Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008820.1 Corchorus olitorius cultivar O-4 contig08847, 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, 633
Length: 1056
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Found at i:315 original size:154 final size:154
Alignment explanation
Indices: 1--1056 Score: 1530
Period size: 154 Copynumber: 6.9 Consensus size: 154
* * *
1 ATTATAGTTAGGCCATACACTATGGAAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
1 ATTATAGTTAGGCCATAAACAATGG--AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
** * *
66 CAAAACGTTACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAACTT
64 CAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
*
131 CACAGTGGACTAATCTCACCAAAAGA
129 CACAGTGGACTAATCTCACCAAAAGT
* * * *
157 ATTATAGTTAGGCCCTAAAAAATGGAAAGAAAAGCTTTGGGGTTTGCCAAATCGAAGACGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
* * *
222 AAACGGAACTAACGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAAATGAGCTAAAAACTTCA
66 AAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
287 CAGTGGGCTAATCTCACCAAAAGT
131 CAGTGGACTAATCTCACCAAAAGT
* * *
311 ATTATAGTAACGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACTATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
** * *
376 AAACGTCACTAACGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
66 AAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
441 CAGTGGACTAATCTCACCAAAAGG
131 CAGTGGACTAATCTCACCAAAAGT
* *
465 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTG-GGTTTGCCAAATCGAAAACGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
** * *
529 AAACAAAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTTCAAATCAGCTAAAAACTTCA
66 AAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
594 CAGTGGACTAATCTCACCAAAA-T
131 CAGTGGACTAATCTCACCAAAAGT
* ** *
617 GATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCAATTGGGGTTTGGGAAATTGAAGACGATT
1 -ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-ATTGAGGTTTGCCAAATCGAAGACGATT
* * *
681 TAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTT
64 CAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
746 CACAGTGGACTAAGCTCACCTATA-T
129 CACAGTGGACTAATCTCACCAAAAGT
*
771 GATTATAGTTAGGCCATAAACAATGGACA-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
1 -ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
* **
835 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAACGCTTC
65 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
900 ACAGTGGACTAATCTCACCAAAAGG
130 ACAGTGGACTAATCTCACCAAAAGT
* * ** *
925 ATTATAGTTAGGCCATTAACAATTGAAAGAAAAGCATTTTGGTTTGCCAAATCGAAGATGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
** * *
990 AAACGTCACTAATGGGTCCC-AATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC
66 AAACGGAACTAATGGGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
1054 ACA
130 ACA
Statistics
Matches: 813, Mismatches: 81, Indels: 14
0.90 0.09 0.02
Matches are distributed among these distances:
152 5 0.01
153 266 0.33
154 521 0.64
156 21 0.03
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (154 bp):
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
AAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAAGT
Found at i:702 original size:307 final size:306
Alignment explanation
Indices: 1--1056 Score: 1564
Period size: 307 Copynumber: 3.4 Consensus size: 306
* * *
1 ATTATAGTTAGGCCATACACTATGGAAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
1 ATTATAGTTAGGCCATAAACAATGG--AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
* * *
66 CAAAACGTTACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAACTT
64 CAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * *
131 CACAGTGGACTAATCTCACCAAAAGAATTATAGTTAGGCCCTAAAAAATGGAAAGAAAAGCT-TT
129 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-TATT
* * *
195 GGGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAACGGGCCCCGATAGGCCCAAAGTAACA
193 -GGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
*
260 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGGCTAATCTCACCAAAAG
257 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAG
* * *
310 TATTATAGTAACGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACTATTC
1 -ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
* *
375 AAAACGTCACTAACGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
440 ACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGG
130 ACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGG
* **
505 GTTTGCCAAATCGAAAACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
195 GTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
* *
570 GTTTCAAATCAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
260 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA-G
* ** * *
618 ATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCAATTGGGGTTTGGGAAATTGAAGACGATTT
