Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010984.1 Corchorus olitorius cultivar O-4 contig11016, 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: 2322
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Found at i:391 original size:154 final size:154
Alignment explanation
Indices: 75--2322 Score: 3212
Period size: 154 Copynumber: 14.6 Consensus size: 154
65 AATAGAACCA
* * * *
75 TTTTGAATCGACATCGATTTGGCAAACCTCAAAAG-TTTTCTTTCCATTGCTTATGAACTAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACCTC-AAAGCTTTTCTTTCCATTGTTTATGGACTAACTA
* * * *
139 TAATCATTTTGGTGAGA-TAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAATTGTAATTTTA
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* * ** *
203 GGCCTTTCGGGGACCACCAGATCCG
130 GGCCTATCGGGGCCCATTAGTTCCG
* * * *
228 TTTTAAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * * * *
293 AATCATTTTGGTGAGA-TATGTCCACTATGAAGTTTTTAACTCTTTTGGAACAATTGTAATTTTG
66 AATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* *
357 GGCCTTTCGGGGCCCATTAGATCCG
130 GGCCTATCGGGGCCCATTAGTTCCG
* * *
382 TTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
447 AATCATTTTGGTGAGA-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
66 AATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* * * * *
511 GGCCTTTC-TGGACCACTAGTTCTG
130 GGCCTATCGGGGCCCATTAGTTCCG
* * *
535 TTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* *
600 AATCATTTTGGTCAGA-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTG
66 AATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* * *
664 GGCCTTTCGGGGCCCATCAGTTCCA
130 GGCCTATCGGGGCCCATTAGTTCCG
* * *
689 TTTTGAATCGACTTCGATTTGGCAAACCTAAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * *
754 AATCATTTTGGTGAGA-AATGTCCACTGTGAAGTTTTTACCTCATTTGGAACAATT-TTAATTTT
66 AATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT-ATTTT
* *
817 GGGCCTTTCGAGGCCCATTAGATT-CG
129 GGGCCTATCGGGGCCCATTAG-TTCCG
* * * *
843 TTTTGAATCGACTTCGATTTGGCAAACCTAAAAGCTTTTCTTT-AAGTTGTTTATGGCCTAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTA
* ** * * *
907 TAATCATTTTGATGTCATTAGTCCACTTTGAAATTCTTAGCTCATTTGGAACACTTGTTA-TTTG
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
*
971 GGCCTATCGGGGCCTATTAGTTCCG
130 GGCCTATCGGGGCCCATTAGTTCCG
* *
996 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGAATAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * * *
1061 AATCATTTTGGTGAGATTAGTCCACAGTAAAGTTTATAGCTCATTTGCAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
** *
1126 GCCTATCGGGGCCCATTAGTGACA
131 GCCTATCGGGGCCCATTAGTTCCG
* * *
1150 TTTTGAATCGTCTTCGATTTGACAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * *
1215 AATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTATAGCTCATTTGGAACACTTGTTATTTTGC
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
*
1280 GCCCATCGGGGCCCATTAGTTCCG
131 GCCTATCGGGGCCCATTAGTTCCG
* * * * *
1304 TTTTGAATCGTCTTCAATTTGGCAAGCCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGACTAACTA
* * *
1368 TAATCATTTTGATGAGATTAGTCCACTATGAAGTTCTTAGCTCAATTT-GAACACTTGTTATTTT
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTT
* *
1432 GGGCCAATCGGGGCCCATTAGTTTCG
129 GGGCCTATCGGGGCCCATTAGTTCCG
* *
1458 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTTTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
1523 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* ** *
1588 GCCTAACGGGGCCCATTAGTGACA
131 GCCTATCGGGGCCCATTAGTTCCG
* *
1612 TTTTGAATCGTCTTCGATTTGGCAAGCCTCAAGGCTTTTCTTTCCATTGTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* *
1677 AATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
**
1742 GCCTATCGGGGCCCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTTCCG
*
1766 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
*
1831 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* **
1896 GCCTATCGCGGCCCATTAGTGACG
131 GCCTATCGGGGCCCATTAGTTCCG
* * *
1920 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTGTGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * * *
1985 AATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCTTTTGGAACACTTGCTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
2050 GCCTATC-GGGCCCATTAGTTCCG
131 GCCTATCGGGGCCCATTAGTTCCG
* * *
2073 CTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
*
2138 AATCACTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* * **
2202 GCCTATCAGGGCCCATTCGTGACG
131 GCCTATCGGGGCCCATTAGTTCCG
*
2226 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
* * *
2291 ATTAATTTTGGTGAGATTGGTCCACTGTGAAG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAG
Statistics
Matches: 1920, Mismatches: 159, Indels: 32
0.91 0.08 0.02
Matches are distributed among these distances:
152 42 0.02
153 562 0.29
154 1305 0.68
155 11 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (154 bp):
TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAACTAT
AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
GCCTATCGGGGCCCATTAGTTCCG
Found at i:949 original size:461 final size:460
Alignment explanation
Indices: 75--2322 Score: 3180
Period size: 461 Copynumber: 4.9 Consensus size: 460
65 AATAGAACCA
* * *
75 TTTTGAATCGACATCGATTTGGCAAACCTCAAAAG-TTTTCTTTCCATTGCTTATGAACTAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACCTC-AAAGCTTTTCTTTCCATTGTTTATGAACTAACTA
* * * *
139 TAATCATTTTGGTGAGA-TAGTCCACTGTGAAGTTTTTAACTCATTTGGAACAATTGTAATTTTA
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* * ** * * *
203 GGCCTTTCGGGGACCACCAGATCCGTTTTAAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
