Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014924.1 Corchorus capsularis cultivar CVL-1 contig14945, 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: 10153
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Found at i:1952 original size:14 final size:14
Alignment explanation
Indices: 1933--1960 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1923 GGTTATTCAT
1933 TGCTTAATATACAA
1 TGCTTAATATACAA
1947 TGCTTAATATACAA
1 TGCTTAATATACAA
1961 AGGCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TGCTTAATATACAA
Found at i:5117 original size:16 final size:16
Alignment explanation
Indices: 5096--5126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5086 TTGAAAAATA
5096 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
5112 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
5127 AATTTGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:5811 original size:199 final size:200
Alignment explanation
Indices: 5463--6317 Score: 1037
Period size: 199 Copynumber: 4.3 Consensus size: 200
5453 CTTTATAATA
* * * *
5463 AGGATCATTATACAATACAATGTCAATGTAAATTTTGGACTCCATAAGTGGGTTAAGAAGTTGAA
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* * * *
5528 ACATACCACATTTCATAATTAATTAAATACTTAATATTAATACATATTCCTTAAG-GGGACACAT
66 ACATACCCCATTTCATAATT-ATTAAATATTTAATATTAATACATATTCCCTAAGAGGTACACAT
* * * *
5592 GTCAACCCTTAAA--CCATGCACGTGCAGTATGCTAAACTCCACTGACGGTGTATTGTATAATTT
130 GTCAACCCTTAAAGTACACGCACGTGCAGTCTGCTAAACTCCACTGACGG-GTATTGTATAAATT
5655 TTCTTAT
194 TTCTTAT
* * * * * *
5662 AGGATTATTATACAACACACTATCATTATAAATTTTGGACTTCATAAGCGGGTTAAGAATTTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
5727 ACATACCCCATTTCATAATTAATTATATATTTAATATTAATACATATTCCCTAAGAGG-ACACAT
66 ACATACCCCATTTCATAATT-ATTAAATATTTAATATTAATACATATTCCCTAAGAGGTACACAT
* * * * *
5791 GTCAACTCTTAAA-T-CATGCACGTGCAGTCTGCTAAAATCTACTGACGGGTATTGTATAATTTT
130 GTCAACCCTTAAAGTACACGCACGTGCAGTCTGCTAAACTCCACTGACGGGTATTGTATAAATTT
*
5854 TCTTAA
195 TCTTAT
* * * * *
5860 AGGATTATTATACAATACATTGTCAGTGTAAA-TTTGGACTCCATAAGCAGATTAAGAAGCTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* * * *
5924 ACATTCCCCATTTC---ATGATTAAATATTTATTATTAATACCTATTCCCTAA-AGGTACACATG
66 ACATACCCCATTTCATAATTATTAAATATTTAATATTAATACATATTCCCTAAGAGGTACACATG
* *
5985 TCAACCCTTAAAGTTAAACCCCGCATGTGCAGTCTGCTAAACTCCACTGAC-GG--TTGTATAAA
131 TCAACCCTTAAAG-T--A-CACGCACGTGCAGTCTGCTAAACTCCACTGACGGGTATTGTATAAA
*
6047 TTTTCTTGT
192 TTTTCTTAT
* * * *
6056 AGGATTATTATACAATACATTGTCAGTGT-AATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
6120 ACATACCCCATTT--T-ATTATTAAATATTTAATATTAATACATATTCCCTAAG-GGTACACATG
66 ACATACCCCATTTCATAATTATTAAATATTTAATATTAATACATATTCCCTAAGAGGTACACATG
* * *
6181 TCAACCCTTAAAGTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTTACGGTGTATTGAATAA
131 TCAACCCTTAAAG-T--A-CACGCACGTGCAGTCTGCTAAACTCCACTGACGG-GTATTGTATAA
*
6246 ATTTTCTTGT
191 ATTTTCTTAT
* * *
6256 AGGATTATTATACAATACACTGCCAATGTAAATTTTGAACTCCATAAGCGAGTTAAGAAGTT
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
6318 TTTGTGCCAA
Statistics
Matches: 581, Mismatches: 58, Indels: 32
0.87 0.09 0.05
Matches are distributed among these distances:
192 3 0.01
193 48 0.08
194 2 0.00
195 3 0.01
196 179 0.31
197 41 0.07
198 50 0.09
199 182 0.31
200 45 0.08
201 28 0.05
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (200 bp):
AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCCATTTCATAATTATTAAATATTTAATATTAATACATATTCCCTAAGAGGTACACATG
TCAACCCTTAAAGTACACGCACGTGCAGTCTGCTAAACTCCACTGACGGGTATTGTATAAATTTT
CTTAT
Found at i:6081 original size:196 final size:199
Alignment explanation
Indices: 5463--6317 Score: 1008
Period size: 196 Copynumber: 4.3 Consensus size: 199
5453 CTTTATAATA
* * ** * *
5463 AGGATCATTATACAATACAATGTCAATGTAAATTTTGGACTCCATAAGTGGGTTAAGAAGTTGAA
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
* * * * *
