Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010723.1 Corchorus capsularis cultivar CVL-1 contig10744, 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: 38374
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3847 original size:34 final size:34
Alignment explanation
Indices: 3809--3876 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
3799 GAGATTTTCA
3809 CAAGACTCTAACCCACTCACACCGAAACCTTGCT
1 CAAGACTCTAACCCACTCACACCGAAACCTTGCT
*
3843 CAAGACTCTAACCCACTCAGACCGAAACCTTGCT
1 CAAGACTCTAACCCACTCACACCGAAACCTTGCT
3877 TGAGCAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.40, G:0.10, T:0.18
Consensus pattern (34 bp):
CAAGACTCTAACCCACTCACACCGAAACCTTGCT
Found at i:3919 original size:29 final size:29
Alignment explanation
Indices: 3886--3949 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3876 TTGAGCAAGG
3886 TTGAACTTGGTCCAAATTGATAGAATCAT
1 TTGAACTTGGTCCAAATTGATAGAATCAT
*
3915 TTGAACTTGGTCCAATTTGATAGAATCAT
1 TTGAACTTGGTCCAAATTGATAGAATCAT
3944 TGTGAA
1 T-TGAA
3950 TAACAGACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (29 bp):
TTGAACTTGGTCCAAATTGATAGAATCAT
Found at i:6323 original size:2 final size:2
Alignment explanation
Indices: 6316--6348 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6306 GCTTAATTAC
6316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6349 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13943 original size:21 final size:22
Alignment explanation
Indices: 13912--13952 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13902 GAATGTAAAT
*
13912 AAATGATTAAAATGGTATTTAA
1 AAATGATTAAAAAGGTATTTAA
13934 AAAT-ATTAAAAAGGTATTT
1 AAATGATTAAAAAGGTATTT
13953 TCTCTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
AAATGATTAAAAAGGTATTTAA
Found at i:15397 original size:7 final size:7
Alignment explanation
Indices: 15387--15415 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
15377 CAAAAGTTTT
15387 GTTGAGA
1 GTTGAGA
15394 GTTGAGA
1 GTTGAGA
15401 GTTGAGA
1 GTTGAGA
15408 G-TGAGA
1 GTTGAGA
15414 GT
1 GT
15416 GTCTTGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GTTGAGA
Found at i:19155 original size:2 final size:2
Alignment explanation
Indices: 19148--19176 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19138 TCACATAATT
19148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19177 GAATTCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29646 original size:6 final size:6
Alignment explanation
Indices: 29590--29642 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
29580 TTTCCTTTAG
*
29590 TTTTG- TTTTG- TTTCGT ATTTTGT TTTTGT TTTTGT TTTTCGT TTTTGT
1 TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT TTTTGT TTTT-GT TTTTGT
29638 GTTTT
1 -TTTT
29643 TGTTAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 9 0.21
6 18 0.43
7 15 0.36
ACGTcount: A:0.02, C:0.04, G:0.17, T:0.77
Consensus pattern (6 bp):
TTTTGT
Found at i:34381 original size:49 final size:49
Alignment explanation
Indices: 34231--34616 Score: 464
Period size: 48 Copynumber: 7.9 Consensus size: 49
34221 TGCATATCCT
* *
34231 AAAACGCCCCTCCCAGACGGAAGGCACTTA-TTTTACTTG-TTGTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT-TTTCCC
*
34279 AAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTG-TTGTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT-TTTCCC
* * * * * * *
34327 AAAATGCCCTTTCCGGATGGAAAGCACCTATTTTTACATGCTATTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
*
34376 AAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
*
34424 AAAACGCCCTTCCCAGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
* * *
34473 TAAACGCCCTTCCCGAACGGAAGGCACTCAATTTTTACTTGCTTTTTCCC
1 AAAACGCCCTTCCCGGACGGAAGGCACT-TATTTTTACTTGCTTTTTCCC
* * * * * *
34523 TAAACGCCCTTCCTGGACGGAAGGCACTT-CTTTTATTTACTTTTTCCT
1 AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
* *
34571 AAAATGCCCTTCCCGGACGGAA-G-ACGTTAATGTTTACTTGCTTTTT
1 AAAACGCCCTTCCCGGACGGAAGGCAC-TT-ATTTTTACTTGCTTTTT
34617 TTTAAAATGC
Statistics
Matches: 296, Mismatches: 35, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
46 2 0.01
47 3 0.01
48 149 0.50
49 95 0.32
50 47 0.16
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.33
Consensus pattern (49 bp):
AAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTTTTTCCC
Found at i:34427 original size:97 final size:97
Alignment explanation
Indices: 34231--34616 Score: 455
Period size: 97 Copynumber: 4.0 Consensus size: 97
34221 TGCATATCCT
* * * *
34231 AAAACGCCCCTCCCAGACGGAAGGCACTTA-TTTTACTTG-TTGTTTCCCAAAATGCCCTTCCCG
1 AAAACGCCCTTTCCGGACGGAAGGCACCTATTTTTACTTGCTT-TTTCCCAAAATGCCCTTCCCG
34294 GACGGAAGGCACTTATTTTACTTG-TTGTTTCCC
65 GACGGAAGGCACTTATTTTACTTGCTT-TTTCCC
* * * * *
34327 AAAATGCCCTTTCCGGATGGAAAGCACCTATTTTTACATGCTATTTCCCAAAATGCCCTTCCCGG
1 AAAACGCCCTTTCCGGACGGAAGGCACCTATTTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGG
34392 ACGGAAGGCACTTATTTTACTTGCTTTTTCCC
66 ACGGAAGGCACTTATTTTACTTGCTTTTTCCC
* * * * * *
34424 AAAACGCCCTTCCCAGACGGAAGGCACTTATTTTTACTTGCTTTTTCCCTAAACGCCCTTCCCGA
1 AAAACGCCCTTTCCGGACGGAAGGCACCTATTTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGG
*
34489 ACGGAAGGCACTCAATTTTTACTTGCTTTTTCCC
66 ACGGAAGGCACT-TA-TTTTACTTGCTTTTTCCC
* * * *
34523 TAAACGCCC-TTCCTGGACGGAAGGCA-CT-TCTTTTATTTACTTTTTCCTAAAATGCCCTTCCC
1 AAAACGCCCTTTCC-GGACGGAAGGCACCTAT-TTTTACTTGCTTTTTCCCAAAATGCCCTTCCC
34585 GGACGGAA-G-ACGTTAATGTTTACTTGCTTTTT
64 GGACGGAAGGCAC-TT-AT-TTTACTTGCTTTTT
34617 TTTAAAATGC
Statistics
Matches: 248, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
96 26 0.10
97 143 0.58
98 42 0.17
99 37 0.15
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.33
Consensus pattern (97 bp):
AAAACGCCCTTTCCGGACGGAAGGCACCTATTTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGG
ACGGAAGGCACTTATTTTACTTGCTTTTTCCC
Done.