Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016305.1 Corchorus olitorius cultivar O-4 contig16338, 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: 8385
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2052 original size:25 final size:25
Alignment explanation
Indices: 2024--2093 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
2014 TAAACGCTCA
*
2024 TGTGCTTGCGTTTGGAAAATGAACC
1 TGTGCTTGCGTTTGGAAAACGAACC
*
2049 TGTGCTGGCGTTTGGAAAACGAACC
1 TGTGCTTGCGTTTGGAAAACGAACC
2074 TGTGCTTGCGTTTGGAAAAC
1 TGTGCTTGCGTTTGGAAAAC
2094 ACATAGGCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (25 bp):
TGTGCTTGCGTTTGGAAAACGAACC
Found at i:2833 original size:6 final size:6
Alignment explanation
Indices: 2822--2873 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
2812 TATATACCTG
* * **
2822 TCGAGC TCGAGC TCGAGC TCGAAC TCG-GTA TCGAAT TCGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC
2870 TCGA
1 TCGA
2874 ATTTTAGCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (6 bp):
TCGAGC
Found at i:2875 original size:18 final size:18
Alignment explanation
Indices: 2822--2876 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2812 TATATACCTG
**
2822 TCGAGCTCGAGCTCGAGC
1 TCGAGCTCGAGCTCGAAT
* *
2840 TCGAACTCG-GTATCGAAT
1 TCGAGCTCGAG-CTCGAAT
2858 TCGAGCTCGAGCTCGAAT
1 TCGAGCTCGAGCTCGAAT
2876 T
1 T
2877 TTAGCTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (18 bp):
TCGAGCTCGAGCTCGAAT
Found at i:6109 original size:24 final size:25
Alignment explanation
Indices: 6077--6189 Score: 102
Period size: 31 Copynumber: 4.1 Consensus size: 25
6067 ATCCTATATA
6077 TACAATTCCTAATGA-TTACTTAGT
1 TACAATTCCTAATGATTTACTTAGT
*
6101 TACAATTCCTAGTGATTTACTTAGTTATAT
1 TACAATTCCTAATGATTTACTTAG-----T
6131 ATACAATTCCTAATGATTTACTTAGTTATAT
1 -TACAATTCCTAATGATTTACTTAG-----T
6162 ATACAATTCCTAATGATTTACTTAGT
1 -TACAATTCCTAATGATTTACTTAGT
6188 TA
1 TA
6190 TATATACAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
24 14 0.17
25 10 0.12
26 1 0.01
30 1 0.01
31 54 0.68
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (25 bp):
TACAATTCCTAATGATTTACTTAGT
Found at i:6126 original size:25 final size:24
Alignment explanation
Indices: 6077--6127 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
6067 ATCCTATATA
6077 TACAATTCCTAATGATTACTTAGT
1 TACAATTCCTAATGATTACTTAGT
*
6101 TACAATTCCTAGTGATTTACTTAGT
1 TACAATTCCTAATGA-TTACTTAGT
6126 TA
1 TA
6128 TATATACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (24 bp):
TACAATTCCTAATGATTACTTAGT
Found at i:6194 original size:33 final size:31
Alignment explanation
Indices: 6101--6211 Score: 195
Period size: 31 Copynumber: 3.5 Consensus size: 31
6091 ATTACTTAGT
*
6101 TACAATTCCTAGTGATTTACTTAGTTATATA
1 TACAATTCCTAATGATTTACTTAGTTATATA
6132 TACAATTCCTAATGATTTACTTAGTTATATA
1 TACAATTCCTAATGATTTACTTAGTTATATA
6163 TACAATTCCTAATGATTTACTTAGTTATATA
1 TACAATTCCTAATGATTTACTTAGTTATATA
6194 TACAATATTCCTAATGAT
1 TAC-A-ATTCCTAATGAT
6212 CTGTGAAAGT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 64 0.83
32 1 0.01
33 12 0.16
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (31 bp):
TACAATTCCTAATGATTTACTTAGTTATATA
Found at i:7189 original size:16 final size:15
Alignment explanation
Indices: 7148--7189 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
7138 AACTAATCAG
7148 ATCATGACTCCACTA
1 ATCATGACTCCACTA
7163 A-CAAT-ACTCCACTAA
1 ATC-ATGACTCCACT-A
7178 ATCATGACTCCA
1 ATCATGACTCCA
7190 ATATCAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (15 bp):
ATCATGACTCCACTA
Done.