Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020372.1 Corchorus olitorius cultivar O-4 contig20405, 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: 8574
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:1121 original size:34 final size:34
Alignment explanation
Indices: 1083--1147 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1073 TCTTGTTAAC
1083 TAGTCCTACTATTATTAGGATTTGGATTAGGAAT
1 TAGTCCTACTATTATTAGGATTTGGATTAGGAAT
*
1117 TAGTCCTATTATTATTAGGATTTGGATTAGG
1 TAGTCCTACTATTATTAGGATTTGGATTAGG
1148 GATATCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.43
Consensus pattern (34 bp):
TAGTCCTACTATTATTAGGATTTGGATTAGGAAT
Found at i:3681 original size:25 final size:24
Alignment explanation
Indices: 3653--3709 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
3643 GTGGATTGTA
*
3653 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
* *
3678 AAATCAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
3702 AAA-AAATT
1 AAATAAATT
3710 CAAGGCTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.14
24 8 0.29
25 16 0.57
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:5145 original size:19 final size:18
Alignment explanation
Indices: 5102--5150 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5092 AGTTATAAAA
5102 TAAAAGA-AAAAAAAACG
1 TAAAAGACAAAAAAAACG
* * *
5119 GAAGAGACAAAAAAATGCG
1 TAAAAGACAAAAAAA-ACG
5138 TAAAAGACAAAAA
1 TAAAAGACAAAAA
5151 CAAAAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 5 0.20
18 7 0.28
19 13 0.52
ACGTcount: A:0.69, C:0.08, G:0.16, T:0.06
Consensus pattern (18 bp):
TAAAAGACAAAAAAAACG
Found at i:5534 original size:67 final size:72
Alignment explanation
Indices: 5426--5580 Score: 216
Period size: 67 Copynumber: 2.2 Consensus size: 72
5416 CAATTGGGTT
*
5426 GGGAGGCATGACG--CCCCCTTAACAATTAAGATTTGCGGAGGCGTCACG-CCCCC-TCACAA-T
1 GGGAGGCATGACGCCCCCCCTTAACAATTAAGATTTGCGGAGGCGTCACGCCCCCCTTAACAATT
5486 TTAAGTG
66 TTAAGTG
* *
5493 GGGAGGCATGACGCCCCCCCTTAACAATTTA-A-TTGGGGAGGCGTCACGCCCCCCTTAACAATT
1 GGGAGGCATGACGCCCCCCCTTAACAATTAAGATTTGCGGAGGCGTCACGCCCCCCTTAACAATT
*
5556 TTAATTG
66 TTAAGTG
*
5563 GGGAGGCATTACGCCCCC
1 GGGAGGCATGACGCCCCC
5581 TTCAATCCAA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
67 28 0.36
68 6 0.08
69 20 0.26
70 24 0.31
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (72 bp):
GGGAGGCATGACGCCCCCCCTTAACAATTAAGATTTGCGGAGGCGTCACGCCCCCCTTAACAATT
TTAAGTG
Found at i:5581 original size:34 final size:33
Alignment explanation
Indices: 5426--5582 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 33
5416 CAATTGGGTT
* *
5426 GGGAGGCATGACGCCCCCTTAACAATTAAGATTTG
1 GGGAGGCATCACGCCCCCTTAACAATTTA-A-TTG
* * * *
5461 CGGAGGCGTCACGCCCCC-TCACAATTTAAGTG
1 GGGAGGCATCACGCCCCCTTAACAATTTAATTG
*
5493 GGGAGGCATGACGCCCCCCCTTAACAATTTAATTG
1 GGGAGGCATCACG--CCCCCTTAACAATTTAATTG
*
5528 GGGAGGCGTCACGCCCCCCTTAACAATTTTAATTG
1 GGGAGGCATCACG-CCCCCTTAACAA-TTTAATTG
*
5563 GGGAGGCATTACGCCCCCTT
1 GGGAGGCATCACGCCCCCTT
5583 CAATCCAATG
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
32 12 0.12
33 1 0.01
34 33 0.32
35 57 0.55
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (33 bp):
GGGAGGCATCACGCCCCCTTAACAATTTAATTG
Found at i:6901 original size:25 final size:25
Alignment explanation
Indices: 6882--6952 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
6872 TAAACGCTCA
* *
6882 TGTGCTTGCGTTTGGAAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
6907 TGTGCTTGCGTTTAGCAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
6932 TGTGCTTGCGTTTAGCAAACG
1 TGTGCTTGCGTTTAGCAAACG
6953 CATGGGCTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (25 bp):
TGTGCTTGCGTTTAGCAAACGAGCC
Found at i:7230 original size:2 final size:2
Alignment explanation
Indices: 7223--7273 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
7213 TCATATAATG
* * *
7223 TA TA TA TA TA CA TA TA TA TA TA TA TA T- TA -A TG TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7263 TA TA CTA TA TA
1 TA TA -TA TA TA
7274 AGTCTAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Done.