Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013944.1 Kokia drynarioides strain JFW-HI SEQ_128974, 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: 14592
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1680 original size:40 final size:40
Alignment explanation
Indices: 1592--1669 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1582 TATCAAAAAA
*
1592 ATCGAATCAAAACTAATCGAATTCCATCTATTCAAATTAG
1 ATCGAATCAAAACTAATCGAATTCCATCCATTCAAATTAG
* * * *
1632 ATCGAATCAAAATTAATTGAATTCCATCCGTTTAAATT
1 ATCGAATCAAAACTAATCGAATTCCATCCATTCAAATT
1670 GGGTTGAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (40 bp):
ATCGAATCAAAACTAATCGAATTCCATCCATTCAAATTAG
Found at i:1931 original size:79 final size:79
Alignment explanation
Indices: 1829--1978 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 79
1819 TTTTGTGGAC
* * *
1829 AAATTCTGTTGAACGAAAGGAATAAAATCCTGAAAAAGAATTGTTCAATTGATTTCTATTTGGAA
1 AAATTCTGTTGAACGAAAGGAATAAAATCCTGAAAAAGAATTATTCAATTAATTTCTATTTGCAA
*
1894 ATAGAAAATCGAAT
66 ACAGAAAATCGAAT
* ** *
1908 AAATTCTGTTGAACGGCAA-GAATAAAATTTTGAAATAGAATTATTCAATTAATTTCTATTTGCA
1 AAATTCTGTTGAAC-GAAAGGAATAAAATCCTGAAAAAGAATTATTCAATTAATTTCTATTTGCA
1972 AACAGAA
65 AACAGAA
1979 TACAATTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 59 0.95
80 3 0.05
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (79 bp):
AAATTCTGTTGAACGAAAGGAATAAAATCCTGAAAAAGAATTATTCAATTAATTTCTATTTGCAA
ACAGAAAATCGAAT
Found at i:10625 original size:21 final size:22
Alignment explanation
Indices: 10587--10651 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
10577 GTTTTTAGTA
*
10587 TCGGTAGAAGAAAT-ACTTGT-T
1 TCGGTAGAAG-AGTCACTTGTAT
10608 TCGGTAGAAGAGTCACTTGTAT
1 TCGGTAGAAGAGTCACTTGTAT
**
10630 T-GGTAGAACTGTCACTTGTAT
1 TCGGTAGAAGAGTCACTTGTAT
10651 T
1 T
10652 AATAGAAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 2 0.05
21 35 0.90
22 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (22 bp):
TCGGTAGAAGAGTCACTTGTAT
Found at i:10657 original size:21 final size:21
Alignment explanation
Indices: 10619--10658 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10609 CGGTAGAAGA
**
10619 GTCACTTGTATTGGTAGAACT
1 GTCACTTGTATTAATAGAACT
10640 GTCACTTGTATTAATAGAA
1 GTCACTTGTATTAATAGAA
10659 GTCTGCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (21 bp):
GTCACTTGTATTAATAGAACT
Found at i:12234 original size:17 final size:18
Alignment explanation
Indices: 12212--12251 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
12202 ATCTCCAATA
12212 AAAAGGCAATGAAAA-TG
1 AAAAGGCAATGAAAATTG
12229 AAAAGGCAATGAAAATTG
1 AAAAGGCAATGAAAATTG
12247 AAAAG
1 AAAAG
12252 AGGTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.60, C:0.05, G:0.23, T:0.12
Consensus pattern (18 bp):
AAAAGGCAATGAAAATTG
Found at i:13535 original size:21 final size:21
Alignment explanation
Indices: 13511--13553 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13501 CGCTATATAA
*
13511 TTAACTTTAATTATTATAATT
1 TTAAATTTAATTATTATAATT
**
13532 TTAAATTTTTTTATTATAATT
1 TTAAATTTAATTATTATAATT
13553 T
1 T
13554 ATTTAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAAATTTAATTATTATAATT
Done.