Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002305.1 Corchorus capsularis cultivar CVL-1 contig02311, 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, 922
Length: 1537
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:703 original size:70 final size:70
Alignment explanation
Indices: 577--833 Score: 302
Period size: 70 Copynumber: 3.7 Consensus size: 70
567 GAATGAAATC
*
577 AAAATTTATGTAATATCATATAATGAACATAGAATG------AAATTATGTAATACCATATAATG
1 AAAA-TTATGTAATACCATATAATGAA-ATAGAATGAAATCAAAATTATGTAATACCATATAATG
636 AACATAG
64 AACATAG
643 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
708 CATAG
66 CATAG
* * ** * * * *
713 AATGAA--AT-CAAAATTACATAAT-ACCATATAATGAAATAGAAAATTATGTAATACCATATAA
1 AA--AATTATGTAATACCATATAATGA-AATAGAATGAAAT-CAAAATTATGTAATACCATATAA
774 TGAA-ATAG
62 TGAACATAG
782 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
834 TGTAATTATG
Statistics
Matches: 160, Mismatches: 17, Indels: 25
0.79 0.08 0.12
Matches are distributed among these distances:
64 8 0.05
65 21 0.13
66 4 0.03
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:0.30
Consensus pattern (70 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
CATAG
Found at i:724 original size:40 final size:39
Alignment explanation
Indices: 643--833 Score: 229
Period size: 30 Copynumber: 5.3 Consensus size: 39
633 ATGAACATAG
643 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
682 AAAATTATGTAATACCATATAATGAACATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAA-ATAGAATGAAATC
**
722 AAAATTACATAATACCATATAATGAAAT---A-G-----
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
752 AAAATTATGTAATACCATATAATGAAAT---A-G-----
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
782 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
821 AAAATTATGTAAT
1 AAAATTATGTAAT
834 TGTAATTATG
Statistics
Matches: 138, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
30 56 0.41
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
39 41 0.30
40 37 0.27
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (39 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
Found at i:809 original size:139 final size:143
Alignment explanation
Indices: 548--833 Score: 492
Period size: 139 Copynumber: 2.0 Consensus size: 143
538 GCCAATTCAA
** *
548 AATACCATATAATGAAATAGAATGAAATCAAAATTTATGTAATATCATATAATGAACATAGAATG
1 AATACCATATAATGAAATAGAATGAAATCAAAATTTACATAATACCATATAATGAACATAGAA-G
613 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
65 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
678 AATCAAAATTATGT
130 AATCAAAATTATGT
692 AATACCATATAATGAACATAGAATGAAATCAAAA-TTACATAATACCATATAATGAA-ATAG-A-
1 AATACCATATAATGAA-ATAGAATGAAATCAAAATTTACATAATACCATATAATGAACATAGAAG
753 AAATTATGTAATACCATATAATGAA-ATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
65 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
817 AATCAAAATTATGT
130 AATCAAAATTATGT
831 AAT
1 AAT
834 TGTAATTATG
Statistics
Matches: 138, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
139 56 0.41
140 25 0.18
142 1 0.01
143 4 0.03
144 35 0.25
145 17 0.12
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (143 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTTACATAATACCATATAATGAACATAGAAGA
AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
ATCAAAATTATGT
Found at i:810 original size:15 final size:15
Alignment explanation
Indices: 732--810 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
722 AAAATTACAT
732 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
747 AATAGAAAATTATGT
1 AATACCATATAATGA
762 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
777 AATAGAAAATTATGT
1 AATACCATATAATGA
792 AATACCATATAATGA
1 AATACCATATAATGA
807 AATA
1 AATA
811 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
Done.