Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016332.1 Corchorus olitorius cultivar O-4 contig16365, 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: 51585
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3209 original size:40 final size:40
Alignment explanation
Indices: 3165--3240 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
3155 ATTTGTCCTT
3165 CCTAATAATTAAAG-AAATAAATTAAAT-TCAGATTTAGCTC
1 CCTAATAATTAAAGTAAA-AAATTAAATCT-AGATTTAGCTC
*
3205 CCTAATAATTAAGGTAAAAAATTAAATCTAGATTTA
1 CCTAATAATTAAAGTAAAAAATTAAATCTAGATTTA
3241 ACCCCTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33
Consensus pattern (40 bp):
CCTAATAATTAAAGTAAAAAATTAAATCTAGATTTAGCTC
Found at i:7200 original size:3 final size:3
Alignment explanation
Indices: 7194--7232 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
7184 TGTCAGCCCT
* *
7194 CAC CAC CAC CAC CAC CAC CAC CAT CAC CAC CTC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
7233 TTCCAATAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.64, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:18656 original size:22 final size:24
Alignment explanation
Indices: 18618--18662 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
18608 AATGTCTCAT
*
18618 TATTATTCTATAATTATTCAAATA
1 TATTATTCTATAATTATTAAAATA
18642 TATTATT-T-TAATTATTAAAAT
1 TATTATTCTATAATTATTAAAAT
18663 TAAAGAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTATTCTATAATTATTAAAATA
Found at i:18851 original size:21 final size:19
Alignment explanation
Indices: 18826--18883 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
18816 ACTGCTCTAA
18826 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
18847 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
18866 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
18884 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:21780 original size:48 final size:49
Alignment explanation
Indices: 21710--21812 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 49
21700 ACGATAAATT
21710 TTTATTTTTTTAAAATAAAGATTAAATAAAGTGTTTTA-CTATTTATGAA
1 TTTATTTTTTT-AAATAAAGATTAAATAAAGTGTTTTATCTATTTATGAA
* * *
21759 TTTAGTTTTTTT-AATAAAGATTGAATAAATTGTTTTATTTTATTTATGAA
1 TTTA-TTTTTTTAAATAAAGATTAAATAAAGTGTTTTA-TCTATTTATGAA
21809 TTTA
1 TTTA
21813 ATAATTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
48 23 0.48
49 4 0.08
50 21 0.44
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (49 bp):
TTTATTTTTTTAAATAAAGATTAAATAAAGTGTTTTATCTATTTATGAA
Found at i:45069 original size:36 final size:36
Alignment explanation
Indices: 44897--45074 Score: 230
Period size: 36 Copynumber: 4.9 Consensus size: 36
44887 GAGGAGGGGC
** * *
44897 CATTCATACTTTGAGGTGGTTGCCGCTGTTGGTAGG
1 CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATAGG
** * *
44933 CATTCATGTTTTGAATTGGTTGCTGCCGTTGGTAGG
1 CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATAGG
*
44969 CATTCATGTTTTGAGGTGGTTGCTGCCGTTGATAGG
1 CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATAGG
* * *
45005 TATTCATGTTTTGAGGTGGTTGCCGTTGTTGATAGG
1 CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATAGG
* *
45041 CATTCATGCTTTGAGGTGGTTGCTGTTGTTGATA
1 CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATA
45075 TGAGAATCGG
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 126 1.00
ACGTcount: A:0.14, C:0.13, G:0.32, T:0.41
Consensus pattern (36 bp):
CATTCATGTTTTGAGGTGGTTGCTGCTGTTGATAGG
Found at i:45902 original size:2 final size:2
Alignment explanation
Indices: 45895--45921 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45885 AAATTACTTG
45895 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 A
45922 GACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45928 original size:2 final size:2
Alignment explanation
Indices: 45923--45950 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45913 ATATATATAG
45923 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
45951 TTAAGTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51209 original size:2 final size:2
Alignment explanation
Indices: 51202--51235 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
51192 CGATAACAAC
51202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51236 TATTACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.