Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004298.1 Kokia drynarioides strain JFW-HI SEQ_117601, 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: 5558
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Found at i:1244 original size:13 final size:13
Alignment explanation
Indices: 1228--1253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1218 ATTTTGCCAA
1228 GGATTTTTTTGTT
1 GGATTTTTTTGTT
1241 GGATTTTTTTGTT
1 GGATTTTTTTGTT
1254 TTCTCTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (13 bp):
GGATTTTTTTGTT
Found at i:2435 original size:23 final size:23
Alignment explanation
Indices: 2368--2444 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
2358 GACAATTTTT
2368 ATATTGTAATTAATCCAACTCAA
1 ATATTGTAATTAATCCAACTCAA
* * * *
2391 ATATTG-GATTCAAATGCTAACTTAT
1 ATATTGTAATT--AAT-CCAACTCAA
2416 ATATTGTAATTAATCCAACTCAA
1 ATATTGTAATTAATCCAACTCAA
2439 ATATTG
1 ATATTG
2445 GATTCAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 3 0.07
23 18 0.43
24 6 0.14
25 12 0.29
26 3 0.07
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATTGTAATTAATCCAACTCAA
Found at i:3708 original size:10 final size:10
Alignment explanation
Indices: 3675--3710 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3665 ATATATACGC
3675 ATACATATAT
1 ATACATATAT
*
3685 ATATATATAT
1 ATACATATAT
*
3695 ATACATAAAT
1 ATACATATAT
3705 ATACAT
1 ATACAT
3711 TTTGATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (10 bp):
ATACATATAT
Found at i:4616 original size:26 final size:23
Alignment explanation
Indices: 4575--4626 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
4565 TATTACATAT
*
4575 AATTAAAAAAATAATATTATTAA
1 AATTAAAAAAATAATATAATTAA
4598 AATTAATAAATAATAAATATAATTAA
1 AATTAA-AAA-AAT-AATATAATTAA
4624 AAT
1 AAT
4627 ATAACAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 3 0.12
26 13 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTAAAAAAATAATATAATTAA
Found at i:4627 original size:22 final size:23
Alignment explanation
Indices: 4571--4636 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
4561 ATTTTATTAC
4571 ATATAATTAAAA-AAATAATATTA
1 ATATAATTAAAATAAATAATA-TA
* *
4594 TTAAAATT--AATAAATAATA-A
1 ATATAATTAAAATAAATAATATA
*
4614 ATATAATTAAAATATAACAATAT
1 ATATAATTAAAATA-AATAATAT
4637 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 12 0.36
23 12 0.36
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATAATTAAAATAAATAATATA
Found at i:4837 original size:19 final size:18
Alignment explanation
Indices: 4808--4854 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4798 AATATATTAT
*
4808 TTATAAAATTTATACATCAA
1 TTAT-AAATTTATAAAT-AA
4828 TTATAAATTTATAAATAA
1 TTATAAATTTATAAATAA
4846 TT-TAAATTT
1 TTATAAATTT
4855 TCTATTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 11 0.42
20 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATAAATTTATAAATAA
Done.