Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012227.1 Kokia drynarioides strain JFW-HI SEQ_127228, 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: 51574
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:31 original size:7 final size:7
Alignment explanation
Indices: 21--131 Score: 89
Period size: 7 Copynumber: 16.0 Consensus size: 7
11 ACCTCAATCT
21 TTAAACC
1 TTAAACC
28 TTAAACC
1 TTAAACC
*
35 -TAAGCC
1 TTAAACC
** *
41 CCAAGCC
1 TTAAACC
*
48 TCAAACC
1 TTAAACC
55 TTAAACC
1 TTAAACC
*
62 CTAAACC
1 TTAAACC
*
69 TCAAACC
1 TTAAACC
*
76 TTAAACA
1 TTAAACC
83 TTAAACC
1 TTAAACC
*
90 CTAAACC
1 TTAAACC
* *
97 TCAAGCC
1 TTAAACC
104 TTAAACC
1 TTAAACC
*
111 CTAAACC
1 TTAAACC
*
118 TCAAACC
1 TTAAACC
*
125 TCAAACC
1 TTAAACC
132 CCAAGCCTCG
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
6 5 0.06
7 78 0.94
ACGTcount: A:0.41, C:0.37, G:0.03, T:0.19
Consensus pattern (7 bp):
TTAAACC
Found at i:50 original size:34 final size:34
Alignment explanation
Indices: 5--132 Score: 96
Period size: 35 Copynumber: 3.7 Consensus size: 34
1 CAAA
* * *
5 CCCCAAACCTCAATCTTTAAACCTTAAACCTAAG
1 CCCCAAACCTCAAACCTTAAACCCTAAACCTAAG
* *
39 CCCCAAGCCTCAAACCTTAAACCCTAAACCTCAAA
1 CCCCAAACCTCAAACCTTAAACCCTAAACCT-AAG
** * * * * *
74 CCTTAAACATTAAACCCTAAA-CCTCAAGCCTTAAA
1 CCCCAAACCTCAAACCTTAAACCCT-AAACC-TAAG
* *
109 CCCTAAACCTCAAACCTCAAACCC
1 CCCCAAACCTCAAACCTTAAACCC
133 CAAGCCTCGA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
34 30 0.41
35 40 0.55
36 3 0.04
ACGTcount: A:0.40, C:0.39, G:0.02, T:0.19
Consensus pattern (34 bp):
CCCCAAACCTCAAACCTTAAACCCTAAACCTAAG
Found at i:81 original size:28 final size:28
Alignment explanation
Indices: 2--131 Score: 147
Period size: 28 Copynumber: 4.7 Consensus size: 28
1 C
* * *
2 AAACCCCAAACCTCAATCTTTAAACCTT
1 AAACCCTAAACCTCAAACCTTAAACCTT
* * * *
30 AAA-CCTAAGCCCCAAGCCTCAAACCTT
1 AAACCCTAAACCTCAAACCTTAAACCTT
*
57 AAACCCTAAACCTCAAACCTTAAACATT
1 AAACCCTAAACCTCAAACCTTAAACCTT
* *
85 AAACCCTAAACCTCAAGCCTTAAACCCT
1 AAACCCTAAACCTCAAACCTTAAACCTT
113 AAA-CCTCAAACCTCAAACC
1 AAACCCT-AAACCTCAAACC
132 CCAAGCCTCG
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 24 0.28
28 61 0.72
ACGTcount: A:0.42, C:0.38, G:0.02, T:0.18
Consensus pattern (28 bp):
AAACCCTAAACCTCAAACCTTAAACCTT
Found at i:132 original size:21 final size:21
Alignment explanation
Indices: 71--152 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
61 CCTAAACCTC
* * *
71 AAACCTTAAACATTAAACCCT
1 AAACCTCAAACCTCAAACCCT
* *
92 AAACCTCAAGCCTTAAACCCT
1 AAACCTCAAACCTCAAACCCT
*
113 AAACCTCAAACCTCAAACCCC
1 AAACCTCAAACCTCAAACCCT
* * *
134 AAGCCTCGAACCCCAAACC
1 AAACCTCAAACCTCAAACC
153 TTTAGATCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.41, C:0.40, G:0.04, T:0.15
Consensus pattern (21 bp):
AAACCTCAAACCTCAAACCCT
