Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014042.1 Corchorus capsularis cultivar CVL-1 contig14063, 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: 17600
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27 TTGATGACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8391 original size:109 final size:109
Alignment explanation
Indices: 8195--8490 Score: 459
Period size: 109 Copynumber: 2.7 Consensus size: 109
8185 ACTATTATAG
*
8195 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTTA-T---TT-AATTAAATCTAATATCTTTATAATTACTT
8260 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
8309 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
8374 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* * **
8418 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
8482 TTTTTACCA
63 TTTTTACCA
8491 TTTTAATTTA
Statistics
Matches: 173, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
108 1 0.01
109 122 0.71
110 7 0.04
111 15 0.09
113 1 0.01
114 27 0.16
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:10303 original size:23 final size:21
Alignment explanation
Indices: 10264--10305 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
10254 TTGAATCTAT
10264 ACAAAATTTTCCACTTTTTTG
1 ACAAAATTTTCCACTTTTTTG
*
10285 ACAAATATTGTTCCTCTTTTT
1 ACAAA-ATT-TTCCACTTTTT
10306 CTCTCTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (21 bp):
ACAAAATTTTCCACTTTTTTG
Found at i:11090 original size:31 final size:32
Alignment explanation
Indices: 11053--11126 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
11043 CGCAGGTAAA
*
11053 AAAAAACAGAGACTTCTGG-TTTTTCTTAACT
1 AAAAAACAGAGACCTCTGGTTTTTTCTTAACT
11084 AAAAAACAGAGACCTCTGGTTTTTTCTTAACT
1 AAAAAACAGAGACCTCTGGTTTTTTCTTAACT
*
11116 -CAAAACAGAGA
1 AAAAAACAGAGA
11127 ATTCCAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 28 0.70
32 12 0.30
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (32 bp):
AAAAAACAGAGACCTCTGGTTTTTTCTTAACT
Found at i:12115 original size:33 final size:33
Alignment explanation
Indices: 12051--12117 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12041 TACACTGAGT
* *
12051 CTCCCCACTAGGACGGCTCCGCTATGACGGAGC
1 CTCCCCACTAGGACGGCTCCGCCAAGACGGAGC
* ** *
12084 CTCCCCACTAGTACTTCTCCGCCAAGGCGGAGC
1 CTCCCCACTAGGACGGCTCCGCCAAGACGGAGC
12117 C
1 C
12118 ATCAGTCCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTCCGCCAAGACGGAGC
Found at i:16664 original size:211 final size:211
Alignment explanation
Indices: 16300--16695 Score: 659
Period size: 211 Copynumber: 1.9 Consensus size: 211
16290 ATTTAATTAC
* *
16300 AAAGCAAATCATTTATTTTTTTAATCAAATAGATTGATTACGTTTAATATTTTTTACTTATTGAA
1 AAAGCAAATCATCTATTTTTTTAATCAAATAGATTGATTACGTTTAATATTTTTGACTTATTGAA
*
16365 TTATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGCTTTAATAGTTGCTTAATTTC
66 TTATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTACTTTAATAGTTGCTTAATTTC
16430 CCTTTTTCGTTTAATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAACTAATTATGC
131 CCTTTTTCGTTTAATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAACTAATTATGC
16495 TTTATTTCCTTTAAGA
196 TTTATTTCCTTTAAGA
*
16511 AAAGCAAATCATCTATTTTTTTTAATCAAATAGATTGATTACGTTTGATA-TTTTGACTTATTGA
1 AAAGCAAATCATCTA-TTTTTTTAATCAAATAGATTGATTACGTTTAATATTTTTGACTTATTGA
* * *
16575 ATTATTTAATTTCAAGCATTATCATAGTCAATAATTACTTATTTACTTTAATAGTTGCTTAATTT
65 ATTATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTACTTTAATAGTTGCTTAATTT
* ** ** *
