Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002298.1 Kokia drynarioides strain JFW-HI SEQ_114331, 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: 17414
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:4501 original size:16 final size:16
Alignment explanation
Indices: 4477--4557 Score: 53
Period size: 16 Copynumber: 5.2 Consensus size: 16
4467 TATTAAATAT
*
4477 AATAAAATTATTATTA
1 AATATAATTATTATTA
*
4493 AATATAA-T-TTAATA
1 AATATAATTATTATTA
* * * *
4507 AAAATAATAATCAAT-
1 AATATAATTATTATTA
* *
4522 AATTTAATCA-TATTTA
1 AATATAATTATTA-TTA
4538 AATATAATTATTATTA
1 AATATAATTATTATTA
4554 AATA
1 AATA
4558 CGATTTAATA
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
14 12 0.25
15 9 0.19
16 25 0.52
17 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAATTATTATTA
Found at i:6537 original size:13 final size:14
Alignment explanation
Indices: 6519--6550 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6509 TCAGTTGAGA
6519 ATAAAA-AAAAAAC
1 ATAAAATAAAAAAC
6532 ATAAAATAAAAAAC
1 ATAAAATAAAAAAC
6546 A-AAAA
1 ATAAAA
6551 GCACAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.09
Consensus pattern (14 bp):
ATAAAATAAAAAAC
Found at i:10423 original size:5 final size:5
Alignment explanation
Indices: 10407--10439 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
10397 TTGACAATGC
10407 TTATT ATTATT TTATT TTATT TTATT TTATT TT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TT
10440 TAATGGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:15551 original size:9 final size:9
Alignment explanation
Indices: 15529--15596 Score: 59
Period size: 9 Copynumber: 7.1 Consensus size: 9
15519 ATTATTTTTT
15529 TTAAAA-TA
1 TTAAAATTA
15537 -TAAAATTA
1 TTAAAATTA
15545 TTAAAATTA
1 TTAAAATTA
15554 TTTAAAATTAA
1 -TTAAAATT-A
*
15565 GTTTAAAATTT
1 --TTAAAATTA
15576 TTAAAATTA
1 TTAAAATTA
15585 TTTTAAAATTA
1 --TTAAAATTA
15596 T
1 T
15597 AATCATTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 17 0.33
10 8 0.16
11 10 0.20
12 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:15580 original size:21 final size:21
Alignment explanation
Indices: 15537--15596 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
15527 TTTTAAAATA
15537 TAAAATTA--TTAAAATTATT
1 TAAAATTAGTTTAAAATTATT
15556 TAAAATTAAGTTTAAAATT-TT
1 TAAAATT-AGTTTAAAATTATT
*
15577 TAAAATTATTTTAAAATTAT
1 TAAAATTAGTTTAAAATTAT
15597 AATCATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 7 0.19
20 11 0.31
21 10 0.28
22 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAAATTAGTTTAAAATTATT
Found at i:17389 original size:6 final size:6
Alignment explanation
Indices: 17364--17408 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
17354 ACAATTCATA
* * *
17364 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
17409 ATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Done.