Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001865.1 Kokia drynarioides strain JFW-HI SEQ_113628, 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: 37450
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3294 original size:23 final size:23
Alignment explanation
Indices: 3264--3307 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3254 TTGATAATGC
*
3264 TTAAATATATATATTTTTAGATA
1 TTAAATATATATATATTTAGATA
3287 TTAAATATATATATATTTAGA
1 TTAAATATATATATATTTAGA
3308 GTATGATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTAAATATATATATATTTAGATA
Found at i:4382 original size:16 final size:17
Alignment explanation
Indices: 4361--4399 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
4351 TCTAATTCCC
4361 TATTTTTTATTTT-TTT
1 TATTTTTTATTTTCTTT
4377 TA-TTTTTATTTTCTTT
1 TATTTTTTATTTTCTTT
4393 TATTTTT
1 TATTTTT
4400 AATTCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 7 0.33
17 4 0.19
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
TATTTTTTATTTTCTTT
Found at i:4384 original size:15 final size:16
Alignment explanation
Indices: 4364--4400 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
4354 AATTCCCTAT
4364 TTTTTATTTT-TTTTA
1 TTTTTATTTTCTTTTA
4379 TTTTTATTTTCTTTTA
1 TTTTTATTTTCTTTTA
4395 TTTTTA
1 TTTTTA
4401 ATTCTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTATTTTCTTTTA
Found at i:4388 original size:21 final size:21
Alignment explanation
Indices: 4373--4420 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
4363 TTTTTTATTT
* *
4373 TTTTTATTTTTATTTTCTTTTA
1 TTTTTAATTCTATTTT-TTTTA
* *
4395 TTTTTAATTCTGTTTCTTTTA
1 TTTTTAATTCTATTTTTTTTA
4416 TTTTT
1 TTTTT
4421 TCTTAGATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTAATTCTATTTTTTTTA
Found at i:4405 original size:15 final size:15
Alignment explanation
Indices: 4364--4418 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
4354 AATTCCCTAT
*
4364 TTTTTATTTTTTTTA
1 TTTTTATTTCTTTTA
4379 TTTTTATTTTCTTTTA
1 TTTTTA-TTTCTTTTA
*
4395 TTTTTAATTCTGTTT-
1 TTTTTATTTCT-TTTA
*
4410 CTTTTATTT
1 TTTTTATTT
4419 TTTCTTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 17 0.50
16 17 0.50
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTATTTCTTTTA
Found at i:12343 original size:16 final size:18
Alignment explanation
Indices: 12324--12356 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12314 GAATTCTATT
12324 TTTA-TTTAATT-TATAA
1 TTTATTTTAATTATATAA
12340 TTTATTTTAATTATATA
1 TTTATTTTAATTATATA
12357 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATTTTAATTATATAA
Found at i:21340 original size:25 final size:26
Alignment explanation
Indices: 21272--21340 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
21262 TTTGTTAGGA
21272 ATGTTTTTA-GTATTTTTGGTGTATT
1 ATGTTTTTATGTATTTTTGGTGTATT
*
21297 ATGTTTTT-TGTAATTTTGGT-T-TT
1 ATGTTTTTATGTATTTTTGGTGTATT
* *
21320 TTTTTTTTATGTATTTGTTGG
1 ATGTTTTTATGTATTT-TTGG
21341 AAAAATGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 8 0.22
24 7 0.19
25 22 0.59
ACGTcount: A:0.13, C:0.00, G:0.19, T:0.68
Consensus pattern (26 bp):
ATGTTTTTATGTATTTTTGGTGTATT
Found at i:22237 original size:6 final size:6
Alignment explanation
Indices: 22226--22252 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22216 ATATCTTGTT
22226 TATAAA TATAAA TATAAA TATAAA TAT
1 TATAAA TATAAA TATAAA TATAAA TAT
22253 TTATATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Done.