Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010852.1 Corchorus capsularis cultivar CVL-1 contig10873, 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: 47364
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4060 original size:29 final size:29
Alignment explanation
Indices: 3999--4060 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3989 AGTCCATGCC
* **
3999 ATTATCTTTTGGATTGGGTGATTAATCCC
1 ATTATCTTTTGGATTGGGTGATTAAGCAA
*
4028 ATTATCTTTTGGATTGGGATGATT-AGGAA
1 ATTATCTTTTGGATTGGG-TGATTAAGCAA
4057 ATTA
1 ATTA
4061 CCATGGCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (29 bp):
ATTATCTTTTGGATTGGGTGATTAAGCAA
Found at i:6307 original size:33 final size:32
Alignment explanation
Indices: 6234--6328 Score: 101
Period size: 33 Copynumber: 3.1 Consensus size: 32
6224 TTTTTACTTA
*
6234 TTTTCTTTCCTTAATATATTA-T-TT-ACTA-
1 TTTTCTTTCCTTAATATATTATTATTAATTAT
* *
6262 -TTGCTTTGCTTAATATATTATTATTAAGTTAT
1 TTTTCTTTCCTTAATATATTATTATTAA-TTAT
*
6294 TTTTCTTTCCTTAATATATTATTATGAAATTAT
1 TTTTCTTTCCTTAATATATTATTAT-TAATTAT
6327 TT
1 TT
6329 ACTACTGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.33
28 1 0.02
29 2 0.04
30 1 0.02
31 2 0.04
33 28 0.52
34 2 0.04
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.59
Consensus pattern (32 bp):
TTTTCTTTCCTTAATATATTATTATTAATTAT
Found at i:10891 original size:93 final size:91
Alignment explanation
Indices: 10730--10915 Score: 282
Period size: 93 Copynumber: 2.0 Consensus size: 91
10720 AGTTTCTTCG
* *
10730 TATAGGGTCTAACACGGCTCGATTTCCGACTAATCAAGAGGATCTAATGTGATTATTGGATACCG
1 TATAGGGTCTAACACGGCTCGATTTCCGACTAACCAAGAAGATCTAATGTGATTATTGGATACCG
10795 AGAAGATTAGTATACAAAACAAAAATAA
66 AGAAGATTAGTA-A-AAAACAAAAATAA
* * * * * *
10823 TATAGGGTCTAACATGGCTCGATTTCGGATTAACCAGGAAGATCTAATGTGGTTATTGGATACTG
1 TATAGGGTCTAACACGGCTCGATTTCCGACTAACCAAGAAGATCTAATGTGATTATTGGATACCG
10888 AGAAGATTAGTAAAAAACAAAAATAA
66 AGAAGATTAGTAAAAAACAAAAATAA
10914 TA
1 TA
10916 ATGTTAGTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
91 15 0.18
92 1 0.01
93 69 0.81
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (91 bp):
TATAGGGTCTAACACGGCTCGATTTCCGACTAACCAAGAAGATCTAATGTGATTATTGGATACCG
AGAAGATTAGTAAAAAACAAAAATAA
Found at i:33881 original size:29 final size:28
Alignment explanation
Indices: 33837--33902 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
33827 AATCCTTCTC
*
33837 TTTTT-TTTTCTTTTTTGTGGTTC-AAGAA
1 TTTTTATTTTCTTTTTT-TGG-CCAAAGAA
33865 TTTTTATTTT-TTATTTTTGGCCAAAAGAA
1 TTTTTATTTTCTT-TTTTTGGCC-AAAGAA
33894 TTTTTATTT
1 TTTTTATTT
33903 AGATAACAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 10 0.30
29 22 0.67
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.64
Consensus pattern (28 bp):
TTTTTATTTTCTTTTTTTGGCCAAAGAA
Found at i:47085 original size:16 final size:16
Alignment explanation
Indices: 47064--47094 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47054 AAATAGCTAA
*
47064 AGTATTGTATTTGATT
1 AGTATTGAATTTGATT
47080 AGTATTGAATTTGAT
1 AGTATTGAATTTGAT
47095 GTGTTGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (16 bp):
AGTATTGAATTTGATT
Done.