Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021298.1 Corchorus olitorius cultivar O-4 contig21331, 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: 46643
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1166 original size:18 final size:18
Alignment explanation
Indices: 1143--1183 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1133 CGTTTCATTG
1143 GATCATGTCACCTATGTA
1 GATCATGTCACCTATGTA
1161 GATCATGTCACCTATGTA
1 GATCATGTCACCTATGTA
1179 GATCA
1 GATCA
1184 AGGAGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (18 bp):
GATCATGTCACCTATGTA
Found at i:14324 original size:29 final size:30
Alignment explanation
Indices: 14290--14365 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
14280 CTCTTAACGA
*
14290 ATGGACAATTTGCACCCTAAACTTTAAT-T
1 ATGGACAATTTGCACCCTAAACTATAATCT
* * *
14319 TTGGACAATTTACACCATAAACTATAATCT
1 ATGGACAATTTGCACCCTAAACTATAATCT
* *
14349 ATGTACAATATGCACCC
1 ATGGACAATTTGCACCC
14366 AATTAGATGG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (30 bp):
ATGGACAATTTGCACCCTAAACTATAATCT
Found at i:14568 original size:31 final size:31
Alignment explanation
Indices: 14530--14588 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
14520 AAGTTTATAG
* *
14530 TGCAAATTGTCCATTCGCTTATAGTTCAAGA
1 TGCAAATTATCCATTCACTTATAGTTCAAGA
14561 TGCAAATTATCCATTCACTTATAGTTCA
1 TGCAAATTATCCATTCACTTATAGTTCA
14589 GTGGGTGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (31 bp):
TGCAAATTATCCATTCACTTATAGTTCAAGA
Found at i:15386 original size:9 final size:9
Alignment explanation
Indices: 15372--15401 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
15362 ACAAATGGAA
15372 TGACATTAT
1 TGACATTAT
15381 TGACATTAT
1 TGACATTAT
15390 TGACATTAT
1 TGACATTAT
15399 TGA
1 TGA
15402 TATATTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (9 bp):
TGACATTAT
Found at i:17422 original size:22 final size:22
Alignment explanation
Indices: 17380--17422 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17370 TTTCTGATTA
**
17380 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
17402 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
17423 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:21092 original size:30 final size:30
Alignment explanation
Indices: 21049--21132 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
21039 GGATTAGTTA
*
21049 TTTATG-CTTTAATTTTCAATTTCCTTTAT
1 TTTATGTCCTTAATTTTCAATTTCCTTTAT
21078 TTTATGTCCTTAATTTTCAATTTCCTTTAT
1 TTTATGTCCTTAATTTTCAATTTCCTTTAT
21108 TTTATGTCCTTAATTTTCAAGTTTC
1 TTTATGTCCTTAATTTTCAA-TTTC
21133 ATTAATAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 6 0.12
30 42 0.81
31 4 0.08
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTATGTCCTTAATTTTCAATTTCCTTTAT
Found at i:21093 original size:14 final size:14
Alignment explanation
Indices: 21070--21124 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
21060 ATTTTCAATT
*
21070 TCCTTTATTTTATG
1 TCCTTAATTTTATG
*
21084 TCCTTAATTTTCAATT
1 TCCTTAATTTT--ATG
*
21100 TCCTTTATTTTATG
1 TCCTTAATTTTATG
21114 TCCTTAATTTT
1 TCCTTAATTTT
21125 CAAGTTTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 22 0.65
16 12 0.35
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.62
Consensus pattern (14 bp):
TCCTTAATTTTATG
Found at i:24041 original size:22 final size:22
Alignment explanation
Indices: 23999--24041 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
23989 TTTCTGATTA
**
23999 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
24021 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
24042 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:31395 original size:17 final size:17
Alignment explanation
Indices: 31369--31406 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31359 ATATTATTAG
31369 ATTT-TATTTATATATT
1 ATTTATATTTATATATT
* *
31385 GTTTATATTTATTTATT
1 ATTTATATTTATATATT
31402 ATTTA
1 ATTTA
31407 ATGATTACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTATATTTATATATT
Found at i:35104 original size:56 final size:56
Alignment explanation
Indices: 34992--35104 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
34982 CCCTTTAAAC
***
34992 GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATACAAAGGCACCTTTTCAT
1 GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATACAAAGGCACCAGATCAT
* * * * * *
35048 GAATAGACATGTCTCTAATTAGAGATGCAATCTCTCATAGAAAGGTATCAGATCAT
1 GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATACAAAGGCACCAGATCAT
35104 G
1 G
35105 TTTGAAACAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (56 bp):
GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATACAAAGGCACCAGATCAT
Done.