Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012610.1 Corchorus capsularis cultivar CVL-1 contig12631, 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: 42245
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1586 original size:19 final size:18
Alignment explanation
Indices: 1534--1597 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
1524 GTGATGTTAT
*
1534 ATATTATACATATAAGATAA
1 ATATTATA-ATATAATA-AA
1554 ATA-TATAA-ATAATAAA
1 ATATTATAATATAATAAA
*
1570 GATATTATAATATAATATAT
1 -ATATTATAATATAATA-AA
1590 ATATTATA
1 ATATTATA
1598 TTGTAAGCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 6 0.16
19 18 0.47
20 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATTATAATATAATAAA
Found at i:3711 original size:1 final size:1
Alignment explanation
Indices: 3705--3739 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
3695 TGCAATATGC
3705 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3740 CTTGCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4024 original size:60 final size:60
Alignment explanation
Indices: 3942--4058 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
3932 TTTGAGCATT
* * **
3942 TTTTTTTTCTCTGGGCCCTTATTTATGCATTTTCGCAAACGTT-GAGCCCTGATTTGAACA
1 TTTTTTTCCTCTGGACCCTTATTTAAACATTTTCGCAAACGTTAG-GCCCTGATTTGAACA
* * *
4002 TTTTTTTCCTTTGGACCCTTATTTAAACATTTTCGCAAATGTTAGGCCCTTATTTGA
1 TTTTTTTCCTCTGGACCCTTATTTAAACATTTTCGCAAACGTTAGGCCCTGATTTGA
4059 GCAATTAGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (60 bp):
TTTTTTTCCTCTGGACCCTTATTTAAACATTTTCGCAAACGTTAGGCCCTGATTTGAACA
Found at i:13081 original size:2 final size:2
Alignment explanation
Indices: 13074--13099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13064 TTATTAGTAC
13074 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13100 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25917 original size:22 final size:22
Alignment explanation
Indices: 25891--25932 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25881 ATTTTACTCT
25891 TCAAAAAAAAAAAAGGAAAAAC
1 TCAAAAAAAAAAAAGGAAAAAC
***
25913 TCAAAACCCAAAAAGGAAAA
1 TCAAAAAAAAAAAAGGAAAA
25933 GTAGAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.10, T:0.05
Consensus pattern (22 bp):
TCAAAAAAAAAAAAGGAAAAAC
Found at i:37994 original size:30 final size:27
Alignment explanation
Indices: 37946--38005 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
37936 AATATTAAAC
*
37946 TTATAATTAATTCCAATTTTATTTATTTAT
1 TTATAATTAATT-CAAATTTA-TTA-TTAT
* *
37976 TTATAATTACTTGAAATTTATTATTAT
1 TTATAATTAATTCAAATTTATTATTAT
38003 TTA
1 TTA
38006 ATCGATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 3 0.11
29 6 0.22
30 11 0.41
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (27 bp):
TTATAATTAATTCAAATTTATTATTAT
Found at i:41531 original size:25 final size:24
Alignment explanation
Indices: 41497--41551 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
41487 TTAATACAGG
*
41497 TATCGACGGATATATTGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
*
41522 TATCGACGGATATATCGATGGATA
1 TATCGACGGATATATCGACGGATA
41546 TATCGA
1 TATCGA
41552 GGTATCGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:41532 original size:12 final size:12
Alignment explanation
Indices: 41497--41551 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
41487 TTAATACAGG
41497 TATCGACGGATA
1 TATCGACGGATA
*
41509 TATTGAACGGATA
1 TATCG-ACGGATA
41522 TATCGACGGATA
1 TATCGACGGATA
*
41534 TATCGATGGATA
1 TATCGACGGATA
41546 TATCGA
1 TATCGA
41552 GGTATCGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (12 bp):
TATCGACGGATA
Done.