Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014931.1 Corchorus olitorius cultivar O-4 contig14964, 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: 14224
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Found at i:949 original size:333 final size:333
Alignment explanation
Indices: 343--1626 Score: 2020
Period size: 333 Copynumber: 3.8 Consensus size: 333
333 AAACTGTGAT
* * *
343 GCTAAAATTTTGCAAAAAAATTGACCCGAAAAATTTTTGCTGAATTTTTGGCCACAATACTCATA
1 GCTAAAATTTTGCAAAAAAACTGACCCG-AAAATTTTTGCTCAATTTTCGGCCACAATACTCATA
408 AAAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCT
65 AAAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCT
*
473 A-TTTTTTCACAATTAATTTTTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCC
130 ATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCC
* *
537 TTATGTCCTATGTGACTGAGATTTGGTTACTTGAATATAGATATTTCATGGAGTCTTGGCGCCAA
195 TTATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAA
* * * *
602 AAATCATTCAAAACTGAGTCGAGGACCCGGAACACGTTTTTAGAGAAAAACTGTGATGGTTACTA
260 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTGTGATGGTTACTA
667 CACGATATC
325 CACGATATC
*
676 GCTAAAATTTTGCAAAAAAACTGACCCGAAAATTTTTGCTCAATTTTCGGCCACAATACTCATAT
1 GCTAAAATTTTGCAAAAAAACTGACCCGAAAATTTTTGCTCAATTTTCGGCCACAATACTCATAA
* * *
741 AAACTATATTATTCAATGCAAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTA
66 AAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTA
806 TTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCCT
131 TTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCCT
*
871 TATGTCCTATGTGACTGAGATTTGGTTACTCAAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
196 TATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
936 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTGTGATGGTTACTAC
261 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTGTGATGGTTACTAC
1001 ACGATATC
326 ACGATATC
1009 GCTAAAATTTTGCAAAAAAACTGACCCGAAAATTTTTGCTCAATTTTCGGCCACAATACTCATAA
1 GCTAAAATTTTGCAAAAAAACTGACCCGAAAATTTTTGCTCAATTTTCGGCCACAATACTCATAA
1074 AAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTA
66 AAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTA
*
1139 TTTTTTTCAGAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCCT
131 TTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCCT
1204 TATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
196 TATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
* *
1269 AATCATTCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTATGATGGTTACTAC
261 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTGTGATGGTTACTAC
*
1334 ACGATGTC
326 ACGATATC
* * *
1342 GCTAAAATTTTG-AAAAAAACTAGACCAGAAATTTTTTTTCTCAATTTTCGGCCACAATACTCAT
1 GCTAAAATTTTGCAAAAAAACT-GACCCGAAA-ATTTTTGCTCAATTTTCGGCCACAATACTCAT
* * *
1406 AAAAAATATAATAATTCAATGCCAGAAAGATTGAAGGG-CTTTCATGCTTCTAATATCATTTTTC
64 AAAAAATAT-ATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-
* * * * ** *
1470 CATCTTTTTTTTTC-CGAATTAACTTCTAATTCAATCGAAACTGGTTTCTGATGCTTC-AAAAAA
127 C--CTATTTTTTTCAC-AATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGC-TCGAAAAAA
* * * ** * * ** * * *
1533 CAAATCCTTATATCCAATATGTTTGAGATTTGATTAGTTTAATATAAATATTTCAAAGAGTTTTG
188 CAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTG
*** *
1598 GCAATAAAAATCATGCAAAACTAAGCCGG
253 GCGCCAAAAATCATGCAAAACTGAGCCGG
1627 ATTCCAAGAA
Statistics
Matches: 887, Mismatches: 55, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
332 105 0.12
333 565 0.64
334 61 0.07
335 29 0.03
337 125 0.14
338 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (333 bp):
GCTAAAATTTTGCAAAAAAACTGACCCGAAAATTTTTGCTCAATTTTCGGCCACAATACTCATAA
AAAATATATAATTCAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTA
TTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAGTTTCCGATGCTCGAAAAAACAAATCCT
TATGTCCTATGTGACTGAGATTTGGTTACTCGAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGAGAAAAACTGTGATGGTTACTAC
ACGATATC
Done.