Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004714.1 Corchorus capsularis cultivar CVL-1 contig04730, 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, 604
Length: 1008
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Found at i:384 original size:153 final size:153
Alignment explanation
Indices: 1--1006 Score: 1491
Period size: 154 Copynumber: 6.6 Consensus size: 153
*
1 GATTCGAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* *
66 TCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGT-AACAAGTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAA-TGAAAGAAAAGC
*
130 TTTGTGGTTTG-TAAATCGAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
153 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* *
218 TCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAGTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAA-TGAAAGAAAAGC
*
283 TTTGTGGTTTG-TAAATCGAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
* * * * **
306 GATTCAAAACAGCACTAATGGGCCCAGTAAGGCCCGAAATATTAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* * * * *
371 ACTTCACAATGGACCAATCTCATCAAAATAATTATAGTTAGGCCCTAAACTATGGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAT-GAAAGAAAAGC
* * **
436 TTTATGTTTTGCCAAATCGAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
* * * * * *
460 GATTCTAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAACCAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* * ** * *
525 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTTCGCCATAAACTATGGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAT-GAAAGAAAAGC
*
590 TTTGTGGTTTGAAAAATCAAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
* *
614 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCAGAATGAGCAAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
679 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAA-TGAAAGAAAAGC
**
744 TTTGTGGTTTGCCAAATCGAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
* * * *
768 GATTCAAAACAGCACAAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* * * *
833 ACTTCACAGTGGACTAATCTCACC-AAACGATTATAATTAGGCCCTAAACAATTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAA-TGAAAGAAAAGC
*
897 TTTGTGGTTTGAAAAATCAAAGAC
130 TTTGTGGTTTGAAAAATCGAAGAC
921 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCT-AAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
985 ACTTCACAATGGACTAATCTCA
66 ACTTCACAATGGACTAATCTCA
1007 TC
Statistics
Matches: 783, Mismatches: 67, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
152 135 0.17
153 280 0.36
154 367 0.47
155 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (153 bp):
GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGAAAGAAAAGCT
TTGTGGTTTGAAAAATCGAAGAC
Found at i:561 original size:307 final size:305
Alignment explanation
Indices: 1--1006 Score: 1543
Period size: 307 Copynumber: 3.3 Consensus size: 305
*
1 GATTCGAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* * *
66 TCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGT-AACAAGTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACATG-GAAAGAAAAGC
* * * *
130 TTTGTGGTTTG-TAAATCGAAGACGATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATA
130 TTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATA
*
194 ACAAGTGTTCTGAATGAGCTAAAATCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
195 ACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CAAAATGATTATAGTTAG
* * *
259 GCCGTAAACAAGTGAAAGAAAAGCTTTGTGGTTTG-TAAATCGAAGAC
259 GCCATAAACAA-TGAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
* * * * **
306 GATTCAAAACAGCACTAATGGGCCCAGTAAGGCCCGAAATATTAAGTGTTCTGAATGAGCTAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
* * * *
371 ACTTCACAATGGACCAATCTCATCAAAATAATTATAGTTAGGCCCTAAACTATGGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAC-ATGGAAAGAAAAGC
* * * *
436 TTTATGTTTTGCCAAATCGAAGACGATTCTAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATA
130 TTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATA
* * * * **
501 ACAAGTGTTCTGAATGAACCAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTTC
195 ACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CAAAATGATTATAGTTAG
*
566 GCCATAAACTATGGAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
259 GCCATAAACAAT-GAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
* *
614 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCAGAATGAGCAAAAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
*
679 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATTGAAAGAAAAGC
66 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAC-ATGGAAAGAAAAGC
*
744 TTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACAAATGGGCCCCGAAAGGCCCAAAATA
130 TTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATA
* * *
809 ACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAACGATTATAATTAGG
195 ACAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAATGATTATAGTTAGG
*
874 CCCTAAACAATTGAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
260 CCATAAACAA-TGAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
921 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCT-AAA
1 GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
985 ACTTCACAATGGACTAATCTCA
66 ACTTCACAATGGACTAATCTCA
1007 TC
Statistics
Matches: 630, Mismatches: 65, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
305 98 0.16
306 49 0.08
307 253 0.40
308 230 0.37
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (305 bp):
GATTCAAAACAGCACTATTGGGCCCTGAAAGGCCCTAAATAACAAGTGTTCTGAATGAGCTAAAA
ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACATGGAAAGAAAAGCT
TTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATAA
CAAGTGTTCTGAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAATGATTATAGTTAGGC
CATAAACAATGAAAGAAAAGCTTTGTGGTTTGAAAAATCAAAGAC
Done.