Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002978.1 Corchorus olitorius cultivar O-4 contig02983, 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, 970
Length: 1618
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:1138 original size:332 final size:328
Alignment explanation
Indices: 18--1618 Score: 1652
Period size: 332 Copynumber: 4.8 Consensus size: 328
8 TTTTTAATAT
* * * *
18 TTTTTTCTAAATTAAGTTCTGATAAAATCGAAACAAGATTCAGATGCTCGTAAAAATATTTCCTT
1 TTTTTTCCAAATTAAGTTCTGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACATTTCCTT
* * *
83 TAATCCAATGTGGCTGAGATTTGATCAGATGAATATAGCTATTTCAATGAGTCTCTGCGCCAAAA
66 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCAAAA
* * * ** * *
148 ATCATGTAAAACTGAGCCGGAGCGCC-GTAACGCGTTTTCAGCCAGAAACTTTTATGGTTAGTAC
131 ATCATGCAAAACTGAGCCGGAGC-CCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTAATAC
* * * *
212 ATGATTTCAGTTAAAAATTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTTCTCAAAAT
195 ATGATTTCAGCTAAAATTTTG-AAAAATTGACCCG-AATATTTTTCCTCAATTTTTGCCCAAAAT
* * * * * * *
277 ATGCATAAATAATACATAAGTGAATGCCAAAAAGATTGGCA-GGCTTTTCACGCTTCTAATATCG
258 ATGCATAAAAAATATATAATTGAACGCCAAAAATATT-GAAGGGCTTTTCACGCTTCAAATATCG
*
341 TATATTTAA
322 T-T-TTTTA
* * * * * * *
350 TTTTTTTCAAATTAATTTCCGATTAAATCGAAGCAAGATTCAGATGCTCGTAAAAGCATATCCTT
1 TTTTTTCCAAATTAAGTTCTGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACATTTCCTT
* *
415 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATATCAATGAGTCTCTGCGCCACAA
66 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCAAAA
* * * * *
480 ATCATGTAAAACTAAGCCGGGGCCCTGGAATGCGTTTTCAGCCAGAACCCATGATGGTTAATATA
131 ATCATGCAAAACTGAGCCGGAGCCCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTAATACA
* * * * * * * * *
545 CGATTTCAGCTAAAATTTTGATAAAACTGA-ACGAAAAGTTTTTCGTTAATTTCTGGCCACAATA
196 TGATTTCAGCTAAAATTTTGA-AAAATTGACCCGAATA-TTTTTCCTCAATTTTTGCCCAAAATA
* * * * * *
609 CT-CATAAAAAATATATAATTTACCGCTAAAACTATTTAAGGGCTTTTCATGCTTCAAATAT-G-
259 -TGCATAAAAAATATATAATTGAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCAAATATCGT
*
671 -GTTT-
323 TTTTTA
* * * *
675 TTTTTTCCAAATTAAGTTCTGAATAAACCGAAAA-AAAATTCATATGCTCGTAAAAAAACATTTC
1 TTTTTTCCAAATTAAGTTCTGATTAAATC-AAAACAAGATTCAGATGCTCGT--AAAAACATTTC
* * ** *
739 CTCAAATCCAATATGGCCAAGATTTGATTAGGTGAATATAGATATTTCAATGAGTCTCTGCGCCA
63 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCA
* * *
804 AAAATCATGCAAAACTGTGTCGGAGCCCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTACT
128 AAAATCATGCAAAACTGAGCCGGAGCCCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTAAT
* * * *
869 ACATGATTTCGGTTAAAATTTTGTAAAAATTGACCCGAATTATTTTTCCACAATTTTTTCCCAAA
193 ACATGATTTCAGCTAAAATTTTG-AAAAATTGACCCGAA-TATTTTTCCTCAATTTTTGCCCAAA
* * * ** *
934 ATATGCATAAAAAATATATGATTGAACGCAAAAAAAATTGGCGGGCTTTTCACGCTTCTAATATC
256 ATATGCATAAAAAATATATAATTGAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCAAATATC
999 GTTTTTCCTA
321 GTTTTT--TA
* **
1009 TTTTTTCCAAATTAATTTCTGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAGATCCTT
1 TTTTTTCCAAATTAAGTTCTGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACATTTCCTT
** * * * *
1074 AAATCCAATAAGGCTGAGATTTGATTAGATAAATATAGATATTTCAATGAGTCCCGGTGCCAAAA
66 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCAAAA
* *
1139 ATCATGCAAAACAGAGCCAGG-GCCGC-GGAACT-CGTTTTCAGCCAGAAACCGTGATGGTTAAT
131 ATCATGCAAAACTGAGCC-GGAGCC-CTGGAA-TGCGTTTTCAGCCAGAAACCATGATGGTTAAT
* * * ** * * * * * * *
1201 ACACGATTTTAGCT-AAATATTTGATAAAACTGAAACGAAAAGTTTTGCGTTAATTTTAGGCCAC
193 ACATGATTTCAGCTAAAAT-TTTGA-AAAATTGACCCGAATA-TTTTTCCTCAATTTTTGCCCAA
* * * *
1265 AATACT-CATAAAAAATATATAATTCAA-GACCAAAACTATTTAAGGGCTTTTCATGCTTCAAAT
255 AATA-TGCATAAAAAATATATAATTGAACG-CCAAAAATATTGAAGGGCTTTTCACGCTTCAAAT
* *
1328 ATGGTTTTTCCTCTTTTT
318 ATCG----T--T-TTTTA
* * *
1346 TTTTTTCCAAATTAAGTTCTGATTAAAT-AGAAACAAAATTTAGATGCTTGTAAAAACATTTTCC
1 TTTTTTCCAAATTAAGTTCTGATTAAATCA-AAACAAGATTCAGATGCTCGTAAAAACA-TTTCC
* * *
1410 TTAAATCCAATGTGACTGAGATTTGACTAGATGAATATAGATATTTCAATGACTCTCTGCGCCAA
64 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCAA
* * * ** * *
1475 AAGTAATGCAAAACTGAGTCGGAGCCCTGGAACACGTTTTCAGCCAGAAACCGTGATGGTTAGTA
129 AAATCATGCAAAACTGAGCCGGAGCCCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTAATA
* * *
1540 CATGAATTT-GGCTAAAATTTTGCAAAAATTGACCCTAAATATTTTTCATCAATTTTTGCCCAAA
194 CATG-ATTTCAGCTAAAATTTTG-AAAAATTGACCC-GAATATTTTTCCTCAATTTTTGCCCAAA
1604 ATATGCATAAAAAAT
256 ATATGCATAAAAAAT
Statistics
Matches: 1039, Mismatches: 186, Indels: 82
0.79 0.14 0.06
Matches are distributed among these distances:
325 39 0.04
326 4 0.00
327 152 0.15
328 72 0.07
329 2 0.00
330 5 0.00
331 77 0.07
332 402 0.39
333 10 0.01
334 41 0.04
336 2 0.00
337 57 0.05
338 161 0.15
339 15 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (328 bp):
TTTTTTCCAAATTAAGTTCTGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACATTTCCTT
AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTCTGCGCCAAAA
ATCATGCAAAACTGAGCCGGAGCCCTGGAATGCGTTTTCAGCCAGAAACCATGATGGTTAATACA
TGATTTCAGCTAAAATTTTGAAAAATTGACCCGAATATTTTTCCTCAATTTTTGCCCAAAATATG
CATAAAAAATATATAATTGAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCAAATATCGTTTT
TTA
Done.