Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014632.1 Corchorus olitorius cultivar O-4 contig14665, 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: 33168
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6699 original size:21 final size:21
Alignment explanation
Indices: 6673--6712 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6663 AGGATGTCCA
*
6673 TATCCAGGGTAGCCCGGCATG
1 TATCCAGGGTAGCCAGGCATG
6694 TATCCAGGGTAGCCAGGCA
1 TATCCAGGGTAGCCAGGCA
6713 AGTAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.17
Consensus pattern (21 bp):
TATCCAGGGTAGCCAGGCATG
Found at i:7989 original size:29 final size:29
Alignment explanation
Indices: 7946--8003 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
7936 AGAAGAACAA
7946 GAAAATGAATAAAAATGGAGTCTTTGGTT
1 GAAAATGAATAAAAATGGAGTCTTTGGTT
7975 GAAAATGGAATAAAAATGGAGTCTTTGGT
1 GAAAAT-GAATAAAAATGGAGTCTTTGGT
8004 GTGTTAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.29
Consensus pattern (29 bp):
GAAAATGAATAAAAATGGAGTCTTTGGTT
Found at i:8941 original size:7 final size:7
Alignment explanation
Indices: 8929--8955 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
8919 TAAGGACCAT
8929 GCTAAAG
1 GCTAAAG
8936 GCTAAAG
1 GCTAAAG
8943 GCTAAAG
1 GCTAAAG
8950 GCTAAA
1 GCTAAA
8956 AGAGAGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (7 bp):
GCTAAAG
Found at i:10814 original size:30 final size:31
Alignment explanation
Indices: 10780--10839 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
10770 GGCGCGTCAC
* * *
10780 GTGTCCTTTTTT-GTACATGTGGCGTGCCAT
1 GTGTCATTTTTTGGTACACGTGGCATGCCAT
10810 GTGTCATTTTTTGGTACACGTGGCATGCCA
1 GTGTCATTTTTTGGTACACGTGGCATGCCA
10840 CATCGGATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (31 bp):
GTGTCATTTTTTGGTACACGTGGCATGCCAT
Found at i:12101 original size:37 final size:37
Alignment explanation
Indices: 12051--12121 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
12041 ACGCATCTAA
12051 CCACAAACCAATTAGTGATAGTTGAAGAGACTCATAG
1 CCACAAACCAATTAGTGATAGTTGAAGAGACTCATAG
12088 CCACAAACCAATTAGTGATAGTTGAAGAGACTCA
1 CCACAAACCAATTAGTGATAGTTGAAGAGACTCA
12122 ACTTAATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (37 bp):
CCACAAACCAATTAGTGATAGTTGAAGAGACTCATAG
Found at i:14221 original size:3 final size:3
Alignment explanation
Indices: 14213--14264 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
14203 TAACCATCTT
* *
14213 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GCG GCG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
14261 GTG G
1 GTG G
14265 GGGAGGAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.04, G:0.67, T:0.29
Consensus pattern (3 bp):
GTG
Found at i:19964 original size:16 final size:16
Alignment explanation
Indices: 19930--19964 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19920 CACCCTTTCA
*
19930 TAAAGACAATCCTAAT
1 TAAAGACAATCATAAT
*
19946 TAAAGACAATCATAGT
1 TAAAGACAATCATAAT
19962 TAA
1 TAA
19965 CACAACATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (16 bp):
TAAAGACAATCATAAT
Done.