Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011298.1 Kokia drynarioides strain JFW-HI SEQ_126278, 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: 9852
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Found at i:137 original size:17 final size:17
Alignment explanation
Indices: 115--152 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
105 CGAATTCAGA
115 GAGCAAGATTTGCCATC
1 GAGCAAGATTTGCCATC
132 GAGCAAGATTTGCCATC
1 GAGCAAGATTTGCCATC
149 GAGC
1 GAGC
153 TAATCTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (17 bp):
GAGCAAGATTTGCCATC
Found at i:9016 original size:30 final size:29
Alignment explanation
Indices: 8973--9375 Score: 311
Period size: 29 Copynumber: 13.8 Consensus size: 29
8963 ATTTCAAGGT
*
8973 TAAAAAT-GAATTTTTGGAAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGG
*
9001 TCAAAAATAGGA-TTTTGGAAG-TTTAGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTTA-GGG
* * ***
9030 TAAAATTGGAATTTTTGGAAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGG
* *
9059 TAAAAATGGAATTTTTAGG-AGTTTTAAGG
1 TAAAAATGGGATTTTT-GGAAGTTTTAGGG
* **
9088 TCAAAAATGGGATTTTTGGAAATTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTTAGGG
** * *
9118 TAAAAATGGGATTTTTAAAAAATTTTGGGGG
1 TAAAAATGGGATTTTT-GGAAGTTTT-AGGG
* * * *
9149 TAAAAATGGAATTTTTTGGATGTTTTTGTG
1 TAAAAATGGGA-TTTTTGGAAGTTTTAGGG
*
9179 TCAAAAATGGGATTTTTGAAAG-TTTAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTTAGGG
*
9208 T-AAAATGGAATTTTTGGAA-TTTTCAGGG
1 TAAAAATGGGATTTTTGGAAGTTTT-AGGG
* ** *
9236 TTAAAATGGGA-TTTTCAAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGG
**
9264 TCAAAAATGGGATTTTTGGAAGTTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTTAGGG
* * *
9294 TAAAGATGGAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGG
* ** * *
9323 TCAAAATAAGATTTTTAGAAG-TTTCGAGG
1 TAAAAATGGGATTTTTGGAAGTTTTAG-GG
9352 TCAAAAATGGGATTTTTGGAAGTT
1 T-AAAAATGGGATTTTTGGAAGTT
9376 AGGGACCTCC
Statistics
Matches: 292, Mismatches: 62, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
27 19 0.07
28 31 0.11
29 138 0.47
30 71 0.24
31 28 0.10
32 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTTAGGG
Found at i:9119 original size:59 final size:59
Alignment explanation
Indices: 8974--9375 Score: 344
Period size: 58 Copynumber: 6.9 Consensus size: 59
8964 TTTCAAGGTT
** * * *
8974 AAAAAT-GAATTTTTGGAAGTTTTAGGGTCAAAAATAGGA-TTTTGGAAGTTTAGGGGT-
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAAATGGGATTTTTAGAAGTTTTGGGGTC
* * * * **
9031 AAAATTGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAGGAGTTTTAAGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTC
* * * *
9090 AAAAATGGGATTTTTGGAAATTCGAGGGTAAAAATGGGATTTTTAAAAAATTTTGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTT-AGAAGTTTT-GGGGTC
* *** * *
9150 AAAAATGGAATTTTTTGGATGTTTTTGTGTCAAAAATGGGATTTTT-GAAAG-TTTAGGGT-
1 AAAAATGGAA-TTTTTGGAAGTTCGAGGGT-AAAAATGGGATTTTTAG-AAGTTTTGGGGTC
* * *
9209 -AAAATGGAATTTTTGGAATTTTC-AGGGTTAAAATGGGATTTTCA-AAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAA-GTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTC
* * * *
9266 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAGATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTC
* * *
9325 -AAAAT-AAGATTTTTAGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTT
1 AAAAATGGA-ATTTTTGGAAG-TTCGAGGGT-AAAAATGGGATTTTTAGAAGTT
9376 AGGGACCTCC
Statistics
Matches: 276, Mismatches: 51, Indels: 34
0.76 0.14 0.09
Matches are distributed among these distances:
55 3 0.01
56 20 0.07
57 27 0.10
58 94 0.34
59 81 0.29
60 18 0.07
61 18 0.07
62 15 0.05
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTC
Done.