Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007198.1 Corchorus capsularis cultivar CVL-1 contig07219, 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: 15364
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:1685 original size:30 final size:31
Alignment explanation
Indices: 1592--1702 Score: 143
Period size: 33 Copynumber: 3.5 Consensus size: 31
1582 TGACACTAAA
*
1592 TCTGTTTTGGATGCTAATAGCATTGAAAATAAT
1 TCTGTTTTGGTTG--AATAGCATTGAAAATAAT
*
1625 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGA--ATAGCATTGAAAATAAT
*
1658 TCTGTTTTGGTTG-ATGGCATTGAAAATAAT
1 TCTGTTTTGGTTGAATAGCATTGAAAATAAT
*
1688 TCTGTTTTGGGTGAA
1 TCTGTTTTGGTTGAA
1703 AAGAAAGAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
30 27 0.39
31 2 0.03
33 41 0.59
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (31 bp):
TCTGTTTTGGTTGAATAGCATTGAAAATAAT
Found at i:10761 original size:14 final size:13
Alignment explanation
Indices: 10742--10777 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
10732 CATCTTATAC
10742 ATTCATTTTTCAAT
1 ATTCATTTTTC-AT
10756 ATTCATTTTTCAT
1 ATTCATTTTTCAT
10769 -TTCATTTTT
1 ATTCATTTTT
10778 TTTTTGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 11 0.50
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTCATTTTTCAT
Found at i:11077 original size:12 final size:13
Alignment explanation
Indices: 11054--11151 Score: 90
Period size: 13 Copynumber: 6.8 Consensus size: 13
11044 TTCGAAAATT
11054 ATTTTTGAAAAAC
1 ATTTTTGAAAAAC
11067 ATTTTTGAAAACCATGACTC
1 ATTTTTG-AAA--A--A--C
11087 ATTTTTGAAAAAC
1 ATTTTTGAAAAAC
11100 ATTTTTGAAAAAAC
1 ATTTTTG-AAAAAC
11114 A-TTTTGAAAAAAC
1 ATTTTTG-AAAAAC
11127 ATTTTTGAAAAAAC
1 ATTTTTG-AAAAAC
*
11141 GTTTTTGAAAA
1 ATTTTTGAAAA
11152 CCATGACTCT
Statistics
Matches: 75, Mismatches: 1, Indels: 18
0.80 0.01 0.19
Matches are distributed among these distances:
13 32 0.43
14 28 0.37
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 3 0.04
20 8 0.11
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
ATTTTTGAAAAAC
Found at i:11124 original size:27 final size:28
Alignment explanation
Indices: 11089--11151 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
11079 CATGACTCAT
11089 TTTTG-AAAAACATTTTTGAAAAAAC-A
1 TTTTGAAAAAACATTTTTGAAAAAACGA
*
11115 TTTTGAAAAAACATTTTTGAAAAAACGT
1 TTTTGAAAAAACATTTTTGAAAAAACGA
11143 TTTTGAAAA
1 TTTTGAAAA
11152 CCATGACTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 5 0.15
27 20 0.59
28 9 0.26
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (28 bp):
TTTTGAAAAAACATTTTTGAAAAAACGA
Found at i:11196 original size:11 final size:12
Alignment explanation
Indices: 11179--11210 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11169 TCCAAGTGCC
11179 TTTTATTATTTA
1 TTTTATTATTTA
11191 -TTTATT-TTTA
1 TTTTATTATTTA
11201 TTTTATTATT
1 TTTTATTATT
11211 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:11203 original size:14 final size:14
Alignment explanation
Indices: 11181--11218 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
11171 CAAGTGCCTT
11181 TTATTA-TTTATTTA
1 TTATTATTTTA-TTA
*
11195 TTTTTATTTTATTA
1 TTATTATTTTATTA
11209 TTATTATTTT
1 TTATTATTTT
11219 TTGGAATGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTATTTTATTA
Done.