Found at i:140 original size:14 final size:14
Alignment explanation
Indices: 49--153 Score: 77
Period size: 14 Copynumber: 7.5 Consensus size: 14
39 CCCCAAGCCT
*
49 CAAACCTTAAACCC
1 CAAACCTCAAACCC
* *
63 TAAACCTCAAACCT
1 CAAACCTCAAACCC
* * *
77 TAAACATTAAACCC
1 CAAACCTCAAACCC
* * *
91 TAAACCTCAAGCCT
1 CAAACCTCAAACCC
* *
105 TAAACC-CTAAACCT
1 CAAACCTC-AAACCC
119 CAAACCTCAAACCC
1 CAAACCTCAAACCC
* *
133 CAAGCCTCGAACCC
1 CAAACCTCAAACCC
147 CAAACCT
1 CAAACCT
154 TTAGATCTTA
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
13 1 0.01
14 71 0.97
15 1 0.01
ACGTcount: A:0.41, C:0.40, G:0.03, T:0.16
Consensus pattern (14 bp):
CAAACCTCAAACCC
Found at i:3296 original size:6 final size:6
Alignment explanation
Indices: 3285--3309 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3275 TTTAAAGCTC
3285 TTCTGG TTCTGG TTCTGG TTCTGG T
1 TTCTGG TTCTGG TTCTGG TTCTGG T
3310 AGAGGAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (6 bp):
TTCTGG
Found at i:12891 original size:24 final size:24
Alignment explanation
Indices: 12864--13107 Score: 184
Period size: 24 Copynumber: 10.2 Consensus size: 24
12854 ATAACAACTC
*
12864 ATATACGTTTATGCTCGTTAGCTT
1 ATATACGTTTATGCTCGTCAGCTT
* * *
12888 ATATACGTTTACGCTCATCAGTTT
1 ATATACGTTTATGCTCGTCAGCTT
** * *
12912 GCACACGTTTATGCTCGTCAACTT
1 ATATACGTTTATGCTCGTCAGCTT
* * * *
12936 ATATACGTCTACGCTCCTTAGCTT
1 ATATACGTTTATGCTCGTCAGCTT
* * * *
12960 GTATACGTTAATGTTCGTCAACTT
1 ATATACGTTTATGCTCGTCAGCTT
* * * *
12984 ACACACATTTATGCTCATCAGCTT
1 ATATACGTTTATGCTCGTCAGCTT
* * *
13008 ATATAGGTTTATGTTCGTCAAC-T
1 ATATACGTTTATGCTCGTCAGCTT
* *
13031 AGCACACGTTTATGCTCGTCAGCTT
1 A-TATACGTTTATGCTCGTCAGCTT
* * *
13056 ACATACGTTTACGTTCGTCAGCTT
1 ATATACGTTTATGCTCGTCAGCTT
** * *
13080 GCACACGTTTATGCTCGTCAACTT
1 ATATACGTTTATGCTCGTCAGCTT
13104 ATAT
1 ATAT
13108 TCATTTACGC
Statistics
Matches: 160, Mismatches: 58, Indels: 4
0.72 0.26 0.02
Matches are distributed among these distances:
23 2 0.01
24 156 0.98
25 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATACGTTTATGCTCGTCAGCTT
Found at i:49144 original size:15 final size:15
Alignment explanation
Indices: 49114--49152 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
49104 AAAAAGCATT
49114 TTTTGAAATAAAAATA
1 TTTT-AAATAAAAATA
49130 TTATTAAAT-AAAATA
1 TT-TTAAATAAAAATA
49145 TTTTAAAT
1 TTTTAAAT
49153 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 6 0.27
17 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTTAAATAAAAATA
Found at i:49930 original size:8 final size:8
Alignment explanation
Indices: 49917--49942 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
49907 TAAATGATAG
49917 ATATGAGA
1 ATATGAGA
49925 ATATGAGA
1 ATATGAGA
49933 ATATGAGA
1 ATATGAGA
49941 AT
1 AT
49943 TTGTATTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
ATATGAGA
Done.