Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008305.1 Corchorus capsularis cultivar CVL-1 contig08326, 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: 10772
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:1963 original size:10 final size:10
Alignment explanation
Indices: 1948--1972 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1938 GTTGCTGCTT
1948 AATTCCAGAA
1 AATTCCAGAA
1958 AATTCCAGAA
1 AATTCCAGAA
1968 AATTC
1 AATTC
1973 TAGAGTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:2923 original size:13 final size:13
Alignment explanation
Indices: 2905--2943 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2895 AATTATTGTT
2905 TGCTTTATTAATC
1 TGCTTTATTAATC
*
2918 TGCTTTATTAATT
1 TGCTTTATTAATC
2931 TGCTTTA-TAATC
1 TGCTTTATTAATC
2943 T
1 T
2944 TTAGATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:2954 original size:6 final size:6
Alignment explanation
Indices: 2943--2969 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2933 CTTTATAATC
2943 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
2970 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:3343 original size:41 final size:40
Alignment explanation
Indices: 3267--3351 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
3257 TTGTTTTTGA
** *
3267 TTTTCCGTTTTTCTAAAAAAAAAAAGTTTTTTTTTTCCGAT
1 TTTTCCGTTTTTCTAAAAAAAAAAAG-AATATTTTTCCGAT
3308 TTTTCCGATTTTTACTAAAAAAAAAAA-AATATTTTTCCGAT
1 TTTTCCG-TTTTT-CTAAAAAAAAAAAGAATATTTTTCCGAT
3349 TTT
1 TTT
3352 AAAATTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
41 21 0.54
42 5 0.13
43 13 0.33
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (40 bp):
TTTTCCGTTTTTCTAAAAAAAAAAAGAATATTTTTCCGAT
Found at i:3421 original size:37 final size:37
Alignment explanation
Indices: 3362--3437 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
3352 AAAATTAGGG
* *
3362 TTTCCGATTTTTCTTTAAAAAAAAAATTTATTTTTCTT
1 TTTCCGATTTTTCTTTAAAAAAAAAA-ATATTTTTATT
*
3400 TTTCCG-TTTTTCCTTT-TAAAAAAAAATATTTTTATT
1 TTTCCGATTTTT-CTTTAAAAAAAAAAATATTTTTATT
3436 TT
1 TT
3438 CTGTTTCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 11 0.32
37 13 0.38
38 10 0.29
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (37 bp):
TTTCCGATTTTTCTTTAAAAAAAAAAATATTTTTATT
Found at i:3438 original size:35 final size:36
Alignment explanation
Indices: 3362--3453 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 36
3352 AAAATTAGGG
* *
3362 TTTCCGATTTTTCTTTAAAAAAAAAATTTATTTTTCTT
1 TTTCCG-TTTTTCTTTTAAAAAAAAA-TTATTTTTCAT
3400 TTTCCGTTTTTCCTTTTAAAAAAAAA-TATTTTT-AT
1 TTTCCGTTTTT-CTTTTAAAAAAAAATTATTTTTCAT
* *
3435 TTTCTGTTTCTGCTTTTAA
1 TTTCCGTTT-TTCTTTTAA
3454 TTTTTATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
35 16 0.33
36 8 0.17
37 5 0.10
38 19 0.40
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.57
Consensus pattern (36 bp):
TTTCCGTTTTTCTTTTAAAAAAAAATTATTTTTCAT
Found at i:5817 original size:12 final size:13
Alignment explanation
Indices: 5776--5820 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
5766 AATTATTGTT
5776 TGCTTTATTAATC
1 TGCTTTATTAATC
*
5789 TGCTTTATTAATT
1 TGCTTTATTAATC
5802 TGCTTTA-TAATC
1 TGCTTTATTAATC
5814 TGCTTTA
1 TGCTTTA
5821 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:5828 original size:6 final size:6
Alignment explanation
Indices: 5817--5843 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5807 TATAATCTGC
5817 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
5844 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:6207 original size:33 final size:33
Alignment explanation
Indices: 6121--6217 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
6111 TGGCTGGTTG
* *
6121 TGGCCGGACATGTCCATGTCGCGTGGCCGGTGA
1 TGGCCGGACATCTCCAAGTCGCGTGGCCGGTGA
* * * *
6154 TGGGCGGGCATC-CCTGAGTCGCGTGGCCGGTGT
1 TGGCCGGACATCTCC-AAGTCGCGTGGCCGGTGA
* *
6187 TGGCCGGACTTCTCCAAGTCGCATGGCCGGT
1 TGGCCGGACATCTCCAAGTCGCGTGGCCGGT
6218 CACCCGCGCC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
32 2 0.04
33 47 0.92
34 2 0.04
ACGTcount: A:0.10, C:0.29, G:0.39, T:0.22
Consensus pattern (33 bp):
TGGCCGGACATCTCCAAGTCGCGTGGCCGGTGA
Done.