Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012891.1 Corchorus capsularis cultivar CVL-1 contig12912, 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: 7524
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:5259 original size:48 final size:47
Alignment explanation
Indices: 5098--5421 Score: 224
Period size: 50 Copynumber: 6.6 Consensus size: 47
5088 TCTTTACCTA
* * * ** * **
5098 CTTTTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTATTAA
1 CTTTTTCCCTAAACGCCCTTCCTGGACGG-AGGCACTT-CTTTTATTTG
* * * * *
5147 CCTTTTCCCAAAACGCCCTTCCCGGACAGAAGGCACTTAATTTTTATTTG
1 CTTTTTCCCTAAACGCCCTTCCTGGAC-GGAGGCACTT--CTTTTATTTG
*
5197 CTTTTTCCCTAAATGCCCTTCCTGGACGGAGGACACTTCTTTTATTTG
1 CTTTTTCCCTAAACGCCCTTCCTGGACGGAGG-CACTTCTTTTATTTG
* ** * * * *
5245 CTTTTT-CCTAAAATGCCCTTCCCAGATGGAAGCCATTTATTTTTTATTTG
1 CTTTTTCCCT-AAACGCCCTTCCTGGACGG-AGGCA-CT-TCTTTTATTTG
*
5295 CTTTTTCCCTAAACGCCCTTCCTGGACGGAAGGCACTTCTTTTGTTTG
1 CTTTTTCCCTAAACGCCCTTCCTGGACGG-AGGCACTTCTTTTATTTG
** * *
5343 CTTTTTCCC-AAAGCGCCCTTCCCAGACGGAAGTCA-TTCATCTTTACTTG
1 CTTTTTCCCTAAA-CGCCCTTCCTGGACGG-AGGCACTTC-T-TTTATTTG
* *
5392 CTATTTCCC-AAAGCGCCCTTCCTAGACGGA
1 CTTTTTCCCTAAA-CGCCCTTCCTGGACGGA
5422 AGCCATTTGT
Statistics
Matches: 230, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
47 9 0.04
48 72 0.31
49 72 0.31
50 74 0.32
51 3 0.01
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (47 bp):
CTTTTTCCCTAAACGCCCTTCCTGGACGGAGGCACTTCTTTTATTTG
Found at i:5299 original size:147 final size:146
Alignment explanation
Indices: 5083--5731 Score: 623
Period size: 147 Copynumber: 4.4 Consensus size: 146
5073 TTTATTAATT
* * * * * * *
5083 TTCAGTCTTTACCTACTTTTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTA-TTAA
1 TTCA-TCTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTT--
* * * * * *
5147 CCTTTTCCCAAAACGCCCTTCCCGGACAGAAGGCACTTAATTTTTATTTGCTTTTTCCCTAAA-T
63 GCTTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTT-ATTTTTACTTGCTATTTCCC-AAAGC
* *
5211 GCCCTTCCTGGACGGAGGACA
126 GCCCTTCCTAGACGGAAGACA
* * * * * *
5232 CTTC-T-TTTATTTGCTTTTTCCTAAAATGCCCTTCCCAGATGGAAGCCATTTATTTTTTATTTG
1 -TTCATCTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTA-TTTTTACTTG
* ** * *
5295 CTTTTTCCCTAAACGCCCTTCCTGGACGGAAGGCACTTCTTTTGT--TTGCTTTTTCCCAAAGCG
64 C-TTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTTATTTT-TACTTGCTATTTCCCAAAGCG
* *
5358 CCCTTCCCAGACGGAAGTCA
127 CCCTTCCTAGACGGAAGACA
* * * *
5378 TTCATCTTTACTTGCTATTTCCCAAAGCGCCCTTCCTAGACGGAAGCCATTTGTTTTTGCTTGCT
1 TTCATCTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCT
* * *
5443 ATCTCCCAAAACACCCTTCCCAGACGGAA-GC-CGTTCATTTTTACTTGCAATTTCCCAAAGCGC
66 -TTTCCCAAAACGCCCTTCCCAGACGGAAGGCAC-TT-ATTTTTACTTGCTATTTCCCAAAGCGC
* *
5506 CCTTCTTAGACGGAAGCCA
128 CCTTCCTAGACGGAAGACA
* *
5525 TTCATCTTTACTTGCTATCTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCC
1 TTCATCTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTG-C
* ** * * * *
5590 ATTTCCCAAAGTGCCCTTCCCAGACGGAAGCCATTTATTTCTACTTGCTATTTCCCAAAGTGCCC
65 TTTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTTATTTTTACTTGCTATTTCCCAAAGCGCCC
*
5655 TTCCTAGACGGAAGCCA
130 TTCCTAGACGGAAGACA
* * * * ** *