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-ATTGAGGTTTGCCAAATCGAAGACGATTC
* *
682 AAAACAG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTT
65 AAAAC-GTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
* * * * * *
746 CACAGTGGACTAAGCTCACCTATATGATTATAGTTAGGCCATAAACAATGGACA-AAAAGCATTG
129 CACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTG
810 AGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAA
194 -GGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAA
* **
875 GTGTTCCAAATGAGATAAACGCTTCACAGTGGACTAATCTCACCAAAAGG
258 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA-G
* * ** *
925 ATTATAGTTAGGCCATTAACAATTGAAAGAAAAGCATTTTGGTTTGCCAAATCGAAGATGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
* *
990 AAACGTCACTAATGGGTCCC-AATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC
66 AAACGTCACTAATGGGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
1054 ACA
130 ACA
Statistics
Matches: 675, Mismatches: 63, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
306 18 0.03
307 473 0.70
308 163 0.24
310 21 0.03
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (306 bp):
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
AAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGGG
TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAG
Found at i:971 original size:461 final size:462
Alignment explanation
Indices: 1--1056 Score: 1577
Period size: 461 Copynumber: 2.3 Consensus size: 462
* * *
1 ATTATAGTTAGGCCA-TACACTATGGAAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
1 ATTATAGTTAGGCCATTA-ACAATGG--AAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGAT
* * *
65 TCAAAACGTTACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAACT
63 TCAAAACGTAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
* *
130 TCACAGTGGACTAATCTCACCAAAAGAATTATAGTTAGGCCCTAAAAAATGGAAAGAAAAGCTTT
128 TCACAGTGGACTAATCTCACCAAAAGAATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCATT
* * *
195 GGGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAACGGGCCCCGATAGGCCCAAAGTAACA
193 GGGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAACGGGCCCCGAAAGGCCCAAAATAACA
* * *
260 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGGCTAATCTCACCAAAAGTATTATAGTAACGCC
258 AGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAAAAGTATTATAGTAACGCC
* **
325 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACTATTCAAAACGTCACTAACG
323 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAACG
* *
390 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
388 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGACTAATCT
455 CACCAAAAGG
453 CACCAAAAGG
* * * *
465 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTA-TTGGGTTTGCCAAATCGAAAACGATTCA
1 ATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGATTCA
** * *
529 AAACAAAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTTCAAATCAGCTAAAAACTTCA
66 AAACGTAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
594 CAGTGGACTAATCTCACCAAAATG-ATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCAATTG
131 CAGTGGACTAATCTCACCAAAA-GAATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGC-ATTG
** * * *
657 GGGTTTGGGAAATTGAAGACGATTTAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAA
194 GGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAACGGGCCCCGAAAGGCCCAAAATAACAA
* * * *
722 GTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCTATA-TGATTATAGTTAGGCC
259 GTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAAAAGT-ATTATAGTAACGCC
* *
786 ATAAACAATGGACA-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
323 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAACG
**
850 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAACGCTTCACAGTGGACTAATCT
388 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGACTAATCT
915 CACCAAAAGG
453 CACCAAAAGG
* * *
925 ATTATAGTTAGGCCATTAACAATTGAAAGAAAAGCATTTTGGTTTGCCAAATCGAAGATGATTCA
1 ATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGATTCA
* * *
990 AAACGTCACTAATGGGTCCC-AATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTC
66 AAACGTAACTAATGGGCCCCGAA-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
1054 ACA
130 ACA
Statistics
Matches: 532, Mismatches: 54, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
460 159 0.30
461 341 0.64
462 10 0.02
464 21 0.04
465 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (462 bp):
ATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAGACGATTCA
AAACGTAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAAGAATTATAGTTAGGCCATAAAAAATGGAAAGAAAAGCATTGGG
GTTTGCCAAATCGAAGACGATTCAAAACAGAACTAACGGGCCCCGAAAGGCCCAAAATAACAAGT
GTCCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCTCACCAAAAGTATTATAGTAACGCCATA
AACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAACGGGC
CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCACAGTGGACTAATCTCAC
CAAAAGG
Done.