Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008184.1 Corchorus capsularis cultivar CVL-1 contig08205, 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: 19091
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:5927 original size:30 final size:30
Alignment explanation
Indices: 5891--5973 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
5881 CAAGGAAGGG
5891 ATGGAATCGCACCAAAGATGCCATTA-GCTA
1 ATGGAATCGCACCAAAGATGCCATTATG-TA
* *
5921 ATGGAATCGCACCTAAGATGCCATTATGTG
1 ATGGAATCGCACCAAAGATGCCATTATGTA
*
5951 ATGAAATCGCACCAAAGATGCCA
1 ATGGAATCGCACCAAAGATGCCA
5974 CTTTATCCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 47 0.98
31 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (30 bp):
ATGGAATCGCACCAAAGATGCCATTATGTA
Found at i:9766 original size:30 final size:30
Alignment explanation
Indices: 9730--9809 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
9720 CAAAAGATCA
9730 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
9760 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
* ***
9790 ATTGATGTCTTTGGTGCGAT
1 AATGGCATCTTTGGTGCGAT
9810 CCCATCTCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:11900 original size:33 final size:33
Alignment explanation
Indices: 11829--11969 Score: 124
Period size: 33 Copynumber: 4.3 Consensus size: 33
11819 AAAGGATCAT
** * *
11829 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCAC
* * ** *
11862 TTGGCCGGTTGTGGCCGGGCATGTCCTTGTCGC
1 GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCAC
*
11895 GTGGCCGG-TGATGGCCGAGCATCTCCAAGTCAC
1 GTGGCCGGTTG-TGGCCGGGCATCTCCAAGTCAC
* * *
11928 ATGGCCGG-TGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTGTGGC-CGGGCATCTCCAAGTCAC
*
11961 TTGGCCGGT
1 GTGGCCGGT
11970 CACAAGTGCT
Statistics
Matches: 88, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
32 5 0.06
33 83 0.94
ACGTcount: A:0.10, C:0.28, G:0.39, T:0.23
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCAC
Found at i:13331 original size:33 final size:33
Alignment explanation
Indices: 13289--13374 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
13279 TTCTTTTCAC
*
13289 CCAAAACATAATTATTTTTAATGCTATAATCAA
1 CCAAAACATAATTATTTTCAATGCTATAATCAA
* *
13322 CCAAAACATAATTATTTGCAATGCTATGATCAA
1 CCAAAACATAATTATTTTCAATGCTATAATCAA
*
13355 CCAAAACAGAATTATTTTCA
1 CCAAAACATAATTATTTTCA
13375 TCACAATTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (33 bp):
CCAAAACATAATTATTTTCAATGCTATAATCAA
Found at i:13449 original size:33 final size:33
Alignment explanation
Indices: 13389--13485 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
13379 AATTAGCATC
**
13389 CAAAACAGATTTAGTATCATCATAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * * *
13422 TAAAACAGATTTAGTGTCATTGCAAACAACTCT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
13455 CAAATTAGGTTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
13486 TCTAAAGACT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:15177 original size:33 final size:33
Alignment explanation
Indices: 15135--15225 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
15125 AGATAAAGGA
15135 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
* * **
15168 TCATTTGGCCGGTTGTGGCCGGGCATGTCCTTG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
*
15201 TCACGTGGCCGG-TGATGGCCGGGCA
1 TCATGTGGCCGGTTG-TGGCCGGGCA
15226 ACTCCAAGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.09, C:0.25, G:0.42, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
Found at i:15243 original size:33 final size:33
Alignment explanation
Indices: 15206--15279 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
15196 CCTTGTCACG
15206 TGGCCGGTGATGGC-CGGGCAACTCCAAGTCGCA
1 TGGCCGGTG-TGGCGCGGGCAACTCCAAGTCGCA
* **
15239 TGGCCGGTGTTGCGCGGGCATGTCCAAGTCGCA
1 TGGCCGGTGTGGCGCGGGCAACTCCAAGTCGCA
15272 TGGCCGGT
1 TGGCCGGT
15280 CACAAGTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.08
33 34 0.92
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.19
Consensus pattern (33 bp):
TGGCCGGTGTGGCGCGGGCAACTCCAAGTCGCA
Found at i:17119 original size:33 final size:33
Alignment explanation
Indices: 17072--17155 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
17062 CTTTTCACCT
* *
17072 AAAATAGAATTATTTTTAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGCTATAATCAACC
* *
17105 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTTCAATGCTATAATCAACC
*
17138 AAAACATAATTATTTTCA
1 AAAACAGAATTATTTTCA
17156 TCACAATTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AAAACAGAATTATTTTCAATGCTATAATCAACC
Found at i:18976 original size:33 final size:33
Alignment explanation
Indices: 18934--19024 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
18924 AGATAAAGGA
18934 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
* * **
18967 TCATTTGGCCGGTTGTGGCCGGGCATGTCCTTG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
*
19000 TCACGTGGCCGG-TGATGGCCGGGCA
1 TCATGTGGCCGGTTG-TGGCCGGGCA
19025 ACTCCAAGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.09, C:0.25, G:0.42, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
Found at i:19042 original size:33 final size:33
Alignment explanation
Indices: 19005--19078 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
18995 CCTTGTCACG
19005 TGGCCGGTGATGGC-CGGGCAACTCCAAGTCGCA
1 TGGCCGGTG-TGGCGCGGGCAACTCCAAGTCGCA
* **
19038 TGGCCGGTGTTGCGCGGGCATGTCCAAGTCGCA
1 TGGCCGGTGTGGCGCGGGCAACTCCAAGTCGCA
19071 TGGCCGGT
1 TGGCCGGT
19079 CACAAGTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.08
33 34 0.92
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.19
Consensus pattern (33 bp):
TGGCCGGTGTGGCGCGGGCAACTCCAAGTCGCA
Done.