Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002065.1 Kokia drynarioides strain JFW-HI SEQ_113974, 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: 61023
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:466 original size:17 final size:18
Alignment explanation
Indices: 432--467 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
422 TGAATTTCTA
432 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
450 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
467 T
1 T
468 AATTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:914 original size:9 final size:9
Alignment explanation
Indices: 900--924 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
890 TGTTTTGTTC
900 TTCTTTTGT
1 TTCTTTTGT
909 TTCTTTTGT
1 TTCTTTTGT
918 TTCTTTT
1 TTCTTTT
925 CTTTATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (9 bp):
TTCTTTTGT
Found at i:8325 original size:22 final size:23
Alignment explanation
Indices: 8296--8353 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 23
8286 CAGAGGGAAA
8296 ATATTTTTAAATATTAATATAAT
1 ATATTTTTAAATATTAATATAAT
8319 -TATTTTTAATTAATATTAATATAAT
1 ATATTTTT-A--AATATTAATATAAT
8344 ATATTTTTAA
1 ATATTTTTAA
8354 TTATATATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 7 0.23
23 2 0.06
25 15 0.48
26 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTTTTAAATATTAATATAAT
Found at i:8338 original size:25 final size:26
Alignment explanation
Indices: 8305--8362 Score: 100
Period size: 25 Copynumber: 2.2 Consensus size: 26
8295 AATATTTTTA
8305 AATATTAATATAAT-TATTTTTAATT
1 AATATTAATATAATATATTTTTAATT
8330 AATATTAATATAATATATTTTTAATT
1 AATATTAATATAATATATTTTTAATT
8356 ATATATT
1 A-ATATT
8363 GATTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 14 0.45
26 12 0.39
27 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATATTAATATAATATATTTTTAATT
Found at i:8688 original size:7 final size:7
Alignment explanation
Indices: 8676--8728 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
8666 GGTGCGCACA
8676 GCACACT
1 GCACACT
8683 GCACACT
1 GCACACT
8690 GCACACT
1 GCACACT
8697 GCACACT
1 GCACACT
8704 GCACACT
1 GCACACT
8711 GCACACT
1 GCACACT
8718 GCACACT
1 GCACACT
8725 GCAC
1 GCAC
8729 CAGGACTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (7 bp):
GCACACT
Found at i:9045 original size:22 final size:22
Alignment explanation
Indices: 9017--9073 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
9007 GAAATTGAAT
9017 ATTTTTATTATAATAAAAGTTA
1 ATTTTTATTATAATAAAAGTTA
** *
9039 ATTTTTATTATTTTAAAAGTTT
1 ATTTTTATTATAATAAAAGTTA
*
9061 A-TATTATTATAAT
1 ATTTTTATTATAAT
9074 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTTTTATTATAATAAAAGTTA
Found at i:9075 original size:24 final size:23
Alignment explanation
Indices: 9030--9081 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
9020 TTTATTATAA
* *
9030 TAAAAGTTAATTTTTATTA-TTT
1 TAAAAGTTAATTATTATAATTTT
9052 TAAAAGTTTATATTATTATAATTTT
1 TAAAAG-TTA-ATTATTATAATTTT
9077 TAAAA
1 TAAAA
9082 AATTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 3 0.12
24 8 0.32
25 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TAAAAGTTAATTATTATAATTTT
Found at i:23893 original size:21 final size:21
Alignment explanation
Indices: 23853--23893 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23843 TATTCTGTGC
* *
23853 TTCTACCGATACATGCAAGAG
1 TTCTACCGAAACAAGCAAGAG
*
23874 TTCTACCGAAACAAGTAAGA
1 TTCTACCGAAACAAGCAAGA
23894 AGATTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (21 bp):
TTCTACCGAAACAAGCAAGAG
Found at i:24497 original size:78 final size:78
Alignment explanation
Indices: 24415--24580 Score: 203
Period size: 78 Copynumber: 2.1 Consensus size: 78
24405 AGTATGTCGG
* *
24415 TCTTACGAGCCAATACAGTATATCGCTA-TTACGAGCCAGT-TCAATAT-TTCGCTCTGACGAGC
1 TCTTACGAGCCAATACAATATATCAC-ACTTACGAGCCAGTAT-AATATATT-GCTCTGACGAGC
24477 TAGTACAGTATATTGC
63 TAGTACAGTATATTGC
* * * * * * *
24493 TCTTACTAGCCAGTTCAATATTTCACACTTACGAGCTAGTATAGTATATTGCTCTTACGAGCTAG
1 TCTTACGAGCCAATACAATATATCACACTTACGAGCCAGTATAATATATTGCTCTGACGAGCTAG
24558 TACAGTATATTGC
66 TACAGTATATTGC
24571 TCTTACGAGC
1 TCTTACGAGC
24581 TAGTTCAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 71 0.95
79 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (78 bp):
TCTTACGAGCCAATACAATATATCACACTTACGAGCCAGTATAATATATTGCTCTGACGAGCTAG
