Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015652.1 Corchorus olitorius cultivar O-4 contig15685, 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: 18067
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:1412 original size:14 final size:14
Alignment explanation
Indices: 1393--1420 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1383 AACACAGCCA
1393 AAGAAGGAAGGAAG
1 AAGAAGGAAGGAAG
1407 AAGAAGGAAGGAAG
1 AAGAAGGAAGGAAG
1421 GTGGGACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (14 bp):
AAGAAGGAAGGAAG
Found at i:7042 original size:7 final size:7
Alignment explanation
Indices: 7030--7065 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
7020 TCACATGATA
7030 TATATAC
1 TATATAC
7037 TATATAC
1 TATATAC
7044 --TATA-
1 TATATAC
7048 TATATAC
1 TATATAC
7055 TATATAC
1 TATATAC
7062 TATA
1 TATA
7066 CTATAATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
5 4 0.15
6 4 0.15
7 18 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAC
Found at i:7050 original size:18 final size:18
Alignment explanation
Indices: 7027--7070 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
7017 GGATCACATG
7027 ATATATATACTATATACT
1 ATATATATACTATATACT
7045 ATATATATACTATATACT
1 ATATATATACTATATACT
7063 ATACTATA
1 ATA-TATA
7071 ATGGGAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATATACTATATACT
Found at i:8204 original size:2 final size:2
Alignment explanation
Indices: 8197--8240 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
8187 TGATCACATA
*
8197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
8240 A
1 A
8241 AAAGTACGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13638 original size:51 final size:51
Alignment explanation
Indices: 13562--13714 Score: 288
Period size: 51 Copynumber: 3.0 Consensus size: 51
13552 TTTTTTTTTT
*
13562 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAAAACGAACTAATATAAA
1 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACACGAACTAATATAAA
13613 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACACGAACTAATATAAA
1 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACACGAACTAATATAAA
*
13664 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACAGGAACTAATATAAA
1 GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACACGAACTAATATAAA
13715 AATTGAGCTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 100 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (51 bp):
GCACCATAACTTTGGGATTCCTTAATCTTAGCTAACACGAACTAATATAAA
Found at i:16001 original size:12 final size:12
Alignment explanation
Indices: 15984--16044 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
15974 TTTAATTTCC
15984 TTTTTTTCTCA-
1 TTTTTTTCTCAT
15995 TTTTTTTCT--T
1 TTTTTTTCTCAT
*
16005 TATTTTTCTCAT
1 TTTTTTTCTCAT
** **
16017 TTTTTACCTTTT
1 TTTTTTTCTCAT
16029 TTTTTTTCTCAT
1 TTTTTTTCTCAT
16041 TTTT
1 TTTT
16045 CCCTTTTAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
10 8 0.22
11 9 0.24
12 20 0.54
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTCTCAT
Found at i:16012 original size:21 final size:22
Alignment explanation
Indices: 15986--16044 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
15976 TAATTTCCTT
15986 TTTTTCTCATTTTTT-TCTTTA
1 TTTTTCTCATTTTTTCTCTTTA
* *
16007 TTTTTCTCATTTTTTACCTTTTTT
1 TTTTTCTCATTTTTT--CTCTTTA
16031 TTTTTCTCATTTTT
1 TTTTTCTCATTTTT
16045 CCCTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 15 0.45
24 18 0.55
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTCTCATTTTTTCTCTTTA
Found at i:16051 original size:21 final size:21
Alignment explanation
Indices: 15984--16051 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
15974 TTTAATTTCC
**
15984 TTTTTTTCTCATTTTTTTCTT
1 TTTTTTTCTCATTTTTCCCTT
* *
16005 TATTTTTCTCATTTTTTACCTTTT
1 TTTTTTTCTCA-TTTTT-CC-CTT
16029 TTTTTTTCTCATTTTTCCCTT
1 TTTTTTTCTCATTTTTCCCTT
16050 TT
1 TT
16052 AAACTCATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.37
22 7 0.18
23 5 0.13
24 12 0.32
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTCTCATTTTTCCCTT
Done.