Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009717.1 Kokia drynarioides strain JFW-HI SEQ_124436, 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: 26526
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:170 original size:17 final size:17
Alignment explanation
Indices: 148--187 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
138 AGGTGGAGAA
* *
148 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
165 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
182 CTTGTT
1 CTTGTT
188 AAGGTGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.47
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:13167 original size:37 final size:36
Alignment explanation
Indices: 13117--13186 Score: 122
Period size: 37 Copynumber: 1.9 Consensus size: 36
13107 TCTGAAAGTT
13117 TGTTGAATGTTGGCAACAATGCAGCGACAATGGAGGA
1 TGTTGAATGTTGGCAACAATGCAGCGAC-ATGGAGGA
*
13154 TGTTGAATGTTGGCAACATTGCAGCGACATGGA
1 TGTTGAATGTTGGCAACAATGCAGCGACATGGA
13187 ACGAGTCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 5 0.16
37 27 0.84
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (36 bp):
TGTTGAATGTTGGCAACAATGCAGCGACATGGAGGA
Found at i:14115 original size:16 final size:16
Alignment explanation
Indices: 14100--14155 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
14090 TTGTTTATAT
* *
14100 ATTTATTTTAAAATAT
1 ATTTATATTAAAATAA
14116 ATTTATATTAATAA-AA
1 ATTTATATTAA-AATAA
*
14132 ATATATATTAAAATAA
1 ATTTATATTAAAATAA
14148 ATTTATAT
1 ATTTATAT
14156 AATTAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.88
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATATTAAAATAA
Found at i:18300 original size:47 final size:47
Alignment explanation
Indices: 18246--18358 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 47
18236 GTCACAGTAA
* *
18246 TGCAAATAAACTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTATAGACAAGCCACCACTTT
18293 TGCAAATAAACTGCCACTTAATAATATTATAGACAAGCCACCACTTT
1 TGCAAATAAACTGCCACTTAATAATATTATAGACAAGCCACCACTTT
* * *
18340 TACAGATAAACTGTCACTT
1 TGCAAATAAACTGCCACTT
18359 CTTCCTCCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (47 bp):
TGCAAATAAACTGCCACTTAATAATATTATAGACAAGCCACCACTTT
Found at i:23935 original size:17 final size:17
Alignment explanation
Indices: 23913--23951 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
23903 AGGTGAAGCA
* *
23913 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
23930 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
23947 CTTGT
1 CTTGT
23952 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:23998 original size:41 final size:41
Alignment explanation
Indices: 23941--24036 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
23931 TTGTTCGTAG
* *
23941 AGAATTCTTGTCAAGGTGGAGATTGTTATAATTAGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
*
23982 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
24023 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
24037 AATAAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
Done.