Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003192.1 Kokia drynarioides strain JFW-HI SEQ_115805, 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, 664
Length: 1108
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Found at i:146 original size:28 final size:29
Alignment explanation
Indices: 73--369 Score: 241
Period size: 30 Copynumber: 10.1 Consensus size: 29
63 GTAAAGTTCG
73 GGGTAAAAA--TAATTTTTTGAGAAGTTT-A
1 GGGTAAAAATGTAA-TTTTTG-GAAGTTTGA
*
101 GAGATAAAAATGTAATTTTTGGAAGTTTGA
1 G-GGTAAAAATGTAATTTTTGGAAGTTTGA
* * * *
131 GAGCAAAAATGTATTTTTTTTTGGAAAG-TTCA
1 GGGTAAAAATGTA---ATTTTTGG-AAGTTTGA
* * *
163 GGGGTTAAAA-GTGATTTTTGGAAGTTTAA
1 -GGGTAAAAATGTAATTTTTGGAAGTTTGA
*
192 GGGTAAAAATGTAA-TTTTGGAAGTTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGA
* * * *
220 GGGCAAAAATGTAATTTTTAGCAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGA
*
249 GGG-CAAAATGTAATTTTTGAGAAGTTTGA
1 GGGTAAAAATGTAATTTTTG-GAAGTTTGA
**
278 GGGTAAAAATGTAATTTTCAAGAAGTTTGA
1 GGGTAAAAATGTAATTTT-TGGAAGTTTGA
* *
308 GGGTAAAAATATAATTTTTAAGAAGTTTGA
1 GGGTAAAAATGTAATTTTT-GGAAGTTTGA
* * *
338 GGGTCAAAATATGATTTTTGGATAGTTT-A
1 GGGTAAAAATGTAATTTTTGGA-AGTTTGA
367 GGG
1 GGG
370 ACCTTTTGGG
Statistics
Matches: 221, Mismatches: 31, Indels: 33
0.78 0.11 0.12
Matches are distributed among these distances:
28 52 0.24
29 66 0.30
30 79 0.36
31 3 0.01
32 12 0.05
33 9 0.04
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTGA
Found at i:150 original size:30 final size:29
Alignment explanation
Indices: 73--369 Score: 191
Period size: 29 Copynumber: 10.1 Consensus size: 29
63 GTAAAGTTCG
*
73 GGGTAAAAAT-AATTTTTTGAGAAGTTT-A
1 GGGTAAAAATGTATTTTTTG-GAAGTTTGA
* *
101 GAGATAAAAATGTAATTTTTGGAAGTTTGA
1 G-GGTAAAAATGTATTTTTTGGAAGTTTGA
* * *
131 GAGCAAAAATGTATTTTTTTTTGGAAAG-TTCA
1 GGGTAAAAATGTA---TTTTTTGG-AAGTTTGA
* *
163 GGGGTTAAAA-GTGA-TTTTTGGAAGTTTAA
1 -GGGTAAAAATGT-ATTTTTTGGAAGTTTGA
* *
192 GGGTAAAAATGTA-ATTTTGGAAGTTTTA
1 GGGTAAAAATGTATTTTTTGGAAGTTTGA
* * * * *
220 GGGCAAAAATGTAATTTTTAGCAGTTTAA
1 GGGTAAAAATGTATTTTTTGGAAGTTTGA
* *
249 GGG-CAAAATGTAATTTTTGAGAAGTTTGA
1 GGGTAAAAATGTATTTTTTG-GAAGTTTGA
***
278 GGGTAAAAATGTAATTTTCAAGAAGTTTGA
1 GGGTAAAAATGT-ATTTTTTGGAAGTTTGA
* **
308 GGGTAAAAATATAATTTTTAAGAAGTTTGA
1 GGGTAAAAATGT-ATTTTTTGGAAGTTTGA
338 GGGTCAAAATATG-A-TTTTTGGATAGTTT-A
1 GGGT-AAAA-ATGTATTTTTTGGA-AGTTTGA
367 GGG
1 GGG
370 ACCTTTTGGG
Statistics
Matches: 217, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
28 52 0.24
29 70 0.32
30 63 0.29
31 8 0.04
32 14 0.06
33 10 0.05
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTATTTTTTGGAAGTTTGA
Found at i:199 original size:90 final size:89
Alignment explanation
Indices: 65--238 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
55 TCATTTAGGT
65 AAAGTTCGGGGTAAAAATAATTTTTTGAGAAGTTTAGAGATAAAAATGTAATTTTTGGAAGTTTG
1 AAAGTTCGGGGTAAAAATAATTTTTTGAGAAGTTTAGAGATAAAAATGTAA-TTTTGGAAGTTTG
*
130 AGAGCAAAAATGTATTTTTTTTTGG
65 AGAGCAAAAATGTAATTTTTTTTGG
* * *
155 AAAGTTCAGGGGTTAAAAGTGA-TTTTTG-GAAGTTTA-AGGGTAAAAATGTAATTTTGGAAGTT
1 AAAGTTC-GGGG-TAAAAATAATTTTTTGAGAAGTTTAGA-GATAAAAATGTAATTTTGGAAGTT
* *
217 TTAGGGCAAAAATGTAATTTTT
63 TGAGAGCAAAAATGTAATTTTT
239 AGCAGTTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 31 0.41
90 27 0.36
91 10 0.13
92 7 0.09
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (89 bp):
AAAGTTCGGGGTAAAAATAATTTTTTGAGAAGTTTAGAGATAAAAATGTAATTTTGGAAGTTTGA
GAGCAAAAATGTAATTTTTTTTGG
Done.