Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011820.1 Corchorus olitorius cultivar O-4 contig11853, 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: 6094
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--118 Score: 62
Period size: 2 Copynumber: 59.5 Consensus size: 2
1 TAT
* * * * *
4 TA TA TA TA TA TA TA TA TA TA TA AA TGA TT TA TG T- TT TC TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA T-A TA
* * * *
47 TA TT TA TA AA T- TA TA -A TA TA TA TA TA AA TA TT TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
86 TA TA -A TA TA TA TA AA AA TA TT TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
119 TAAAATCCTA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
1 6 0.07
2 77 0.90
3 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:80 original size:28 final size:29
Alignment explanation
Indices: 46--118 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 29
36 GTTTTCTGAT
*
46 ATATTTATAAAT-TATAATATATATATAA
1 ATATTTATAAATATATAATATATATAAAA
74 ATATTTAT-AATATATAATATATATAAAA
1 ATATTTATAAATATATAATATATATAAAA
102 ATATTTATATAATATAT
1 ATATTTATA-AATATAT
119 TAAAATCCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 3 0.07
28 31 0.76
30 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATTTATAAATATATAATATATATAAAA
Found at i:83 original size:21 final size:21
Alignment explanation
Indices: 57--119 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
47 TATTTATAAA
57 TTATAATATATATATAAATAT
1 TTATAATATATATATAAATAT
*
78 TTATAATATATA-ATATATA-
1 TTATAATATATATATAAATAT
* * *
97 TAAAAATATTTATATAATATAT
1 TTATAATATATATATAA-ATAT
119 T
1 T
120 AAAATCCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 9 0.26
20 9 0.26
21 15 0.44
22 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATAATATATATATAAATAT
Found at i:2319 original size:4 final size:4
Alignment explanation
Indices: 2310--2370 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
2300 GTTATAAGAC
* * * * *
2310 ATAT ATAT ATAT ATAT ACAT ACAT ACAT ACAT ACAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2358 ATAT ATAT ATAT A
1 ATAT ATAT ATAT A
2371 CACATACATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:6082 original size:18 final size:18
Alignment explanation
Indices: 6059--6094 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6049 CTCCTCTTGC
*
6059 ATGAAAACACTTTTTTTA
1 ATGAAAACAATTTTTTTA
6077 ATGAAAACAATTTTTTTA
1 ATGAAAACAATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTTTTTTA
Done.