Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006002.1 Kokia drynarioides strain JFW-HI SEQ_120432, 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: 28598
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2130 original size:30 final size:31
Alignment explanation
Indices: 2067--2140 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
2057 AAAATTAGAG
* * * * *
2067 AAAAAAATTTTAAGTCTCTTGAAAGTTGAT-
1 AAAAAAATTTTGAGCCCCTTAAAAATTGATA
*
2097 AAAAAAATTTTGAGCCCCTTAAAAATTGGTA
1 AAAAAAATTTTGAGCCCCTTAAAAATTGATA
2128 AAAAAAATTTTGA
1 AAAAAAATTTTGA
2141 TTTTTAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (31 bp):
AAAAAAATTTTGAGCCCCTTAAAAATTGATA
Found at i:5261 original size:3 final size:3
Alignment explanation
Indices: 5228--5282 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
5218 GCAAAAGGCC
5228 GAG GA- GAG GA- GAG GA- GAG GA- GAG GA- GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
5271 GAG GAG G-G GAG G
1 GAG GAG GAG GAG G
5283 GGGGTTGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 12 0.26
3 34 0.74
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:5284 original size:5 final size:5
Alignment explanation
Indices: 5228--5281 Score: 72
Period size: 5 Copynumber: 10.2 Consensus size: 5
5218 GCAAAAGGCC
5228 GAGGA GAGGA GAGGA GAGGA GAGGA GAGGA GGAGGA GGAGGA GGAGGA
1 GAGGA GAGGA GAGGA GAGGA GAGGA GAGGA -GAGGA -GAGGA -GAGGA
*
5276 GGGGA G
1 GAGGA G
5282 GGGGGTTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 30 0.64
6 17 0.36
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (5 bp):
GAGGA
Found at i:15314 original size:17 final size:16
Alignment explanation
Indices: 15279--15321 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
15269 ATACTTTGAT
* *
15279 TGTTATTTAAATTAGA
1 TGTTATTTAAATGAAA
15295 TGTTATTTCAAATGAAA
1 TGTTATTT-AAATGAAA
15312 TGTTGATTTA
1 TGTT-ATTTA
15322 TATTGAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 11 0.48
18 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (16 bp):
TGTTATTTAAATGAAA
Found at i:15399 original size:29 final size:30
Alignment explanation
Indices: 15367--15424 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
15357 GAATTGTTTG
15367 GATA-CAAGTTAAAG-AGAAGGGCTTATTTA
1 GATACCAA-TTAAAGTAGAAGGGCTTATTTA
**
15396 GATACCAATTAAAGTTTAAGGGCTTATTT
1 GATACCAATTAAAGTAGAAGGGCTTATTT
15425 GGGTGTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (30 bp):
GATACCAATTAAAGTAGAAGGGCTTATTTA
Found at i:26710 original size:27 final size:27
Alignment explanation
Indices: 26671--26723 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
26661 ACTGATTCAA
26671 AATTTATCACTCTACATG-TATATGTTG
1 AATTTATCACTCTACA-GATATATGTTG
* *
26698 AATTTCTCTCTCTACAGATATATGTT
1 AATTTATCACTCTACAGATATATGTT
26724 AATCTTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (27 bp):
AATTTATCACTCTACAGATATATGTTG
Done.