Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019138.1 Corchorus olitorius cultivar O-4 contig19171, 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, 971
Length: 1619
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:1170 original size:617 final size:596
Alignment explanation
Indices: 1--1379 Score: 1734
Period size: 617 Copynumber: 2.3 Consensus size: 596
* * * * *
1 TTTTGGCCACAATACTCATAAAAATATATAAAATCCATCGCCAAAACGATGGAAGGATTTTTCAC
1 TTTTGGCCA-AATACTCATAAAAAAATATAAAATTCAACGCCAAAACAATGAAAGGATTTTTCAC
*
66 GTATTTAATATCGTTCTTTTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAGATGCT
65 GTATTTAATATCGTTCTTTTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAGATACT
* * *
131 CGTTAAAAAAATACTTAAATCCAATGTGGCTGCTACTTGATTATCTGAATATCGATATTCCTAGA
130 CGTTAAAAAAATACTTAAATCCAATGTGGCTGCTACTTGATTATATGAATATAGATATTCCGAGA
* * * * ** *
196 AGTCTTAGCGCCAAAAATATTCCAAGATTTCGTCTAAAATTTTGAAAAAATTGACCCGAATGTTT
195 AGTCTTAGCGCCAAAAATAATACAAAACTGAGTCTAAAATTTTGAAAAAACTG--CCGAATGTTT
* ** *
261 TTTCTTCAAGTTCTGGCCAAATACTTATAAAATTATATAATTCAATGCCAAAATATTGAAGGGCT
258 TTTCCTCAAGTTCTGGAAAAATACTTATAAAATTATATAATTCAATGCCAAAAGATTGAAGGGCT
* * * * *
326 TTCCACGCTTCTTATATCATTTTTTTAATATTTTTTTGAATTAATTTCTATTTAAATCGAAACAA
323 TTCCACGCTTCTAATATCATTTTTTAAATATTTTTTAGAATTAATTTATATTTAAATCCAAACAA
* *
391 GATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCTGGATGAATTT
388 GATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAATAT
456 AGATATTTCAAGGAGACTGGGAGACAAAAAACATGCAAAACTGAGTCGGGGTCCCGAAACGCGTT
453 AGATATTTCAAGGAGACTGGGAGACAAAAAACATGCAAAACTGAGTCGGGGTCCCGAAACGCGTT
* * *
521 TTTAGCCAAAAACCGTGACGGTTAGTACACGATTTCGGCTAAAACTTTGCAAAAACTGA-TCTGA
518 TTTAGCCAAAAACCGTGACGGTTAGAACACGATTGCGGCTAAAACTTTGAAAAAACTGACTC-G-
585 AAAAAAATTTCCTCAAT
581 -AAAAAATTTCCTCAAT
* *
602 TTTTGGCGATAATACTCATAAAAAAATATAAAATTCAACGCCAAAACAATGAAAGGATTTTTCTC
1 TTTTGGCCA-AATACTCATAAAAAAATATAAAATTCAACGCCAAAACAATGAAAGGATTTTTCAC
667 GTATTTAATATCGTTCTTTTTTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAGATA
65 GTATTTAATATCGTTC--TTTTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAGATA
*
732 CTCGTTAAAAAAATACTTAAATCCAATGTGGCTGCTATTTGATTATATGAATATAGATATTCCGA
128 CTCGTTAAAAAAATACTTAAATCCAATGTGGCTGCTACTTGATTATATGAATATAGATATTCCGA
* *
797 GAAGTCTTAGCGCCAAATATAATACAAAACTGAG-CTGAGGCCCCGGAACGAGTTTTTAGCCAAA
193 GAAGTCTTAGCGCCAAAAATAATACAAAACTGAGTCT-A--------AA--A--TTTT-G-AAAA
* *
861 AACTG-TG-ATGGTTAGTTTTCCTCAATTTCTGGAAAAATACTTATAAAAATTATATAATTCAAT
243 AACTGCCGAAT-GTT--TTTTCCTCAAGTTCTGGAAAAATACTTAT-AAAATTATATAATTCAAT
924 GCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCA-TTTTTAAATATTTTTTAGAATTAAT
304 GCC-AAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTAAATATTTTTTAGAATTAAT
988 TTATATTTAAATCCAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATG
368 TTATATTTAAATCCAAACAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATG
* * * *
1053 GGATTTGGCCGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAACTGTG
433 GGATTTGGCCGGATGAATATAGATATTTCAAGGAGACTGGGAGACAAAAAACATGCAAAACTGAG
* * * *
1118 TCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAGAACACGATTGCGGCTAAAAT
498 TCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGACGGTTAGAACACGATTGCGGCTAAAAC
* ***
1183 TTTGAAAAAATTGACTCGAAAGTTTTTCCTCAAT
563 TTTGAAAAAACTGACTCGAAAAAATTTCCTCAAT
* * * * * * * *
1217 TTCTGGCCAAATACTTAT-AAAAATTATATAATTCAATGCCAAAA-AGGTTGAAAGG-CTTTCCA
1 TTTTGGCCAAATACTCATAAAAAAATATAAAATTCAACGCCAAAACA--ATGAAAGGATTTTTCA
* * * ** * **
