Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014740.1 Corchorus capsularis cultivar CVL-1 contig14761, 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: 28267
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:15349 original size:35 final size:35
Alignment explanation
Indices: 15310--15383 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
15300 ACCTGATTCA
* *
15310 CTGAATCTAACTTTGAAGATGCTACACCTAGTCAT
1 CTGAATCCAACTTTGAAGATGCTACACCGAGTCAT
* *
15345 CTGAATCCAATTTTGAAGATGCTGCACCGAGTCAT
1 CTGAATCCAACTTTGAAGATGCTACACCGAGTCAT
15380 CTGA
1 CTGA
15384 TTTACCGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (35 bp):
CTGAATCCAACTTTGAAGATGCTACACCGAGTCAT
Found at i:16037 original size:50 final size:50
Alignment explanation
Indices: 15962--16091 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
15952 TCATTACAAG
* * * *
15962 CCAATTATTCGAT-AAATCCCTGGGTAAATAACTCTGAAATACCATGACAT
1 CCAATTATTCGATCAAA-CCCAGGGTAAATAACACCGAAATACCACGACAT
* * *
16012 CCAATTATTCGATCAAACCCAGGGTAAATAACACCGAAATCCCGCGCCAT
1 CCAATTATTCGATCAAACCCAGGGTAAATAACACCGAAATACCACGACAT
* *
16062 --GATTAATCGATCAAACCCAGGGTAAATAAC
1 CCAATTATTCGATCAAACCCAGGGTAAATAAC
16092 GCCGCCGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 28 0.40
50 39 0.56
51 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.22
Consensus pattern (50 bp):
CCAATTATTCGATCAAACCCAGGGTAAATAACACCGAAATACCACGACAT
Found at i:21649 original size:12 final size:13
Alignment explanation
Indices: 21603--21660 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
21593 CCCGTTGAGG
21603 AAATGTTTTAT-T
1 AAATGTTTTATAT
*
21615 -ACTGCTTTTATAT
1 AAATG-TTTTATAT
**
21628 AAATACTTTATA-
1 AAATGTTTTATAT
21640 AAATGTTTTA-AT
1 AAATGTTTTATAT
21652 AAATGTTTT
1 AAATGTTTT
21661 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 4 0.11
12 23 0.64
13 7 0.19
14 2 0.06
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (13 bp):
AAATGTTTTATAT
Found at i:23880 original size:29 final size:28
Alignment explanation
Indices: 23844--23898 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
23834 CATGCATGTC
23844 AAAAATTAAAATTATT-ATTATTATTATT
1 AAAAATT-AAATTATTGATTATTATTATT
* *
23872 AAAATATTAATTTATTGATTTTTATTA
1 AAAA-ATTAAATTATTGATTATTATTA
23899 AATTAGGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AAAAATTAAATTATTGATTATTATTATT
Found at i:27038 original size:38 final size:38
Alignment explanation
Indices: 26996--27144 Score: 253
Period size: 38 Copynumber: 3.9 Consensus size: 38
26986 GGCTGTGCAT
26996 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* *
27034 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* *
27072 AGTGGACCCGTGCCTCAGGGGGTTAAACTGCTGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
*
27110 AGTGGACTCGCGCCTCAGGGGGTTAAACTGATGGT
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGT
27145 CAGGGGGTTA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 105 1.00
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.21
Consensus pattern (38 bp):
AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:27149 original size:20 final size:20
Alignment explanation
Indices: 27124--27164 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27114 GACTCGCGCC
27124 TCAGGGGGTTAAACTGATGG
1 TCAGGGGGTTAAACTGATGG
*
27144 TCAGGGGGTTAAACTGTTGG
1 TCAGGGGGTTAAACTGATGG
27164 T
1 T
27165 AAGAGTGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.10, G:0.39, T:0.29
Consensus pattern (20 bp):
TCAGGGGGTTAAACTGATGG
Found at i:27183 original size:58 final size:58
Alignment explanation
Indices: 27086--27197 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
27076 GACCCGTGCC
*
27086 TCAGGGGGTTAAACTGCTGGTAAGAGTGGACTCGCGCCTCAGGGGGTTAAACTGATGG
1 TCAGGGGGTTAAACTGCTGGTAAGAGTGGACCCGCGCCTCAGGGGGTTAAACTGATGG
* *
27144 TCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCGTGCCTCAGGGGGTTAAACTG
1 TCAGGGGGTTAAACTGCTGGTAAGAGTGGACCCGCGCCTCAGGGGGTTAAACTG
27198 TTGGCAAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (58 bp):
TCAGGGGGTTAAACTGCTGGTAAGAGTGGACCCGCGCCTCAGGGGGTTAAACTGATGG
Found at i:27216 original size:6 final size:6
Alignment explanation
Indices: 27205--27235 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
27195 CTGTTGGCAA
*
27205 GATTGT GATTGT GATTGT GATTGC GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT G
27236 GTCCAGCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.03, G:0.35, T:0.45
Consensus pattern (6 bp):
GATTGT
Found at i:28008 original size:2 final size:2
Alignment explanation
Indices: 28001--28032 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27991 TAAGTTGAAC
28001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28033 AACAATGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.