TACAGTATATTGC
Found at i:24576 original size:52 final size:52
Alignment explanation
Indices: 24378--24584 Score: 227
Period size: 52 Copynumber: 4.0 Consensus size: 52
24368 CGATCCCAGT
* * * * * * * *
24378 CAGTATATCGCTCTTACGAACTATTTCAGTATGTCGGTCTTACGAGCCAATA
1 CAGTATATCGCTCTTACGAGCCAGTTCAATATTTCGCTCTTACGAGCTAGTA
* *
24430 CAGTATATCGCTATTACGAGCCAGTTCAATATTTCGCTCTGACGAGCTAGTA
1 CAGTATATCGCTCTTACGAGCCAGTTCAATATTTCGCTCTTACGAGCTAGTA
* * * *
24482 CAGTATATTGCTCTTACTAGCCAGTTCAATATTTCACACTTACGAGCTAGTA
1 CAGTATATCGCTCTTACGAGCCAGTTCAATATTTCGCTCTTACGAGCTAGTA
* * * * *
24534 TAGTATATTGCTCTTACGAGCTAGTACAGTATATT-GCTCTTACGAGCTAGT
1 CAGTATATCGCTCTTACGAGCCAGTTCAATAT-TTCGCTCTTACGAGCTAGT
24585 TCAATATTTC
Statistics
Matches: 131, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
52 129 0.98
53 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (52 bp):
CAGTATATCGCTCTTACGAGCCAGTTCAATATTTCGCTCTTACGAGCTAGTA
Found at i:24581 original size:26 final size:26
Alignment explanation
Indices: 24378--24584 Score: 184
Period size: 26 Copynumber: 8.0 Consensus size: 26
24368 CGATCCCAGT
* * * *
24378 CAGTATATCGCTCTTACGAACTATTT
1 CAGTATATTGCTCTTACGAGCTAGTA
* * * * *
24404 CAGTATGTCGGTCTTACGAGCCAATA
1 CAGTATATTGCTCTTACGAGCTAGTA
* * * *
24430 CAGTATATCGCTATTACGAGCCAGTT
1 CAGTATATTGCTCTTACGAGCTAGTA
* *
24456 CAATAT-TTCGCTCTGACGAGCTAGTA
1 CAGTATATT-GCTCTTACGAGCTAGTA
* * *
24482 CAGTATATTGCTCTTACTAGCCAGTT
1 CAGTATATTGCTCTTACGAGCTAGTA
* * *
24508 CAATAT-TTCACACTTACGAGCTAGTA
1 CAGTATATT-GCTCTTACGAGCTAGTA
*
24534 TAGTATATTGCTCTTACGAGCTAGTA
1 CAGTATATTGCTCTTACGAGCTAGTA
24560 CAGTATATTGCTCTTACGAGCTAGT
1 CAGTATATTGCTCTTACGAGCTAGT
24585 TCAATATTTC
Statistics
Matches: 144, Mismatches: 33, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
25 3 0.02
26 137 0.95
27 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (26 bp):
CAGTATATTGCTCTTACGAGCTAGTA
Found at i:25325 original size:3 final size:3
Alignment explanation
Indices: 25310--25369 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
25300 CCGGTCATGT
*
25310 GAA GAA CAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
25358 GAA GAA GAA GAA
1 GAA GAA GAA GAA
25370 AAATATCGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:26315 original size:17 final size:18
Alignment explanation
Indices: 26288--26321 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
26278 TATCATATTA
26288 GATTAAATTGCATTTAGG
1 GATTAAATTGCATTTAGG
26306 GATT-AATTGCATTTAG
1 GATTAAATTGCATTTAG
26322 TTATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (18 bp):
GATTAAATTGCATTTAGG
Found at i:47097 original size:13 final size:14
Alignment explanation
Indices: 47068--47097 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47058 TACGTTGCTC
47068 TGACATTTAACCTT
1 TGACATTTAACCTT
47082 TGACATTTAA-CTT
1 TGACATTTAACCTT
47095 TGA
1 TGA
47098 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (14 bp):
TGACATTTAACCTT
Found at i:50436 original size:12 final size:12
Alignment explanation
Indices: 50414--50456 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
50404 AAAGACAAGT
50414 GGAAGAAGAGGAA
1 GGAA-AAGAGGAA
50427 GGAAAAGAGGAA
1 GGAAAAGAGGAA
*
50439 GAAAAAGAGGAA
1 GGAAAAGAGGAA
50451 GGAAAA
1 GGAAAA
50457 AAAGCTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
GGAAAAGAGGAA
Found at i:50928 original size:17 final size:17
Alignment explanation
Indices: 50908--50955 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
50898 CACATTCCCT
*
50908 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* *
50925 TTGTCACTGCATTTGCA
1 TTGTCATTGCATTTGAA
*
50942 TTGTCATTACATTT
1 TTGTCATTGCATTT
50956 CCATTTGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:50960 original size:17 final size:17
Alignment explanation
Indices: 50889--50967 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 17
50879 TGCTAGTAAT
** *
50889 CATTGTCACCACATTCC
1 CATTGTCATTACATTTC
* * *
50906 CTTTGTCATTGCATTTT
1 CATTGTCATTACATTTC
* * * *
50923 AATTGTCACTGCATTTG
1 CATTGTCATTACATTTC
50940 CATTGTCATTACATTTC
1 CATTGTCATTACATTTC
50957 CATTTGTCATT
1 CA-TTGTCATT
50968 GTAATTTAAT
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
17 39 0.83
18 8 0.17
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (17 bp):
CATTGTCATTACATTTC
Done.