Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001808.1 Kokia drynarioides strain JFW-HI SEQ_113545, 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: 44864
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:5458 original size:26 final size:26
Alignment explanation
Indices: 5435--5486 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5425 GGATAATATA
*
5435 AATGTGATATATATAGTAAGAATAAT
1 AATGTGATATATATAATAAGAATAAT
*
5461 AATGTGATATATATAATTAGAATAAT
1 AATGTGATATATATAATAAGAATAAT
5487 TACATATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (26 bp):
AATGTGATATATATAATAAGAATAAT
Found at i:6396 original size:18 final size:19
Alignment explanation
Indices: 6372--6414 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
6362 ATTGTCTGAA
*
6372 ATTTTTTAT-AAATTTCA-
1 ATTTTTTTTGAAATTTCAG
*
6389 ATTTTTTTTGAAATTTGAG
1 ATTTTTTTTGAAATTTCAG
6408 ATTTTTT
1 ATTTTTT
6415 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTTTTTTTGAAATTTCAG
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6883--6921 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6873 TTTTTTATAT
*
6883 GATTTTTTAATTATTTTTAA
1 GATTTTTAAATTATTTTTAA
*
6903 GATTTTTAAATTTTTTTTA
1 GATTTTTAAATTATTTTTA
6922 CAATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
GATTTTTAAATTATTTTTAA
Found at i:11660 original size:20 final size:20
Alignment explanation
Indices: 11635--11676 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11625 TAAGATTGAA
11635 TATTTATATGATATGA-ATAT
1 TATTTAT-TGATATGATATAT
*
11655 TATTTATTGATGTGATATAT
1 TATTTATTGATATGATATAT
11675 TA
1 TA
11677 AGTAGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (20 bp):
TATTTATTGATATGATATAT
Found at i:16754 original size:8 final size:8
Alignment explanation
Indices: 16741--16770 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16731 TAATTTTAAT
16741 AAATAAAA
1 AAATAAAA
16749 AAATAAAA
1 AAATAAAA
*
16757 AAATATAA
1 AAATAAAA
16765 AAATAA
1 AAATAA
16771 TATATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAATAAAA
Found at i:17574 original size:47 final size:47
Alignment explanation
Indices: 17505--17599 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
17495 CTGTATTTAA
17505 AATAAGTTATATTACTTAAGGATATTTTAGTTTTTTTAGTACAAGTT
1 AATAAGTTATATTACTTAAGGATATTTTAGTTTTTTTAGTACAAGTT
17552 AATAAGTTATATTACTTAAGGATATTTTAGTTTTTTTAGTACAAGTT
1 AATAAGTTATATTACTTAAGGATATTTTAGTTTTTTTAGTACAAGTT
17599 A
1 A
17600 TACATATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (47 bp):
AATAAGTTATATTACTTAAGGATATTTTAGTTTTTTTAGTACAAGTT
Found at i:24966 original size:19 final size:20
Alignment explanation
Indices: 24922--24966 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
24912 ATAATAATAA
* *
24922 AACAA-AAGTTCAAGTAAAG
1 AACAATAAGTCCAAGTAAAC
24941 AAC-ATAAGTCCAAGT-AAC
1 AACAATAAGTCCAAGTAAAC
24959 AACAATAA
1 AACAATAA
24967 CACAACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (20 bp):
AACAATAAGTCCAAGTAAAC
Found at i:25920 original size:42 final size:41
Alignment explanation
Indices: 25863--25956 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
25853 AAAAATTGAT
* **
25863 TTTGAGTTTAATTTATGGGTGTTTTATAAAAATAAAATAATA
1 TTTGGGTTTAATTTATGAAT-TTTTATAAAAATAAAATAATA
* * * * *
25905 TTTGGGTTTAGTTTATGAATTTTTTTAAGAATGAAATTATA
1 TTTGGGTTTAATTTATGAATTTTTATAAAAATAAAATAATA
25946 TTTGGGTTTAA
1 TTTGGGTTTAA
25957 AAAATATTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 27 0.63
42 16 0.37
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (41 bp):
TTTGGGTTTAATTTATGAATTTTTATAAAAATAAAATAATA
Found at i:28687 original size:16 final size:16
Alignment explanation
Indices: 28646--28677 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28636 AGATAGATTC
28646 AATATTTCAATTTTTT
1 AATATTTCAATTTTTT
28662 AATATTTCAATTTTTT
1 AATATTTCAATTTTTT
28678 TTTCTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTTCAATTTTTT
Found at i:29330 original size:60 final size:57
Alignment explanation
Indices: 29142--29385 Score: 151
Period size: 57 Copynumber: 4.2 Consensus size: 57
29132 AAAAAATTTA
** * ** *
29142 GTGTTGGCCATTGCA-TGGTCGACACCACCTTTTTAATCTGACAAAAAAT--TTTTTTG
1 GTGTTGGCCA-TGCATTGACCGACACAACCTTTTT-ATCAAATAAAAAATAATTTTTTG
** * * * * *
29198 GTGTTGGCCATGCATTGGTCGACATC-A-CTTTTCTTTTAGATAGAAAAACAA-TTTTTA
1 GTGTTGGCCATGCATTGACCGACA-CAACCTTTT-TATCAAATA-AAAAATAATTTTTTG
* * * *
29255 ATGTTGACCATTGCA-TGGCCGAGACAACCTTTTTTATCAAATAAAAAATCAAATTTTTTTG
1 GTGTTGGCCA-TGCATTGACCGACACAACC-TTTTTATCAAATAAAAAAT--AA-TTTTTTG
* * *
29316 GTGTTGGCCATGCATTGACCGACACCATCTTTTTATCAGATAAAAAATAATTTTTTG
1 GTGTTGGCCATGCATTGACCGACACAACCTTTTTATCAAATAAAAAATAATTTTTTG
* *
29373 GTGTCGGTCATGC
1 GTGTTGGCCATGC
29386 TTTTTATCTT
Statistics
Matches: 149, Mismatches: 24, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
55 13 0.09
56 27 0.18
57 45 0.30
58 13 0.09
59 6 0.04
60 22 0.15
61 23 0.15
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (57 bp):
GTGTTGGCCATGCATTGACCGACACAACCTTTTTATCAAATAAAAAATAATTTTTTG
Found at i:33756 original size:13 final size:12
Alignment explanation
Indices: 33730--33777 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
33720 TCTTACTTTC
33730 AATTATTCATAA
1 AATTATTCATAA
*
33742 AATTAGTTCAAAAA
1 AATTA-TTC-ATAA
33756 AATTATTCATAA
1 AATTATTCATAA
*
33768 AATCATTCAT
1 AATTATTCAT
33778 CATTCACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 17 0.55
13 6 0.19
14 8 0.26
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (12 bp):
AATTATTCATAA
Found at i:33759 original size:14 final size:14
Alignment explanation
Indices: 33730--33769 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
33720 TCTTACTTTC
33730 AATTATTCAT--AA
1 AATTATTCATAAAA
33742 AATTAGTTCA-AAAA
1 AATTA-TTCATAAAA
33756 AATTATTCATAAAA
1 AATTATTCATAAAA
33770 TCATTCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 11 0.46
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (14 bp):
AATTATTCATAAAA
Done.