Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023288.1 Corchorus olitorius cultivar O-4 contig23321, 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: 14057
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:168 original size:2 final size:2
Alignment explanation
Indices: 161--191 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
151 ACTTTAATGT
161 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
192 ATTATTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1611 original size:23 final size:22
Alignment explanation
Indices: 1548--1665 Score: 109
Period size: 22 Copynumber: 5.4 Consensus size: 22
1538 GGGAGATTAA
*
1548 CAAAATCTCATAGGGAAGGTTA-
1 CAAAATTTCATA-GGAAGGTTAT
*
1570 CAAAATTTCGTAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
1593 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
1615 CAAAGTTTCATATGGAA-TTTAT
1 CAAAATTTCATA-GGAAGGTTAT
1637 CAAAATTTCATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
1658 CAAAATTT
1 CAAAATTT
1666 TTCATAGCGT
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
21 20 0.25
22 44 0.55
23 16 0.20
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:4751 original size:21 final size:21
Alignment explanation
Indices: 4725--4795 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
4715 GTGTAAACTC
4725 GTACAGTACCTAATCTAATCT
1 GTACAGTACCTAATCTAATCT
* * *
4746 GTACAGTGTAATCTGTACCTAA-CT
1 GTACA--GT-ACCT-AATCTAATCT
4770 CGTACAGTACCTAATCTAATCT
1 -GTACAGTACCTAATCTAATCT
4792 GTAC
1 GTAC
4796 CTAACTCACA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 14 0.37
22 5 0.13
23 4 0.11
24 5 0.13
25 10 0.26
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (21 bp):
GTACAGTACCTAATCTAATCT
Found at i:4793 original size:32 final size:30
Alignment explanation
Indices: 4754--4819 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 30
4744 CTGTACAGTG
* *
4754 TAATCTGTACCTAACTCGTACAGTACCTAATC
1 TAATCTGTACCTAACTC--ACAATACATAATC
4786 TAATCTGTACCTAACTCACAATACATAATC
1 TAATCTGTACCTAACTCACAATACATAATC
4816 TAAT
1 TAAT
4820 TTATACAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 15 0.47
32 17 0.53
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (30 bp):
TAATCTGTACCTAACTCACAATACATAATC
Found at i:4795 original size:16 final size:16
Alignment explanation
Indices: 4730--4799 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
4720 AACTCGTACA
4730 GTACCTAATCTAATCT
1 GTACCTAATCTAATCT
* *
4746 GTA-C-AGTGTAATCT
1 GTACCTAATCTAATCT
*
4760 GTACCTAACTCGT-A-CA
1 GTACCTAA-TC-TAATCT
4776 GTACCTAATCTAATCT
1 GTACCTAATCTAATCT
4792 GTACCTAA
1 GTACCTAA
4800 CTCACAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 12 0.29
15 5 0.12
16 22 0.52
17 2 0.05
18 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (16 bp):
GTACCTAATCTAATCT
Found at i:10597 original size:22 final size:22
Alignment explanation
Indices: 10572--10627 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
10562 AGTTTAGGAC
10572 GTGCATATTTTA-CTCTTTTAAT
1 GTGCATATTTTATCT-TTTTAAT
* *
10594 GTGCTTTAGTTTATCTTTTTAAT
1 GTGC-ATATTTTATCTTTTTAAT
*
10617 GTGCATTTTTT
1 GTGCATATTTT
10628 GAAAAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 8 0.30
23 17 0.63
24 2 0.07
ACGTcount: A:0.18, C:0.11, G:0.12, T:0.59
Consensus pattern (22 bp):
GTGCATATTTTATCTTTTTAAT
Done.