Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009818.1 Corchorus capsularis cultivar CVL-1 contig09839, 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: 12162
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:2528 original size:35 final size:35
Alignment explanation
Indices: 2489--2648 Score: 230
Period size: 35 Copynumber: 4.6 Consensus size: 35
2479 TTACTAAACG
* * * *
2489 TAATTACCCTGAATTAAGTTGCTTATTTAATTACT
1 TAATTACCCTGAATTAAGTTGATTACTGACTTACT
* * *
2524 TAATTACCCTTAATTAAGTGGATTACTGGCTTACT
1 TAATTACCCTGAATTAAGTTGATTACTGACTTACT
* *
2559 TAATTACCCTGAATTAAATTGATTACTGACTCACT
1 TAATTACCCTGAATTAAGTTGATTACTGACTTACT
*
2594 TAATTACCCTGAATTAAGTTGATTACTTACTTACT
1 TAATTACCCTGAATTAAGTTGATTACTGACTTACT
2629 TAATTACCCTGAATTAAGTT
1 TAATTACCCTGAATTAAGTT
2649 ACTTATTACT
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 110 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (35 bp):
TAATTACCCTGAATTAAGTTGATTACTGACTTACT
Found at i:5611 original size:36 final size:36
Alignment explanation
Indices: 5524--5651 Score: 106
Period size: 36 Copynumber: 3.6 Consensus size: 36
5514 CAAAATAATT
* **
5524 AACTGAAGAAA-GACCACCCTGGATCATTCCAAACTGA
1 AACTGAAGAAACGACCACCCTCGATCATT-CTGACT-A
5561 AA-TGAA-AAACGACCACCCTCGATCATTCTGACGTA
1 AACTGAAGAAACGACCACCCTCGATCATTCTGAC-TA
* * * * *
5596 AACTGAAGAGA-GACCACCCTGGGTCA-ACTGAAATA
1 AACTGAAGAAACGACCACCCTCGATCATTCTG-ACTA
5631 AACTGAAG-AACGACCACCCTC
1 AACTGAAGAAACGACCACCCTC
5652 AATTACCACC
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
34 1 0.01
35 31 0.41
36 39 0.52
37 4 0.05
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (36 bp):
AACTGAAGAAACGACCACCCTCGATCATTCTGACTA
Found at i:6893 original size:15 final size:15
Alignment explanation
Indices: 6873--6908 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6863 CTTTACCTCT
6873 TTTCTTCTCTTGCTC
1 TTTCTTCTCTTGCTC
* *
6888 TTTCTTCTTTTTCTC
1 TTTCTTCTCTTGCTC
6903 TTTCTT
1 TTTCTT
6909 TTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTCTTCTCTTGCTC
Found at i:6907 original size:12 final size:11
Alignment explanation
Indices: 6888--6921 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6878 TCTCTTGCTC
6888 TTTC-TTCTTT
1 TTTCTTTCTTT
6898 TTCTCTTTCTTT
1 TT-TCTTTCTTT
6910 TTTCTTTCTTT
1 TTTCTTTCTTT
6921 T
1 T
6922 CTTTTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 12 0.55
12 8 0.36
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:6928 original size:15 final size:16
Alignment explanation
Indices: 6880--6928 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
6870 TCTTTTCTTC
* *
6880 TCTTGCTCTTTCTTCT
1 TCTTTCTCTTTCTTTT
6896 T-TTTCTCTTTCTTTTT
1 TCTTTCTCTTTC-TTTT
6912 TCTTTCT-TTTCTTTT
1 TCTTTCTCTTTCTTTT
6927 TC
1 TC
6929 GATTGCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 15 0.52
16 9 0.31
17 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (16 bp):
TCTTTCTCTTTCTTTT
Found at i:7746 original size:16 final size:17
Alignment explanation
Indices: 7725--7792 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 17
7715 GCAATTCAAC
7725 TTTTTTCTCTTTTC-TT
1 TTTTTTCTCTTTTCATT
*
7741 TTTTTTTTCTTTTCATT
1 TTTTTTCTCTTTTCATT
**
7758 TTTCAT-TCTTTTCACTT
1 TTTTTTCTCTTTTCA-TT
*
7775 TTTCTTTTTCCTTTTCAT
1 TTT-TTTCT-CTTTTCAT
7793 GTGGGAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 21 0.50
17 11 0.26
18 1 0.02
19 2 0.05
20 7 0.17
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCTCTTTTCATT
Found at i:10828 original size:35 final size:35
Alignment explanation
Indices: 10789--10951 Score: 281
Period size: 35 Copynumber: 4.7 Consensus size: 35
10779 TTTTTACTAA
* * *
10789 ACTTAATTACCCTGAATTAAGTTGCTTATTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
10824 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
10859 ACTTAATTACCCTGAATTAAGTTGATTACTGCCTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
10894 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
10929 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
10952 ACTTATTACT
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 121 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Done.