Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007170.1 Corchorus capsularis cultivar CVL-1 contig07191, 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: 26844
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:2924 original size:23 final size:23
Alignment explanation
Indices: 2894--2971 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
2884 CCGCGCAACA
* **
2894 CCGGCCACATGACTTGGAGATGC
1 CCGGCCACATGACTCGGCCATGC
***
2917 CCGGCCACATGACTCGGCCACAA
1 CCGGCCACATGACTCGGCCATGC
2940 CCGGCCACATGACTCGGCCATGC
1 CCGGCCACATGACTCGGCCATGC
2963 CCGGCCACA
1 CCGGCCACA
2972 ACCGGCCACA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.22, C:0.41, G:0.26, T:0.12
Consensus pattern (23 bp):
CCGGCCACATGACTCGGCCATGC
Found at i:2936 original size:13 final size:13
Alignment explanation
Indices: 2918--2959 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
2908 TGGAGATGCC
2918 CGGCCACATGACT
1 CGGCCACATGACT
2931 CGGCCACA--AC-
1 CGGCCACATGACT
2941 CGGCCACATGACT
1 CGGCCACATGACT
2954 CGGCCA
1 CGGCCA
2960 TGCCCGGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 2 0.08
13 14 0.54
ACGTcount: A:0.24, C:0.43, G:0.24, T:0.10
Consensus pattern (13 bp):
CGGCCACATGACT
Found at i:9400 original size:32 final size:33
Alignment explanation
Indices: 9361--9427 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
9351 CCGGCCATTG
*
9361 CTTGGAGAAG-CCGTG-CAACACCGGCCACATGA
1 CTTGGAGAAGCCCG-GCCAACACCGACCACATGA
* *
9393 CTTGGAGATGCCCGGCCACCACCGACCACATGA
1 CTTGGAGAAGCCCGGCCAACACCGACCACATGA
9426 CT
1 CT
9428 CGGCCATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.13
Consensus pattern (33 bp):
CTTGGAGAAGCCCGGCCAACACCGACCACATGA
Found at i:9422 original size:33 final size:33
Alignment explanation
Indices: 9379--9491 Score: 136
Period size: 33 Copynumber: 3.4 Consensus size: 33
9369 AGCCGTGCAA
* **
9379 CACCGGCCACATGACTTGGAGATGCCCGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
* *
9412 CACCGACCACATGACTCGGCCATGCCTGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
* *
9445 AACCGGCCACTTGACTCGGCCATGCCCGGCCAC
1 CACCGGCCACATGACTCGGCCATGCCCGGCCAC
* * *
9478 AATCAGCCACATGA
1 CACCGGCCACATGA
9492 TCCTTTAACT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.23, C:0.42, G:0.23, T:0.12
Consensus pattern (33 bp):
CACCGGCCACATGACTCGGCCATGCCCGGCCAC
Found at i:15752 original size:15 final size:15
Alignment explanation
Indices: 15734--15832 Score: 92
Period size: 15 Copynumber: 6.6 Consensus size: 15
15724 TTTCGGTGTT
*
15734 ATCATCTTTGGTGCC
1 ATCATCTTCGGTGCC
*
15749 ATCACCTTCGGTGCC
1 ATCATCTTCGGTGCC
* *
15764 GTTGAT-TTCGGTGCC
1 -ATCATCTTCGGTGCC
* * *
15779 ACCATCTTGGGTGCT
1 ATCATCTTCGGTGCC
* *
15794 ATCATCTTGGGTGAC
1 ATCATCTTCGGTGCC
*
15809 ATCATCTTTGGTGCC
1 ATCATCTTCGGTGCC
15824 ATCATCTTC
1 ATCATCTTC
15833 TTCCATGGCA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
14 2 0.03
15 62 0.94
16 2 0.03
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.36
Consensus pattern (15 bp):
ATCATCTTCGGTGCC
Found at i:17077 original size:18 final size:18
Alignment explanation
Indices: 17056--17160 Score: 104
Period size: 18 Copynumber: 5.8 Consensus size: 18
17046 AAGTGAGGCA
* * *
17056 ACTTGGTGCAGTGTGGCC
1 ACTTGGTGCGGTGCGACC
17074 ACTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
17092 ATTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