16640 CCTTTTTTTTTTTAATGAAAATGAATCTTCTGTTTTTACTTAAAGATTTTCAATAA
130 CCCTTTTTCGTTTAATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAA
16696 GTTGTAAGGT
Statistics
Matches: 171, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
211 138 0.81
212 33 0.19
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (211 bp):
AAAGCAAATCATCTATTTTTTTAATCAAATAGATTGATTACGTTTAATATTTTTGACTTATTGAA
TTATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTACTTTAATAGTTGCTTAATTTC
CCTTTTTCGTTTAATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAACTAATTATGC
TTTATTTCCTTTAAGA
Found at i:17132 original size:137 final size:137
Alignment explanation
Indices: 16874--17259 Score: 465
Period size: 137 Copynumber: 2.8 Consensus size: 137
16864 CCAAAAGCTA
* * * *
16874 ATGATTATTTAATTTTGCCACAAATAAATAAATCAGTTAGT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATGTTAC--AAAAA-AAATT
* * * *
16938 GATTGAACATCCAAATAAGTAAATGAATCAAGTTAGTCCTTAGTTAACTTTGCCAATCAAAGTTA
63 GATTGAACATCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTCAACTTTGCCAATCAAAGTTA
17003 TAATTGATGG
128 TAATTGATGG
*
17013 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATATTAC-AAAAAAATTGAT
1 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATGTTACAAAAAAAATTGAT
*
17077 TGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTT-GATCAACTTTGTCAATCAAAGTTAT
66 TGAACAT-CTAAATAAATAAATGAATCAAGTTAGTCGTTAG-TCAACTTTGCCAATCAAAGTTAT
*
17141 AATTGATTG
129 AATTGATGG
* * * *
17150 ATGATTATTTGATTTTGT-CATAAATGAATGAATCAATTAGTAATCATGTTAGCAAAAAAAATAG
1 ATGATTATTT-ATTTTTTCCATAAATAAATAAATCAATTAGTAATTATGTTA-C--AAAAAA-A-
* ** *
17214 ATTGATTGAACATACTAAATAAATTAGGGAATCAAATTAGTCGTTA
60 ATTGATTGAACAT-CTAAATAAATAAATGAATCAAGTTAGTCGTTA
17260 ATTAATTGCC
Statistics
Matches: 215, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
136 16 0.07
137 100 0.47
138 7 0.03
139 37 0.17
140 9 0.04
141 5 0.02
142 1 0.00
143 40 0.19
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (137 bp):
ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATGTTACAAAAAAAATTGAT
TGAACATCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTCAACTTTGCCAATCAAAGTTATAA
TTGATGG
Found at i:17436 original size:167 final size:166
Alignment explanation
Indices: 17120--17438 Score: 417
Period size: 167 Copynumber: 1.9 Consensus size: 166
17110 GTCGTTGATC
* * * ** * *
17120 AACTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTGATTTTGTCATAAATGAATGAATCA
1 AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
* * * * *
17185 ATTAGTAATCATGTTAGCAAAAAAAATAGATTGATTGAACATACTAAATAAATTAGGGAATCAAA
66 ATTAGTAATCATGTTAGC-AAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAA
* *
17250 TTAGTCGTTAATTAATTGCCAAAAAAAATTAGTAATT
130 TTAGTCGCTAATAAATTGCCAAAAAAAATTAGTAATT
*
17287 AACTTTGCCAATCAAAGTTATAACTAATTGGTGATTATTACATTTTGCCATAAATAAATGAATCA
1 AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
* * * *
17352 ATTAGTAATTATGTTAGC-AAAAAATAAATTGATTCAACATGCTAAATAAATAAATGAACCAAGT
66 ATTAGTAATCATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAAT
17416 TAGTC-CTAAGTCAAAATTGCCAA
131 TAGTCGCTAA-T--AAATTGCCAA
17439 TCAAAGTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
164 3 0.02
165 44 0.34
167 83 0.64
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (166 bp):
AACTTTGCCAATCAAAGTTATAACTAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
ATTAGTAATCATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAAT
TAGTCGCTAATAAATTGCCAAAAAAAATTAGTAATT
Done.