Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005999.1 Corchorus capsularis cultivar CVL-1 contig06017, 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: 11490
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:30 original size:8 final size:9
Alignment explanation
Indices: 3--46 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
1 AG
*
3 TATAGATTA
1 TATATATTA
12 TATTATATTA
1 TA-TATATTA
22 TAT-TATTA
1 TATATATTA
30 TATATATATA
1 TATATAT-TA
40 TATATAT
1 TATATAT
47 ATTTGAGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 8 0.26
9 6 0.19
10 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATTA
Found at i:35 original size:2 final size:2
Alignment explanation
Indices: 10--48 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 AGTATAGAT
10 TA TA T- TA TA T- TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48 T
1 T
49 TTGAGTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2074 original size:15 final size:15
Alignment explanation
Indices: 2054--2083 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2044 CTACCCCCAG
2054 GTTCACTTTTATCAA
1 GTTCACTTTTATCAA
2069 GTTCACTTTTATCAA
1 GTTCACTTTTATCAA
2084 ATAACTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
GTTCACTTTTATCAA
Found at i:4155 original size:6 final size:6
Alignment explanation
Indices: 4144--4182 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
4134 TATAATCTGC
4144 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
4183 GCTTTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:10359 original size:10 final size:10
Alignment explanation
Indices: 10344--10368 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10334 GTCCCTGCTC
10344 AATTCCAGAA
1 AATTCCAGAA
10354 AATTCCAGAA
1 AATTCCAGAA
10364 AATTC
1 AATTC
10369 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:11303 original size:12 final size:12
Alignment explanation
Indices: 11278--11323 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
11268 TTAATTATTG
11278 TTTGCTTTATTAA
1 TTTGCTTTA-TAA
*
11291 TTTGTTTTATAA
1 TTTGCTTTATAA
11303 TTTGCTTTATAA
1 TTTGCTTTATAA
*
11315 TCTGCTTTA
1 TTTGCTTTA
11324 GATTTAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (12 bp):
TTTGCTTTATAA
Found at i:11331 original size:6 final size:6
Alignment explanation
Indices: 11320--11346 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11310 TATAATCTGC
11320 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
11347 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.