Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016327.1 Corchorus capsularis cultivar CVL-1 contig16348, 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: 12686
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:177 original size:24 final size:24
Alignment explanation
Indices: 145--190 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
135 TTGGGAAAAA
145 TATATGACGGCGTTTAAACGCCTC
1 TATATGACGGCGTTTAAACGCCTC
* *
169 TATATGACGGTGTTTAGACGCC
1 TATATGACGGCGTTTAAACGCC
191 GTAATATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (24 bp):
TATATGACGGCGTTTAAACGCCTC
Found at i:197 original size:24 final size:24
Alignment explanation
Indices: 146--198 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
136 TGGGAAAAAT
*
146 ATATGACGGCGTTTAAACGCCTCT
1 ATATGACGGCGTTTAAACGCCTCA
* *
170 ATATGACGGTGTTTAGACGCCGT-A
1 ATATGACGGCGTTTAAACGCC-TCA
194 ATATG
1 ATATG
199 GATAGCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (24 bp):
ATATGACGGCGTTTAAACGCCTCA
Found at i:2980 original size:33 final size:33
Alignment explanation
Indices: 2953--3049 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
2943 TGGCCGATTG
*
2953 TGGCCGGACATGTCC-ATGTCGCGTGGCCGGTGA
1 TGGCCGGACATCTCCGA-GTCGCGTGGCCGGTGA
* *
2986 TGGCCGGGCATCTCCGAGTCGCGTGGCCGGTGT
1 TGGCCGGACATCTCCGAGTCGCGTGGCCGGTGA
* * * * *
3019 TTGCCGGGCTTCTCCAAGTCGCATGGCCGGT
1 TGGCCGGACATCTCCGAGTCGCGTGGCCGGT
3050 CACTAGTGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.30, G:0.38, T:0.23
Consensus pattern (33 bp):
TGGCCGGACATCTCCGAGTCGCGTGGCCGGTGA
Found at i:10998 original size:17 final size:17
Alignment explanation
Indices: 10973--11005 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10963 TGCATTATTT
10973 AAATACAAAGCATACAC
1 AAATACAAAGCATACAC
*
10990 AAATCCAAAGCATACA
1 AAATACAAAGCATACA
11006 GAAAACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.24, G:0.06, T:0.12
Consensus pattern (17 bp):
AAATACAAAGCATACAC
Found at i:12494 original size:21 final size:21
Alignment explanation
Indices: 12451--12494 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12441 AAGAAGGGGG
* *
12451 TTGCTAAATACTGCCCTATTT
1 TTGCTAAATACCGCCCTAGTT
12472 TTGCTAAATACCGTCCC-AGTT
1 TTGCTAAATACCG-CCCTAGTT
12493 TT
1 TT
12495 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (21 bp):
TTGCTAAATACCGCCCTAGTT
Found at i:12577 original size:33 final size:33
Alignment explanation
Indices: 12540--12615 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
12530 TTTTTACACT
*
12540 AGCCTCCCCACTA-GGACGGCTCAGCCACGGCGG
1 AGCCTCCCCACTAGGGA-GGCTCAACCACGGCGG
*
12573 AGCCTTCCCACTAGGGAGGCTCAACCACGGCGG
1 AGCCTCCCCACTAGGGAGGCTCAACCACGGCGG
12606 AGCCTCCCCA
1 AGCCTCCCCA
12616 GGCAGCTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.20, C:0.42, G:0.28, T:0.11
Consensus pattern (33 bp):
AGCCTCCCCACTAGGGAGGCTCAACCACGGCGG
Done.