Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016499.1 Corchorus capsularis cultivar CVL-1 contig16520, 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: 18051
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:4623 original size:3 final size:3
Alignment explanation
Indices: 4615--4686 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
4605 GATTTCAGTT
* * *
4615 ATC ATC ATC ACC ATC ATC ATC ATC ATC ATC CTC ATC ATC ATC CTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
4663 CTC ATC ATC -TGA ATC ATC ATC ATC
1 ATC ATC ATC AT-C ATC ATC ATC ATC
4687 TTTTCCCTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 1 0.02
3 55 0.96
4 1 0.02
ACGTcount: A:0.29, C:0.38, G:0.01, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:8210 original size:330 final size:327
Alignment explanation
Indices: 7556--8214 Score: 771
Period size: 329 Copynumber: 2.0 Consensus size: 327
7546 CACGTGTACT
* * *
7556 GATTACACGCTTTATTGTCAAGCTCATAAGCAAACATATCCACAATATATCACCTTACTCCACAT
1 GATTACACGCTTTATTGTCAAGCTCATAAGCAAACATATCCACAATAAATCAACTCACTCCACAT
* * * * * * *
7621 TTAGAAAAAAGATATGATAATAACCTAAAGTAATCCCACCATACCCTCCAAAACAAAAATGTGTT
66 TTAGAAAAAAAACATAATAATAACCTAAAATAAACCCACCACACCCTCCAAAACAAAAACGTGTT
* * * * *
7686 TAAGGAGCAAGGCGGACAATCTGACACACAAAAGAGAAAAAGGACTCAACTTTCCACAGACACGT
131 TAAGGAGCAAGGCGGAAAATCAGACACACAAAAGAGAAAAAGGACCCAACATTCCACA-ACACAT
* **
7751 GGAAGAGATCAATTAAAGAACTCAGTCCTTCCACACTAATTCAGTTATATCCAACACATAAACGA
195 GGAAGAGATCAATTAAAGAACTAAGGAC-TCCACACTAATTCAGTTATATCCAACACATAAACGA
* * * * * *
7816 CAAACGAAGCTGATCAGGTACAAAAATTAATAATCACAGATACGATAATTTTAACACGTATCTCA
259 CAAACAAAGCCGATCAGGTACAAAAATTAACAATCACAGATACCATAATTTGAACACATATCTCA
7881 CTGA
324 CTGA
* * *
7885 GATTAC-CTCTTTATTGTTAAGCTCATAAGCAAACATATCCACATTAAATCAACTCACTCCACAT
1 GATTACACGCTTTATTGTCAAGCTCATAAGCAAACATATCCACAATAAATCAACTCACTCCACAT
* *
7949 TTAGACAAAAAAACATAATGATAACCTAAAATAAACCCACCACACCCTCCAAAATAAAAACGTGT
66 TTAGA-AAAAAAACATAATAATAACCTAAAATAAACCCACCACACCCTCCAAAACAAAAACGTG-
** *
8014 TTAAGGAATAAGGAAGCAAGGCGGAAAATCAGACACGA-GGAAGAGAATAAGGACCCAAACATTC
129 TT------TAAGG-AGCAAGGCGGAAAATCAGACAC-ACAAAAGAGAAAAAGGACCC-AACATTC
* * *
8078 CAC-ACACAT-GCAGA-ATCAA-T-CA-AATTAAGGAC-CCA-ATCTAATTCAGTTATATCCAAA
185 CACAACACATGGAAGAGATCAATTAAAGAACTAAGGACTCCACA-CTAATTCAGTTATATCC-AA
* *
8135 GACATAAACGACAAACAAAGCCGATCAGGTACAGAAATTAACAATCACAGATACCATAATTTGAA
248 CACATAAACGACAAACAAAGCCGATCAGGTACAAAAATTAACAATCACAGATACCATAATTTGAA
*
8200 CATATATCTCACTGA
313 CACATATCTCACTGA
8215 CCCAGAACTG
Statistics
Matches: 279, Mismatches: 38, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
328 58 0.21
329 75 0.27
330 75 0.27
331 6 0.02
332 1 0.00
333 1 0.00
334 5 0.02
335 4 0.01
336 10 0.04
337 34 0.12
338 10 0.04
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.21
Consensus pattern (327 bp):
GATTACACGCTTTATTGTCAAGCTCATAAGCAAACATATCCACAATAAATCAACTCACTCCACAT
TTAGAAAAAAAACATAATAATAACCTAAAATAAACCCACCACACCCTCCAAAACAAAAACGTGTT