5672 TTTAT-TTTCGCTTGCTATTTCCCAAAACGCCCATCCCGGACGGAAGGTATTTATTCTTAC
1 TTCATCTTT-ACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTAC
5732 CTGCCATCTC
Statistics
Matches: 420, Mismatches: 63, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
144 1 0.00
145 12 0.03
146 69 0.16
147 288 0.69
148 45 0.11
149 2 0.00
150 3 0.01
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (146 bp):
TTCATCTTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCT
TTTCCCAAAACGCCCTTCCCAGACGGAAGGCACTTATTTTTACTTGCTATTTCCCAAAGCGCCCT
TCCTAGACGGAAGACA
Found at i:5747 original size:49 final size:48
Alignment explanation
Indices: 5101--5746 Score: 535
Period size: 49 Copynumber: 13.2 Consensus size: 48
5091 TTACCTACTT
* * * * * *
5101 TTTCCCAAAACGCCCTTCCCGGATGGAAGGCGTTTATTTTTA-TTAACCT-
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTT--GCTA
* * * * * * *
5150 TTTCCCAAAACGCCCTTCCCGGACAGAAGGCACTTAATTTTTATTTGCTT
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA-TTTA-TTTTACTTGCTA
* ** * * * * * *
5200 TTTCCCTAAA-TGCCCTTCCTGGACGGAGGACACTTCTTTTATTTGCTT
1 TTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTA
* ** * * *
5248 TTTCCTAAAATGCCCTTCCCAGATGGAAGCCATTTATTTTTTATTTGCTT
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTA--TTTTACTTGCTA
** * * * ** *
5298 TTTCCCTAAA-CGCCCTTCCTGGACGGAAGGCACTTCTTTTGTTTGCTT
1 TTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTA
* *
5346 TTTCCCAAAGCGCCCTTCCCAGACGGAAGTCATTCATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTAT-TTTACTTGCTA
* * *
5395 TTTCCCAAAGCGCCCTTCCTAGACGGAAGCCATTTGTTTTTGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTT-ATTTTACTTGCTA
* * * * * *
5444 TCTCCCAAAACACCCTTCCCAGACGGAAGCCGTTCATTTTTACTTGCAA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTTGCTA
** *
5493 TTTCCCAAAGCGCCCTTCTTAGACGGAAGCCATTCATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTAT-TTTACTTGCTA
* *
5542 TCTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCCA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTTGCTA
*
5591 TTTCCCAAAGTGCCCTTCCCAGACGGAAGCCATTTATTTCTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTT-TACTTGCTA
* * *
5640 TTTCCCAAAGTGCCCTTCCTAGACGGAAGCCATTTATTTTCGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTT-ACTTGCTA
* * * ** * *
5689 TTTCCCAAAACGCCCATCCCGGACGGAAGGTATTTATTCTTACCTGCCA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATT-TTACTTGCTA
*
5738 TCTCCCAAA
1 TTTCCCAAA
5747 ATGCCTTTTC
Statistics
Matches: 499, Mismatches: 81, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
47 6 0.01
48 79 0.16
49 334 0.67
50 72 0.14
51 8 0.02
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (48 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTA
Found at i:6934 original size:27 final size:27
Alignment explanation
Indices: 6904--6962 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
6894 CTCAAAAGAG
6904 AACCAGAAGAGGGTGGGGTGCACTCAC
1 AACCAGAAGAGGGTGGGGTGCACTCAC
6931 AACCAGAAGAGGGTGGGGTGCACTCAC
1 AACCAGAAGAGGGTGGGGTGCACTCAC
6958 AACCA
1 AACCA
6963 AAACAGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.34, T:0.10
Consensus pattern (27 bp):
AACCAGAAGAGGGTGGGGTGCACTCAC
Done.