Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021711.1 Corchorus olitorius cultivar O-4 contig21744, 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: 10527
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Found at i:1917 original size:21 final size:21
Alignment explanation
Indices: 1891--1961 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
1881 TGCTAGGAGT
1891 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
1912 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
1933 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
1954 TCATTGGA
1 TCATTGGA
1962 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:2243 original size:65 final size:65
Alignment explanation
Indices: 2156--2284 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
2146 CTTGCTATTG
* * *
2156 ATTCCAACTTTCTGCACTAGCCCAGGC-ATGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 ATTCAAACTTTCTACACTAGCCCAGGCGA-GGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
2220 A
65 A
**
2221 ATTCAAACTTTCTACACTAGCCCAGGCGAGGGTAGGCCATTGGTACCCCATGCATGGGTAGGAC
1 ATTCAAACTTTCTACACTAGCCCAGGCGAGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
2285 CAGTTTTTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 57 0.98
66 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (65 bp):
ATTCAAACTTTCTACACTAGCCCAGGCGAGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGACA
Found at i:2393 original size:11 final size:11
Alignment explanation
Indices: 2361--2399 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2351 AAAAAGGATC
*
2361 TTTCCTAGCTC
1 TTTCCTAGCTT
*
2372 CTTCCTAGCTT
1 TTTCCTAGCTT
2383 TTTCCTAGCTT
1 TTTCCTAGCTT
2394 TTTCCT
1 TTTCCT
2400 TTACTCTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.08, C:0.33, G:0.08, T:0.51
Consensus pattern (11 bp):
TTTCCTAGCTT
Found at i:2495 original size:18 final size:18
Alignment explanation
Indices: 2472--2529 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
2462 TAAACATAAG
2472 TTGAGTTGATTAATAAAA
1 TTGAGTTGATTAATAAAA
* * *
2490 TTGAG-TG-TAAACATAAG
1 TTGAGTTGATTAATA-AAA
2507 TTGAGTTGATTAATAAAA
1 TTGAGTTGATTAATAAAA
2525 TTGAG
1 TTGAG
2530 GTTTTTACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 9 0.29
18 14 0.45
19 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (18 bp):
TTGAGTTGATTAATAAAA
Found at i:2506 original size:35 final size:35
Alignment explanation
Indices: 2460--2529 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2450 CAACCCCTCT
2460 TGTAAACATAAGTTGAGTTGATTAATAAAATTGAG
1 TGTAAACATAAGTTGAGTTGATTAATAAAATTGAG
2495 TGTAAACATAAGTTGAGTTGATTAATAAAATTGAG
1 TGTAAACATAAGTTGAGTTGATTAATAAAATTGAG
2530 GTTTTTACCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTAAACATAAGTTGAGTTGATTAATAAAATTGAG
Found at i:2522 original size:17 final size:17
Alignment explanation
Indices: 2467--2522 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2457 TCTTGTAAAC
2467 ATAAGTTGAGTTGATTA
1 ATAAGTTGAGTTGATTA
* *
2484 ATAAAATTGAG-TG-TAAA
1 AT-AAGTTGAGTTGAT-TA
2501 CATAAGTTGAGTTGATTA
1 -ATAAGTTGAGTTGATTA
2519 ATAA
1 ATAA
2523 AATTGAGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 1 0.03
17 16 0.53
18 12 0.40
19 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (17 bp):
ATAAGTTGAGTTGATTA
Done.