCCTCGGCTCAGTTTTGATATATTTTTGGCCAAGACTCATTGAATATCTATATCC
ATCTAATCAAATTCCAGGCACAGTTGATTTAAAGACTTGTTTTTACGAGCATCAAAACCTTA
Done.