Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014316.1 Corchorus capsularis cultivar CVL-1 contig14337, 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: 60862
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1390 original size:15 final size:16
Alignment explanation
Indices: 1363--1392 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1353 TGCAGAAGGT
1363 AGAAAAGCTCTGAAGC
1 AGAAAAGCTCTGAAGC
1379 AGAAAA-CTCTGAAG
1 AGAAAAGCTCTGAAG
1393 AATCAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (16 bp):
AGAAAAGCTCTGAAGC
Found at i:8670 original size:58 final size:58
Alignment explanation
Indices: 8605--8723 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
8595 AACTACTTGC
* *
8605 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAAGCAAAAGTTAGAGCAAAA
*
8663 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAAGCAAAAGTTAGAGCAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAAGCAAAAGTTAGAGCAAAA
8721 AAA
1 AAA
8724 AAATCCCCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.17
Consensus pattern (58 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAAGCAAAAGTTAGAGCAAAA
Found at i:13963 original size:15 final size:16
Alignment explanation
Indices: 13936--13965 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13926 TGCAGAAGGT
13936 AGAAAAGCTCTGAAGC
1 AGAAAAGCTCTGAAGC
13952 AGAAAA-CTCTGAAG
1 AGAAAAGCTCTGAAG
13966 AATCAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (16 bp):
AGAAAAGCTCTGAAGC
Found at i:13977 original size:15 final size:15
Alignment explanation
Indices: 13959--13995 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13949 AGCAGAAAAC
13959 TCTGAAGAATCAAGA
1 TCTGAAGAATCAAGA
* *
13974 TCTGAGGAATCAATA
1 TCTGAAGAATCAAGA
13989 TCTGAAG
1 TCTGAAG
13996 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (15 bp):
TCTGAAGAATCAAGA
Found at i:17220 original size:11 final size:11
Alignment explanation
Indices: 17204--17233 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17194 GAAGTTCGTG
*
17204 TTTGAAGATTA
1 TTTGAAGATAA
17215 TTTGAAGATAA
1 TTTGAAGATAA
17226 TTTGAAGA
1 TTTGAAGA
17234 ATTGAAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:17232 original size:22 final size:22
Alignment explanation
Indices: 17204--17263 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17194 GAAGTTCGTG
*
17204 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
17226 TTTGAAGA--A-TTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
17245 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
17264 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:17250 original size:18 final size:19
Alignment explanation
Indices: 17216--17254 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
17206 TGAAGATTAT
*
17216 TTGAAGATAATTTGAAGAA
1 TTGAAGACAATTTGAAGAA
17235 TTGAAGACAA-TTGAAGAA
1 TTGAAGACAATTTGAAGAA
17253 TT
1 TT
17255 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.31
Consensus pattern (19 bp):
TTGAAGACAATTTGAAGAA
Found at i:18636 original size:21 final size:20
Alignment explanation
Indices: 18612--18659 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
18602 TAGATTTAGA
* *
18612 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
18633 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
18653 TTTAATT
1 TTTAATT
18660 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:32134 original size:32 final size:32
Alignment explanation
Indices: 32077--32137 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
32067 GGAGCGTTTA
*
32077 GTGGCGTTTTGTTCGAAGAACGCCCCTATATG
1 GTGGCGTTTTGTTCGAAAAACGCCCCTATATG
*
32109 GTGGCGTTTTGTTC-ATAAAATGCCCCTAT
1 GTGGCGTTTTGTTCGA-AAAACGCCCCTAT
32138 TTTGTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (32 bp):
GTGGCGTTTTGTTCGAAAAACGCCCCTATATG
Found at i:35112 original size:21 final size:21
Alignment explanation
Indices: 35086--35125 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35076 TCGACGCTCA
35086 GGTGGAGGAGGCGGCTGTTCT
1 GGTGGAGGAGGCGGCTGTTCT
35107 GGTGGAGGAGGCGGCTGTT
1 GGTGGAGGAGGCGGCTGTT
35126 GTGTAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.55, T:0.23
Consensus pattern (21 bp):
GGTGGAGGAGGCGGCTGTTCT
Found at i:43244 original size:26 final size:26
Alignment explanation
Indices: 43196--43257 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
43186 AATGAGAGGG
*** *
43196 AAAGAAGAAGAAAAAGTTTGGAAAGA
1 AAAGAAGAAGAAAAAGAAGGGAAACA
* *
43222 AAAGAAGAAGAAAAGGAAGGGAATCA
1 AAAGAAGAAGAAAAAGAAGGGAAACA
43248 AAAGAAGAAG
1 AAAGAAGAAG
43258 CGATGAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.63, C:0.02, G:0.29, T:0.06
Consensus pattern (26 bp):
AAAGAAGAAGAAAAAGAAGGGAAACA
Found at i:51887 original size:18 final size:18
Alignment explanation
Indices: 51842--51887 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
51832 TTTTTTAATT
51842 TTAAAATA-TTAAAGTACA
1 TTAAAATATTTAAAGTA-A
51860 TTAAAA-ATTTAAAGT-A
1 TTAAAATATTTAAAGTAA
51876 TTAAAGATATTT
1 TTAAA-ATATTT
51888 TAACTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 2 0.08
18 17 0.68
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (18 bp):
TTAAAATATTTAAAGTAA
Found at i:55205 original size:53 final size:52
Alignment explanation
Indices: 55125--55228 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 52
55115 ATTTTTCATC
* * *
55125 AAGTTTTCAAAGTATTCAATTTAGGTCTTTTTTAAATTGGGAAAGTTCCCATT
1 AAGTTTTCAAAGTACTCAATTTAGGTC-TTTTCAAAGTGGGAAAGTTCCCATT
*
55178 AAGTTTTCAAAGTGCTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAT
1 AAGTTTTCAAAGTACTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAT
55229 CGAGTCTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 22 0.47
53 25 0.53
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (52 bp):
AAGTTTTCAAAGTACTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATT
Done.