Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011533.1 Corchorus olitorius cultivar O-4 contig11566, 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: 3318
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:517 original size:154 final size:154
Alignment explanation
Indices: 237--1248 Score: 1571
Period size: 154 Copynumber: 6.6 Consensus size: 154
227 TTGGCGCATC
* * *
237 ATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGCGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
302 TCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
367 CGAAGACAATTCAAAACGGAACTA
131 CGAAGACAATTCAAAACGGAACTA
* * * *
391 ATGGGCCCCGATAGGCACAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTAGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
456 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
* **
521 CGAAGACGATTCAAAACGTCACTA
131 CGAAGACAATTCAAAACGGAACTA
545 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
610 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
* *
675 CGAAGACAATTCAAAATGGCACTA
131 CGAAGACAATTCAAAACGGAACTA
* *
699 ATGGGCCGCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* *
764 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCATTG-GGAATTGACAAA
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAA
* *
827 TTGAAGACGATTCAAAACGGAACTA
130 TCGAAGACAATTCAAAACGGAACTA
* * *
852 ATGGGACCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* ** * * * * *
917 TCTCACCAAAATGATTATAGTTAGGCCTTGCACAATGGAAAGAAAGGCATCGAAGG-TTACCGAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAA
* **
981 TCGAAGACGATTCAAAACGTCACTA
130 TCGAAGACAATTCAAAACGGAACTA
* * * *
1006 ATGGTCTCCGATAGGCCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTAACAGTGGACTAA
1 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
1071 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAATAAAAGCATTGAGGTTTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
*
1136 CGAAGACAATTCAAAACAGAACTA
131 CGAAGACAATTCAAAACGGAACTA
* *
1160 ATGGGCCTCGATAGGCCCAAAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGAC
1 ATGGGCCCCGATAGGCCC---AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
1225 TAATCTCACCAAAACGATTATAGT
63 TAATCTCACCAAAATGATTATAGT
1249 GATGTGCCAA
Statistics
Matches: 778, Mismatches: 72, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
152 2 0.00
153 139 0.18
154 571 0.73
156 2 0.00
157 64 0.08
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
CGAAGACAATTCAAAACGGAACTA
Found at i:1100 original size:461 final size:462
Alignment explanation
Indices: 237--1248 Score: 1625
Period size: 461 Copynumber: 2.2 Consensus size: 462
227 TTGGCGCATC
* * * *
237 ATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATTGCGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* * *
302 TCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGACAAAT
* * *
367 CGAAGACAATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATTACAAGTGTTCCAAATGA
131 CGAAGACAATTCAAAACGGAACTAATGGGACCCGAAAGGCACAAAATAACAAGTGTTCCAAATGA
432 GCTAAAAACTTCAAAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
196 GCTAAAAACTTCAAAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
497 GAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
261 GAAAAGCATCGAGGATTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
*
562 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
326 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGATTA
*
627 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAAT
391 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAAC
* *
692 GGCACTA
456 AGAACTA
*
699 ATGGGCCGCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
1 ATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
764 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCATTG-GGAATTGACAAA
66 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-ATTGACAAA
* * * *
827 TTGAAGACGATTCAAAACGGAACTAATGGGACCCGAAAGGCCCAAAATAACAAGTGTTCCAATTG
130 TCGAAGACAATTCAAAACGGAACTAATGGGACCCGAAAGGCACAAAATAACAAGTGTTCCAAATG
* * * **
892 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCTTGCACAATGGAA
195 AGCTAAAAACTTCAAAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* * * * *
957 AGAAAGGCATCGAAGG-TTACCGATTCGAAGACGATTCAAAACGTCACTAATGGTCTCCGATAGG
260 AGAAAAGCATCG-AGGATTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG
*
1021 CCCAAAATAACAAGTGTTCCATATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGAT
324 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGAT
*
1086 TATAGTTAGGCCATAAACAATGGAAATAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAA
389 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAA
1151 ACAGAACTA
454 ACAGAACTA
* * *
1160 ATGGGCCTCGATAGGCCCAAAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGAC
1 ATGGGCCCCGATAGG--C-ACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
1225 TAATCTCACCAAAACGATTATAGT
63 TAATCTCACCAAAATGATTATAGT
1249 GATGTGCCAA
Statistics
Matches: 508, Mismatches: 37, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
460 2 0.00
461 335 0.66
462 103 0.20
463 1 0.00
464 67 0.13
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (462 bp):
ATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGACAAAT
CGAAGACAATTCAAAACGGAACTAATGGGACCCGAAAGGCACAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCAAAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCATCGAGGATTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGACTAATCTCACCAAAATGATTA
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAAC
AGAACTA
Done.