Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006241.1 Kokia drynarioides strain JFW-HI SEQ_120812, 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: 32365
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 159 characters in sequence are not A, C, G, or T
Found at i:3889 original size:24 final size:25
Alignment explanation
Indices: 3862--3915 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
3852 TCATCTCCAA
* * *
3862 TAACCTTCCACCTTTTATCTT-TTT
1 TAACCTTCAACCTTTCATCTTCTTG
*
3886 TAACCTTTAACCTTTCATCTTCTTG
1 TAACCTTCAACCTTTCATCTTCTTG
3911 TAACC
1 TAACC
3916 CATTTTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (25 bp):
TAACCTTCAACCTTTCATCTTCTTG
Found at i:7280 original size:15 final size:15
Alignment explanation
Indices: 7260--7299 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
7250 TTTATTTTTG
7260 TTTTAATATTTTCAT-
1 TTTTAAT-TTTTCATA
*
7275 TTTTAATTTTTTATA
1 TTTTAATTTTTCATA
7290 TTTTAATTTT
1 TTTTAATTTT
7300 CCCCTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTTCATA
Found at i:12304 original size:52 final size:52
Alignment explanation
Indices: 12154--12393 Score: 385
Period size: 51 Copynumber: 4.7 Consensus size: 52
12144 ATAAATAAAG
*
12154 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
12206 AAAAGGTCCGATGACTATGT-TCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
*
12257 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGG-TT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * *
12308 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGATTGCTTCATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * * *
12360 AAGATGTCTGATGACTATGTGTCATTGTGAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
12394 TAAAAGGAAT
Statistics
Matches: 176, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
51 97 0.55
52 79 0.45
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
Found at i:12333 original size:103 final size:103
Alignment explanation
Indices: 12154--12393 Score: 392
Period size: 103 Copynumber: 2.3 Consensus size: 103
12144 ATAAATAAAG
12154 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATG
1 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATG
*
12219 ACTATGTTCATCGTGAGTATATGAATCCTTTATGGATT
66 ACTATGTTCATCGTGAGTATATGAATCCTTCATGGATT
12257 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGG-TTAAAAGGTCCGATG
1 AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATG
* *
12321 ACTATGTGTCATCGTGAGTATATGATTGCTTCATGGATT
66 ACTATGT-TCATCGTGAGTATATGAATCCTTCATGGATT
* * ** *
12360 AAGATGTCTGATGACTATGTGTCATTGTGAGTAT
1 AAAAGGTCCAATGACTATGTGTCATCGTGAGTAT
12394 TAAAAGGAAT
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
102 22 0.17
103 106 0.83
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (103 bp):
AAAAGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATG
ACTATGTTCATCGTGAGTATATGAATCCTTCATGGATT
Found at i:16866 original size:5 final size:6
Alignment explanation
Indices: 16835--16890 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
16825 AGTTGTTTTA
* * * *
16835 TTTATT TTTATT TTTAGT TGTACT TTTA-T TTTATT TTTGATT GTTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT-ATT -TTTATT
16884 TTTATT T
1 TTTATT T
16891 GTGAGACCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
5 5 0.12
6 28 0.68
7 6 0.15
8 2 0.05
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (6 bp):
TTTATT
Found at i:16885 original size:24 final size:24
Alignment explanation
Indices: 16816--16890 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
16806 ATTGATCTCA
* *
16816 TTTATTTCTAGTTGT-TTTATTTATT
1 TTTATTTTTAGTTGTACTT-TTTA-T
16841 TTTATTTTTAGTTGTAC-TTTTAT
1 TTTATTTTTAGTTGTACTTTTTAT
*
16864 TTTATTTTT-GATTGTTCATTTTTAT
1 TTTATTTTTAG-TTGTAC-TTTTTAT
16889 TT
1 TT
16891 GTGAGACCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 1 0.02
23 15 0.35
24 4 0.09
25 23 0.53
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (24 bp):
TTTATTTTTAGTTGTACTTTTTAT
Found at i:18984 original size:53 final size:53
Alignment explanation
Indices: 18904--19009 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
18894 GATGAGAGTA
18904 AACCATTAGAGATTATTCAAGAAAACAACTTGGAGAACACCATTGAAGCCGTC
1 AACCATTAGAGATTATTCAAGAAAACAACTTGGAGAACACCATTGAAGCCGTC
18957 AACCATTAGAGATTATTCAAGAAAACAACTTGGAGAACACCATTGAAGCCGTC
1 AACCATTAGAGATTATTCAAGAAAACAACTTGGAGAACACCATTGAAGCCGTC
19010 TTTGAAGCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (53 bp):
AACCATTAGAGATTATTCAAGAAAACAACTTGGAGAACACCATTGAAGCCGTC
Found at i:23619 original size:36 final size:36
Alignment explanation
Indices: 23534--23630 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
23524 TACACAATCA
*
23534 GCATGATTTCACACGACCGTGTGCCCTACACGACCT
1 GCATGATTTCACATGACCGTGTGCCCTACACGACCT
* * * * * *
23570 GTATGATTTCACATGATCGTGTGGCCTACATGGCTT
1 GCATGATTTCACATGACCGTGTGCCCTACACGACCT
* *
23606 GCATGATTTCACATGGCCATGTGCC
1 GCATGATTTCACATGACCGTGTGCC
23631 TCACATGGCC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (36 bp):
GCATGATTTCACATGACCGTGTGCCCTACACGACCT
Found at i:29099 original size:29 final size:29
Alignment explanation
Indices: 29042--29110 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
29032 TATTATTTTT
* * *
29042 AGTTAAATTTGACCCTCAACCTTTAAAAA
1 AGTTAAATTTAACCATCAACCTTCAAAAA
* *
29071 AGTTGAATTTAACCATCAACCTTCCAAAACG
1 AGTTAAATTTAACCATCAACCTT-CAAAA-A
29102 AGTTAAATT
1 AGTTAAATT
29111 GTTGTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 20 0.62
30 4 0.12
31 8 0.25
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (29 bp):
AGTTAAATTTAACCATCAACCTTCAAAAA
Found at i:31442 original size:64 final size:65
Alignment explanation
Indices: 31368--31505 Score: 235
Period size: 64 Copynumber: 2.1 Consensus size: 65
31358 CGTTGGTTTA
31368 TTCTTTTTGTATTGGGAAAATGAGAAGAATTGTTAG-A-AGAAGAAGAAGAAGAAGAAGTGTCTT
1 TTCTTTTTGTATTGGGAAAATGAGAAGAATTGTTAGAAGAGAAGAAGAAGAAGAAGAAG-GTCTT
31431 C
65 C
*
31432 TTCTTTTTGTATTGGGAAAATGAGAAGAATTGTTAGAAGGAGAAGAAGAAGAAGAAGAAGGTTTT
1 TTCTTTTTGTATTGGGAAAATGAGAAGAATTGTTAGAA-GAGAAGAAGAAGAAGAAGAAGGTCTT
31497 C
65 C
31498 TTCTTTTT
1 TTCTTTTT
31506 CTTCTTCTTA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
64 36 0.51
65 1 0.01
66 13 0.19
67 20 0.29
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (65 bp):
TTCTTTTTGTATTGGGAAAATGAGAAGAATTGTTAGAAGAGAAGAAGAAGAAGAAGAAGGTCTTC
Done.