Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011696.1 Corchorus olitorius cultivar O-4 contig11729, 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, 621
Length: 1036
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Found at i:460 original size:154 final size:154
Alignment explanation
Indices: 2--1033 Score: 1624
Period size: 154 Copynumber: 6.7 Consensus size: 154
1 T
*
2 TAATCTACACCAAAATGAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATTGAGGTTTG
1 TAATCT-CACCAAAATG-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CTTTGAGGTTTG
67 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
63 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
132 AAATGAGCTAAAAACTTCACAGTGGAC
128 AAATGAGCTAAAAACTTCACAGTGGAC
*
159 TAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCC
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTG-CC
*
224 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
*
289 ATGAGCTAAAAATTTCACAGTGGAC
130 ATGAGCTAAAAACTTCACAGTGGAC
314 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
** * *
379 AATCGAAGACGATTCAAAACGTCAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
444 TGAGCTAAAAACTTCACAGTGGAC
131 TGAGCTAAAAACTTCACAGTGGAC
* * *
468 TAATCTCATCAAATTGATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
* *
533 AATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAATAAGTGTT-CAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
597 TTGAGCTAAGAACTTCATAGTGGAC
131 -TGAGCTAAAAACTTCACAGTGGAC
* * *
622 TAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAATAGCTTTGAGGTTTGCC
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCC
* *
686 AAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATGGGCCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* * *
751 ATGATCCT--TAACTTCATAGTGGAC
130 ATGA-GCTAAAAACTTCACAGTGGAC
* * * * *
775 TAATCTCACCAAATTGATTATAGTTAGGCCTTAAACAATGGAAATAAAAGCATTGAGGTTTGTCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
**
840 AATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
905 TGAGCTAAAAACTTCACAGTGGAC
131 TGAGCTAAAAACTTCACAGTGGAC
* * * * *
929 TAATCTAACCAAAATGATTATATTTAGTCCCTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
* *
994 AATCGAAGACGATTTCAAAACCG-ACTAATGGGCCCTGATA
66 AATCGAAGACGA-TTCAAAACGGAACTAATGGGCCCCGATA
1034 TGC
Statistics
Matches: 811, Mismatches: 55, Indels: 21
0.91 0.06 0.02
Matches are distributed among these distances:
152 3 0.00
153 138 0.17
154 456 0.56
155 199 0.25
156 9 0.01
157 6 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (154 bp):
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGAC
Found at i:920 original size:307 final size:307
Alignment explanation
Indices: 2--1033 Score: 1622
Period size: 307 Copynumber: 3.3 Consensus size: 307
1 T
2 TAATCTACACCAAAATGAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATTGAGGTTTG
1 TAATCT-CACCAAAATG-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTTG
67 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
63 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
* *
132 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAA
128 AAATGAGCT-AAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAA
* *
197 TGGAAAGAAAAGCTTTGAGGTTTGCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCG
192 TGGAAAGAAAAGCTTTGAGGTTTG-CCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCG
*
262 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAC
256 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
314 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
** * *
379 AATCGAAGACGATTCAAAACGTCAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
444 TGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAATTGATTATAGTTAGGCCATAAACAAAGG
131 TGAGCT-AAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATGG
509 AAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAG
195 AAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAG
* * *
574 GCCCAAAATAATAAGTGTT-CAAATTGAGCTAAGAACTTCATAGTGGAC
260 GCCCAAAATAACAAGTGTTCCAAA-TGAGCTAAAAACTTCACAGTGGAC
* * * *
622 TAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAATAGCTTTGAGGTTTGCC
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCC
* *
686 AAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATGGGCCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
* * * *
751 ATGATCCT-TAACTTCATAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCTTAAACAATG
130 ATGA-GCTAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATG
* * * **
815 GAAATAAAAGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATA
194 GAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATA
880 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
259 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * * *
929 TAATCTAACCAAAATGATTATATTTAGTCCCTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
* *
994 AATCGAAGACGATTTCAAAACCG-ACTAATGGGCCCTGATA
66 AATCGAAGACGA-TTCAAAACGGAACTAATGGGCCCCGATA
1034 TGC
Statistics
Matches: 664, Mismatches: 50, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
306 1 0.00
307 237 0.36
308 216 0.33
309 160 0.24
310 34 0.05
311 10 0.02
312 6 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (307 bp):
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGG
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
Found at i:926 original size:461 final size:461
Alignment explanation
Indices: 2--1033 Score: 1662
Period size: 461 Copynumber: 2.2 Consensus size: 461
1 T
2 TAATCTACACCAAAATGAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATTGAGGTTTG
1 TAATCT-CACCAAAATG-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTTG
67 CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
63 CCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
132 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAA
127 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAA
*
197 TGGAAAGAAAAGCTTTGAGGTTTGCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCG
192 TGGAAAGAAAAGCTTTGAGGTTTGCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
* *
262 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACCAAA
257 ATAGGCCCAAAATAACAAGTGTTCCAAATGACCT-AAAACTTCACAGTGGACTAATCTCACCAAA
*
327 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGAT
321 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
* *
392 TCAAAACGTCAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACT
386 TCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
457 TCACAGTGGAC
451 TCACAGTGGAC
* * * *
468 TAATCTCATCAAATTGATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
*
533 AATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAATAAGTGTT-CAAA
66 AATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
597 TTGAGCTAAGAACTTCATAGTGGACTAATCTCA-TCAAAATGATTATAGTTAGGCCATAAACAAC
130 -TGAGCTAAAAACTTCACAGTGGACTAATCTCACT-AAAATGATTATAGTTAGGCCATAAACAA-
* * *
661 T-TAAAGAATAGCTTTGAGGTTTG-CCAAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCG
192 TGGAAAGAAAAGCTTTGAGGTTTGCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
* * *
724 ATGGGCCCAAAATAACAAGTGTTCCAAATGATCCT-TAACTTCATAGTGGACTAATCTCACCAAA
257 ATAGGCCCAAAATAACAAGTGTTCCAAATGA-CCTAAAACTTCACAGTGGACTAATCTCACCAAA
* * * *
788 TTGATTATAGTTAGGCCTTAAACAATGGAAATAAAAGCATTGAGGTTTGTCAAATCGAAGACGAT
321 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
853 TCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
386 TCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
918 TCACAGTGGAC
451 TCACAGTGGAC
* * * *
929 TAATCTAACCAAAATGATTATATTTAGTCCCTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
*
994 AATCGAAGACGATTTCAAAACCG-ACTAATGGGCCCTGATA
66 AATCGAAGACGA-TTCAAAA-CGAACTAATGGGCCCCGATA
1034 TGC
Statistics
Matches: 527, Mismatches: 32, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
461 245 0.46
462 81 0.15
463 153 0.29
464 34 0.06
465 8 0.02
466 6 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (461 bp):
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCTTTGAGGTTTGCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAATGACCTAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
ACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGAC
Done.