Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010572.1 Corchorus capsularis cultivar CVL-1 contig10593, 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: 2442
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:550 original size:209 final size:209
Alignment explanation
Indices: 300--696 Score: 713
Period size: 209 Copynumber: 1.9 Consensus size: 209
290 ATTCAGAGGC
300 TCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATATTTCAA
1 TCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATATTTCAA
365 GGAGTATTTCTGCAAAAAATCATGCTAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAACCAAGA
66 GGAGTATTTCTGCAAAAAATCATGCTAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAACCAAGA
*
430 ACCGTGATGGATAACACACGATTTCGGCTAAAAACTGACCCGAAAAATTATTTCTCAAGCTTCTA
131 ACCGTGATGGATAACACACGATTTCAGCTAAAAACTGACCCGAAAAATTATTTCTCAAGCTTCTA
495 GCCAAGAACCGTGT
196 GCCAAGAACCGTGT
* * *
509 TCGTAAAAATAAATCTTTAAATCCAACGTGGTTGTGATTTGGTTTGCTGAATACAGATATTTCAA
1 TCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATATTTCAA
* * *
574 GGAGTATTTCTGCAAAATATCATGTTAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAGCCAAGA
66 GGAGTATTTCTGCAAAAAATCATGCTAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAACCAAGA
* *
639 ACCGTGATGGATAAGACACGATTTCAGCTAAAAACTGACCCGAAATATTATTTCTCAA
131 ACCGTGATGGATAACACACGATTTCAGCTAAAAACTGACCCGAAAAATTATTTCTCAA
697 TTTTTCCCAA
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 179 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (209 bp):
TCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATATTTCAA
GGAGTATTTCTGCAAAAAATCATGCTAAACTGAGTCGGGTCCCCGAAACGCGTTTTTAACCAAGA
ACCGTGATGGATAACACACGATTTCAGCTAAAAACTGACCCGAAAAATTATTTCTCAAGCTTCTA
GCCAAGAACCGTGT
Found at i:1011 original size:41 final size:41
Alignment explanation
Indices: 954--1031 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
944 TTTTTAGCTC
*
954 AGAACCGTAATGGATAATACACGATTTCGGCTAAAAAGCCA
1 AGAACCGTAATGGATAACACACGATTTCGGCTAAAAAGCCA
*
995 AGAACCGTGATGGATAACACACGATTTCGGCTAAAAA
1 AGAACCGTAATGGATAACACACGATTTCGGCTAAAAA
1032 CTGACCAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (41 bp):
AGAACCGTAATGGATAACACACGATTTCGGCTAAAAAGCCA
Found at i:1730 original size:322 final size:323
Alignment explanation
Indices: 990--2442 Score: 2285
Period size: 322 Copynumber: 4.5 Consensus size: 323
980 TCGGCTAAAA
*
990 AGCCAAGAACCGTGATGGATAACACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
1 AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
1055 TTTTTTTCGCAAAATATATTCA-GAAATATATTTAATTCAACGCCAAAAAAATTCACGGGATTTT
66 -TTTTTTCGCAAAATATATTCAGGAAA-ATATTTAATTCAACGCCAAAAAAATTCACGGGATTTT
* ** * *
1119 CCTGCTTCTAATTTCGTTTTTCTTTTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGTT
129 CCCGCTTCTAATTTCGTTTTTCCATTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGAT
* *
1184 TCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTTAGATTTGTTTCGCTGAATACAGA
194 TCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGA
1249 TATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTTT
259 TATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTTT
1314 AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
1 AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
*
1379 TTTTTTCGCAAAATATATTCAGAAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTTCC
66 TTTTTTCGCAAAATATATTCAGGAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTTCC
1444 CGCTTCTAATTTCGTTTTTCCATTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTC
131 CGCTTCTAATTTCGTTTTTCCATTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTC
* *
1509 AGAGGCTCGTAAAAATCAATCTTTAAATCCAACGTGGTTGAGA-TTGGTTCGCTGAATACAGATA
196 AGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATA
* *
1573 TTTCAAGGAGTATTTATGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCATTTTT
261 TTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTTT
* * *
1636 AGCCAAGAACCCTGATGGATAATACACGATTTCAGCTAAAAACTGACCCGA-AATATTATTTCTC
1 AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAA-ATTATTTCTC
* * * * * * * *
1700 AATTTTTCCCAAGATATATTAAGGAAAATATTTATTTCAACGCTAAAAAAATTGAAGGGATTTTC
65 ATTTTTTCGCAAAATATATTCAGGAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTTC
* *
1765 CCGCTTCTAATTTTG-TTTTCCATTTAATTTTTCGAATTTATTTCTAATTAAATCGAAACAAGAT
130 CCGCTTCTAATTTCGTTTTTCCATTT-TTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGAT
* * *
1829 TCAGATGCTCTTAAAAATAAATCCATAAATCCAACGTGGTTGAGA-TTGGTTCGCTGAATACAGA
194 TCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGA
* * *
1893 TATTTCAAGGAGTATTTCTGCAAAAAATCATGATAAGCTGAGTCGGGTCCCCGAAACGCGTTTTT
259 TATTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTTT
*
1958 AGCCAAGAACCGTGATTCGGCTAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCT
1 AGCCAAGAACCGTGA-T-GGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCT
* *
2023 CATTTTTTCGCAAAACATATTCTGGAAAATATTTAATTCAACG-CAAAAAAATTCACGGGATTTT
64 CATTTTTTCGCAAAATATATTCAGGAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTT
* * * *
2087 CCCGCTTCTAATTTAGTTTTTCC--TTTTTTTTCGAATTTATTACTAATTAAATGGAAACAAGTT
129 CCCGCTTCTAATTTCGTTTTTCCATTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGAT
* *
2150 TCAGAGGCTCGTAAAAATAAATACTTAAATCCAACGTGGTTGAGATTTGGTTTGCTGAATACAGA
194 TCAGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGA
* * *
2215 TATTTCAATGAGTATTTCTG-AAAAATATCATGTTAAACTGAGTCGGGTCCCCGAAACGCGTTTT
259 TATTTCAAGGAGTATTTCTGCAAAAA-ATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTT
2279 T
323 T
* * * * *
2280 AGCCAAGAACCGTGATCGATAAGACACGATTTCAGCTAAAAACTTACCAGAAAAATTATTTCTCA
1 AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
* * * * *
2345 ATTTTTAGTAGAATATATTCAGGAAAATATTTAATTCAATGCCAAAAAAATTCACGGGATTTTCC
66 TTTTTTCGCAAAATATATTCAGGAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTTCC
2410 CGCTTCTAAATTTCGTTTTTCCATTTTTTTTTC
131 CGCTTCT-AATTTCGTTTTTCCATTTTTTTTTC
Statistics
Matches: 1038, Mismatches: 78, Indels: 26
0.91 0.07 0.02
Matches are distributed among these distances:
320 77 0.07
321 123 0.12
322 483 0.47
323 194 0.19
324 159 0.15
325 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (323 bp):
AGCCAAGAACCGTGATGGATAATACACGATTTCGGCTAAAAACTGACCAGAGAAATTATTTCTCA
TTTTTTCGCAAAATATATTCAGGAAAATATTTAATTCAACGCCAAAAAAATTCACGGGATTTTCC
CGCTTCTAATTTCGTTTTTCCATTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTC
AGAGGCTCGTAAAAATAAATCCTTAAATCCAACGTGGTTGAGATTTGGTTCGCTGAATACAGATA
TTTCAAGGAGTATTTCTGCAAAAAATCATGCTAAACTGAGACGGGTCCCCGAAACGCGTTTTT
Done.