Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007600.1 Kokia drynarioides strain JFW-HI SEQ_122231, 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: 13417
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:2171 original size:21 final size:22
Alignment explanation
Indices: 2127--2177 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2117 GTACTAATAT
2127 AATAGCAAAATGAAATCAAAAC
1 AATAGCAAAATGAAATCAAAAC
*
2149 AATATCAAAATGATAA-C-AAAC
1 AATAGCAAAATGA-AATCAAAAC
2170 AATAGCAA
1 AATAGCAA
2178 CAAACAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.63, C:0.14, G:0.08, T:0.16
Consensus pattern (22 bp):
AATAGCAAAATGAAATCAAAAC
Found at i:2483 original size:25 final size:28
Alignment explanation
Indices: 2448--2501 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2438 TTATAGGAAC
*
2448 TTGATCAAA-TTAG-TTCTACTATTAAA
1 TTGATCAAATTTAGCTTATACTATTAAA
2474 TTGAT-AAATTTAGTCTTATACTATTAAA
1 TTGATCAAATTTAG-CTTATACTATTAAA
2502 AAGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 9 0.38
28 12 0.50
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (28 bp):
TTGATCAAATTTAGCTTATACTATTAAA
Found at i:2585 original size:23 final size:21
Alignment explanation
Indices: 2534--2585 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2524 GGAATAGAGT
2534 TAATATTTATTGTATAAAAAA
1 TAATATTTATTGTATAAAAAA
*
2555 T-ATCATTTATTGTTTAACAAAA
1 TAAT-ATTTATTGTATAA-AAAA
2577 TGAATATTT
1 T-AATATTT
2586 TTAAAGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 5 0.19
23 4 0.15
24 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (21 bp):
TAATATTTATTGTATAAAAAA
Found at i:3626 original size:3 final size:3
Alignment explanation
Indices: 3620--3648 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3610 ATAATAATAA
3620 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3649 ATAACATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4839 original size:29 final size:30
Alignment explanation
Indices: 4795--4935 Score: 103
Period size: 30 Copynumber: 4.7 Consensus size: 30
4785 CCCTAAACTA
* * *
4795 TCCAAAAATCATATTTTGACCCTGAACTTT
1 TCCAAAAATTACATTTTAACCCTGAACTTT
* * *
4825 TCC-AAAATTCCATTTTTAA-CATCGTA-TTT
1 TCCAAAAATTACA-TTTTAACCCT-GAACTTT
*
4854 TCCAAAAATTACATTTTAACTCCTAAACTTT
1 TCCAAAAATTACATTTTAAC-CCTGAACTTT
* * **
4885 T-CTAAAATTCCATATTTAACCCT-AAAATT
1 TCCAAAAATTACAT-TTTAACCCTGAACTTT
*
4914 TCCAAAAATTACATTTTTACCC
1 TCCAAAAATTACATTTTAACCC
4936 CAAAACTTCC
Statistics
Matches: 86, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
29 32 0.37
30 42 0.49
31 12 0.14
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
TCCAAAAATTACATTTTAACCCTGAACTTT
Found at i:4893 original size:60 final size:58
Alignment explanation
Indices: 4785--4935 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 58
4775 CCCTAAAAGT
* * * * * *
4785 CCCTAAACTATCCAAAAATCATATTTTGACCCTGAACTTTTCCAAAATTCCATTTTTAA
1 CCCTAAA-TTTCCAAAAATTACATTTTAACCCTAAACTTTTCCAAAATTCCATATTTAA
* * *
4844 CATCGT-ATTTTCCAAAAATTACATTTTAACTCCTAAACTTTTCTAAAATTCCATATTTAA
1 C--CCTAAATTTCCAAAAATTACATTTTAAC-CCTAAACTTTTCCAAAATTCCATATTTAA
*
4904 CCCTAAAATTTCCAAAAATTACATTTTTACCC
1 CCCT-AAATTTCCAAAAATTACATTTTAACCC
4936 CAAAACTTCC
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
58 2 0.03
59 21 0.28
60 50 0.67
61 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (58 bp):
CCCTAAATTTCCAAAAATTACATTTTAACCCTAAACTTTTCCAAAATTCCATATTTAA
Found at i:4940 original size:29 final size:29
Alignment explanation
Indices: 4852--4951 Score: 110
Period size: 30 Copynumber: 3.4 Consensus size: 29
4842 AACATCGTAT
*
4852 TTTCCAAAAATTACATTTTAACTCCTAAAC
1 TTTCCAAAAATTACATTTTAAC-CCTAAAA
* * *
4882 TTTTCTAAAATTCCATATTTAACCCTAAAA
1 TTTCCAAAAATTACAT-TTTAACCCTAAAA
* *
4912 TTTCCAAAAATTACATTTTTACCCCAAAA
1 TTTCCAAAAATTACATTTTAACCCTAAAA
* *
4941 CTTCCACAAAT
1 TTTCCAAAAAT
4952 AACCACTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.34
30 32 0.55
31 6 0.10
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTAACCCTAAAA
Found at i:12758 original size:11 final size:11
Alignment explanation
Indices: 12742--12774 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12732 TGGTCACATG
12742 GCTGATGTGGC
1 GCTGATGTGGC
12753 GCTGATGTGGC
1 GCTGATGTGGC
*
12764 GATGATGTGGC
1 GCTGATGTGGC
12775 ATGCTGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.12, C:0.15, G:0.45, T:0.27
Consensus pattern (11 bp):
GCTGATGTGGC
Found at i:12972 original size:6 final size:6
Alignment explanation
Indices: 12935--12966 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
12925 TTTAAAAACA
12935 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
12967 ACTTTTGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Done.