Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020879.1 Corchorus olitorius cultivar O-4 contig20912, 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, 733
Length: 1223
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Found at i:394 original size:154 final size:154
Alignment explanation
Indices: 1--1223 Score: 1784
Period size: 154 Copynumber: 7.9 Consensus size: 154
* * * *
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAACCTTCAAAGTGGACTAATCTTACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * * *
66 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
** *
131 TGGAACTAATGGGCCCTGATAGGC
131 CAGAACTAATGGGCCCCGATAGGC
* * * * * * *
155 CCAAAAGTAAAAAGTGTTTCAATTGAGCTAAAAACTTCATAGTGGACTAATCTTACCGAAATGGT
1 CCAAAA-TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
220 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGGTTTCCAAATCGAAGACGATTCAAA
65 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAA
* *
285 ACAAAACTAATTGGCCCCGATAGGC
130 ACAGAACTAATGGGCCCCGATAGGC
* *
310 CCAAAATAACTAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
375 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
**
440 TGGAACTAATGGGCCCCGATAGGC
131 CAGAACTAATGGGCCCCGATAGGC
* * * *
464 CCAAAATAACAAGTATTCGAAATGAGCTAAAAACTTCACAGTGCACTAATCTCACCAAAATGATA
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * * *
529 ACAGTTAGGGCATAAAGAATGGAAAGAAACGCATTGAAGGTTG-CAAATAGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
* ** * *
593 AATCACTAATGGGCCCCAATAGGG
131 CAGAACTAATGGGCCCCGATAGGC
* * *
617 CAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAACGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * *
682 ATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGACGGTTGCCAAATTGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
747 CAGAACTAATGGGCCCCGATAGGC
131 CAGAACTAATGGGCCCCGATAGGC
* * *
771 CAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAAGGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* *
836 ATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGACGGTTCGCCAAATCGAAGACGATTCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTT-GCCAAATCGAAGACGATTCAAA
901 ACA-AACTAATGGGCCCCGATAGGC
130 ACAGAACTAATGGGCCCCGATAGGC
925 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
990 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGGTTGCCAAAATCGAAGACGATTCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCC-AAATCGAAGACGATTCAAA
*
1055 ACGGAACTAATGGGCCCCGATAGGC
130 ACAGAACTAATGGGCCCCGATAGGC
* * *
1080 CCAAAATAACAACTGTTCCAAATGAGCTAAAAAACTTCACTGTGGACCTAAAGTCTCACCAGGTA
1 CCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGA-CT-AA-TCTCACCA--AA
* * *
1145 ATAAGTTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
60 ATGA-TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGA
*
1210 TTCAAAACGGAACT
124 TTCAAAACAGAACT
Statistics
Matches: 968, Mismatches: 89, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
153 138 0.14
154 519 0.54
155 208 0.21
156 16 0.02
157 2 0.00
158 2 0.00
159 8 0.01
161 31 0.03
162 44 0.05
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (154 bp):
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
CAGAACTAATGGGCCCCGATAGGC
Found at i:698 original size:307 final size:307
Alignment explanation
Indices: 1--1217 Score: 1817
Period size: 307 Copynumber: 3.9 Consensus size: 307
* * *
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAACCTTCAAAGTGGACTAATCTTACCAAAATGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * *
66 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * * * * *
131 TGGAACTAATGGGCCCTGATAGGCCCAAAAGTAAAAAGTGTTTCAATTGAGCTAAAAACTTCATA
131 CGGAACTAATGGGCCCCGATAGGCCCAAAA-TAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* * * *
196 GTGGACTAATCTTACCGAAATGGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGG
195 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGG
* *
261 TTTCCAAATCGAAGACGATTCAAAACAAAACTAATTGGCCCCGATAGGC
260 TTGCCAAATCGAAGACGATTCAAAAC-AAACTAATGGGCCCCGATAGGC
** *
310 CCAAAATAACTAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
375 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * *
440 TGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCGAAATGAGCTAAAAACTTCACAG
131 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * * * * *
505 TGCACTAATCTCACCAAAATGATAACAGTTAGGGCATAAAGAATGGAAAGAAACGCATTGAAGGT
196 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGT
* * *
570 TG-CAAATAGAAGACGATTCAAAA-AATCACTAATGGGCCCCAATAGGG
261 TGCCAAATCGAAGACGATTCAAAACAA--ACTAATGGGCCCCGATAGGC
* *
617 CAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAACGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * *
682 ATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGACGGTTGCCAAATTGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* *
747 CAGAACTAATGGGCCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
131 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * * *
812 TGGACTAAACTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGACGGT
