Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000620.1 Corchorus capsularis cultivar CVL-1 contig00620, 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: 16302
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Found at i:164 original size:2 final size:2
Alignment explanation
Indices: 157--201 Score: 63
Period size: 2 Copynumber: 21.0 Consensus size: 2
147 ATTGTTTTAA
157 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT GAT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT -AT AT
200 AT
1 AT
202 GATGTTCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 34 0.85
3 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:187 original size:7 final size:7
Alignment explanation
Indices: 157--204 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
147 ATTGTTTTAA
157 ATATAT-
1 ATATATG
163 ATATAT-
1 ATATATG
169 ATATAT-
1 ATATATG
175 ATATATG
1 ATATATG
182 ATATATG
1 ATATATG
189 ATATATG
1 ATATATG
196 ATATATG
1 ATATATG
203 AT
1 AT
205 GTTCTAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 18 0.44
7 23 0.56
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (7 bp):
ATATATG
Found at i:795 original size:13 final size:13
Alignment explanation
Indices: 773--806 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
763 TTTTTACCAG
773 ATTATTTATATAT
1 ATTATTTATATAT
* *
786 ATTGTTTATATTT
1 ATTATTTATATAT
799 ATTATTTA
1 ATTATTTA
807 ATAATTACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
ATTATTTATATAT
Found at i:1333 original size:12 final size:12
Alignment explanation
Indices: 1316--1341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1306 GGGCCTTGAA
1316 TCGTAATTTTAT
1 TCGTAATTTTAT
1328 TCGTAATTTTAT
1 TCGTAATTTTAT
1340 TC
1 TC
1342 CAATGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (12 bp):
TCGTAATTTTAT
Found at i:2018 original size:15 final size:15
Alignment explanation
Indices: 1998--2029 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1988 TCGGGTTATC
1998 GTCACTTGGATCCAG
1 GTCACTTGGATCCAG
2013 GTCACTTGGATCCAG
1 GTCACTTGGATCCAG
2028 GT
1 GT
2030 TTAATGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (15 bp):
GTCACTTGGATCCAG
Found at i:13303 original size:286 final size:281
Alignment explanation
Indices: 12791--13362 Score: 961
Period size: 286 Copynumber: 2.0 Consensus size: 281
12781 CATGGTATTT
12791 GAGCAGTTCTACTTTAGTTTTTTTGTCTATGTCTTACCTTCCAAGTTCCAATTGTCTTTCCAGAG
1 GAGCAGTTCTACTTTAGTTTTTTTGTCTATGTCTTA-C--CC-A-TTCCAATTGTCTTTCCAGAG
*
12856 ATTTTTCATGTTGTGGTTGCTATGTTGCATTGCTGCAGTTGTTATTTTGTCATTGATATTTTCCT
61 ATTTTTCATGTCGTGGTTGCTATGTTGCATTGCTGCAGTTGTTATTTTGTCATTGATATTTTCCT
12921 GATTCATCGCCTTGTCTCATTACCGTTGCCTCTAATATGGCCAGATGTTCTTGCTGCTCATTCCA
126 GATTCATCGCCTTGTCTCATTACCGTTGCCTCTAATATGGCCAGATGTTCTTGCTGCTCATTCCA
* *
12986 CATACTTATAATGGCACAGTCAATAAATGTGTGGAAGCTTTATCTCACCACATGCTGATGCAATT
191 CATACTTAGAATGGCACAGTCAACAAATGTGTGGAAGCTTTATCTCACCACATGCTGATGCAATT
13051 GTCGGTCTTTTGTGGGGTGTAATCCC
256 GTCGGTCTTTTGTGGGGTGTAATCCC
*
13077 GAGCAGTTCTACTTTAG-TTTTTTGTTTATGTCTTA-CC-TTCCAATTGTCTTTCCAGAGATTTT
1 GAGCAGTTCTACTTTAGTTTTTTTGTCTATGTCTTACCCATTCCAATTGTCTTTCCAGAGATTTT
13139 TCATGTCGTGGTTGCTATGTTGCATTGCTGCAGTTGTTATTTTGTCATTGATATTTTCCTGATTC
66 TCATGTCGTGGTTGCTATGTTGCATTGCTGCAGTTGTTATTTTGTCATTGATATTTTCCTGATTC
13204 ATCGCCTTGTCTCATTTACCGTTTACCGTTGCCTCTAATATGGCCAGATGTTCTTGCTGCTCATT
131 ATCGCCTTGTCTC----A----TTACCGTTGCCTCTAATATGGCCAGATGTTCTTGCTGCTCATT
*
13269 CCACATACTTAGAATGGCACAGTGAACAAATGTGTGGAAGCTTTATCTCACCACATGCTGATGCA
188 CCACATACTTAGAATGGCACAGTCAACAAATGTGTGGAAGCTTTATCTCACCACATGCTGATGCA
13334 ATTGTCGGTCTTTTGTGGGGTGTAATCCC
253 ATTGTCGGTCTTTTGTGGGGTGTAATCCC
13363 ATGCAGCCAA
Statistics
Matches: 273, Mismatches: 5, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
278 102 0.37
281 2 0.01
282 1 0.00
285 17 0.06
286 151 0.55
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (281 bp):
GAGCAGTTCTACTTTAGTTTTTTTGTCTATGTCTTACCCATTCCAATTGTCTTTCCAGAGATTTT
TCATGTCGTGGTTGCTATGTTGCATTGCTGCAGTTGTTATTTTGTCATTGATATTTTCCTGATTC
ATCGCCTTGTCTCATTACCGTTGCCTCTAATATGGCCAGATGTTCTTGCTGCTCATTCCACATAC
TTAGAATGGCACAGTCAACAAATGTGTGGAAGCTTTATCTCACCACATGCTGATGCAATTGTCGG
TCTTTTGTGGGGTGTAATCCC
Found at i:14423 original size:26 final size:26
Alignment explanation
Indices: 14366--14415 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
14356 CCCTGTCGAT
* *
14366 AACTGTATGCAACTATAACATTGGAC
1 AACTTTATGCAACTACAACATTGGAC
14392 AACTTTATGCAACTACAACATTGG
1 AACTTTATGCAACTACAACATTGG
14416 GATTCTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (26 bp):
AACTTTATGCAACTACAACATTGGAC
Done.