130 GGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* * *
268 TTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TATGTCCACTATGAAGTTTTTAA
195 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAG
* * * * * *
332 CTCTTTTGGAACAATTGTAATTTTGGGCCTTTCGGGGCCCATTAGATCCGTTTTGAATCGACTTC
259 CTCATTTGGAACACTT-TTATTTTGGGCCTATCGGGGCCCATTAG-TACGTTTTGAATCGTCTTC
* *
397 GATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
322 GATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAG
* * * *
462 A-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTTTC-TGGACC
387 ATTA-GTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
*
525 ACTAGTTCTG
451 ATTAGTTCTG
* *
535 TTTTGAATCGACTTCGATTTGGCAAACCTCAAAACTTTTCTTTCCATTGTTTATGAACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGAACTAACTAT
* *
600 AATCATTTTGGTCAGA-TATGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTG
66 AATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
* * *
664 GGCCTTTCGGGGCCCATCAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTAAAAGCTTTTC
130 GGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
729 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-AATGTCCACTGTGAAGTTTTTAC
195 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA-GTCCACTGTGAAGTTTTTAG
* * * * *
793 CTCATTTGGAACAATTTTAATTTTGGGCCTTTCGAGGCCCATTAGATTCGTTTTGAATCGACTTC
259 CTCATTTGGAACACTTTT-ATTTTGGGCCTATCGGGGCCCATTAG-TACGTTTTGAATCGTCTTC
* * *
858 GATTTGGCAAACCTAAAAGCTTTTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGT
322 GATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTTGATGA
* * * *
922 CATTAGTCCACTTTGAAATTCTTAGCTCATTTGGAACACTTGTTA-TTTGGGCCTATCGGGGCCT
386 GATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
*
986 ATTAGTTCCG
451 ATTAGTTCTG
*
996 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGAA-TAACTA
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTAT-GAACTAACTA
* * * *
1060 TAATCATTTTGGTGAGATTAGTCCACAGTAAAGTTTATAGCTCATTTGCAACACTTGTTATTTTG
65 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
** * * *
1125 GGCCTATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGACAAACCTCAAGGCTTTTC
130 GGCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTC
* *
1190 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTATAGC
195 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
* * * *
1255 TCATTTGGAACACTTGTTATTTTGCGCCCATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCA
260 TCATTTGGAACACTT-TTATTTTGGGCCTATCGGGGCCCATTAG-TACGTTTTGAATCGTCTTCG
* * *
1320 ATTTGGCAAGCCTCAAAGCTATTCTTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGAG
323 ATTTGGCAAACCTCAAAGCTTTTCTTTCCA-TTGTTTATGGCCTAACTATAATCATTTTGATGAG
* *
1384 ATTAGTCCACTATGAAGTTCTTAGCTCAATTT-GAACACTTGTTATTTTGGGCCAATCGGGGCCC
387 ATTAGTCCACTGTGAAGTTCTTAGCTC-ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
1448 ATTAGTT-TCG
451 ATTAGTTCT-G
* * *
1458 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTTTTTATGGACTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGAACTAACTAT
1523 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* ** * * *
1588 GCCTAACGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAGCCTCAAGGCTTTTCT
131 GCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCT
* *
1653 TTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCT
196 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
*
1718 CATTTGGAACACCTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGA
261 CATTTGGAACA-CTTTTATTTTGGGCCTATCGGGGCCCATTAGT-ACGTTTTGAATCGTCTTCGA
* * *
1783 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGAT
324 TTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGAT
*
1848 TAGTCCACTGTGAAGTT-TTAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGCGGCCCAT
389 TAGTCCACTGTGAAGTTCTT-AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
*
1912 TAGTGAC-G
453 TAGT-TCTG
* * **
1920 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTGTGGCCTAACTAT
1 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGAACTAACTAT
* * * *
1985 AATCAATTTGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCTTTTGGAACACTTGCTATTTTGG
66 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
** *
2050 GCCTATC-GGGCCCATTAGTTCCGCTTTGAATCGACTTCGATTTGGCAAACCTCAATGCTTTTCT
131 GCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCT
* *
2114 TTCCATTGTTTATGGACTAACTATAATCACTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCT
196 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
* *
2178 CATTTGGAACACTTGTTATTTTGGGCCTATCAGGGCCCATTCGTGACGTTTTGAATCGTCTTCGA
261 CATTTGGAACACTT-TTATTTTGGGCCTATCGGGGCCCATTAGT-ACGTTTTGAATCGTCTTCGA
* * * * *
2243 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATATTAATTTTGGTGAGAT
324 TTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGAT
*
2308 TGGTCCACTGTGAAG
389 TAGTCCACTGTGAAG
Statistics
Matches: 1633, Mismatches: 133, Indels: 44
0.90 0.07 0.02
Matches are distributed among these distances:
459 5 0.00
460 232 0.14
461 815 0.50
462 578 0.35
463 3 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (460 bp):
TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGAACTAACTAT
AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
GCCTATCGGGGCCCATTAGTTCCATTTTGAATCGACTTCGATTTGGCAAACCTCAAAGCTTTTCT
TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
CATTTGGAACACTTTTATTTTGGGCCTATCGGGGCCCATTAGTACGTTTTGAATCGTCTTCGATT
TGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTA
GTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAG
TTCTG
Done.