Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010473.1 Kokia drynarioides strain JFW-HI SEQ_125373, 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: 5893
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Found at i:5135 original size:29 final size:29
Alignment explanation
Indices: 5103--5358 Score: 200
Period size: 29 Copynumber: 8.8 Consensus size: 29
5093 GGAGGTTCAA
* *
5103 GGGTAAAAATGAAAATTTTGGAAATTTTG
1 GGGTAAAAATGGAATTTTTGGAAATTTTG
** * **
5132 GGGTTAAAAAT-TCATTTTTGGAAGTTCGG
1 GGG-TAAAAATGGAATTTTTGGAAATTTTG
* *
5161 GGGTAAAAATGGAATTTTTGGGAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAATTTTG
* * * *
5190 GGGTCAAAATGGTATTTTTGG-AAGTTCG
1 GGGTAAAAATGGAATTTTTGGAAATTTTG
* * * *
5218 AGGGTAAAATTTGAATTTTTGGGAGTTTTG
1 -GGGTAAAAATGGAATTTTTGGAAATTTTG
*
5248 GGGTCAAAAAT-GAGATTTTTGG-AAGTTTG
1 GGGT-AAAAATGGA-ATTTTTGGAAATTTTG
* *
5277 AGGGTAAAAATGGAATTTTTAG-AATTTATT
1 -GGGTAAAAATGGAATTTTTGGAAATTT-TG
* *
5307 GGGTAAACAAT-GAGATTTTTGGAAGTTTGG
1 GGGTAAA-AATGGA-ATTTTTGGAAATTTTG
5337 GGGTAAAAATGGAATTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
5359 TAGTTTAGGG
Statistics
Matches: 181, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.06
29 116 0.64
30 50 0.28
31 4 0.02
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAATTTTG
Found at i:5287 original size:88 final size:88
Alignment explanation
Indices: 5145--5368 Score: 260
Period size: 88 Copynumber: 2.5 Consensus size: 88
5135 TTAAAAATTC
* * * *
5145 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGGAGTTTTG-GGGTCAAAATGGTATTTTT
1 ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAG-TTTGAGGGTAAAAATGGAATTTTT
* * *
5209 GGAAGTTCGAGGGTAAA-ATTTGA-
65 AGAAGTTAGAGGGTAAACA-ATGAG
* *
5232 ATTTTTGGGAGTTTTGGGGTCAAAAAT-GAGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTT
1 ATTTTTGGAAGTTTGGGGGT-AAAAATGGA-ATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTT
* **
5296 TAGAATTTATTGGGTAAACAATGAG
64 TAGAAGTTAGAGGGTAAACAATGAG
5321 ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGATAGTTT-AGGG
1 ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA-AGTTTGAGGG
5369 ACCTCCAAGG
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
87 23 0.20
88 67 0.58
89 26 0.22
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (88 bp):
ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTA
GAAGTTAGAGGGTAAACAATGAG
Found at i:5293 original size:59 final size:59
Alignment explanation
Indices: 5089--5357 Score: 314
Period size: 58 Copynumber: 4.6 Consensus size: 59
5079 AAAATAAAGA
* * * * * * **
5089 TTTTGGAGGTTCAAGGGTAAAAATGAAAATTTTGGAAATTTTGGGGTTAAAAAT-TCAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAATTTTGGGGTCAAAAATGAGAT
* *
5147 TTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGGAGTTTTGGGGTC-AAAATG-GTAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAATTTTGGGGTCAAAAATGAG-AT
* * *
5205 TTTTGGAAGTTCGAGGGTAAAATTTGAATTTTTGGGAGTTTTGGGGTCAAAAATGAGAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAATTTTGGGGTCAAAAATGAGAT
* * *
5264 TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTT-AGAATTTATTGGGT-AAACAATGAGAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAATTT-TGGGGTCAAA-AATGAGAT
* *
5323 TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGG
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGG
5358 ATAGTTTAGG
Statistics
Matches: 184, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.03
58 95 0.52
59 83 0.45
60 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (59 bp):
TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAATTTTGGGGTCAAAAATGAGAT
Done.