1279 CGCT-TCTAATATCATTTTTAAAATATTTTTTGAATTAATTTCTATTTAAATCGAAACAAGATTC
64 CG-TATTTAATATCGTTCTT----T-TTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTC
* *
1343 AGATACTCG-TAAAATCACATACTTGAATCCAATGTGG
123 AGATACTCGTTAAAA--AAATACTTAAATCCAATGTGG
1380 ATGGGATTTG
Statistics
Matches: 675, Mismatches: 70, Indels: 50
0.85 0.09 0.06
Matches are distributed among these distances:
601 73 0.11
602 2 0.00
603 135 0.20
611 4 0.01
612 1 0.00
613 42 0.06
614 20 0.03
615 30 0.04
616 69 0.10
617 264 0.39
618 35 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (596 bp):
TTTTGGCCAAATACTCATAAAAAAATATAAAATTCAACGCCAAAACAATGAAAGGATTTTTCACG
TATTTAATATCGTTCTTTTTTTTCAAATTTATTTCTCCTTAAATCGAAACAAGATTCAGATACTC
GTTAAAAAAATACTTAAATCCAATGTGGCTGCTACTTGATTATATGAATATAGATATTCCGAGAA
GTCTTAGCGCCAAAAATAATACAAAACTGAGTCTAAAATTTTGAAAAAACTGCCGAATGTTTTTT
CCTCAAGTTCTGGAAAAATACTTATAAAATTATATAATTCAATGCCAAAAGATTGAAGGGCTTTC
CACGCTTCTAATATCATTTTTTAAATATTTTTTAGAATTAATTTATATTTAAATCCAAACAAGAT
TCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAATATAGA
TATTTCAAGGAGACTGGGAGACAAAAAACATGCAAAACTGAGTCGGGGTCCCGAAACGCGTTTTT
AGCCAAAAACCGTGACGGTTAGAACACGATTGCGGCTAAAACTTTGAAAAAACTGACTCGAAAAA
ATTTCCTCAAT
Found at i:1477 original size:330 final size:330
Alignment explanation
Indices: 876--1546 Score: 1137
Period size: 330 Copynumber: 2.0 Consensus size: 330
866 TGATGGTTAG
*
876 TTTTCCTCAATTTCTGGAAAAATACTTATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGG
1 TTTTCCTCAATTTCTGGAAAAATACTTATAAAAATTATATAATTCAATGCCAAAAAGATTGAAAG
941 GCTTTCCACGCTTCTAATATCATTTTTAAATATTTTTTAGAATTAATTTATATTTAAATCCAAAC
66 GCTTTCCACGCTTCTAATATCATTTTTAAATATTTTTTAGAATTAATTTATATTTAAATCCAAAC
1006 AAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAAT
131 AAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAAT
* * ** * *
1071 ATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAACTGTGTCGGGGTCCCGGAACGCG
196 ATAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAACTCAGTCGGGATCCCGAAACGCG
* * *
1136 TTTTTAGCCAAAAACGGTGATGGTTAGAACACGATTGCGGCTAAAATTTTGAAAAAATTGACTCG
261 TTTTTAGCCAAAAACCGTGATGGTTAGAACACGATTGCGGCAAAAATTTTGAAAAAATTGACCCG
1201 AAAGT
326 AAAGT
** *
1206 TTTTCCTCAATTTCTGGCCAAATACTTATAAAAATTATATAATTCAATGCCAAAAAGGTTGAAAG
1 TTTTCCTCAATTTCTGGAAAAATACTTATAAAAATTATATAATTCAATGCCAAAAAGATTGAAAG
* *
1271 GCTTTCCACGCTTCTAATATCATTTTTAAAATATTTTTT-GAATTAATTTCTATTTAAATCGAAA
66 GCTTTCCACGCTTCTAATATCATTTTT-AAATATTTTTTAGAATTAATTTATATTTAAATCCAAA
*
1335 CAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCTGGATGAA
130 CAAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAA
*
1400 TTTAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAACTCAGTCGGGATCCCGAAACGC
195 TATAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAACTCAGTCGGGATCCCGAAACGC
** * *
1465 GTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGAAAAATTTGACCC
260 GTTTTTAGCCAAAAACCGTGATGGTTAGAACACGATTGCGGCAAAAATTTTGAAAAAATTGACCC
1530 GAAAGT
325 GAAAGT
1536 TTTTCCTCAAT
1 TTTTCCTCAAT
1547 ATTTAATATC
Statistics
Matches: 319, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
330 308 0.97
331 11 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (330 bp):
TTTTCCTCAATTTCTGGAAAAATACTTATAAAAATTATATAATTCAATGCCAAAAAGATTGAAAG
GCTTTCCACGCTTCTAATATCATTTTTAAATATTTTTTAGAATTAATTTATATTTAAATCCAAAC
AAGATTCAGATACTCGTAAAATCACATACTTGAATCCAATGTGGATGGGATTTGGCCGGATGAAT
ATAGATATTTCAAGGAGTCTGGGAGACAAAAAACATGCAAAACTCAGTCGGGATCCCGAAACGCG
TTTTTAGCCAAAAACCGTGATGGTTAGAACACGATTGCGGCAAAAATTTTGAAAAAATTGACCCG
AAAGT
Done.