Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015391.1 Corchorus olitorius cultivar O-4 contig15424, 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, 922
Length: 1538
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Found at i:207 original size:53 final size:53
Alignment explanation
Indices: 1--358 Score: 643
Period size: 52 Copynumber: 6.8 Consensus size: 53
1 TAATTACTAAATC-TTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
*
53 TAATTACTAAATCTTTTT-AAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
**
105 TAATTACTAAATCTTTTT-AAATGTTCGGAGGGACAGCCCTCATAGGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
*
157 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
210 TAATTACTAAATC-TTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
262 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
*
315 TAATTACTAAATCTTTTTAAACTGTTCGGAGGGACAGCCCTCAT
1 TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCAT
359 AACATACTTG
Statistics
Matches: 296, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
52 165 0.56
53 131 0.44
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (53 bp):
TAATTACTAAATCTTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
Found at i:209 original size:105 final size:105
Alignment explanation
Indices: 1--359 Score: 648
Period size: 105 Copynumber: 3.4 Consensus size: 105
*
1 TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCCTAATTACTAAATC
1 TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATACGTCTCCCTAATTACTAAATC
66 TTTTT-AAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
66 TTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
* *
105 TAATTACTAAATCTTTTTAAATGTTCGGAGGGACAGCCCTCATAGGTCTCCCTAATTACTAAATC
1 TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATACGTCTCCCTAATTACTAAATC
170 TTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
66 TTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
*
210 TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCCTAATTACTAAATC
1 TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATACGTCTCCCTAATTACTAAATC
*
275 TTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCCC
66 TTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
*
315 TAATTACTAAATCTTTTTAAACTGTTCGGAGGGACAGCCCTCATA
1 TAATTACTAAATC-TTTTAAAATGTTCGGAGGGACAGCCCTCATA
360 ACATACTTGA
Statistics
Matches: 244, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
104 67 0.27
105 148 0.61
106 29 0.12
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (105 bp):
TAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATACGTCTCCCTAATTACTAAATC
TTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCCC
Found at i:761 original size:56 final size:56
Alignment explanation
Indices: 701--812 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
691 AAAACAGAAG
701 AACATAATCAAGCAATCATCCAGAAGCCAACAAAAAATCAGCAACAACAAGCAAAC
1 AACATAATCAAGCAATCATCCAGAAGCCAACAAAAAATCAGCAACAACAAGCAAAC
*
757 AACATAATCAAGCAATCATCCGGAAGCCAACAAAAAATCAGCAACAACAAGCAAAC
1 AACATAATCAAGCAATCATCCAGAAGCCAACAAAAAATCAGCAACAACAAGCAAAC
813 GGCAACACAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.54, C:0.27, G:0.10, T:0.09
Consensus pattern (56 bp):
AACATAATCAAGCAATCATCCAGAAGCCAACAAAAAATCAGCAACAACAAGCAAAC
Found at i:1393 original size:52 final size:52
Alignment explanation
Indices: 1308--1535 Score: 384
Period size: 52 Copynumber: 4.3 Consensus size: 52
1298 TCACACTATG
* *
1308 CTAATTACTAATTTCTTTTTAAAATGTTTGGAGGGACAGCCCTCATCCGTCTCC
1 CTAATTACTAA-ATC-TTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
*
1362 CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCTGTCTCC
1 CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
1414 CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
1 CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
* **
1466 CTAATTACTAAATCTTTTTAAATGTTCGGAGGGACAGCCCTCATAGGTCTCC
1 CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
1518 CTAATTACTAAATCTTTT
1 CTAATTACTAAATCTTTT
1536 TAA
Statistics
Matches: 167, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
52 154 0.92
53 2 0.01
54 11 0.07
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (52 bp):
CTAATTACTAAATCTTTTAAAATGTTCGGAGGGACAGCCCTCATCCGTCTCC
Done.