196 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGT
877 TCGCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCCGATAGGC
261 T-GCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCCGATAGGC
*
925 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* *
990 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGGTTGCCAAAATCGAAGACGATTCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC-AAATCGAAGACGATTCAAA
*
1055 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTAAAAAACTTCAC
130 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCAC
* * * *
1120 TGTGGACCTAAAGTCTCACCAGGTAATAAGTTATAGTTAGGCCATAAACAATGGAACGAAAAGCA
194 AGTGGA-CT-AA-TCTCACCA--AAATGA-TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
*
1185 TTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
253 TTGAAGGTTGCCAAATCGAAGACGATTCAAAAC
1218 GGAACT
Statistics
Matches: 820, Mismatches: 75, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
305 2 0.00
307 276 0.34
308 208 0.25
309 237 0.29
310 18 0.02
311 2 0.00
312 2 0.00
313 7 0.01
315 27 0.03
316 41 0.05
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (307 bp):
CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGT
TGCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCCGATAGGC
Found at i:872 original size:461 final size:461
Alignment explanation
Indices: 1--1223 Score: 1793
Period size: 461 Copynumber: 2.6 Consensus size: 461
* * * *
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAACCTTCAAAGTGGACTAATCTTACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * * *
66 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
* * * * * *
131 TGGAACTAATGGGCCCTGATAGGCCCAAAAGTAAAAAGTGTTTCAATTGAGCTAAAAACTTCATA
131 AGGAACTAATGGGCCCCGATAGG-CCAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACA
* ** *
196 GTGGACTAATCTTACCGAAATGGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGG
195 GTGGACTAATCTCACC-AAAAAGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGG
* * * * *
261 TTTCCAAATCGAAGACGATTCAAAACAAAACTAATTGGCCCCGATAGGCCCAAAATAACTAGTGT
259 TTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCAAAAATAACAAGTGT
* *
326 TCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
324 TCCAAATGAGCTAAAAACATCACAGTGGACTAAACTCACCAAAAGGATTATAGTTAGGCCATAAA
* **
391 CAATGGAAAGAAAAGCATTGAGGGTT-GCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
389 CAATGGAAAGAAAAGCATTGACGGTTCGCCAAATCGAAGACGATTCAAAA-CAAACTAATGGGCC
455 CCGATAGGC
453 CCGATAGGC
* * * *
464 CCAAAATAACAAGTATTCGAAATGAGCTAAAAACTTCACAGTGCACTAATCTCACCAAAATGATA
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * * * *
529 ACAGTTAGGGCATAAAGAATGGAAAGAAACGCATTGAAGGTTG-CAAATAGAAGACGATTCAAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
*** * *
593 AATCACTAATGGGCCCCAATAGGGCAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAG
131 AGGAACTAATGGGCCCCGATAGGCCAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * *
658 TGGACTAATCTCACCAAAACGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGACGGT
196 TGGACTAATCTCACCAAAAAG-TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGT
*
723 TGCCAAATTGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCAAAAATAACAAGTGTT
260 TGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCAAAAATAACAAGTGTT
*
788 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAAGGATTATAGTTAGGCCATAAAC
325 CCAAATGAGCTAAAAACATCACAGTGGACTAAACTCACCAAAAGGATTATAGTTAGGCCATAAAC
*
853 AATGGAAAGAAAGGCATTGACGGTTCGCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCC
390 AATGGAAAGAAAAGCATTGACGGTTCGCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCC
918 GATAGGC
455 GATAGGC
925 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
1 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
990 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAAGGTTGCCAAAATCGAAGACGATTCAAA
66 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCC-AAATCGAAGACGATTCAAA
* * * *
1055 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTAAAAAACTTCAC
130 AAGGAACTAATGGGCCCCGATAGGCCAAAAATAAAAAGTGTTCCAAATGAGCT-AAAAACTTCAC
* *
1120 TGTGGACCTAAAGTCTCACCAGGTAATAAGTTATAGTTAGGCCATAAACAATGGAACGAAAAGCA
194 AGTGGA-CT-AA-TCTCACCA---AA-AAGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* *
1185 TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT
252 TTGAAGGTTGCCAAATCGAAGACGATTCAAAACAGAACT
Statistics
Matches: 675, Mismatches: 73, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
460 4 0.01
461 355 0.53
462 59 0.09
463 156 0.23
464 16 0.02
465 2 0.00
466 2 0.00
467 8 0.01
470 71 0.11
471 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (461 bp):
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAAA
AGGAACTAATGGGCCCCGATAGGCCAAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACCAAAAAGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGGTT
GCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCAAAAATAACAAGTGTTC
CAAATGAGCTAAAAACATCACAGTGGACTAAACTCACCAAAAGGATTATAGTTAGGCCATAAACA
ATGGAAAGAAAAGCATTGACGGTTCGCCAAATCGAAGACGATTCAAAACAAACTAATGGGCCCCG
ATAGGC
Done.