Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013921.1 Kokia drynarioides strain JFW-HI SEQ_128951, 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: 5998
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:2879 original size:11 final size:11
Alignment explanation
Indices: 2862--2924 Score: 69
Period size: 11 Copynumber: 5.7 Consensus size: 11
2852 GGCCCCCCTT
*
2862 TTTAATTT-AT
1 TTTAATTTAAA
2872 TTTAAATTTAAA
1 TTT-AATTTAAA
2884 -TTAATTTTAAA
1 TTTAA-TTTAAA
2895 TTTAAATTT-AA
1 TTT-AATTTAAA
2906 TTTAATTTAAA
1 TTTAATTTAAA
2917 TTTAATTT
1 TTTAATTT
2925 CAAAATTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
10 10 0.22
11 28 0.61
12 6 0.13
13 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:2883 original size:6 final size:6
Alignment explanation
Indices: 2872--2934 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
2862 TTTAATTTAT
*
2872 TTTAAA TTTAAA -TTAAT TTTAAA TTTAAA TTT-AA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
2917 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
2935 AAAGTCCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 19 0.38
6 27 0.54
7 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:2890 original size:17 final size:18
Alignment explanation
Indices: 2865--2934 Score: 94
Period size: 17 Copynumber: 4.1 Consensus size: 18
2855 CCCCCTTTTT
2865 AATTT-ATTTTAAATTTA
1 AATTTAATTTTAAATTTA
2882 AA-TTAATTTTAAATTTA
1 AATTTAATTTTAAATTTA
2899 AATTTAA-TTT-AATTTA
1 AATTTAATTTTAAATTTA
* *
2915 AATTTAATTTCAAAATTA
1 AATTTAATTTTAAATTTA
2933 AA
1 AA
2935 AAAGTCCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 15 0.32
17 21 0.45
18 11 0.23
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAATTTTAAATTTA
Found at i:2924 original size:5 final size:5
Alignment explanation
Indices: 2862--2924 Score: 63
Period size: 5 Copynumber: 11.6 Consensus size: 5
2852 GGCCCCCCTT
* *
2862 TTTAA TTTAT TTTAAA TTTAA ATTAA TTTTAAA TTTAAA TTTAA TTTAA
1 TTTAA TTTAA TTT-AA TTTAA TTTAA -TTT-AA TTT-AA TTTAA TTTAA
2911 TTTAAA TTTAA TTT
1 TTT-AA TTTAA TTT
2925 CAAAATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 28 0.56
6 20 0.40
7 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTAA
Found at i:3665 original size:24 final size:23
Alignment explanation
Indices: 3628--3677 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3618 TTTTAAGTAT
* *
3628 TAAATGTCTGTTAATATTAATAA
1 TAAATGTCTATTAATAATAATAA
*
3651 TAAATGTGCTATTAATAATGATAA
1 TAAATGT-CTATTAATAATAATAA
3675 TAA
1 TAA
3678 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (23 bp):
TAAATGTCTATTAATAATAATAA
Found at i:4779 original size:29 final size:29
Alignment explanation
Indices: 4736--5150 Score: 353
Period size: 29 Copynumber: 14.4 Consensus size: 29
4726 GGAGGTCCTT
*
4736 GAACTGTCGAAAAATTCCATTTTTACCCTC
1 GAACT-TCCAAAAATTCCATTTTTACCCTC
*
4766 GAACTTCCAAAAATCCCATTTTTGACCC-C
1 GAACTTCCAAAAATTCCATTTTT-ACCCTC
* *
4795 GAAACTTCAAAAAAATCCATTTTTA----C
1 G-AACTTCCAAAAATTCCATTTTTACCCTC
4821 ---C--CCAAAAATTCCATTTTTTACCC-C
1 GAACTTCCAAAAATTCCA-TTTTTACCCTC
*
4845 AAAACTTCCAAAAATTCCATTTTTACCCTC
1 -GAACTTCCAAAAATTCCATTTTTACCCTC
* *
