Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021228.1 Corchorus olitorius cultivar O-4 contig21261, 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: 44291
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:12062 original size:20 final size:20
Alignment explanation
Indices: 12037--12076 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12027 TTAGGTTCAA
12037 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
12057 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
12077 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:12818 original size:3 final size:3
Alignment explanation
Indices: 12810--12919 Score: 220
Period size: 3 Copynumber: 36.7 Consensus size: 3
12800 AGTTAAATAA
12810 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12906 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
12920 ATACTAGTAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 107 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:15066 original size:19 final size:19
Alignment explanation
Indices: 15042--15078 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15032 CTGTTTAGTA
15042 ACTGTATAAATGAGATTAC
1 ACTGTATAAATGAGATTAC
* *
15061 ACTGTATATATTAGATTA
1 ACTGTATAAATGAGATTA
15079 GGTACTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (19 bp):
ACTGTATAAATGAGATTAC
Found at i:16062 original size:7 final size:7
Alignment explanation
Indices: 16050--16087 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
16040 GTTAGCTATA
16050 GCTAGCT
1 GCTAGCT
16057 GCTAGCT
1 GCTAGCT
16064 GCTAGCT
1 GCTAGCT
16071 GCTAGCT
1 GCTAGCT
16078 GCTAGCT
1 GCTAGCT
16085 GCT
1 GCT
16088 GTTGTTCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
GCTAGCT
Found at i:18088 original size:2 final size:2
Alignment explanation
Indices: 18081--18116 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18071 CTAAAACTAG
18081 TA TA 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 TA TA
18117 CATGGTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34039 original size:39 final size:39
Alignment explanation
Indices: 33983--34059 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
33973 TATATAAAAG
33983 TACGAATAAGGGAAAACTTTATGTTTTCCGATTGTACCC
1 TACGAATAAGGGAAAACTTTATGTTTTCCGATTGTACCC
* *
34022 TACGAATAAGGGGAAACTTTATTTTTTCCGATTGTACC
1 TACGAATAAGGGAAAACTTTATGTTTTCCGATTGTACC
34060 TTTCTTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (39 bp):
TACGAATAAGGGAAAACTTTATGTTTTCCGATTGTACCC
Found at i:36530 original size:37 final size:37
Alignment explanation
Indices: 36482--36555 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
36472 TTTATTATGT
36482 TTTTTTACACCTGAACATTTGACTTAATGGTAAGGTG
1 TTTTTTACACCTGAACATTTGACTTAATGGTAAGGTG
*
36519 TTTTTTACACCTGAACATTTGGCTTAATGGTAAGGTG
1 TTTTTTACACCTGAACATTTGACTTAATGGTAAGGTG
36556 CATGCTCCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (37 bp):
TTTTTTACACCTGAACATTTGACTTAATGGTAAGGTG
Found at i:42807 original size:2 final size:2
Alignment explanation
Indices: 42800--42829 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42790 CCAAATATGC
42800 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
42830 GTTAACCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.