Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011539.1 Corchorus olitorius cultivar O-4 contig11572, 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, 840
Length: 1401
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:170 original size:22 final size:22
Alignment explanation
Indices: 127--170 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
117 GCTCATTTGG
* *
127 TTGGGCCGATCGGGGTCTATTA
1 TTGGGCCGATCGGGGCCCATTA
*
149 TTGGGCCTATCGGGGCCCATTA
1 TTGGGCCGATCGGGGCCCATTA
171 GTTCCGTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.30
Consensus pattern (22 bp):
TTGGGCCGATCGGGGCCCATTA
Found at i:507 original size:154 final size:154
Alignment explanation
Indices: 182--1400 Score: 1746
Period size: 154 Copynumber: 8.0 Consensus size: 154
172 TTCCGTTTCG
* * * * *
182 AATCATCTTCGATTTGACAAACCTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATGATAA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
*
247 TTTT-TGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTGATTTAGAACACTTGTTATTTTGGGCC
66 TTTTGT-TGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCC
* *
311 TATCGGGGTCCATTAGTTCCGTTTTG
129 TATCGGGGTCCATTAGTGCCGTATTG
*
337 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * *
402 TTTTGTTGAGATTAGTCCACCGTGATGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCAA
66 TTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTA
* * *
467 TCGGGGCCCATTAATGACGTATTG
131 TCGGGGTCCATTAGTGCCGTATTG
*
491 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACAATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
556 TTTTAG-TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCT
66 TTTT-GTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCT
** * *
620 ATCATGGTCCATTAGTTCCGTTTTG
130 ATCGGGGTCCATTAGTGCCGTATTG
*
645 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
710 TTTTGGTGAGAATAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAGACTTGTTATTTTGGGCCTA
66 TTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTA
* *
775 TCGGGGCCCATTAGTGACGTATTG
131 TCGGGGTCCATTAGTGCCGTATTG
*
799 AATCTTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* *
864 TTTT-TGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTCGGCCT
66 TTTTGT-TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCT
* *
928 ATCGGGGTCCATTAGTTCCGTTTTG
130 ATCGGGGTCCATTAGTGCCGTATTG
*
953 AATCATCTTCGATTTGG-------CAA----------TCCATTGTTTATGGCCTAACTATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * *
1001 TTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTA
66 TTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTA
*
1065 TCGGGGTCCATTAGTGCCGTCTTG
131 TCGGGGTCCATTAGTGCCGTATTG
*
1089 AATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTTTCCATTGTTTATCGGCCTAACTATAATC
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT-GGCCTAACTATAATC
* * *
1153 ATTTT-TGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTTGGCC
65 ATTTTGT-TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCC
* * *
1217 TATCGGGGCCCATTAATGACGTATTG
129 TATCGGGGTCCATTAGTGCCGTATTG
* *
1243 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCCTAACAATAATCA
1 AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
* * * * *
1308 TTTTGGTGACATTAGTCAACTGTGAAGTGTTTAGCTGATTTAGAACACTTGTTATTTTGGGCCTA
66 TTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTA
* *
1373 TCGGGGTCCATTAGTTCCGTTTTG
131 TCGGGGTCCATTAGTGCCGTATTG
1397 AATC
1 AATC
1401 G
Statistics
Matches: 960, Mismatches: 78, Indels: 53
0.88 0.07 0.05
Matches are distributed among these distances:
136 44 0.05
137 81 0.08
143 3 0.00
147 3 0.00
152 12 0.01
153 73 0.08
154 642 0.67
155 101 0.11
156 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
AATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
TTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTA
TCGGGGTCCATTAGTGCCGTATTG
Found at i:683 original size:308 final size:308
Alignment explanation
Indices: 23--1387 Score: 1978
Period size: 308 Copynumber: 4.5 Consensus size: 308
13 TATTAAATTT
*
23 TCTTCGATTTGGCAAACCTTCAATGCTTTTCTTTCCATTGTTTATTGCCTAACTATAATCATTTT
1 TCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
* * * * ** **
88 GCTGAGATTAGTCAACTTTGAAGTTTCTAGCTCATTTGGTTGGGCCGATCGGGGTCTATTATTGG
65 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA--T--TTGGAAC-A-C-TTGT-TATT-TTGG
** * * *
153 GCCTATCGGGGCCCATTAGTTCCGT-TTCGAATCATCTTCGATTTGACAAACCTCAATGATTTTC
121 GCCTATCGGGGCCCATTAGTGACGTATT-GAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTC
* *
217 TTTCCATTGTTTATGGCCTAACTATGATAATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTTAG
185 TTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAG-TTTTTAG
*
282 CTGATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
249 CTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
342 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
1 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* * * *
407 TTGAGATTAGTCCACCGTGATGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCAATCGGG
66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
*
472 GCCCATTAATGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
131 GCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
* *
537 TATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
196 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