4875 GAACTTCCAAAAATCCCATTTTTAACCTC
1 GAACTTCCAAAAATTCCATTTTTACCCTC
* *
4904 AAAACTTTCAAAAATTCCATTTTTACACC-C
1 -GAACTTCCAAAAATTCCATTTTTAC-CCTC
** *
4934 GAACTTCCAAAAACCCCATTTTTAACCCTA
1 GAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
4964 AAACTTCTAAAAATTTCATTTTTACCCTC
1 GAACTTCCAAAAATTCCATTTTTACCCTC
*
4993 GAACTTCCAAAAATCCCATTTTTGA-CCTC
1 GAACTTCCAAAAATTCCATTTTT-ACCCTC
* *
5022 AAAACTTCCAAAAAATTCTATTTTTGA-CCTC
1 -GAACTTCC-AAAAATTCCATTTTT-ACCCTC
* *
5053 AAAACTTCCAAAAATTCTATTTTTACCCTC
1 -GAACTTCCAAAAATTCCATTTTTACCCTC
*
5083 GAA---CCAAAAATGCCATTTTTTACCC-C
1 GAACTTCCAAAAATTCCA-TTTTTACCCTC
* *
5109 AAAACTTCCCAAAATTCCATTTTTACCCTC
1 -GAACTTCCAAAAATTCCATTTTTACCCTC
*
5139 GAACCTCCAAAA
1 GAACTTCCAAAA
5151 TCTCCAGTTT
Statistics
Matches: 317, Mismatches: 41, Indels: 55
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.03
21 6 0.02
22 1 0.00
24 1 0.00
26 12 0.04
27 11 0.03
28 1 0.00
29 124 0.39
30 121 0.38
31 30 0.09
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
GAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:4808 original size:30 final size:29
Alignment explanation
Indices: 4745--5190 Score: 340
Period size: 30 Copynumber: 15.5 Consensus size: 29
4735 TGAACTGTCG
4745 AAAAATTCCATTTTTACCCTCG-AACTTCC
1 AAAAATTCCATTTTTACCC-CGAAACTTCC
* *
4774 AAAAATCCCATTTTTGACCCCGAAACTTCA
1 AAAAATTCCATTTTT-ACCCCGAAACTTCC
*
4804 AAAAAATCCATTTTTA---C----C--CC
1 AAAAATTCCATTTTTACCCCGAAACTTCC
*
4824 AAAAATTCCATTTTTTACCCCAAAACTTCC
1 AAAAATTCCA-TTTTTACCCCGAAACTTCC
4854 AAAAATTCCATTTTTACCCTCG-AACTTCC
1 AAAAATTCCATTTTTACCC-CGAAACTTCC
* * * *
4883 AAAAATCCCATTTTTAACCTCAAAACTTTC
1 AAAAATTCCATTTTT-ACCCCGAAACTTCC
4913 AAAAATTCCATTTTTACACCCG-AACTTCC
1 AAAAATTCCATTTTTAC-CCCGAAACTTCC
** ** *
4942 AAAAACCCCATTTTTAACCCTAAAACTTCT
1 AAAAATTCCATTTTT-ACCCCGAAACTTCC
*
4972 AAAAATTTCATTTTTACCCTCG-AACTTCC
1 AAAAATTCCATTTTTACCC-CGAAACTTCC
* * *
5001 AAAAATCCCATTTTTGACCTCAAAACTTCC
1 AAAAATTCCATTTTT-ACCCCGAAACTTCC
* * *
5031 AAAAAATTCTATTTTTGACCTCAAAACTTCC
1 -AAAAATTCCATTTTT-ACCCCGAAACTTCC
*
5062 AAAAATTCTATTTTTACCCTCG-AA---CC
1 AAAAATTCCATTTTTACCC-CGAAACTTCC
* *
5088 AAAAATGCCATTTTTTACCCCAAAACTTCC
1 AAAAATTCCA-TTTTTACCCCGAAACTTCC
* *
5118 CAAAATTCCATTTTTACCCTCG-AACCTCC
1 AAAAATTCCATTTTTACCC-CGAAACTTCC
* *
5147 -AAAATCTCCAGTTTTGACCTCGAAAC-TCTC
1 AAAAAT-TCCA-TTTTTACCCCGAAACTTC-C
5177 -AAAATTACCATTTT
1 AAAAATT-CCATTTT
5191 GTGCCCGGGT
Statistics
Matches: 340, Mismatches: 43, Indels: 68
0.75 0.10 0.15
Matches are distributed among these distances:
20 10 0.03
21 6 0.02
22 1 0.00
24 1 0.00
26 12 0.04
27 11 0.03
28 6 0.02
29 128 0.38
30 137 0.40
31 28 0.08
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCGAAACTTCC
Found at i:4833 original size:20 final size:21
Alignment explanation
Indices: 4804--4854 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
4794 CGAAACTTCA
*
4804 AAAAAATCCA-TTTTTACCCC
1 AAAAATTCCATTTTTTACCCC
4824 AAAAATTCCATTTTTTACCCC
1 AAAAATTCCATTTTTTACCCC
*
4845 AAAACTTCCA
1 AAAAATTCCA
4855 AAAATTCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATTCCATTTTTTACCCC
Found at i:4835 original size:50 final size:50
Alignment explanation