TAAGGAGCAAGGCGGAAAATCAGACACACAAAAGAGAAAAAGGACCCAACATTCCACAACACATG
GAAGAGATCAATTAAAGAACTAAGGACTCCACACTAATTCAGTTATATCCAACACATAAACGACA
AACAAAGCCGATCAGGTACAAAAATTAACAATCACAGATACCATAATTTGAACACATATCTCACT
GA
Found at i:8407 original size:42 final size:42
Alignment explanation
Indices: 8348--8431 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
8338 ATTCAGATAT
* *
8348 ATCTAACATATAGAGGACAAACAAAGAAGAACAGGTGCAGAA
1 ATCTAACATACAAAGGACAAACAAAGAAGAACAGGTGCAGAA
*
8390 ATCTAACATACAAAGGACAAACAAAGAAGACCAGGTGCAGAA
1 ATCTAACATACAAAGGACAAACAAAGAAGAACAGGTGCAGAA
8432 TTTAACAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (42 bp):
ATCTAACATACAAAGGACAAACAAAGAAGAACAGGTGCAGAA
Found at i:14655 original size:6 final size:6
Alignment explanation
Indices: 14646--14679 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
14636 GCACCATGGC
*
14646 CATCCA CATCCA CATCCA CATCCA CCTCCA CATC
1 CATCCA CATCCA CATCCA CATCCA CATCCA CATC
14680 ACCTTCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCCA
Found at i:14813 original size:18 final size:18
Alignment explanation
Indices: 14765--14807 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
14755 CTCTTCATTC
14765 TCTTCAGCACCATTCTGT
1 TCTTCAGCACCATTCTGT
*
14783 TCTTTAGCACCATTCTGT
1 TCTTCAGCACCATTCTGT
14801 TCTTCAG
1 TCTTCAG
14808 GGCCATATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (18 bp):
TCTTCAGCACCATTCTGT
Found at i:15884 original size:7 final size:7
Alignment explanation
Indices: 15864--15896 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
15854 TCGAGTTCGA
15864 AGAG-AG
1 AGAGAAG
*
15870 AGAAAAG
1 AGAGAAG
15877 AGAGAAG
1 AGAGAAG
15884 AGAGAAG
1 AGAGAAG
15891 AGAGAA
1 AGAGAA
15897 AATTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 3 0.12
7 21 0.88
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:17831 original size:25 final size:25
Alignment explanation
Indices: 17803--17858 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
17793 CAAATCTCAC
17803 TTTTAGGTTTCGAATTTTAATCATA
1 TTTTAGGTTTCGAATTTTAATCATA
* *
17828 TTTTAGTTTTTGAATTTTAATCATA
1 TTTTAGGTTTCGAATTTTAATCATA
17853 TCTTTA
1 T-TTTA
17859 TTATTTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTTAGGTTTCGAATTTTAATCATA
Found at i:17962 original size:66 final size:66
Alignment explanation
Indices: 17869--17993 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
17859 TTATTTAGTC
*
17869 TCCCACAAATTGGCAAGACCCCAAATTAT-TATTTAATTAATTATGTTT-TTATGATTTTTCTAG
1 TCCCACAAATTGGCAAGAACCCAAATTATCT-TTTAATTAATTAT-TTTATTATGATTTTTCTAG
17932 ACT
64 ACT
* * * *
17935 TCCCACAAATTGGCAA-AATCTAGAATTATCTTTTAATTATTTATTTTATTATTATTTTT
1 TCCCACAAATTGGCAAGAACCCA-AATTATCTTTTAATTAATTATTTTATTATGATTTTT
17994 ATAATTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 6 0.12
66 44 0.86
67 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (66 bp):
TCCCACAAATTGGCAAGAACCCAAATTATCTTTTAATTAATTATTTTATTATGATTTTTCTAGAC
T
Done.