Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009310.1 Corchorus capsularis cultivar CVL-1 contig09331, 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: 17774
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:852 original size:2 final size:2
Alignment explanation
Indices: 845--874 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
835 AAAGGGAGTA
845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
875 TTCTGATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5186 original size:31 final size:28
Alignment explanation
Indices: 5111--5189 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 28
5101 TTGCACACTT
5111 GTGTAACGTATAGGGACCAAAATGGAGCA
1 GTGTAA-GTATAGGGACCAAAATGGAGCA
* *
5140 GTTTTAAATATAGGGACCAAAATGGA-CAAAA
1 G-TGTAAGTATAGGGACCAAAATGGAGC---A
5171 CGTGTAAGTATAGGGACCA
1 -GTGTAAGTATAGGGACCA
5190 TTTCCGTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 19 0.46
30 4 0.10
31 16 0.39
32 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.20
Consensus pattern (28 bp):
GTGTAAGTATAGGGACCAAAATGGAGCA
Found at i:5503 original size:1 final size:1
Alignment explanation
Indices: 5499--5525 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5489 TTTTTTCAAA
5499 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
5526 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10467 original size:7 final size:7
Alignment explanation
Indices: 10455--10480 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10445 GTGATGGAAC
10455 ATGTTCA
1 ATGTTCA
10462 ATGTTCA
1 ATGTTCA
10469 ATGTTCA
1 ATGTTCA
10476 ATGTT
1 ATGTT
10481 AAGATCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (7 bp):
ATGTTCA
Found at i:13690 original size:35 final size:39
Alignment explanation
Indices: 13644--13725 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 39
13634 TTAATTAAAC
* *
13644 AAAGAGGAATAT-ATTATTGT-GCCAAAAA-AAAAGAA-
1 AAAGAGCAATATGATTATTGTGGCCAAAAATAAAAAAAG
* *
13679 AAAGAGCAATATGTTTCTTGTGGCCAAAAATAAAAAAAG
1 AAAGAGCAATATGATTATTGTGGCCAAAAATAAAAAAAG
13718 AAAGAGCA
1 AAAGAGCA
13726 TAGAAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 11 0.28
36 6 0.15
37 8 0.21
38 6 0.15
39 8 0.21
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.20
Consensus pattern (39 bp):
AAAGAGCAATATGATTATTGTGGCCAAAAATAAAAAAAG
Found at i:15017 original size:4 final size:4
Alignment explanation
Indices: 15008--15032 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
14998 GATAGTAAAT
15008 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
15033 AAGCGGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Done.