Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002095.1 Corchorus capsularis cultivar CVL-1 contig02099, 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, 673
Length: 1123
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:646 original size:104 final size:104
Alignment explanation
Indices: 524--793 Score: 382
Period size: 104 Copynumber: 2.6 Consensus size: 104
514 GCCAATTCAA
*
524 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATATCATATAATGAACATAGAATG-
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
**
588 AAATTATGTAATACCATATAATGAACATAGAAAATTATGT
66 AAATTACATAATACCATATAATGAA-ATAGAAAATTATGT
628 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATG-
693 AATCAAAATTACATAATACCATATAATGAAATAGAAAATTATGT
65 ----AAAATTACATAATACCATATAATGAAATAGAAAATTATGT
737 AATACCATATAATGAAAT---A-G-----AAAATTATGTAATACCATATAATGAA-ATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
792 AA
66 AA
794 TCAAAATTAT
Statistics
Matches: 157, Mismatches: 3, Indels: 22
0.86 0.02 0.12
Matches are distributed among these distances:
94 3 0.02
99 8 0.05
100 26 0.17
104 63 0.40
105 1 0.01
106 1 0.01
109 32 0.20
110 23 0.15
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (104 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
AAATTACATAATACCATATAATGAAATAGAAAATTATGT
Found at i:682 original size:70 final size:70
Alignment explanation
Indices: 553--808 Score: 309
Period size: 70 Copynumber: 3.7 Consensus size: 70
543 GAATGAAATC
*
553 AAAATTATGTAATATCATATAATGAACATAGAATG------AAATTATGTAATACCATATAATGA
1 AAAATTATGTAATACCATATAATGAA-ATAGAATGAAATCAAAATTATGTAATACCATATAATGA
612 ACATAG
65 ACATAG
618 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
683 CATAG
66 CATAG
* * ** * * * *
688 AATGAA--AT-CAAAATTACATAAT-ACCATATAATGAAATAGAAAATTATGTAATACCATATAA
1 AA--AATTATGTAATACCATATAATGA-AATAGAATGAAAT-CAAAATTATGTAATACCATATAA
749 TGAA-ATAG
62 TGAACATAG
757 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
809 TGTAATTATG
Statistics
Matches: 160, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
64 8 0.05
65 25 0.16
67 2 0.01
68 1 0.01
69 41 0.26
70 80 0.50
71 1 0.01
72 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (70 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
CATAG
Found at i:731 original size:30 final size:30
Alignment explanation
Indices: 683--788 Score: 169
Period size: 30 Copynumber: 3.6 Consensus size: 30
673 ATATAATGAA
* * **
683 CATAGAATGAAAT-CAAAATTACATAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
712 CATATAATGAAATAGAAAATTATGTAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
742 CATATAATGAAATAGAAAATTATGTAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
772 CATATAATGAAATAGAA
1 CATATAATGAAATAGAA
789 TGAAATCAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 12 0.17
30 60 0.83
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.27
Consensus pattern (30 bp):
CATATAATGAAATAGAAAATTATGTAATAC
Found at i:785 original size:15 final size:15
Alignment explanation
Indices: 707--785 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
697 AAAATTACAT
707 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
722 AATAGAAAATTATGT
1 AATACCATATAATGA
737 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
752 AATAGAAAATTATGT
1 AATACCATATAATGA
767 AATACCATATAATGA
1 AATACCATATAATGA
782 AATA
1 AATA
786 GAATGAAATC
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (15 bp):
AATACCATATAATGA
Found at i:788 original size:139 final size:142
Alignment explanation
Indices: 524--808 Score: 497
Period size: 139 Copynumber: 2.0 Consensus size: 142
514 GCCAATTCAA
** *
524 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATATCATATAATGAACATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAA-GA
589 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
654 ATCAAAATTATGT
130 ATCAAAATTATGT
667 AATACCATATAATGAACATAGAATGAAATCAAAATTACATAATACCATATAATGAA-ATAG-A-A
1 AATACCATATAATGAA-ATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGA
729 AATTATGTAATACCATATAATGAA-ATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
793 ATCAAAATTATGT
130 ATCAAAATTATGT
806 AAT
1 AAT
809 TGTAATTATG
Statistics
Matches: 138, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
139 56 0.41
140 25 0.18
142 1 0.01
143 20 0.14
144 36 0.26
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (142 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGAA
ATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAAA
TCAAAATTATGT
Found at i:1085 original size:17 final size:17
Alignment explanation
Indices: 1065--1098 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1055 TAGGAAAATG
1065 AAAAATAGATAAAAAAA
1 AAAAATAGATAAAAAAA
1082 AAAAATAGATAAAAAAA
1 AAAAATAGATAAAAAAA
1099 GGGAAAGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAGATAAAAAAA
Done.