Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010324.1 Corchorus capsularis cultivar CVL-1 contig10345, 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: 14360
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1012 original size:4 final size:4
Alignment explanation
Indices: 1003--1031 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
993 AAAAATATGT
1003 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1032 TCGATAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2986 original size:19 final size:21
Alignment explanation
Indices: 2950--2991 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2940 TTTCTTCTAT
2950 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
2970 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
2990 TT
1 TT
2992 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:6391 original size:22 final size:22
Alignment explanation
Indices: 6351--6394 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6341 TTGTTTTTCC
* *
6351 GTTTTTGTTTCATTTTTGTTTT
1 GTTTTTGTTACATTGTTGTTTT
*
6373 GTTTTTGTTACGTTGTTGTTTT
1 GTTTTTGTTACATTGTTGTTTT
6395 TTGAAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.18, T:0.73
Consensus pattern (22 bp):
GTTTTTGTTACATTGTTGTTTT
Found at i:8448 original size:2 final size:2
Alignment explanation
Indices: 8443--8467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8433 TATATATATA
8443 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
8468 TGATTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:14091 original size:34 final size:34
Alignment explanation
Indices: 14047--14150 Score: 129
Period size: 34 Copynumber: 2.9 Consensus size: 34
14037 ACTCGTAATA
*
14047 TTAATATATAATTGGAATTGGACTAAGAAAA-CC
1 TTAATATATAATTGGAATTGGACTAAAAAAACCC
*
14080 TGTAATATATAATTTGAATTGGACTAATAAAATTCAACCC
1 T-TAATATATAATTGGAATTGGACT-A-AAAA---AACCC
14120 TTAATATATAATTGGAATTGGACTAAAAAAA
1 TTAATATATAATTGGAATTGGACTAAAAAAA
14151 TTCAATTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
33 1 0.02
34 24 0.39
35 1 0.02
36 3 0.05
37 4 0.07
38 1 0.02
39 24 0.39
40 3 0.05
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (34 bp):
TTAATATATAATTGGAATTGGACTAAAAAAACCC
Found at i:14127 original size:39 final size:37
Alignment explanation
Indices: 14047--14155 Score: 136
Period size: 39 Copynumber: 2.9 Consensus size: 37
14037 ACTCGTAATA
*
14047 TTAATATATAATTGGAATTGGACT-AAGAA---AACC
1 TTAATATATAATTGGAATTGGACTAAAAAATTCAACC
*
14080 TGTAATATATAATTTGAATTGGACTAATAAAATTCAACCC
1 T-TAATATATAATTGGAATTGGACTAA-AAAATTCAA-CC
14120 TTAATATATAATTGGAATTGGACTAAAAAAATTCAA
1 TTAATATATAATTGGAATTGGACT-AAAAAATTCAA
14156 TTTGATTACT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
33 1 0.02
34 22 0.34
35 1 0.02
36 3 0.05
39 33 0.51
40 5 0.08
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (37 bp):
TTAATATATAATTGGAATTGGACTAAAAAATTCAACC
Done.