5528 ACATACCACATTTCATAATTAATTAAATACTTAATATTAATACATATTCCTTAAGGGGACACATG
66 ACATACCCCATTTC---A-TAATTAAATATTTAATATTAATACATATTCCCTAAAGGTACACATG
* * *
5593 TCAACCC-----TTAAACCATGCACGTGCAGTATGCTAAACTCCACTGACGGTGTATTGTATAAT
127 TCAACCCTTAAATTAAACCACGCACGTGCAGTCTGCTAAACTCCACTGACGGTG-ATTGTATAAA
5653 TTTTCTTAT
191 TTTTCTTAT
* * * * * * * *
5662 AGGATTATTATACAACACACTATCATTATAAATTTTGGACTTCATAAGCGGGTTAAGAATTTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
5727 ACATACCCCATTTCATAATTAATTATATATTTAATATTAATACATATTCCCTAAGAGG-ACACAT
66 ACATACCCCATTTCATAATT-A--A-ATATTTAATATTAATACATATTCCCTAA-AGGTACACAT
* * * *
5791 GTCAACTCTTAAA-T----CATGCACGTGCAGTCTGCTAAAATCTACTGACGG-GTATTGTATAA
126 GTCAACCCTTAAATTAAACCACGCACGTGCAGTCTGCTAAACTCCACTGACGGTG-ATTGTATAA
* *
5850 TTTTTCTTAA
190 ATTTTCTTAT
* * *
5860 AGGATTATTATACAATACATTGTCAGTGTAAA-TTTGGACTCCATAAGCAGATTAAGAAGCTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
* * * *
5924 ACATTCCCCATTTCATGATTAAATATTTATTATTAATACCTATTCCCTAAAGGTACACATGTCAA
66 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAAGGTACACATGTCAA
* *
5989 CCCTTAAAGTTAAACCCCGCATGTGCAGTCTGCTAAACTCCACTGAC-G-G-TTGTATAAATTTT
131 CCCTTAAA-TTAAACCACGCACGTGCAGTCTGCTAAACTCCACTGACGGTGATTGTATAAATTTT
*
6051 CTTGT
195 CTTAT
* *
6056 AGGATTATTATACAATACATTGTCAGTGT-AATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
* * *
6120 ACATACCCCATTTTATTATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAA
66 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAAGGTACACATGTCAA
* * *
6185 CCCTTAAAGTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTTACGGTGTATTGAATAAATTT
131 CCCTTAAA-TTAAACCACGCACGTGCAGTCTGCTAAACTCCACTGACGGTG-ATTGTATAAATTT
*
6250 TCTTGT
194 TCTTAT
* *
6256 AGGATTATTATACAATACACTGCCAATGTAAATTTTGAACTCCATAAGC-GAGTTAAGAAGTT
1 AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGA-TTAAGAAGTT
6318 TTTGTGCCAA
Statistics
Matches: 576, Mismatches: 56, Indels: 46
0.85 0.08 0.07
Matches are distributed among these distances:
192 3 0.01
193 44 0.08
194 1 0.00
195 8 0.01
196 182 0.32
197 46 0.08
198 51 0.09
199 165 0.29
200 47 0.08
201 28 0.05
203 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
AGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGATTAAGAAGTTGAC
ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAAGGTACACATGTCAA
CCCTTAAATTAAACCACGCACGTGCAGTCTGCTAAACTCCACTGACGGTGATTGTATAAATTTTC
TTAT
Found at i:7431 original size:21 final size:21
Alignment explanation
Indices: 7405--7451 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7395 TCTTCTAAAC
* *
7405 TTTTTACTTACATTATAAAGT
1 TTTTTAATAACATTATAAAGT
* *
7426 TTTTTAATAACCTTATTAAGT
1 TTTTTAATAACATTATAAAGT
7447 TTTTT
1 TTTTT
7452 TAGGAACCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTAATAACATTATAAAGT
Found at i:7450 original size:22 final size:21
Alignment explanation
Indices: 7417--7477 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
7407 TTTACTTACA
*
7417 TTATAAAGTTTTTTAATAACC
1 TTATTAAGTTTTTTAATAACC
**
7438 TTATTAAGTTTTTTTAGGAACC
1 TTATTAAG-TTTTTTAATAACC
* *
7460 ATATTAAGGTTTTTAATA
1 TTATTAAGTTTTTTAATA
7478 TACAACCTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TTATTAAGTTTTTTAATAACC
Found at i:8028 original size:27 final size:27
Alignment explanation
Indices: 7997--8050 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7987 ACATAAATTT
*
7997 AGTAACCTCACATTCTTAGAATTTTTA
1 AGTAACCTCACATTCTTAGAAATTTTA
***
8024 AGTAACCTTGTATTCTTAGAAATTTTA
1 AGTAACCTCACATTCTTAGAAATTTTA
8051 GCATAGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (27 bp):
AGTAACCTCACATTCTTAGAAATTTTA
Found at i:9033 original size:15 final size:15
Alignment explanation
Indices: 9013--9042 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9003 TTGATAGTCT
9013 AAATTAAAAAATTCA
1 AAATTAAAAAATTCA
*
9028 AAATTAAAATATTCA
1 AAATTAAAAAATTCA
9043 TTTTGATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAAAATTCA
Done.