Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002469.1 Corchorus capsularis cultivar CVL-1 contig02475, 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, 639
Length: 1066
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:658 original size:31 final size:30
Alignment explanation
Indices: 576--821 Score: 224
Period size: 31 Copynumber: 7.4 Consensus size: 30
566 AATGAAATAG
* *
576 AATGAAAT-CAAAATTATGTAATATCATAT
1 AATGAAATAGAAAATTATGTAATACCATAT
605 AATGAACATAGAATGAAATTATGTAATACCATAT
1 AATGAA-ATAG-A--AAATTATGTAATACCATAT
639 AATGAACATAGAAAATTATGTAATACCATAT
1 AATGAA-ATAGAAAATTATGTAATACCATAT
670 AATGAAATAGAATGAAATCAAAATTATGTAATACCATAT
1 AATGAAAT---A-G-----AAAATTATGTAATACCATAT
**
709 AATGAACATAGAATGAAATCAAAATTACATAATACCATAT
1 AATGAA-AT---A-G-----AAAATTATGTAATACCATAT
749 AATGAAATAGAAAAGTTATGTAATACCATAT
1 AATGAAATAGAAAA-TTATGTAATACCATAT
780 AATGAAATAGAAAATTATGTAATACCATAT
1 AATGAAATAGAAAATTATGTAATACCATAT
810 AATGAAATAGAA
1 AATGAAATAGAA
822 TGAAATCAAA
Statistics
Matches: 195, Mismatches: 6, Indels: 31
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.03
30 36 0.18
31 53 0.27
32 1 0.01
33 2 0.01
34 30 0.15
35 1 0.01
36 1 0.01
39 28 0.14
40 37 0.19
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.28
Consensus pattern (30 bp):
AATGAAATAGAAAATTATGTAATACCATAT
Found at i:678 original size:104 final size:105
Alignment explanation
Indices: 556--826 Score: 377
Period size: 104 Copynumber: 2.6 Consensus size: 105
546 GCCAATTCAA
*
556 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATATCATATAATGAACATAGAATG-
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
**
620 AAATTATGTAATACCATATAATGAACATAGAAAA-TTATGT
66 AAATTACATAATACCATATAATGAA-ATAGAAAAGTTATGT
660 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATG-
725 AATCAAAATTACATAATACCATATAATGAAATAGAAAAGTTATGT
65 ----AAAATTACATAATACCATATAATGAAATAGAAAAGTTATGT
770 AATACCATATAATGAAAT---A-G-----AAAATTATGTAATACCATATAATGAA-ATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
825 AA
66 AA
827 TCAAAATTAT
Statistics
Matches: 157, Mismatches: 3, Indels: 23
0.86 0.02 0.13
Matches are distributed among these distances:
95 3 0.02
100 8 0.05
101 26 0.17
104 63 0.40
106 1 0.01
107 1 0.01
109 8 0.05
110 47 0.30
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (105 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAACATAGAATGA
AAATTACATAATACCATATAATGAAATAGAAAAGTTATGT
Found at i:695 original size:39 final size:39
Alignment explanation
Indices: 650--841 Score: 229
Period size: 39 Copynumber: 5.3 Consensus size: 39
640 ATGAACATAG
650 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
689 AAAATTATGTAATACCATATAATGAACATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAA-ATAGAATGAAATC
**
729 AAAATTACATAATACCATATAATGAAAT---A-G--A--
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
*
760 AAAGTTATGTAATACCATATAATGAAAT---A-G-----
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
790 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
829 AAAATTATGTAAT
1 AAAATTATGTAAT
842 TGTAATTATG
Statistics
Matches: 137, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
30 27 0.20
31 27 0.20
33 2 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:0.10, T:0.29
Consensus pattern (39 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
Found at i:800 original size:30 final size:30
Alignment explanation
Indices: 715--821 Score: 162
Period size: 30 Copynumber: 3.6 Consensus size: 30
705 ATATAATGAA
* * **
715 CATAGAATGAAAT-CAAAATTACATAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
744 CATATAATGAAATAGAAAAGTTATGTAATAC
1 CATATAATGAAATAGAAAA-TTATGTAATAC
775 CATATAATGAAATAGAAAATTATGTAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
805 CATATAATGAAATAGAA
1 CATATAATGAAATAGAA
822 TGAAATCAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
29 12 0.17
30 32 0.44
31 28 0.39
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (30 bp):
CATATAATGAAATAGAAAATTATGTAATAC
Found at i:821 original size:140 final size:142
Alignment explanation
Indices: 556--841 Score: 497
Period size: 140 Copynumber: 2.0 Consensus size: 142
546 GCCAATTCAA
** *
556 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATATCATATAATGAACATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAA-GA
621 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
686 ATCAAAATTATGT
130 ATCAAAATTATGT
699 AATACCATATAATGAACATAGAATGAAATCAAAATTACATAATACCATATAATGAA-ATAGAA-A
1 AATACCATATAATGAA-ATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGA
*
762 AGTTATGTAATACCATATAATGAA-ATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
826 ATCAAAATTATGT
130 ATCAAAATTATGT
839 AAT
1 AAT
842 TGTAATTATG
Statistics
Matches: 138, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
140 56 0.41
141 24 0.17
143 22 0.16
144 36 0.26
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (142 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGAA
ATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAAA
TCAAAATTATGT
Done.