Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011929.1 Corchorus olitorius cultivar O-4 contig11962, 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, 674
Length: 1124
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Found at i:283 original size:154 final size:154
Alignment explanation
Indices: 2--369 Score: 610
Period size: 154 Copynumber: 2.4 Consensus size: 154
1 A
*
2 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
67 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
66 AAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
*
132 AATAACAAGTGTTCTAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
156 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATTGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* ** * * *
221 AAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAATACGTCATTAATGGGCCCCGATTGGCCCAA
66 AAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
286 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
310 AAAAACTTTACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
370 CCCCGATAGG
Statistics
Matches: 198, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 198 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (154 bp):
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATGAGCT
Found at i:440 original size:99 final size:99
Alignment explanation
Indices: 265--468 Score: 345
Period size: 99 Copynumber: 2.1 Consensus size: 99
255 ATACGTCATT
* * * * **
265 AATGGGCCCCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTTACGGTGGACTA
1 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
330 ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
364 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
1 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
*
429 ATCTCAGCAAAATGATTATAGTTAGGCCATAAAC
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
463 AATGGA
1 AATGGA
469 AAGAAAAGCA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (99 bp):
AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
Found at i:560 original size:253 final size:253
Alignment explanation
Indices: 111--622 Score: 907
Period size: 253 Copynumber: 2.0 Consensus size: 253
101 AAACGGAACT
* * *
111 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTA
1 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
* *
176 ATCTCACCAAAATGATTATTGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTAGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAA
* *
241 TCGAAGAAGATTCAATACGTCATTAATGGGCCCCGATTGGCCCAAAATAACAAGTGTTCCAAATG
131 TCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
306 AGCTAAAAACTTTACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
196 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
364 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
1 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
* *
429 ATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAA
* *
494 TCGAAGAAGATTCAATACGTCGCTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
131 TCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
559 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
196 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
617 AATGGA
1 AATGGA
623 AAGAAAAGCA
Statistics
Matches: 246, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
253 246 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (253 bp):
AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAA
TCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
Found at i:644 original size:154 final size:154
Alignment explanation
Indices: 364--1124 Score: 1227
Period size: 154 Copynumber: 4.9 Consensus size: 154
354 GGCCATAAAC
* *
364 AATGGACCCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTA
1 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
429 ATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
*
494 TCGAAGAAGATTCAATACGTCGCT
131 TCGAAGAAGATTCAATACGTCACT
* *
518 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTA
1 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
583 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* * **
648 TCGAAGACGATTCAAAACGGAACT
131 TCGAAGAAGATTCAATACGTCACT
* *
672 AATGGACCACGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTA
1 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * *
737 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGATGATTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* *
802 TCGAAGAAGATTCAATACATCATT
131 TCGAAGAAGATTCAATACGTCACT
* * *
826 AATGGGCCCCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTA
1 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* *
891 ATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCGAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* * * *
956 TCGAATACGATTCAAAACGTCACA
131 TCGAAGAAGATTCAATACGTCACT
* * * *
980 AACGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAGAAACTTCAAAGTTGACTA
1 AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* *
1045 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA-CATTGAGGTTTTCCTAA
66 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
1109 TCGAAGAAGATTCAAT
131 TCGAAGAAGATTCAAT
Statistics
Matches: 557, Mismatches: 50, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
153 28 0.05
154 529 0.95
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
AATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGAAGATTCAATACGTCACT
Found at i:757 original size:407 final size:407
Alignment explanation
Indices: 2--776 Score: 1361
Period size: 407 Copynumber: 1.9 Consensus size: 407
1 A
2 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
67 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
*
132 AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTG
131 AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* * **
197 TTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAATACGTC
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGA
* * * * * *
262 ATTAATGGGCCCCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTTACGGTGGA
261 ACTAATGGACCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
327 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGACCCCGATAGGCCAAAAATAACA
326 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGACCCCGATAGGCCAAAAATAACA
392 AGTGTTCCAAATGAGCT
391 AGTGTTCCAAATGAGCT
*
409 AAAAACTTCAAAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *** *
474 AAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAATACGTCGCTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
539 AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
131 AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* *
604 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGA
*
669 ACTAATGGACCACGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGA
261 ACTAATGGACCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
734 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
326 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
777 AAGAAAAGTA
Statistics
Matches: 347, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
407 347 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (407 bp):
AAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAA
AATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTAGCCAAATCGAAGAAGATTCAAAACGGA
ACTAATGGACCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGACCCCGATAGGCCAAAAATAACA
AGTGTTCCAAATGAGCT
Done.