Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006001.1 Kokia drynarioides strain JFW-HI SEQ_120430, 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: 14304
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:869 original size:34 final size:38
Alignment explanation
Indices: 800--872 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
790 TTACATCATT
*
800 ACATAACATAATCATTATATATATATATCACAATTATA
1 ACATAACATAATCATTATATATATATATAACAATTATA
*
838 ACATTACATAAT-ATTA-ATAT-TATA-AACAATTATA
1 ACATAACATAATCATTATATATATATATAACAATTATA
872 A
1 A
873 AACAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 10 0.30
35 4 0.12
36 4 0.12
37 4 0.12
38 11 0.33
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (38 bp):
ACATAACATAATCATTATATATATATATAACAATTATA
Found at i:1403 original size:15 final size:16
Alignment explanation
Indices: 1364--1407 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1354 GTTTAAAAAC
* *
1364 TTAGCAAAAAATAAAT
1 TTAGAAAAAAATCAAT
*
1380 TTAGGAAAAAATCAAT
1 TTAGAAAAAAATCAAT
1396 TTA-AAAAAAATC
1 TTAGAAAAAAATC
1408 CAAAACAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (16 bp):
TTAGAAAAAAATCAAT
Found at i:4457 original size:7 final size:6
Alignment explanation
Indices: 4432--4499 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
4422 AACGGTGCAT
* * *
4432 AATAAA AATAAA ACTAAA AATGAA AATGAA AATAAA AATTAAA AATTGAAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AA-TAAA AA-T--AAA
*
4484 AATAAT AA-AAA AATAA
1 AATAAA AATAAA AATAA
4500 GCTTTGGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 4 0.08
6 34 0.65
7 8 0.15
8 1 0.02
9 5 0.10
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:4490 original size:25 final size:24
Alignment explanation
Indices: 4436--4494 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
4426 GTGCATAATA
4436 AAAAT-AAAACTAAAAATGAAAATG
1 AAAATAAAAACTAAAAATGAAAA-G
*
4460 AAAATAAAAATTAAAAATTGAAAA-
1 AAAATAAAAACTAAAAA-TGAAAAG
4484 AATAATAAAAA
1 AA-AATAAAAA
4495 AATAAGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 7 0.23
25 18 0.58
26 6 0.19
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAATAAAAACTAAAAATGAAAAG
Found at i:4717 original size:30 final size:30
Alignment explanation
Indices: 4683--4774 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
4673 ATACGCCCAA
* * *
4683 GTGTCTAGCTCATGTGCCACAGACGGTCGT
1 GTGTCTAGCTCGTGTGCCACACACGGCCGT
*
4713 GTGTCTAGCTCGTGTGCCACACACGACCGT
1 GTGTCTAGCTCGTGTGCCACACACGGCCGT
*
4743 GTGTCTATCTCGTGTGCCACACACGGCCGT
1 GTGTCTAGCTCGTGTGCCACACACGGCCGT
4773 GT
1 GT
4775 TTCAAGCTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.26
Consensus pattern (30 bp):
GTGTCTAGCTCGTGTGCCACACACGGCCGT
Found at i:7310 original size:13 final size:13
Alignment explanation
Indices: 7292--7316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7282 AAAAGTATTT
7292 ATTAATTAAAAAC
1 ATTAATTAAAAAC
7305 ATTAATTAAAAA
1 ATTAATTAAAAA
7317 TTAAAAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:7634 original size:18 final size:17
Alignment explanation
Indices: 7611--7644 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
7601 TTTTTTATAA
7611 AATTAATTCAAAAAAATT
1 AATTAATT-AAAAAAATT
7629 AATTAATTAAAAAAAT
1 AATTAATTAAAAAAAT
7645 GATCCCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTAATTAAAAAAATT
Found at i:11972 original size:75 final size:73
Alignment explanation
Indices: 11893--12169 Score: 280
Period size: 75 Copynumber: 3.8 Consensus size: 73
11883 TATTTTTAAA
* * *
11893 AAATTAAATTTATTGCTTTAAAATAATTTATTGTTCTTTAAATATGTTTTATTTAATTTAAATTA
1 AAATTAAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTTTT-TTTAATTTAAATTA
11958 TATATATTTT
65 TATAT-TTTT
* * * * *
11968 AAATTTAATTTATTGTTTTAAATTGATTTATTATTCTTTAAACATGTATTTTTAA-TTAAA--CT
1 AAATTAAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTTTTTTTAATTTAAATTAT
*
12030 CTATTTTT
66 ATATTTTT
* * *
12038 GAATTTAATTTATTGCTTTTAATTGA--T-TTATTCTTTAAATATGTATTTTTTTAATTTAAATT
1 AAATTAAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATG--TTTTTTTAATTTAAATT
*
12100 ACTATTTTTTT
64 A-TATATTTTT
* * * *
12111 AAAATTAAATTTTTTG-TTTTAATTGATTTATTATTCTTTATATAGGTCTTCTTTTAATT
1 -AAATTAAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGT-TT-TTTTAATT
12170 AATTTTTTAA
Statistics
Matches: 168, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
67 15 0.09
68 1 0.01
69 8 0.05
70 32 0.19
71 4 0.02
73 22 0.13
74 18 0.11
75 46 0.27
76 22 0.13
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.58
Consensus pattern (73 bp):
AAATTAAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTTTTTTTAATTTAAATTAT
ATATTTTT
Found at i:11998 original size:18 final size:18
Alignment explanation
Indices: 11893--11999 Score: 67
Period size: 18 Copynumber: 5.7 Consensus size: 18
11883 TATTTTTAAA
*
11893 AAATTAAATTTATTGCTTT
1 AAATT-AATTTATTGTTTT
*
11912 AAAATAATTTATTGTTCTTT
1 AAATTAATTTATTG-T-TTT
**
11932 AAATATGTTTTATT-TAATTT
1 AAAT-TAATTTATTGT--TTT
* *
11952 AAATT-ATATA-TATTTT
1 AAATTAATTTATTGTTTT
11968 AAATTTAATTTATTGTTTT
1 AAA-TTAATTTATTGTTTT
*
11987 AAATTGATTTATT
1 AAATTAATTTATT
12000 ATTCTTTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
16 6 0.09
17 3 0.04
18 26 0.38
19 14 0.20
20 13 0.19
21 7 0.10
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (18 bp):
AAATTAATTTATTGTTTT
Found at i:12118 original size:22 final size:21
Alignment explanation
Indices: 12081--12121 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12071 TTTAAATATG
*
12081 TATTTTTTTAATTTAAATTAC
1 TATTTTTTTAAATTAAATTAC
12102 TATTTTTTTAAAATTAAATT
1 TATTTTTTT-AAATTAAATT
12122 TTTTGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTTTAAATTAAATTAC
Found at i:12218 original size:31 final size:31
Alignment explanation
Indices: 12160--12218 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
12150 ATATAGGTCT
* *
12160 TCTTTTAATTAATTTTTTAATTTAAATTTAA
1 TCTTTTAATTAATATTTTAATTAAAATTTAA
*
12191 TCTTTTAAATTGATATTTTAA-TAAAATT
1 TCTTTT-AATTAATATTTTAATTAAAATT
12219 GGATTGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.50
32 12 0.50
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TCTTTTAATTAATATTTTAATTAAAATTTAA
Done.