Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006066.1 Corchorus capsularis cultivar CVL-1 contig06084, 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: 28068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:9 original size:1 final size:1
Alignment explanation
Indices: 4--45 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
1 AAC
4 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46 GGTGCCAACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2449 original size:29 final size:29
Alignment explanation
Indices: 2412--2477 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2402 CCATCTCATA
**
2412 ATATATTTTTTATTAAT-TTAATTATATGT
1 ATATATTTTTT-TTAATGAAAATTATATGT
**
2441 ATATATTTTTTTTGGTGAAAATTATATGT
1 ATATATTTTTTTTAATGAAAATTATATGT
2470 ATATATTT
1 ATATATTT
2478 ATATATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (29 bp):
ATATATTTTTTTTAATGAAAATTATATGT
Found at i:4534 original size:20 final size:20
Alignment explanation
Indices: 4509--4549 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4499 AGACTCAATT
4509 GACACTAAATCGTAAATAGA
1 GACACTAAATCGTAAATAGA
4529 GACACTAAATCGTAAATAGA
1 GACACTAAATCGTAAATAGA
4549 G
1 G
4550 CGACCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
GACACTAAATCGTAAATAGA
Found at i:4558 original size:20 final size:20
Alignment explanation
Indices: 4509--4558 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4499 AGACTCAATT
*
4509 GACACTAAATCGTAAATAGA
1 GACACCAAATCGTAAATAGA
*
4529 GACACTAAATCGTAAATAGA
1 GACACCAAATCGTAAATAGA
4549 G-CGACCAAAT
1 GAC-ACCAAAT
4559 TGATACCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (20 bp):
GACACCAAATCGTAAATAGA
Found at i:20620 original size:266 final size:262
Alignment explanation
Indices: 19915--20706 Score: 1498
Period size: 262 Copynumber: 3.0 Consensus size: 262
19905 CCTTTGTTTC
19915 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
1 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
19980 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
66 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
20045 CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
131 CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
20110 AACTACCATAAATAAATCATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCA
196 AACTACCATAAATAAATCATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCA
20175 CA
261 CA
20177 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
1 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
20242 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
66 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
20307 CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
131 CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
20372 AACTACCAT-AATAAACTACACTCTACCTACCAAACTTACGAC-AATAAACCAAATTACAAACTA
196 AACTACCATAAATAAA-T-CA-TCTACCTACCAAA--TAC-ACAAATAAACCAAATTACAAACTA
20435 AACTCACA
255 AACTCACA
20443 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
1 TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
20508 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
66 TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
*
20573 CATTACAATCAGAATAAATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGA
131 CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
*
20638 AACTATCATAAATAAATCATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCA
196 AACTACCATAAATAAATCATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCA
20703 CA
261 CA
20705 TC
1 TC
20707 TCTATATGTC
Statistics
Matches: 520, Mismatches: 2, Indels: 16
0.97 0.00 0.03
Matches are distributed among these distances:
261 8 0.02
262 239 0.46
263 2 0.00
264 26 0.05
265 2 0.00
266 235 0.45
267 8 0.02
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (262 bp):
TCACTTTTCAGCTCTCTATACATCTCAAAATTCAGAAACTCTTGACCCCTTGCTTGATCCTCACA
TTCCAACCTTAAATGAGGAACACCTTAATATTCCTTTTTTTTTTGAGTGAGTACATGTGAAATCT
CATTACAATCAGAATAAATCTCTATATGTCCAAACATTTAAATGAGAAATCAACTCAAACTAAGA
AACTACCATAAATAAATCATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCA
CA
Found at i:20790 original size:114 final size:114
Alignment explanation
Indices: 20590--20934 Score: 681
Period size: 114 Copynumber: 3.0 Consensus size: 114
20580 ATCAGAATAA
*
20590 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTATCATAAATAAAT
1 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
20655 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
66 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
20704 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
1 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
20769 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
66 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
20818 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
1 ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
20883 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
66 CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
20932 ATC
1 ATC
20935 CTCACATTCC
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 230 1.00
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.22
Consensus pattern (114 bp):
ATCTCTATATGTCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATAAAT
CATCTACCTACCAAATACACAAATAAACCAAATTACAAACTAAACTCAC
Done.