Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014913.1 Corchorus capsularis cultivar CVL-1 contig14934, 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: 11811
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:3487 original size:33 final size:33
Alignment explanation
Indices: 3409--3487 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
3399 TTGCAAAGAG
* *
3409 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTACAATGATACTAAACC
** * *
3442 TAATTTAAGTGTTGTTTACAATGATACTAAATC
1 TGTTTTAGGTGTTGTTTACAATGATACTAAACC
3475 TGTTTTAGGTGTT
1 TGTTTTAGGTGTT
3488 ATTGGTGATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTACAATGATACTAAACC
Found at i:3504 original size:33 final size:33
Alignment explanation
Indices: 3462--3548 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
3452 GTTGTTTACA
* *
3462 ATGATACTAAATCTGTTTTAGG-TG-TTATTGGTG
1 ATGAAACTAAATCTGTTTT-GGATGCTAATT-GTG
*
3495 ATGACACTAAATCTGTTTTGGATGCTAATTGTG
1 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
3528 ATGAAAAC-AAATCTGTTTTGG
1 ATG-AAACTAAATCTGTTTTGG
3549 TAGATCATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 2 0.04
33 39 0.81
34 7 0.15
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (33 bp):
ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
Found at i:3576 original size:33 final size:33
Alignment explanation
Indices: 3539--3647 Score: 200
Period size: 33 Copynumber: 3.3 Consensus size: 33
3529 TGAAAACAAA
*
3539 TCTGTTTTGGTAGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
3572 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
3605 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
3638 TCTGTTTTGG
1 TCTGTTTTGG
3648 GTGAAAAGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:4030 original size:30 final size:30
Alignment explanation
Indices: 3990--4048 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3980 CAAGGGGGAG
3990 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
4020 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
4049 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:5984 original size:22 final size:22
Alignment explanation
Indices: 5959--6001 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5949 TTTTAAATCG
5959 CAAA-CCCTAATTTTTTTTTTTT
1 CAAATCCC-AATTTTTTTTTTTT
*
5981 CAAATCGCAATTTTTTTTTTT
1 CAAATCCCAATTTTTTTTTTT
6002 AGAAAAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.58
Consensus pattern (22 bp):
CAAATCCCAATTTTTTTTTTTT
Found at i:6302 original size:21 final size:20
Alignment explanation
Indices: 6256--6302 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
6246 TAAAGAAATT
* *
6256 AATT-AAAAGAAAGCAATTA
1 AATTAAAAACAAAGCAAGTA
*
6275 AACTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGC-AAGTA
6296 AATTAAA
1 AATTAAA
6303 TCTAAATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (20 bp):
AATTAAAAACAAAGCAAGTA
Found at i:6993 original size:19 final size:18
Alignment explanation
Indices: 6969--7004 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6959 TGAAGATTTC
6969 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
6988 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7005 ATTATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:9276 original size:11 final size:10
Alignment explanation
Indices: 9258--9291 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
9248 AATTGTCTTC
9258 AAATCTTCAA
1 AAATCTTCAA
9268 AATATCTTCAA
1 AA-ATCTTCAA
9279 GAAATCTTCAA
1 -AAATCTTCAA
9290 AA
1 AA
9292 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Done.