**
602 ACTTGTTATTTTGGGCCTATCATGGTCCATTAGTTCCGTTTTGAATCG
261 ACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
650 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
1 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* * *
715 GTGAGAATAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAGACTTGTTATTTTGGGCCTATCGGG
66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
*
780 GCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTT
131 GCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
*
845 TATGGCCTAACTATAATCATTTTTGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
196 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
* *
910 ACTTGTTATTTTCGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCA
261 ACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
958 TCTTCGATTTGG-------CAA----------TCCATTGTTTATGGCCTAACTATAATCATTTTG
1 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
*
1006 GTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGG
66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
* * * *
1070 GTCCATTAGTGCCGTCTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCTTTCCATTGTT
131 GCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
* *
1134 TATCGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAA
196 TAT-GGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
* * * ** * *
1199 CACTTGTTATTTTTGGCCTATCGGGGCCCATTAATGACGTATTGAATCT
260 CACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
* *
1248 TCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCCTAACAATAATCATTTTG
1 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
* * * * *
1313 GTGACATTAGTCAACTGTGAAGTGTTTAGCTGATTTAGAACACTTGTTATTTTGGGCCTATCGGG
66 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
*
1378 GTCCATTAGT
131 GCCCATTAGT
1388 TCCGTTTTGA
Statistics
Matches: 959, Mismatches: 67, Indels: 51
0.89 0.06 0.05
Matches are distributed among these distances:
289 18 0.02
290 167 0.17
291 82 0.09
297 3 0.00
301 3 0.00
307 79 0.08
308 389 0.41
309 111 0.12
310 6 0.01
311 2 0.00
312 1 0.00
313 1 0.00
314 5 0.01
316 1 0.00
318 73 0.08
319 18 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (308 bp):
TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTG
GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
GCCCATTAGTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAAC
ACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCG
Found at i:1358 original size:444 final size:445
Alignment explanation
Indices: 528--1400 Score: 1498
Period size: 444 Copynumber: 2.0 Consensus size: 445
518 TGCTTTTCTT
528 TCCATTGTTTATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
1 TCCATTGTTTATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* * *
593 ATTTAGAACACTTGTTATTTTGGGCCTATCATGGTCCATTAGTTCCGTTTTGAATCGTCTTCGAT
66 ATTTAGAACACTTGTTATTTTGGGCCTATCAGGGTCCATTAGTGCCGTCTTGAATCGTCTTCGAT
658 TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAAT
131 TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAAT
*
723 AGTCCACTGTGAAGTTTTTAGCTCATTTAGAAGACTTGTTATTTTGGGCCTATCGGGGCCCATTA
196 AGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
* * *
788 GTGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCT
261 ATGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCCT
* * * * *
853 AACTATAATCATTTTTGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTA
326 AACAATAATCATTTTGGTAACATTAGTCAACTGTGAAGTGTTTAGCTCATTTAGAACACTTGTTA
918 TTTTCGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAA
391 TTTTCGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAA
* * *
973 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTC
1 TCCATTGTTTATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* *
1038 ATTTGGAACACTTGTTATTTT-GGCCTATCGGGGTCCATTAGTGCCGTCTTGAATCGTCTTCGAT
66 ATTTAGAACACTTGTTATTTTGGGCCTATCAGGGTCCATTAGTGCCGTCTTGAATCGTCTTCGAT
* *
1102 TTGGCAAACCTCAATGC-TTTCTTTCCATTGTTTATCGGCCTAACTATAATCATTTTTGTGAGAT
131 TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT-GGCCTAACTATAATCATTTTGGTGAGAA
* * *
1166 TAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGCCCATT
195 TAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATT
1231 AATGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCC
260 AATGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCC
* *
1296 TAACAATAATCATTTTGGTGACATTAGTCAACTGTGAAGTGTTTAGCTGATTTAGAACACTTGTT
325 TAACAATAATCATTTTGGTAACATTAGTCAACTGTGAAGTGTTTAGCTCATTTAGAACACTTGTT
*
1361 ATTTTGGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATC
390 ATTTTCGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATC
1401 G
Statistics
Matches: 402, Mismatches: 25, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
443 18 0.04
444 302 0.75
445 82 0.20
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (445 bp):
TCCATTGTTTATGGCCTAACAATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
ATTTAGAACACTTGTTATTTTGGGCCTATCAGGGTCCATTAGTGCCGTCTTGAATCGTCTTCGAT
TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAAT
AGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTA
ATGACGTATTGAATCTTCTTCGATTTGGCAAACCTCAATGCTTTCCTTTCCATTGTTTATGGCCT
AACAATAATCATTTTGGTAACATTAGTCAACTGTGAAGTGTTTAGCTCATTTAGAACACTTGTTA
TTTTCGGCCTATCGGGGTCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAA
Done.