Indices: 4772--4872 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
4762 CCTCGAACTT
*
4772 CCAAAAATCCCATTTTTGACCCCGAAACTTCAAAAAAATCCATTTTTACC
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAAAATCCATTTTTACC
* * * *
4822 CCAAAAATTCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACC
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAAAATCCATTTTTACC
4872 C
1 C
4873 TCGAACTTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (50 bp):
CCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAAAATCCATTTTTACC
Found at i:4916 original size:59 final size:59
Alignment explanation
Indices: 4822--5138 Score: 344
Period size: 59 Copynumber: 5.4 Consensus size: 59
4812 CATTTTTACC
* * *
4822 CCAAAAATTCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTT
*
4881 CCAAAAATCCCATTTTTAACCTCAAAACTTTCAAAAATTCCATTTTTACACC-CGAACTT
1 CCAAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTAC-CCTCGAACTT
* * *
4940 CCAAAAACCCCATTTTTAACC-CTAAAACTTCTAAAAATTTCATTTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTAACCTC-AAAACTTCCAAAAATTCCATTTTTACCCTCGAACTT
* * *
4999 CCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAAATTCTATTTTTGA-CCTCAAAACTT
1 CCAAAAATCCCATTTTTAACCTCAAAACTTCC-AAAAATTCCATTTTT-ACCCTC-GAACTT
* * * * * *
5060 CCAAAAATTCTATTTTTACCCTC-GAA---CCAAAAATGCCATTTTTTACCC-CAAAACTT
1 CCAAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATTCCA-TTTTTACCCTC-GAACTT
* * *
5116 CCCAAAATTCCATTTTTACCCTC
1 CCAAAAATCCCATTTTTAACCTC
5139 GAACCTCCAA
Statistics
Matches: 226, Mismatches: 23, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
56 38 0.17
57 9 0.04
58 3 0.01
59 129 0.57
60 22 0.10
61 25 0.11
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
CCAAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTT
Found at i:5156 original size:29 final size:28
Alignment explanation
Indices: 4825--5190 Score: 255
Period size: 29 Copynumber: 12.5 Consensus size: 28
4815 TTTTACCCCA
4825 AAAATTCCATTTTTTACCC-CAAAACTTCC
1 AAAATTCCA-TTTTTACCCTC-AAACTTCC
*
4854 AAAAATTCCATTTTTACCCTCGAACTTCC
1 -AAAATTCCATTTTTACCCTCAAACTTCC
* * *
4883 AAAAATCCCATTTTTAACCTCAAAACTTTCA
1 -AAAATTCCATTTTTACCCTC-AAAC-TTCC
*
4914 AAAATTCCATTTTTACACC-CGAACTTCC
1 AAAATTCCATTTTTAC-CCTCAAACTTCC
** * *
4942 AAAAACCCCATTTTTAACCCTAAAACTTCTA
1 -AAAATTCCATTTTT-ACCCTCAAACTTC-C
* *
4973 AAAATTTCATTTTTACCCTCGAACTTCC
1 AAAATTCCATTTTTACCCTCAAACTTCC
*
5001 AAAAATCCCATTTTTGA-CCTCAAAACTTCC
1 -AAAATTCCATTTTT-ACCCTC-AAACTTCC
*
5031 AAAAAATTCTATTTTTGA-CCTCAAAACTTCC
1 --AAAATTCCATTTTT-ACCCTC-AAACTTCC
* * *
5062 AAAAATTCTATTTTTACCCTCGAAC--CA
1 -AAAATTCCATTTTTACCCTCAAACTTCC
*
5089 AAAATGCCATTTTTTACCC-CAAAACTTCCC
1 AAAATTCCA-TTTTTACCCTC-AAACTT-CC
* *
5119 AAAATTCCATTTTTACCCTCGAACCTCC
1 AAAATTCCATTTTTACCCTCAAACTTCC
*
5147 AAAATCTCCAGTTTTGA-CCTCGAAAC-TCTC
1 AAAAT-TCCA-TTTTTACCCTC-AAACTTC-C
5177 AAAATTACCATTTT
1 AAAATT-CCATTTT
5191 GTGCCCGGGT
Statistics
Matches: 276, Mismatches: 36, Indels: 49
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.03
27 13 0.05
28 10 0.04
29 111 0.40
30 101 0.37
31 33 0.12
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTCAAACTTCC
Done.