Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003940.1 Kokia drynarioides strain JFW-HI SEQ_117022, 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: 46582
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2693 original size:34 final size:34
Alignment explanation
Indices: 2637--2734 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
2627 ATGTCATTTT
* *
2637 TACATACTAA-TTCTTCAATTTGAAAACTTAAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTAAAA
*
2670 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTAAAA
* *
2704 TACATATTAATTTCTTGAGCTTGAAAACTTA
1 TACATACTAATTTCTTGAGTTTGAAAACTTA
2735 CGAAATGAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 10 0.17
34 49 0.83
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (34 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTAAAA
Found at i:8713 original size:19 final size:20
Alignment explanation
Indices: 8686--8726 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
8676 AAACACCAAC
* *
8686 TTAAGAAAAAAA-TATCAAA
1 TTAAAAAAAAAAGCATCAAA
8705 TTAAAAAAAAAAGCATCAAA
1 TTAAAAAAAAAAGCATCAAA
8725 TT
1 TT
8727 TATATACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (20 bp):
TTAAAAAAAAAAGCATCAAA
Found at i:14322 original size:18 final size:18
Alignment explanation
Indices: 14299--14340 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
14289 TTACAAAATC
*
14299 ACAAGCACAGTACTGGGA
1 ACAAGCACAATACTGGGA
*
14317 ACAAGCTCAATACTGGGA
1 ACAAGCACAATACTGGGA
*
14335 AAAAGC
1 ACAAGC
14341 TTGGGCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (18 bp):
ACAAGCACAATACTGGGA
Found at i:22188 original size:20 final size:19
Alignment explanation
Indices: 22116--22218 Score: 75
Period size: 20 Copynumber: 5.3 Consensus size: 19
22106 AATTCAAGTC
*
22116 TTTATGATTTTTTATAA-C
1 TTTATGATTTTTTATAATT
* * *
22134 TTTATAAGTTTGTATCAATT
1 TTTATGATTTTTTAT-AATT
*
22154 TTAAT-ACTTTTTTATAATT
1 TTTATGA-TTTTTTATAATT
*
22173 TTTATGATTTTCTTATGATT
1 TTTATGATTTT-TTATAATT
* *
22193 TTTATAGAATTTTAATACATT
1 TTTAT-GATTTTTTATA-ATT
22214 TTTAT
1 TTTAT
22219 AAAATAGTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
18 12 0.18
19 15 0.23
20 26 0.39
21 13 0.20
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTATGATTTTTTATAATT
Found at i:23250 original size:12 final size:11
Alignment explanation
Indices: 23224--23257 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
23214 ATTTTGTTCA
23224 ATTTAATTTTT
1 ATTTAATTTTT
*
23235 ATTTGATTTGTT
1 ATTTAATTT-TT
23247 ATTTAATTTTT
1 ATTTAATTTTT
23258 TTATTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:29060 original size:27 final size:27
Alignment explanation
Indices: 29022--29073 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
29012 GTAGCCTATA
*
29022 TTTCCATATCTGTATCATTGGACCATG
1 TTTCCATATCTGCATCATTGGACCATG
29049 TTTCCATATCTGCATCATTGGACCA
1 TTTCCATATCTGCATCATTGGACCA
29074 CTCAAGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (27 bp):
TTTCCATATCTGCATCATTGGACCATG
Found at i:29785 original size:4 final size:4
Alignment explanation
Indices: 29778--29814 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
29768 ATAAATACGA
29778 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
29815 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:32055 original size:46 final size:47
Alignment explanation
Indices: 31988--32081 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
31978 GTATGCTTAG
*
31988 TTAGGATAAAAGTGGAGGGATG-AAGGGTATTCATTCACTTAACCTA
1 TTAGGAGAAAAGTGGAGGGATGTAAGGGTATTCATTCACTTAACCTA
* * *
32034 TTAGGAGAAAAGTGGAGGGATGTAGGGGTATTCATTCAGTTAATCTA
1 TTAGGAGAAAAGTGGAGGGATGTAAGGGTATTCATTCACTTAACCTA
32081 T
1 T
32082 CCGAACTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 21 0.49
47 22 0.51
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
TTAGGAGAAAAGTGGAGGGATGTAAGGGTATTCATTCACTTAACCTA
Found at i:35161 original size:3 final size:3
Alignment explanation
Indices: 35148--35180 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
35138 CAAGCACATA
35148 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35181 CTTTCCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44912 original size:13 final size:13
Alignment explanation
Indices: 44894--44938 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
44884 AATTAAAAAC
44894 CTTGAATTTCAAA
1 CTTGAATTTCAAA
*
44907 CTTGAATCTCAAA
1 CTTGAATTTCAAA
* * *
44920 TTTTAAATTCAAA
1 CTTGAATTTCAAA
44933 CTTGAA
1 CTTGAA
44939 CCCTAAACCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (13 bp):
CTTGAATTTCAAA
Found at i:44951 original size:22 final size:22
Alignment explanation
Indices: 44926--44973 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
44916 CAAATTTTAA
44926 ATTCAAACTT-GAACCCTAAACC
1 ATTCAAA-TTCGAACCCTAAACC
* * *
44948 ATTCGAATTCGAACCTTAAAGC
1 ATTCAAATTCGAACCCTAAACC
44970 ATTC
1 ATTC
44974 GAGTTTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (22 bp):
ATTCAAATTCGAACCCTAAACC
Done.