Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014467.1 Corchorus olitorius cultivar O-4 contig14500, 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: 6128
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Found at i:5045 original size:55 final size:55
Alignment explanation
Indices: 4939--5105 Score: 186
Period size: 55 Copynumber: 3.1 Consensus size: 55
4929 GTACAAGTGT
* * *
4939 TTAAGATGAGCCAGTGTGGTCTTTCATAA-AAGTTTTCAGC-AATCTA-AGTTGATC
1 TTAAGATGACCCAGTGCGGTCTTTCATAAGAAGTTTTCA-CTGATC-AGAGTTGATC
4993 TTCAA-ATGACCCAGTGC-GTCCTTTCATAAGAAGTTTTCACTGATCAGAGTTGATC
1 TT-AAGATGACCCAGTGCGGT-CTTTCATAAGAAGTTTTCACTGATCAGAGTTGATC
* *
5048 TTAAGTTGACCCCGTGCGGTCTTTCA-AAGAAGTTTTTCGA-TGATCAGAGTTGATC
1 TTAAGATGACCCAGTGCGGTCTTTCATAAGAAG-TTTTC-ACTGATCAGAGTTGATC
5103 TTA
1 TTA
5106 TTTCAAGAAG
Statistics
Matches: 99, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
53 2 0.02
54 31 0.31
55 63 0.64
56 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (55 bp):
TTAAGATGACCCAGTGCGGTCTTTCATAAGAAGTTTTCACTGATCAGAGTTGATC
Found at i:5208 original size:106 final size:105
Alignment explanation
Indices: 5069--5490 Score: 641
Period size: 106 Copynumber: 4.0 Consensus size: 105
5059 CCGTGCGGTC
* *
5069 TTTCAAAGAAGTTTTTCGATGATCAGAGTTGATCTTATTTCAAGAAGATTTTTATGATCAGAGTT
1 TTTC-AAGAAG-TTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTT
* ** *
5134 GATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCA
64 GATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
5176 TTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTATGATCAGAGTTG
1 TTT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTG
*
5241 ATCTCATTTCCAGAAGTTTTCGATGATCAGAGTTGATCTCG
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
** * *
5282 TTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TTATGATCAGAGTTG
*
5346 ATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
*
5387 TTTCAAGAAGTTTT-GATGATCAGAGTTGATCTTATTTCAAGAAGTTTTTTTAATGATCAGAGTT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTTT-ATGATCAGAGTT
*
5451 GATCTTATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
64 GATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
5491 TCACATTGAT
Statistics
Matches: 289, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
104 28 0.10
105 111 0.38
106 140 0.48
107 9 0.03
108 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (105 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
Found at i:5250 original size:141 final size:139
Alignment explanation
Indices: 5069--5490 Score: 664
Period size: 141 Copynumber: 3.0 Consensus size: 139
5059 CCGTGCGGTC
* *
5069 TTTCAAAGAAGTTTTTCGATGATCAGAGTTGATCTTATTTCAAGAAGATTTTTATGATCAGAGTT
1 TTTC-AAGAAGTTTTT-GATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTGATGATCAGAGTT
5134 GATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGATGATC
63 GATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTT-CAAGAAGTTTTCGATGATC
5199 AGAGTTGATCTCA
127 AGAGTTGATCTCA
* * *
5212 TTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAGAAGTTTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-GATGATCAGAGTTGA
* *
5277 TCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGA
65 TCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGA
*
5342 GTTGATCTCG
130 GTTGATCTCA
* *
5352 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTGATGATCAGAGTTGAT
1 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGAT
** *
5417 CTTATTTCAAGAAGTTTTTTTAATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAG
66 CTCGTTTCAAGAAG-TTTTTT-ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAG
5482 AGTTGATCT
129 AGTTGATCT
5491 TCACATTGAT
Statistics
Matches: 258, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
139 28 0.11
140 84 0.33
141 132 0.51
142 10 0.04
143 4 0.02
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (139 bp):
TTTCAAGAAGTTTTTGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTGATGATCAGAGTTGAT
CTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAG
TTGATCTCA
Found at i:5491 original size:35 final size:35
Alignment explanation
Indices: 5069--5490 Score: 596
Period size: 35 Copynumber: 11.9 Consensus size: 35
5059 CCGTGCGGTC
*
5069 TTTCAAAGAAGTTTTTCGATGATCAGAGTTGATCTTA
1 TTTC-AAGAAG-TTTTCGATGATCAGAGTTGATCTCA
* *
5106 TTTCAAGAAGATTTT-TATGATCAGAGTTGATCTCG
1 TTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTCA
**
5141 TTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
5176 TTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* **
5212 TTTCAATAAGTTTTTTATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
5247 TTTCCAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
** *
5282 TTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
5317 TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
5352 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
5387 TTTCAAGAAGTTTT-GATGATCAGAGTTGATCTTA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
** *
5421 TTTCAAGAAGTTTTTTTAATGATCAGAGTTGATCTTA
1 TTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCA
5458 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
5491 TCACATTGAT
Statistics
Matches: 351, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
34 32 0.09
35 239 0.68
36 47 0.13
37 33 0.09
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Done.