Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008806.1 Kokia drynarioides strain JFW-HI SEQ_123489, 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: 37174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1002 original size:46 final size:48
Alignment explanation
Indices: 933--1048 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 48
923 GGCCTTTACA
*
933 AAAACTCAAATTTTATTA-TTTATTTATAAAT-A-AAATGGAATAAAAT
1 AAAACCCAAATTTTATTATTTTATTTATAAATAATAAAT-GAATAAAAT
*
979 AAAACCCAAATTTTATTTGTTATTTATTTATAAATAAATAAATGAATAAAAT
1 AAAACCCAAATTTTA-TT-AT-TTTATTTATAAAT-AATAAATGAATAAAAT
*
1031 AAAATCCAAATTTTATTA
1 AAAACCCAAATTTTATTA
1049 AACCCAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
46 14 0.24
47 2 0.03
50 13 0.22
51 2 0.03
52 24 0.41
53 4 0.07
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (48 bp):
AAAACCCAAATTTTATTATTTTATTTATAAATAATAAATGAATAAAAT
Found at i:1041 original size:52 final size:50
Alignment explanation
Indices: 948--1047 Score: 157
Period size: 52 Copynumber: 2.0 Consensus size: 50
938 TCAAATTTTA
948 TTATTTATTTATAAATAAAATGGAATAAAATAAAACCCAAATTTTATTTG
1 TTATTTATTTATAAATAAAATGGAATAAAATAAAACCCAAATTTTATTTG
*
998 TTATTTATTTATAAATAAATAAAT-GAATAAAATAAAATCCAAATTTTATT
1 TTATTTATTTATAAAT--A-AAATGGAATAAAATAAAACCCAAATTTTATT
1048 AAACCCAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 16 0.35
52 26 0.57
53 4 0.09
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (50 bp):
TTATTTATTTATAAATAAAATGGAATAAAATAAAACCCAAATTTTATTTG
Found at i:1060 original size:33 final size:32
Alignment explanation
Indices: 1023--1092 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
1013 TAAATAAATG
**
1023 AATAAAA-TAAAATCCAAATTTTATTAAACCCAA
1 AATAAAATTAAAAAACAAATTTTA--AAACCCAA
1056 AATAAAAATTAAAAAACAAATTTTAAAACCCAA
1 AAT-AAAATTAAAAAACAAATTTTAAAACCCAA
1089 AATA
1 AATA
1093 CCCAATACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 1 0.03
33 14 0.42
34 4 0.12
35 14 0.42
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (32 bp):
AATAAAATTAAAAAACAAATTTTAAAACCCAA
Found at i:2071 original size:24 final size:23
Alignment explanation
Indices: 1989--2065 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1979 CTCTTATATT
* *
1989 TTATTTATTTTGCATGATTTTAT
1 TTATTTAATTTGCATGATTTTAA
2012 TTATTTAATTTGCATGATTTTAA
1 TTATTTAATTTGCATGATTTTAA
* *
2035 TTTGTTTAATTTTCATGATTTTAA
1 -TTATTTAATTTGCATGATTTTAA
2059 TTATTTA
1 TTATTTA
2066 CTTTTTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 27 0.56
24 21 0.44
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (23 bp):
TTATTTAATTTGCATGATTTTAA
Found at i:2085 original size:15 final size:15
Alignment explanation
Indices: 2028--2087 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
2018 AATTTGCATG
* *
2028 ATTTTAATTTGTTTA
1 ATTTTTATTTTTTTA
* **
2043 ATTTTCATGATTTTA
1 ATTTTTATTTTTTTA
2058 ATTATTTACTTTTTTTA
1 ATT-TTTA-TTTTTTTA
2075 ATTTTTATTTTTT
1 ATTTTTATTTTTT
2088 ACCCATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 20 0.56
16 7 0.19
17 9 0.25
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTTTATTTTTTTA
Found at i:6595 original size:11 final size:9
Alignment explanation
Indices: 6555--6635 Score: 67
Period size: 9 Copynumber: 8.6 Consensus size: 9
6545 GAATTTCACC
6555 AAAAAAA-A
1 AAAAAAAGA
*
6563 AAATAAAGA
1 AAAAAAAGA
*
6572 AGAAGAAAGA
1 A-AAAAAAGA
6582 AAAACAAGAGA
1 AAAA-AA-AGA
6593 AAAAAAAGA
1 AAAAAAAGA
6602 AAGAAGAAAGA
1 AA-AA-AAAGA
6613 AAAAAAA-A
1 AAAAAAAGA
*
6621 GAGAAAAAGA
1 -AAAAAAAGA
6631 AAAAA
1 AAAAA
6636 GAGTGGTCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.12
9 22 0.37
10 17 0.28
11 14 0.23
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:6596 original size:32 final size:33
Alignment explanation
Indices: 6560--6637 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 33
6550 TCACCAAAAA
*
6560 AAAAAATAAAG-AAGAAGAAAG-AAAAACAAGAG
1 AAAAAA-AAAGAAAGAAGAAAGAAAAAAAAAGAG
6592 -AAAAAAAAGAAAGAAGAAAGAAAAAAAAAGAG
1 AAAAAAAAAGAAAGAAGAAAGAAAAAAAAAGAG
*
6624 AAAAAGAAA-AAAGA
1 AAAAAAAAAGAAAGA
6638 GTGGTCAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 15 0.37
32 15 0.37
33 7 0.17
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (33 bp):
AAAAAAAAAGAAAGAAGAAAGAAAAAAAAAGAG
Found at i:6606 original size:31 final size:33
Alignment explanation
Indices: 6561--6637 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
6551 CACCAAAAAA
* *
6561 AAAAATAAAG-AAGAAGAAAG-AAAAACAAGAG
1 AAAAAGAAAGAAAGAAGAAAGAAAAAAAAAGAG
6592 AAAAA-AAAGAAAGAAGAAAGAAAAAAAAAGAG
1 AAAAAGAAAGAAAGAAGAAAGAAAAAAAAAGAG
6624 AAAAAGAAA-AAAGA
1 AAAAAGAAAGAAAGA
