Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005165.1 Corchorus capsularis cultivar CVL-1 contig05183, 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: 3328
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Found at i:489 original size:31 final size:31
Alignment explanation
Indices: 451--618 Score: 152
Period size: 31 Copynumber: 5.5 Consensus size: 31
441 TTTGGTTAAT
451 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
482 TGCTCAAATAAGGGCTTGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA
*
511 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
** * **
542 TGCTCAAATAAGGGCCCGACCTTT-T-AATT
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* *
571 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
602 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
619 GGCATCAAAA
Statistics
Matches: 104, Mismatches: 23, Indels: 20
0.71 0.16 0.14
Matches are distributed among these distances:
28 2 0.02
29 37 0.36
30 9 0.09
31 54 0.52
32 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:541 original size:60 final size:60
Alignment explanation
Indices: 455--617 Score: 281
Period size: 60 Copynumber: 2.7 Consensus size: 60
445 GTTAATTGCT
* ** *
455 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGACCTTTTAATTTGGC
515 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGACCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGACCTTTTAATTTGGC
*
575 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
618 TGGCATCAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGACCTTTTAATTTGGC
Found at i:699 original size:31 final size:31
Alignment explanation
Indices: 657--824 Score: 109
Period size: 31 Copynumber: 5.5 Consensus size: 31
647 AACTGACGCC
*
657 AGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTTCGATAAGATT
* ** * *
688 AGGTCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGATAAGATT
* *
717 AGACCCTTATTTGAGCATTTTCGATAAGGTT
1 AGGCCCTTATTTGAGCATTTTCGATAAGATT
** * *
748 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGATAAGATT
* * *
777 GGGCCCTTATTTGACCATTTTGGCA-AACG-TT
1 AGGCCCTTATTTGAGCATTTTCG-ATAA-GATT
808 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
825 ATTAGCCCCT
Statistics
Matches: 101, Mismatches: 26, Indels: 20
0.69 0.18 0.14
Matches are distributed among these distances:
29 41 0.41
30 3 0.03
31 55 0.54
32 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAAGATT
Found at i:729 original size:29 final size:29
Alignment explanation
Indices: 692--789 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
682 AACATTAGGT
*
692 CCTTATTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGGCCAAATTAAAAGATCAGGC
** * * *
721 CCTTATTTGAG-CATTTTCGATAAGGTTAGGC
1 CCTTATTTG-GCCAAATT--AAAAGATCAGGC
*
752 CCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGGCCAAATTAAAAGATCAGGC
781 CCTTATTTG
1 CCTTATTTG
790 ACCATTTTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 30 0.57
30 2 0.04
31 21 0.40
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (29 bp):
CCTTATTTGGCCAAATTAAAAGATCAGGC
Found at i:735 original size:60 final size:60
Alignment explanation
Indices: 660--820 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
650 TGACGCCAGG
* *
660 CCCTTATTTGAGCATTTTCGATAACATTAGGTCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
720 CCCTTATTTGAGCATTTTCGATAAGGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* *
780 CCCTTATTTGACCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
821 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:2692 original size:19 final size:21
Alignment explanation
Indices: 2663--2704 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2653 ATAAAATATG
2663 AACTAAAATTG-AAATAATTA
1 AACTAAAATTGCAAATAATTA
*
2683 AACT-AAATTGCAAGTAATTA
1 AACTAAAATTGCAAATAATTA
2703 AA
1 AA
2705 ATAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGCAAATAATTA
Done.