Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013412.1 Corchorus capsularis cultivar CVL-1 contig13433, 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: 22425
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2646 original size:40 final size:40
Alignment explanation
Indices: 2620--2700 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
2610 CATATTCATG
**
2620 AGGTATCTGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTA
1 AGGTATCTGTCTGCCTTTGAAGTAAAACATAATTGAAGTA
**
2660 AGGTATCTGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTA
1 AGGTATCTGTCTGCCTTTGAAGTAAAACATAATTGAAGTA
2700 A
1 A
2701 AAAAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (40 bp):
AGGTATCTGTCTGCCTTTGAAGTAAAACATAATTGAAGTA
Found at i:2729 original size:52 final size:53
Alignment explanation
Indices: 2667--2771 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
2657 GTAAGGTATC
2667 TGTCTGCCTTTGAAGTAAAAGGTAATTGAAGT-AAAAAAAAGAAATATCAAAA
1 TGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTAAAAAAAAAGAAATATCAAAA
2719 TGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTAAAAAAAAAGAAATATCAAAA
1 TGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTAAAAAAAAAGAAATATCAAAA
2772 ATAAATAACG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 32 0.62
53 20 0.38
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (53 bp):
TGTCTGCCTTTGAAGTAAAAGGTAATTGAAGTAAAAAAAAAGAAATATCAAAA
Found at i:6462 original size:29 final size:30
Alignment explanation
Indices: 6430--6492 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
6420 TTGTCCTCCG
6430 AACTCCAATCTT-GGACATTTTGCCCCCTA
1 AACTCCAATCTTGGGACATTTTGCCCCCTA
* * * *
6459 AACTTCAATTTTGGGACGTTTTGCCCCCTC
1 AACTCCAATCTTGGGACATTTTGCCCCCTA
6489 AACT
1 AACT
6493 TAACCGCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (30 bp):
AACTCCAATCTTGGGACATTTTGCCCCCTA
Found at i:6598 original size:13 final size:13
Alignment explanation
Indices: 6580--6607 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6570 CAAACCGCTG
6580 ACATGGCAATGCC
1 ACATGGCAATGCC
6593 ACATGGCAATGCC
1 ACATGGCAATGCC
6606 AC
1 AC
6608 GTCAGCGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.14
Consensus pattern (13 bp):
ACATGGCAATGCC
Found at i:6690 original size:29 final size:30
Alignment explanation
Indices: 6639--6710 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
6629 TTAGGTTGAA
*
6639 GGGGCAAAACGTCCCAAAATTGAAGTTCAT
1 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
* * *
6669 GGGGCAAAATGT-CCAAGATTGAAGTTCGG
1 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
6698 GGGGCAAAACGTC
1 GGGGCAAAACGTC
6711 TAAATCCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (30 bp):
GGGGCAAAACGTCCCAAAATTGAAGTTCAG
Found at i:8008 original size:20 final size:19
Alignment explanation
Indices: 7963--8020 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
7953 AATCTCACGG
7963 GATATCCGTCGATATATCC
1 GATATCCGTCGATATATCC
*
7982 GTGTATCCGTCGATATTTAT-C
1 G-ATATCCGTCGATA--TATCC
8003 GATAT-C-TCGATATATCC
1 GATATCCGTCGATATATCC
8020 G
1 G
8021 TAAATATCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 2 0.06
18 6 0.18
19 2 0.06
20 15 0.45
21 2 0.06
22 3 0.09
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATCCGTCGATATATCC
Found at i:8027 original size:10 final size:10
Alignment explanation
Indices: 8014--8039 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8004 ATATCTCGAT
8014 ATATCCGTAA
1 ATATCCGTAA
8024 ATATCCGTAA
1 ATATCCGTAA
8034 ATATCC
1 ATATCC
8040 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:9900 original size:2 final size:2
Alignment explanation
Indices: 9889--9927 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
9879 CTTTGCGACG
9889 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
9928 ATCTATCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11065 original size:11 final size:11
Alignment explanation
Indices: 11037--11070 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
11027 TGATAACTAG
*
11037 TATATAATATA
1 TATATATTATA
11048 TATATATTATA
1 TATATATTATA
11059 TATATATGTATA
1 TATATAT-TATA
11071 CTTGGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TATATATTATA
Found at i:11729 original size:13 final size:13
Alignment explanation
Indices: 11711--11742 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11701 ATTTTTAAAA
11711 AATATAATAATAT
1 AATATAATAATAT
11724 AATATAATAATAT
1 AATATAATAATAT
11737 AA-ATAA
1 AATATAA
11743 ATGTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATAATAATAT
Done.