Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007303.1 Corchorus capsularis cultivar CVL-1 contig07324, 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: 33378
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:14747 original size:21 final size:21
Alignment explanation
Indices: 14721--14773 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
14711 GCACTGGAGT
14721 ACATGGGTCG-CAAGGCAAACC
1 ACATGGGTCGCCAA-GCAAACC
*
14742 ACATGGGTCGCCAAGCATACC
1 ACATGGGTCGCCAAGCAAACC
14763 ACATGGG-CGCC
1 ACATGGGTCGCC
14774 CAGCGCTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.28, C:0.32, G:0.28, T:0.11
Consensus pattern (21 bp):
ACATGGGTCGCCAAGCAAACC
Found at i:17309 original size:25 final size:24
Alignment explanation
Indices: 17280--17330 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
17270 GTTGAATTGT
*
17280 AATAAATCTAATAATAAAGATATTA
1 AATAAATCTAAAAATAAA-ATATTA
* *
17305 AATAAATTTAAAAATTAAATATTA
1 AATAAATCTAAAAATAAAATATTA
17329 AA
1 AA
17331 AAAAATTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAATCTAAAAATAAAATATTA
Found at i:17770 original size:17 final size:16
Alignment explanation
Indices: 17748--17793 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
17738 TGAAAAAATA
17748 ATATTATTATAATTTT
1 ATATTATTATAATTTT
17764 -TA-TATTATAATTTT
1 ATATTATTATAATTTT
*
17778 -TA-TATTATAATATT
1 ATATTATTATAATTTT
17792 AT
1 AT
17794 TTAGTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATTATAATTTT
Found at i:17771 original size:14 final size:14
Alignment explanation
Indices: 17752--17788 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
17742 AAAATAATAT
17752 TATTATAATTTTTA
1 TATTATAATTTTTA
17766 TATTATAATTTTTA
1 TATTATAATTTTTA
17780 TATTATAAT
1 TATTATAAT
17789 ATTATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATAATTTTTA
Found at i:23977 original size:11 final size:11
Alignment explanation
Indices: 23961--23995 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
23951 AGGATTCGGG
23961 AAAAAAAAAGA
1 AAAAAAAAAGA
23972 AAAAAAAAAGA
1 AAAAAAAAAGA
*
23983 AAAGAAGAAAGA
1 AAA-AAAAAAGA
23995 A
1 A
23996 GAGTAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:26813 original size:6 final size:6
Alignment explanation
Indices: 26802--26832 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
26792 TTTGGGAGAA
26802 TGGATT TGGATT TGGATT TGGATT TGG-TT TG
1 TGGATT TGGATT TGGATT TGGATT TGGATT TG
26833 ATATATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (6 bp):
TGGATT
Found at i:28705 original size:67 final size:67
Alignment explanation
Indices: 28597--28731 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
28587 AGCTGGCGCT
* *
28597 TAGTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAACTATTCAAGCAATTTATTTAAT
1 TAGTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAGCAACTTATTTAAT
28662 TG
66 TG
* ** *
28664 TAGTGGGAGAATTTGTGTTTTAGAATGAACCTTTTGGGGTAAAATATTCAAGGAACTTATTTAAT
1 TAGTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAGCAACTTATTTAAT
28729 TG
66 TG
28731 T
1 T
28732 GGCTCTACGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.38
Consensus pattern (67 bp):
TAGTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAGCAACTTATTTAAT
TG
Found at i:29975 original size:14 final size:15
Alignment explanation
Indices: 29953--29985 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29943 GTTCGATTCG
*
29953 ATTTTTTTAAA-TAT
1 ATTTATTTAAACTAT
29967 ATTTATTTAAACTAT
1 ATTTATTTAAACTAT
29982 ATTT
1 ATTT
29986 TAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTTAAACTAT
Found at i:30031 original size:9 final size:9
Alignment explanation
Indices: 30001--30084 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 9
29991 TTTATTTATT
30001 TATATATAA
1 TATATATAA
30010 TA-A-A-AA
1 TATATATAA
*
30016 CATATATAA
1 TATATATAA
*
30025 TATATATTA
1 TATATATAA
*
30034 TATATTTTAA
1 TATA-TATAA
*
30044 -ATATAT-T
1 TATATATAA
* *
30051 TATAGAAAA
1 TATATATAA
30060 TATATTTATAA
1 TATA--TATAA
30071 TATATATAA
1 TATATATAA
30080 TATAT
1 TATAT
30085 TTTAAATTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 16
0.66 0.14 0.19
Matches are distributed among these distances:
6 3 0.05
7 2 0.04
8 8 0.15
9 32 0.58
10 3 0.05
11 7 0.13
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (9 bp):
TATATATAA
Done.