6638 GTGGTCAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 4 0.10
31 15 0.36
32 20 0.48
33 3 0.07
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (33 bp):
AAAAAGAAAGAAAGAAGAAAGAAAAAAAAAGAG
Found at i:6617 original size:22 final size:22
Alignment explanation
Indices: 6579--6632 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
6569 AGAAGAAGAA
*
6579 AGAAAAA-CAAGAGAAAAAAAAG
1 AGAAAAAGAAAGA-AAAAAAAAG
*
6601 A-AAGAAGAAAGAAAAAAAAAG
1 AGAAAAAGAAAGAAAAAAAAAG
6622 AGAAAAAGAAA
1 AGAAAAAGAAA
6633 AAAGAGTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (22 bp):
AGAAAAAGAAAGAAAAAAAAAG
Found at i:7811 original size:49 final size:50
Alignment explanation
Indices: 7758--7864 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 50
7748 GTGAAAGGAA
*
7758 AGATTGAA-ATCGTAACGACGAATCTTATACTCTAAAGATAAGGAGAA-C
1 AGATTGAAGATCGCAACGACGAATCTTATACTCTAAAGATAAGGAGAAGC
* * * * *
7806 TAGATT-AAGGTCGCAACGACGAATCTTATACTTTGACGATGAGGAGAAGC
1 -AGATTGAAGATCGCAACGACGAATCTTATACTCTAAAGATAAGGAGAAGC
7856 AGATTGAAG
1 AGATTGAAG
7865 CCGCAAAAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.04
49 43 0.88
50 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (50 bp):
AGATTGAAGATCGCAACGACGAATCTTATACTCTAAAGATAAGGAGAAGC
Found at i:10082 original size:24 final size:24
Alignment explanation
Indices: 10054--10116 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
10044 AGAAATAATC
10054 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * *
10078 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
*
10102 TTTCAGTCAAACTCT
1 TTTCAGTTAAACTCT
10117 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:12071 original size:24 final size:24
Alignment explanation
Indices: 12043--12129 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
12033 AGAAATAATC
* *
12043 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
*
12067 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
12091 TTTCAATTAAACTATATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
12115 TTTCAGTCAAACTCT
1 TTTCAATTAAACTCT
12130 TATTAGTCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:25820 original size:27 final size:27
Alignment explanation
Indices: 25770--25821 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
25760 TGGTAAATCT
* *
25770 TGTGGCAGCATTGGAGGAATATTATCC
1 TGTGGCAGCAATGGAGGAAGATTATCC
* *
25797 TGTGGCAGCAATGGTGGTAGATTAT
1 TGTGGCAGCAATGGAGGAAGATTAT
25822 TATTGTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.31
Consensus pattern (27 bp):
TGTGGCAGCAATGGAGGAAGATTATCC
Found at i:36533 original size:55 final size:55
Alignment explanation
Indices: 36445--36609 Score: 237
Period size: 55 Copynumber: 3.0 Consensus size: 55
36435 GTGTGCTATG
* * *
36445 TAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGTAGTATTTCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
36500 TAACAATCGATTTAAACATATAAACAA-CTGATTCAAAAGAAGCAGTATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATC-GATTCAAAAGAAGCAGTATTCCAACA
* *
36555 TGACAA-CTGATTTAAACATATCAAA-AATCGATTTAAAAGAAGCAGTATTCCAACA
1 TAACAATC-GATTTAAACATAT-AAACAATCGATTCAAAAGAAGCAGTATTCCAACA
36610 ATTAAGAAGA
Statistics
Matches: 101, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
54 2 0.02
55 95 0.94
56 4 0.04
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.25
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
Found at i:36864 original size:6 final size:6
Alignment explanation
Indices: 36853--36887 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
36843 ACATCCATTA
*
36853 CATTTC CATTTC CATTTC CATTTT CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
36888 TCATACCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
CATTTC
Found at i:36880 original size:18 final size:18
Alignment explanation
Indices: 36853--36911 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
36843 ACATCCATTA
*
36853 CATTTCCATTTCCATTTC
1 CATTTCCATTTCCATTTT
*
36871 CATTTTCATTTCCATTTT
1 CATTTCCATTTCCATTTT
*
36889 CA-TACCATTAT-CATTTT
1 CATTTCCATT-TCCATTTT
36906 CATTTC
1 CATTTC
36912 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTTCCATTTCCATTTT
Found at i:36888 original size:12 final size:12
Alignment explanation
Indices: 36853--36910 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
36843 ACATCCATTA
*
36853 CATTTCCATTTC
1 CATTTCCATTTT
36865 CATTTCCATTTT
1 CATTTCCATTTT
36877 CATTTCCATTTT
1 CATTTCCATTTT
* *
36889 CA-TACCATTAT
1 CATTTCCATTTT
*
36900 CATTTTCATTT
1 CATTTCCATTT
36911 CATATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 9 0.23
12 30 0.77
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTTCCATTTT
Done.