Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011618.1 Corchorus olitorius cultivar O-4 contig11651, 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, 903
Length: 1506
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Found at i:315 original size:156 final size:156
Alignment explanation
Indices: 3--1506 Score: 2256
Period size: 156 Copynumber: 9.7 Consensus size: 156
1 TG
* ** * *
3 TGGTTTGCCAAATCGAAGACCA-TTCCAAAACCAAACTAATGGACCCCGAATGGCCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
*
67 AAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
*
132 CATAAACAATGGAAAGAAAAGCTTTA
131 CATAAACAATGGAAAGAAAAGCATTA
* * * *
158 TGGTTTGCCAAATCGAAGACAATTTTTAAAACCTAACTAATGGGCCTCGAATGGTCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* * * *
223 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAGTGGTCATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
288 CATAAACAATGGAAAGAAAAGCATTA
131 CATAAACAATGGAAAGAAAAGCATTA
*
314 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* *
379 AAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
444 CATAAACAATGGAAAG-AAAGCA-T-
131 CATAAACAATGGAAAGAAAAGCATTA
* *
467 T-GTTTGCCAAATCGAAGACGATTTTTAAAACCTAACTAATGGGCCCCAAATGGCCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* * * * *
531 AAGTCTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAAGTGGTCATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
596 CATAAACAATGGAAAGAAAAGCATTA
131 CATAAACAATGGAAAGAAAAGCATTA
* * *
622 TTGTTTGCCAAATCGAAGACGACTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* *
687 AAGTGTTCAAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGG
66 AAGTGTTC-AAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGG
* *
752 CCATAAACAATGGAAAGAAAAACATTG
130 CCATAAACAATGGAAAGAAAAGCATTA
* * * * *
779 TGGTTTGTCAAATCAAAAGACGA--TTCAAAACCGAACTAATAGACCCCGAATGGCCCAAAATAA
1 TGGTTTGCCAAATC-GAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAA
842 CAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGG
65 CAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGG
907 CCATAAACAATGGAAAGAAAAGCATTA
130 CCATAAACAATGGAAAGAAAAGCATTA
* * * ** * *
934 TGATTTACCAAATCGAAGATGATTTTTAAAATTGAACTAATGGGCTCCGAATGGTCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* * * * * *
999 AAGTGTTCAAAATGAGTTAAAAACTTCACAATGGCCTAGTCTAACAAAAATGATTATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
*
1064 CATAAACAATGGAAAGAAAAGCATTG
131 CATAAACAATGGAAAGAAAAGCATTA
* * * * *
1090 TGGTTTGCCAATTCGAAAACGA--TTCAAAACAGAACTAATGGACCCCGAATGGCCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
*
1153 AAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
** * *
1218 CATAAACCTTGGAAAGAAAAGGATTG
131 CATAAACAATGGAAAGAAAAGCATTA
* *
1244 TTGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
* *
1309 AAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGC
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
* *
1374 CAAAAACAATGGAAAGAAAAGCATTG
131 CATAAACAATGGAAAGAAAAGCATTA
* * * * * *
1400 TGGTTTGTCAAATCGAAGATGA--TTCAAAACCGAACTAATAGACCCCGAATCGCCCAAAATAAC
1 TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
1463 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTA
66 AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTA
Statistics
Matches: 1220, Mismatches: 118, Indels: 23
0.90 0.09 0.02
Matches are distributed among these distances:
152 134 0.11
153 7 0.01
154 221 0.18
155 118 0.10
156 646 0.53
157 87 0.07
158 7 0.01
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (156 bp):
TGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAAC
AAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCATTA
Found at i:1210 original size:310 final size:309
Alignment explanation
Indices: 5--1506 Score: 2366
Period size: 310 Copynumber: 4.8 Consensus size: 309
1 TGTG
* ** * * *
5 GTTTGCCAAATCGAAGACCA-TTCCAAAACCAAACTAATGGACCCCGAATGGCCCAAAATAACAA
1 GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
* * *
69 GTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCA
66 GTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCA
* * * * *
134 TAAACAATGGAAAGAAAAGCTTTATGGTTTGCCAAATCGAAGACAATTTTTAAAACCTAACTAAT
131 TAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAAT
* * * *
199 GGGCCTCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTC
194 GGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATC
* *
264 TTACCAAAGTGGTCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT
259 TTACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT
315 GGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACA
1 -GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACA
380 AGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCC
65 AGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCC
* *
445 ATAAACAATGGAAAG-AAAGCA-T-T-GTTTGCCAAATCGAAGACGATTTTTAAAACCTAACTAA
130 ATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAA
* * * *
506 TGGGCCCCAAATGGCCCAAAATAACAAGTCTTCAAAATGAGCTAAGAACTTTACAATGGACTAAT
193 TGGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAAT
* *
571 CTTACCAAAGTGGTCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATT
258 CTTACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTA-T
*
624 GTTTGCCAAATCGAAGACGACTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
1 GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
689 GTGTTCAAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCC
66 GTGTTC-AAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCC
* * *
754 ATAAACAATGGAAAGAAAAACATTGTGGTTTGTCAAATCAAAAGACGATTCAAAACCGAACTAAT
130 ATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATC-GAAGACGATTCAAAACCGAACTAAT
*
819 AGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATC
194 GGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATC
*
884 TTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT
259 TTACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT
* * ** *
935 GATTTACCAAATCGAAGATGATTTTTAAAATTGAACTAATGGGCTCCGAATGGTCCAAAATAACA
1 G-TTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACA
* * * *
1000 AGTGTTCAAAATGAGTTAAAAACTTCACAATGGCCTAGTCTAACAAAAATGATTATAGTTAGGCC
65 AGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCC
* * *
1065 ATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAATTCGAAAACGATTCAAAACAGAACTAATG
130 ATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATG
*
1130 GACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCT
195 GACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCT
* ** * *
1195 TACCAAAATGATTATAGTTAGGCCATAAACCTTGGAAAGAAAAGGATTGTT
260 TACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-AT
1246 GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
1 GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
1311 GTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCA
66 GTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCA
* * * *
1376 AAAACAATGGAAAGAAAAGCATTGTGGTTTGTCAAATCGAAGATGATTCAAAACCGAACTAATAG
131 TAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGG
*
1441 ACCCCGAATCGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTT
196 ACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTT
1506 A
261 A
Statistics
Matches: 1110, Mismatches: 71, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
308 217 0.20
309 75 0.07
310 379 0.34
311 119 0.11
312 302 0.27
313 11 0.01
314 7 0.01
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (309 bp):
GTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAA
GTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCA
TAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGG
ACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTT
ACCAAAATGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAT
Done.