Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003293.1 Kokia drynarioides strain JFW-HI SEQ_115966, 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: 8842
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:4199 original size:11 final size:11
Alignment explanation
Indices: 4170--4216 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
4160 ACCTTTTATT
*
4170 TTTTCACTC-A
1 TTTTCTCTCAA
*
4180 TTCTCTCTCAA
1 TTTTCTCTCAA
4191 TTTTCTCTCAA
1 TTTTCTCTCAA
*
4202 TTTTTCTCTAAA
1 -TTTTCTCTCAA
4214 TTT
1 TTT
4217 CAAACAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 7 0.23
11 14 0.45
12 10 0.32
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTCTCTCAA
Found at i:4208 original size:12 final size:12
Alignment explanation
Indices: 4183--4216 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4173 TCACTCATTC
4183 TCTCTCAA-TTT
1 TCTCTCAATTTT
4194 TCTCTCAATTTT
1 TCTCTCAATTTT
*
4206 TCTCTAAATTT
1 TCTCTCAATTT
4217 CAAACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.56
Consensus pattern (12 bp):
TCTCTCAATTTT
Found at i:4391 original size:18 final size:18
Alignment explanation
Indices: 4368--4437 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
4358 GTTAATTTTT
4368 ATTTTTTTATATTATTTA
1 ATTTTTTTATATTATTTA
* *
4386 ATTTTTATA-ATTTAATT-
1 ATTTTTTTATA-TTATTTA
* *
4403 ATTTTTTAATAATATTTA
1 ATTTTTTTATATTATTTA
*
4421 ATTATTTTATATTATTT
1 ATTTTTTTATATTATTT
4438 TTATAATTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.30
18 28 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTTATATTATTTA
Found at i:4400 original size:14 final size:15
Alignment explanation
Indices: 4371--4450 Score: 53
Period size: 14 Copynumber: 5.1 Consensus size: 15
4361 AATTTTTATT
4371 TTTTTATATTATTTAA
1 TTTTTATA-TATTTAA
4387 TTTTTATA-ATTTAATTA
1 TTTTTATATATTT-A--A
4404 TTTTTTAATAATATTTAA
1 -TTTTT-AT-ATATTTAA
4422 TTATTT-TATA-TT-A
1 TT-TTTATATATTTAA
4435 TTTTTATA-ATTTAA
1 TTTTTATATATTTAA
4449 TT
1 TT
4451 AAATTGTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 24
0.69 0.00 0.31
Matches are distributed among these distances:
12 4 0.08
13 7 0.13
14 9 0.17
15 4 0.08
16 9 0.17
17 3 0.06
18 9 0.17
19 2 0.04
20 2 0.04
21 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTATATATTTAA
Found at i:4447 original size:18 final size:18
Alignment explanation
Indices: 4360--4451 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 18
4350 TGGTAAAAGT
*
4360 TAATTTTTATT-TTTTTA
1 TAATTTATATTATTTTTA
4377 T-A-TTAT-TTAATTTTTA
1 TAATTTATATT-ATTTTTA
4393 TAATTTA-ATTATTTTT-
1 TAATTTATATTATTTTTA
* **
4409 TAA-TAATATT-TAATTA
1 TAATTTATATTATTTTTA
4425 T--TTTATATTATTTTTA
1 TAATTTATATTATTTTTA
4441 TAATTTA-ATTA
1 TAATTTATATTA
4452 AATTGTTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 22
0.66 0.08 0.26
Matches are distributed among these distances:
14 2 0.04
15 14 0.25
16 20 0.35
17 12 0.21
18 9 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTTATATTATTTTTA
Found at i:6128 original size:18 final size:18
Alignment explanation
Indices: 6107--6150 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
6097 CCAATCGCCG
6107 CCTCAATTCCT-ATAGCCA
1 CCTCAATT-CTAATAGCCA
*
6125 CCTCAATTCTAATCGCCA
1 CCTCAATTCTAATAGCCA
6143 CCTCAATT
1 CCTCAATT
6151 TTCACCGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.27, C:0.39, G:0.05, T:0.30
Consensus pattern (18 bp):
CCTCAATTCTAATAGCCA
Done.