Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003938.1 Kokia drynarioides strain JFW-HI SEQ_117020, 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: 2981
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Found at i:37 original size:23 final size:24
Alignment explanation
Indices: 1--62 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
*
1 TTTTTTTT-TTAATTTATTA-GAA
1 TTTTTTTTATAAATTTATTATGAA
23 TTTTTTTTATAAATTT-TTATGAA
1 TTTTTTTTATAAATTTATTATGAA
*
46 -TATTTTTATAATATTTA
1 TTTTTTTTATAA-ATTTA
63 ATAAGAGACG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTTTTTTATAAATTTATTATGAA
Found at i:39 original size:10 final size:11
Alignment explanation
Indices: 26--61 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
16 ATTAGAATTT
26 TTTTTATAA-A
1 TTTTTATAATA
36 TTTTTATGAATA
1 TTTTTAT-AATA
48 TTTTTATAATA
1 TTTTTATAATA
59 TTT
1 TTT
62 AATAAGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 9 0.38
12 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TTTTTATAATA
Found at i:2101 original size:29 final size:27
Alignment explanation
Indices: 2069--2137 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
2059 ATATATATAT
2069 TATAAAAATTTCTAATAAATTATAAAACA
1 TATAAAAATTTC-AAT-AATTATAAAACA
* *
2098 TATATAAAATTATCAATAATTGTAAAACT
1 TATA-AAAATT-TCAATAATTATAAAACA
2127 TATAAAAATTT
1 TATAAAAATTT
2138 TCAAAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
28 6 0.17
29 18 0.50
30 9 0.25
31 2 0.06
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (27 bp):
TATAAAAATTTCAATAATTATAAAACA
Found at i:2167 original size:2 final size:2
Alignment explanation
Indices: 2160--2184 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2150 CTAATAAATA
2160 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 A
2185 AATTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2735 original size:38 final size:37
Alignment explanation
Indices: 2666--2761 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 37
2656 TCGTCAGTTT
*
2666 TTTTTATAATTTATTAGGAATTTTTTGAAGTTTTTATA
1 TTTTTATAATTTATTAGGAATTTTATGAAGTTTTT-TA
*
2704 TTTTTATAAATTT-TTATGAATGTTTAT-AAGTTTTTT-
1 TTTTTAT-AATTTATTAGGAAT-TTTATGAAGTTTTTTA
2740 TTTTT-TAATTTATTA-GAATTTT
1 TTTTTATAATTTATTAGGAATTTT
2762 TTTTATAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
33 3 0.06
34 9 0.17
35 4 0.08
36 5 0.09
37 1 0.02
38 22 0.42
39 9 0.17
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (37 bp):
TTTTTATAATTTATTAGGAATTTTATGAAGTTTTTTA
Found at i:2761 original size:23 final size:23
Alignment explanation
Indices: 2735--2796 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
2725 GTTTATAAGT
* *
2735 TTTTTTTTTTTAATTTATTA-GAA
1 TTTTTTTTATAAATTT-TTATGAA
2758 TTTTTTTTATAAATTTTTATGAA
1 TTTTTTTTATAAATTTTTATGAA
*
2781 -TATTTTTATAATATTT
1 TTTTTTTTATAA-ATTT
2797 AATAAGAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (23 bp):
TTTTTTTTATAAATTTTTATGAA
Done.