Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022028.1 Corchorus olitorius cultivar O-4 contig22061, 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: 6549
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:4277 original size:54 final size:54
Alignment explanation
Indices: 4213--4321 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
4203 AGAAACAGGG
* *
4213 TTCAGATGATCCAGTGTGGTCATTCAAAGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCAAAGAAGTTTTCAATGATCAGAGTTGATC
* * *
4267 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGGGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCAAAGAAGTTTTCAATGATCAGAGTTGATC
4321 T
1 T
4322 CGTTTCAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (54 bp):
TTCAGATGATCCAGTGCGGTCATTCAAAGAAGTTTTCAATGATCAGAGTTGATC
Found at i:4338 original size:35 final size:35
Alignment explanation
Indices: 4292--4985 Score: 808
Period size: 35 Copynumber: 19.8 Consensus size: 35
4282 GCGGTCATTC
*
4292 CAAGAAGTTTTCGATGATCAGGGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
4327 CAAGAAATTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
4362 CAAGAAGTTTTTGGTGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* ** *
4397 CAGGAAGTTTTTTATGATCAGAGTTGATCTCATTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTC-GTTT
* * * *
4433 CAAGATGTTTT-TATGGTCAGAGTTGATCTTGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
4467 CAAGAAGTTTT-TATGATCAGAGTTGATTTAC-TTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCT-CGTTT
* * * *
4501 CAAGAAGTTTTCGTTGATCAGAATTGATATCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
4536 CAAGAAGTTTTTTTTTTATGATCAGAGTTGATCTC-ATT
1 CAAGAAG----TTTTCGATGATCAGAGTTGATCTCGTTT
* *
4574 CGAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTT
1 C-AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
4609 CAATAAGTTTTCGATGATCAGAGTGGATCTCGTTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** * * *
4644 CAAGAAGTTTTTTATGATCTGATTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
4679 CAAGAAGTTTCCAATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
4714 CAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
4749 CAAGAAGTTTCCAATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* **
4784 CAAGAAGTTTT-TATGATCAGAGTTGATCTTATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
4818 CAAGAAATTTTTGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* * *
4853 CAAGCAGTTTTTGATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
*
4888 CAAAAAGTTTTCGATGATC-GTAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAG-AGTTGATCTCGTTT
* * *
4923 CAAGAAATTTTTGATGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
4958 CAAGAAGTTTTCGATGATCAGAGTTGAT
1 CAAGAAGTTTTCGATGATCAGAGTTGAT
4986 TTTCAATTTG
Statistics
Matches: 567, Mismatches: 78, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
34 103 0.18
35 423 0.75
36 13 0.02
38 3 0.01
39 25 0.04
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
Found at i:4382 original size:70 final size:70
Alignment explanation
Indices: 4292--4985 Score: 898
Period size: 70 Copynumber: 9.9 Consensus size: 70
4282 GCGGTCATTC
* * * *
4292 CAAGAAGTTTTCGATGATCAGGGTTGATCTCGTTTCAAGAAATTTTCGATGATCAGAGTTGATCT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
4357 CGTTT
66 CGTTT
* * **
4362 CAAGAAGTTTTTGGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATCT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
*
4427 CATTTT
66 C-GTTT
* * ** * *
4433 CAAGATGTTTTT-ATGGTCAGAGTTGATCTTGTTTCAAGAAGTTTT-TATGATCAGAGTTGATTT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
4496 AC-TTT
66 -CGTTT
* * * * * **
4501 CAAGAAGTTTTCGTTGATCAGAATTGATATCATTTCAAGAAGTTTTTTTTTTATGATCAGAGTTG
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAG----TTTTCGATGATCAGAGTTG
*
4566 ATCTC-ATT
62 ATCTCGTTT
* *
4574 CGAAGAAGTTTTT-ATGATCAGAGTTGATCTCCTTTCAATAAGTTTTCGATGATCAGAGTGGATC
1 C-AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
*
4638 TCGTTC
65 TCGTTT
* * * * *
4644 CAAGAAGTTTTTTATGATCTGATTTGATCTCCTTTCAAGAAGTTTCCAATGATCAGAGTTGATCT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
4709 CGTTT
66 CGTTT
* * *
4714 CAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTCCAATGATCAGAGTTGATCT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
4779 CGTTT
66 CGTTT
** * *
4784 CAAGAAGTTTTT-ATGATCAGAGTTGATCTTATTTCAAGAAATTTTTGATGATCAGAGTTGATCT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
4848 CGTTT
66 CGTTT
* *
4853 CAAGCAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAAAAGTTTTCGATGATC-GTAGTTGATC
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAG-AGTTGATC
4917 TCGTTT
65 TCGTTT
*
4923 CAAGAAATTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGAT
1 CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGAT
4986 TTTCAATTTG
Statistics
Matches: 549, Mismatches: 61, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
68 13 0.02
69 135 0.25
70 327 0.60
71 15 0.03
73 32 0.06
74 27 0.05
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (70 bp):
CAAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
CGTTT
Done.