Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015186.1 Corchorus olitorius cultivar O-4 contig15219, 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: 5684
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2103 original size:16 final size:17
Alignment explanation
Indices: 2082--2127 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
2072 AATTGCAAAT
2082 AAATAAATATTCAAGA-
1 AAATAAATATTCAAGAG
*
2098 AAAT-AATAATCAAGAG
1 AAATAAATATTCAAGAG
*
2114 AAACAAATA-TCAAG
1 AAATAAATATTCAAG
2128 TGATGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (17 bp):
AAATAAATATTCAAGAG
Found at i:3379 original size:6 final size:6
Alignment explanation
Indices: 3365--3476 Score: 143
Period size: 6 Copynumber: 17.7 Consensus size: 6
3355 TGAACTCAAC
* *
3365 CATCAT CATCTT CATCTT CATCTT CATCTT CATGCTCTT CATCAT CATCTT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CA---TCTT CATCTT CATCTT
*
3416 CATCTT CATCTT CATCTT CATGCTCTT CATCAT CATCTT CATCTT CATCTT
1 CATCTT CATCTT CATCTT CA---TCTT CATCTT CATCTT CATCTT CATCTT
3467 CATCTT CATC
1 CATCTT CATC
3477 CTCTGCCTGG
Statistics
Matches: 95, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
6 83 0.87
9 12 0.13
ACGTcount: A:0.19, C:0.34, G:0.02, T:0.46
Consensus pattern (6 bp):
CATCTT
Found at i:3418 original size:39 final size:39
Alignment explanation
Indices: 3365--3480 Score: 223
Period size: 39 Copynumber: 3.0 Consensus size: 39
3355 TGAACTCAAC
3365 CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCTT
1 CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCTT
3404 CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCTT
1 CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCTT
*
3443 CATCATCATCTTCATCTTCATCTTCATCTTCATCCTCT
1 CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCT
3481 GCCTGGGGGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.18, C:0.34, G:0.02, T:0.46
Consensus pattern (39 bp):
CATCATCATCTTCATCTTCATCTTCATCTTCATGCTCTT
Found at i:3786 original size:27 final size:29
Alignment explanation
Indices: 3748--3816 Score: 106
Period size: 27 Copynumber: 2.4 Consensus size: 29
3738 CATGCTGTTT
3748 TCTTCATACTCTTCTGCATC-A-TATTCA
1 TCTTCATACTCTTCTGCATCAAGTATTCA
3775 TCTTCATACTCTTCTGCATCATAGTATTCA
1 TCTTCATACTCTTCTGCATCA-AGTATTCA
*
3805 TATTCATACTCT
1 TCTTCATACTCT
3817 GGCAATAGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 20 0.53
29 1 0.03
30 17 0.45
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.45
Consensus pattern (29 bp):
TCTTCATACTCTTCTGCATCAAGTATTCA
Found at i:5604 original size:48 final size:48
Alignment explanation
Indices: 5536--5644 Score: 202
Period size: 48 Copynumber: 2.3 Consensus size: 48
5526 GTTCATTGTG
*
5536 ATTGA-TTTACTAATGAAACATATACTAAATTTAAAATTTTAGTTCTT
1 ATTGATTTTACTAAGGAAACATATACTAAATTTAAAATTTTAGTTCTT
5583 ATTGATTTTACTAAGGAAACATATACTAAATTTAAAATTTTAGTTCTT
1 ATTGATTTTACTAAGGAAACATATACTAAATTTAAAATTTTAGTTCTT
5631 ATTGATTTTACTAA
1 ATTGATTTTACTAA
5645 ATTTAAAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
47 5 0.08
48 55 0.92
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (48 bp):
ATTGATTTTACTAAGGAAACATATACTAAATTTAAAATTTTAGTTCTT
Done.