Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011913.1 Kokia drynarioides strain JFW-HI SEQ_126911, 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: 7073
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Found at i:5419 original size:10 final size:10
Alignment explanation
Indices: 5404--5458 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
5394 AAAAAAAATT
5404 ATAATTTTTA
1 ATAATTTTTA
5414 ATAATTTTT-
1 ATAATTTTTA
5423 A-AATTTTT-
1 ATAATTTTTA
5431 A-AATTTTTA
1 ATAATTTTTA
* **
5440 TTAAAATTTA
1 ATAATTTTTA
5450 ATAATTTTT
1 ATAATTTTT
5459 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 15 0.41
9 1 0.03
10 21 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:5429 original size:8 final size:8
Alignment explanation
Indices: 5406--5439 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
5396 AAAAAATTAT
5406 AATTTTTAA
1 AATTTTT-A
5415 TAATTTTTA
1 -AATTTTTA
5424 AATTTTTA
1 AATTTTTA
5432 AATTTTTA
1 AATTTTTA
5440 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 1 0.04
10 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AATTTTTA
Found at i:5463 original size:19 final size:18
Alignment explanation
Indices: 5410--5477 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
5400 AATTATAATT
*
5410 TTTAATAA-TTTTTAAATT
1 TTTAATAATTTTTTAAA-A
*
5428 TTTAA-ATTTTTATTAAAA
1 TTTAATAATTTT-TTAAAA
5446 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTT-TAAAA
*
5465 TTT-ATTATTTTTT
1 TTTAATAATTTTTT
5478 GTTTTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 2 0.05
18 22 0.52
19 18 0.43
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATAATTTTTTAAAA
Found at i:5476 original size:18 final size:19
Alignment explanation
Indices: 5410--5468 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
5400 AATTATAATT
*
5410 TTTAATAA-TTTT-TAAAT
1 TTTAATAATTTTTCTAAAA
* *
5427 TTTTA-AATTTTTATTAAAA
1 TTTAATAATTTTT-CTAAAA
5446 TTTAATAATTTTTCTAAAA
1 TTTAATAATTTTTCTAAAA
5465 TTTA
1 TTTA
5469 TTATTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
19 17 0.50
20 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATAATTTTTCTAAAA
Found at i:5503 original size:18 final size:18
Alignment explanation
Indices: 5465--5503 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5455 TTTTCTAAAA
* **
5465 TTTATTATTTTTTGTTTT
1 TTTATTATTTTTTCTACT
5483 TTTATTATTTTTTCTACT
1 TTTATTATTTTTTCTACT
5501 TTT
1 TTT
5504 TAATAAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATTATTTTTTCTACT
Done.