** *
17110 ACTTGGTATGGTGCGGCC
1 ACTTGGTGCGGTGCGACC
* *
17128 ACTGGGTGTGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
17146 A-TTGGGTGTGGTGCG
1 ACTT-GGTGCGGTGCG
17161 GCTATTGGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
17 1 0.01
18 73 0.99
ACGTcount: A:0.10, C:0.21, G:0.42, T:0.27
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:17161 original size:36 final size:36
Alignment explanation
Indices: 17072--17174 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
17062 TGCAGTGTGG
* * * *
17072 CCACTTGGTGCGGTGCGACCATTTGGTGCGGTGCGA
1 CCACTTGGTGTGGTGCGGCCATTGGGTGTGGTGCGA
* *
17108 CCACTTGGTATGGTGCGGCCACTGGGTGTGGTGCGA
1 CCACTTGGTGTGGTGCGGCCATTGGGTGTGGTGCGA
*
17144 CCA-TTGGGTGTGGTGCGGCTATTGGGTGTGG
1 CCACTT-GGTGTGGTGCGGCCATTGGGTGTGG
17175 CGCCTGGTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 2 0.04
36 55 0.96
ACGTcount: A:0.10, C:0.20, G:0.43, T:0.27
Consensus pattern (36 bp):
CCACTTGGTGTGGTGCGGCCATTGGGTGTGGTGCGA
Found at i:17167 original size:18 final size:18
Alignment explanation
Indices: 17078--17174 Score: 97
Period size: 18 Copynumber: 5.4 Consensus size: 18
17068 GTGGCCACTT
* * *
17078 GGTGCGGTGCGACCATTT
1 GGTGTGGTGCGGCCATTG
* *
17096 GGTGCGGTGCGACCACTT-
1 GGTGTGGTGCGGCCA-TTG
* *
17114 GGTATGGTGCGGCCACTG
1 GGTGTGGTGCGGCCATTG
*
17132 GGTGTGGTGCGACCATTG
1 GGTGTGGTGCGGCCATTG
*
17150 GGTGTGGTGCGGCTATTG
1 GGTGTGGTGCGGCCATTG
17168 GGTGTGG
1 GGTGTGG
17175 CGCCTGGTGC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.01
18 65 0.96
19 2 0.03
ACGTcount: A:0.09, C:0.19, G:0.45, T:0.27
Consensus pattern (18 bp):
GGTGTGGTGCGGCCATTG
Found at i:22721 original size:36 final size:36
Alignment explanation
Indices: 22674--22743 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
22664 GTCACATCAA
22674 TGAAACTCCTATAATGCAAACTTGTATGCAAAATTG
1 TGAAACTCCTATAATGCAAACTTGTATGCAAAATTG
22710 TGAAACTCCTATAATGCAAACTTGTATGCAAAAT
1 TGAAACTCCTATAATGCAAACTTGTATGCAAAAT
22744 GTAATTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (36 bp):
TGAAACTCCTATAATGCAAACTTGTATGCAAAATTG
Found at i:23269 original size:55 final size:54
Alignment explanation
Indices: 23180--23342 Score: 238
Period size: 55 Copynumber: 3.0 Consensus size: 54
23170 CAAGACTTTC
* *
23180 TTCAAGGAACACTGGGAGATCACGAAGATTTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGAACACG-AGATCTCAAGCGAGTGTCAGCATTGAAGCT
*
23235 TTCAAGGAATACTGGGAGAACACTGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGAACAC-GAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* *
23290 TTCAAGGAACACTGGTA-AATCACGGAGATCTCAAGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGAA-CAC-GAGATCTCAAGCGAGTGTCAGCATTGAAG
23343 ATTGATAAGA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
54 2 0.02
55 96 0.97
56 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (54 bp):
TTCAAGGAACACTGGGAGAACACGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:23739 original size:17 final size:17
Alignment explanation
Indices: 23717--23755 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
23707 CTCATGGTAC
23717 CTAGGTAGTATGAGGTG
1 CTAGGTAGTATGAGGTG
23734 CTAGGTAGTATGAGGTG
1 CTAGGTAGTATGAGGTG
*
23751 ATAGG
1 CTAGG
23756 CTGCATCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.41, T:0.28
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTG
Done.