Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005033.1 Corchorus capsularis cultivar CVL-1 contig05051, 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, 944
Length: 1574
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:934 original size:333 final size:332
Alignment explanation
Indices: 1--1574 Score: 2120
Period size: 333 Copynumber: 4.7 Consensus size: 332
* *
1 AAAATTCACGCAAAACGGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
1 AAAATTCACGCAAAACGGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * *
66 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATATTTCTTCAATTTCTGACGGA
66 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAATTTTTGGCGGA
* *
131 AATAATCATATAAAATATATAATTCTACGCCGAAAAAGATATAAGGGGTTTTCACTCTTCTAACA
131 AATAATCATATAAAATATATAATTCAACACC-AAAAAGATATAAGGGGTTTTCACTCTTCTAACA
* * *
196 TGATTTTCCTATTTTTTTCTGACTTAATTTCGAATGAAATTGAAAACGGTTTCCGATGCTCGTAA
195 TGATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGGTTTCCGATGCTCGTAA
* * ** * * *
261 AAACAAATACTTAAATCCCATTTGGCTGATATTTGGTAACATGAATATAGATATTTCAAGGAGTC
260 AAACAAATCCTTAAATCCAACGTGGCTGAGATTCGGTAACATGAATAAAGATATTTCAAGGAGTC
326 TAGGCACC
325 TAGGCACC
* * ** * *
334 AAAAATAACAAAAAACTGAGCCG-GGTCCCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTA
1 AAAATTCACGCAAAACGGAGCCGAGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G---
* * * *
398 GTTAGTAAACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTAC-TCAATTTTT
61 GTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTT-CTTCAATTTTT
* * ** *
462 GGAC-GAAATAATCATAAAAAATATATAATTCAACACCAGAAAGATATAAGGACTTTTCACACTT
125 GG-CGGAAATAATCATATAAAATATATAATTCAACACCAAAAAGATATAAGGGGTTTTCACTCTT
* * * * *
526 CTAACATCGATTTCCCTATTTTTATCTGAGTTAATTGCTAATGAAAATGAAAACGGTTTCTGATG
189 CTAACAT-GATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGGTTTCCGATG
* *
591 CTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTCGGTTACATGAATAAATATATTTCA
253 CTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTCGGTAACATGAATAAAGATATTTCA
*
656 AGGAGTCTCGGCACC
318 AGGAGTCTAGGCACC
* * *
671 AAAATTCACGCAAAACAGAGCCGAGGCCCCGGAACGCGTTTTCAACCAAAAACCGTGATGGTTAG
1 AAAATTCACGCAAAACGGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
*
736 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAATTTGTGGCGGA
66 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAATTTTTGGCGGA
* * *
801 AATACTCATATAAAATATATAATTCCACGCCAAAAAGATATAAGGGGTTTTCACTCTTCTAACAT
131 AATAATCATATAAAATATATAATTCAACACCAAAAAGATATAAGGGGTTTTCACTCTTCTAACAT
* * *
866 GATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAATTGAACACGGTTTTCCGATGCTCTTAA
196 GATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGG-TTTCCGATGCTCGTAA
* * * * *
931 AAACAAATGCTTCAATCCAACGTGGTTGAGATTCGGTTACATGAATAAATATATTTCAAGGAGTC
260 AAACAAATCCTTAAATCCAACGTGGCTGAGATTCGGTAACATGAATAAAGATATTTCAAGGAGTC
* * *
996 TCGACACA
325 TAGGCACC
* * *
1004 AAAATTCACGCAAAACGGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGGTTAG
1 AAAATTCACGCAAAACGGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* *
1069 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAGTTTTTTGCGGA
66 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAATTTTTGGCGGA
* * * *
1134 AATACTCATATAAAATATATAATTCCACTCCAAAAAGATATAATGGGTTTTCACTCTTCTAACAT
131 AATAATCATATAAAATATATAATTCAACACCAAAAAGATATAAGGGGTTTTCACTCTTCTAACAT
*
1199 GATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGGGTTCCGATGCTCGTAAA
196 GATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGGTTTCCGATGCTCGTAAA
* * * *
1264 AACAAATCCTTAAATACC-ATGTGGCTGATATTCGGTAACATGAATATAGATATATCAAGGAGTC
261 AACAAATCCTTAAAT-CCAACGTGGCTGAGATTCGGTAACATGAATAAAGATATTTCAAGGAGTC
1328 TAGGCACC
325 TAGGCACC
* * * *
1336 AAAAATCACACAAAACTGAGCCAAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G-TAG
1 AAAATTCACGCAAAACGGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * * * *
1399 TACACGATTTCAACTAAAATTTTGCAAAAAATGTCCCGAAATATTTTTCCTT-AATTTTTTGCCG
66 TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTT-CTTCAATTTTTGGCGG
* * * ** * *
1463 AAAAAATCATAAAAAAATATATAATTGAACACCTGAAAGATATAAGGGCTTTTCACACTTCTAAC
130 AAATAATCAT-ATAAAATATATAATTCAACACCAAAAAGATATAAGGGGTTTTCACTCTTCTAAC
* * * * *
1528 ATTAATTTCCCTA-TTTTTTCTTAATTAATTGCTAATCAAAATGAAAA
194 A-TGATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAA
Statistics
Matches: 1097, Mismatches: 128, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
330 65 0.06
331 81 0.07
332 179 0.16
333 481 0.44
334 1 0.00
336 31 0.03
337 255 0.23
338 4 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (332 bp):
AAAATTCACGCAAAACGGAGCCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
TACACGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCTTCAATTTTTGGCGGA
AATAATCATATAAAATATATAATTCAACACCAAAAAGATATAAGGGGTTTTCACTCTTCTAACAT
GATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAATTGAAAACGGTTTCCGATGCTCGTAAA
AACAAATCCTTAAATCCAACGTGGCTGAGATTCGGTAACATGAATAAAGATATTTCAAGGAGTCT
AGGCACC
Done.