Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010479.1 Kokia drynarioides strain JFW-HI SEQ_125381, 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: 51811
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:102 original size:14 final size:15
Alignment explanation
Indices: 78--107 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
68 TCAAATTAAC
78 TAACAAAAAATTTTA
1 TAACAAAAAATTTTA
93 TAAC-AAAAATTTTA
1 TAACAAAAAATTTTA
107 T
1 T
108 TTCATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TAACAAAAAATTTTA
Found at i:426 original size:11 final size:10
Alignment explanation
Indices: 401--425 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
391 TTAAATATAT
401 AAAAATTAAA
1 AAAAATTAAA
411 AAAAATTAAA
1 AAAAATTAAA
421 AAAAA
1 AAAAA
426 ACACGTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:1962 original size:103 final size:103
Alignment explanation
Indices: 1823--2009 Score: 295
Period size: 103 Copynumber: 1.8 Consensus size: 103
1813 CTTTTCGTTT
* * * *
1823 CCATAGCTAATTTTTTTTCTCGAGCACCAGAGCTTTCATTCT-CAAGCCAACAACTTGCAACAAA
1 CCATAGCTAATTATTTTTCTCGAGCACCAAAACTTTCATTCTCCAA-ACAACAACTTGCAACAAA
*
1887 AAACCCACTGGTTAAACTTACGTTATTCCTTTTCTCGAG
65 AAACCCACTAGTTAAACTTACGTTATTCCTTTTCTCGAG
*
1926 CCATAGCTTATTATTTTTCTCGAGCACCAAAACTTTCATTCTCCAAACAACAACTTGCAACAAAA
1 CCATAGCTAATTATTTTTCTCGAGCACCAAAACTTTCATTCTCCAAACAACAACTTGCAACAAAA
*
1991 AACCCACTAGTTCAACTTA
66 AACCCACTAGTTAAACTTA
2010 TGCTACATCT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
103 73 0.96
104 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (103 bp):
CCATAGCTAATTATTTTTCTCGAGCACCAAAACTTTCATTCTCCAAACAACAACTTGCAACAAAA
AACCCACTAGTTAAACTTACGTTATTCCTTTTCTCGAG
Found at i:3889 original size:11 final size:11
Alignment explanation
Indices: 3873--3903 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3863 TTCTGACTTT
3873 GAAAAATTATA
1 GAAAAATTATA
3884 GAAAAA-TATA
1 GAAAAATTATA
3894 GAAAAATTAT
1 GAAAAATTAT
3904 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:4383 original size:23 final size:23
Alignment explanation
Indices: 4357--4414 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
4347 ACACTAGCGC
4357 GCTTACTATTTCGCA-CTTCGTGT
1 GCTTACTATTTCGCACCTT-GTGT
*
4380 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTATTTCGCACCTTGTGT
*
4403 GCCTACTGATTT
1 GCTTACT-ATTT
4415 ACGCTATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.43
Consensus pattern (23 bp):
GCTTACTATTTCGCACCTTGTGT
Found at i:14266 original size:24 final size:24
Alignment explanation
Indices: 14230--14281 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
14220 TTTTAGTGTT
*
14230 TATTTTTAAATTTATTAAATA-ATA
1 TATTTTTAAATTTA-AAAATATATA
*
14254 TATTTTTATATTTAAAAATATATA
1 TATTTTTAAATTTAAAAATATATA
14278 TATT
1 TATT
14282 CTCTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTTTAAATTTAAAAATATATA
Found at i:23996 original size:54 final size:54
Alignment explanation
Indices: 23933--24040 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
23923 TATATTTACT
*
23933 CAAACAAGTAAGTTCGTTTTTAAAAATTTGAAAACATCGACACAAATGAAATTC
1 CAAACAAGTAAGTTCATTTTTAAAAATTTGAAAACATCGACACAAATGAAATTC
23987 CAAACAAGTAAGTTCATTTTTAAAAATTTGAAAACATCGACACAAATGAAATTC
1 CAAACAAGTAAGTTCATTTTTAAAAATTTGAAAACATCGACACAAATGAAATTC
24041 ATCTTACAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (54 bp):
CAAACAAGTAAGTTCATTTTTAAAAATTTGAAAACATCGACACAAATGAAATTC
Found at i:32812 original size:29 final size:29
Alignment explanation
Indices: 32779--32861 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
32769 AAAATTATAT
32779 CTAAATTTTAAATTTAAAAAATA-AAAAG
1 CTAAATTTTAAATTTAAAAAATATAAAAG
*
32807 ACTAAAATTTTAAAATT-AAAAATATAAAAG
1 -CT-AAATTTTAAATTTAAAAAATATAAAAG
* *
32837 CTAAATTCTCAATTTATAAAGAATA
1 CTAAATTTTAAATTTA-AAA-AATA
32862 CAGGACCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.22
29 11 0.24
30 20 0.44
31 4 0.09
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (29 bp):
CTAAATTTTAAATTTAAAAAATATAAAAG
Found at i:36128 original size:138 final size:138
Alignment explanation
Indices: 35914--36191 Score: 484
Period size: 138 Copynumber: 2.0 Consensus size: 138
35904 GCTTTGACTC
* * * *
35914 CATCGAATCTTGATGTTCTACTTTGTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTG
1 CATCGAATCTTGACGATCTACTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTA
*
35979 GCTGCCGCAGTTTACTCTCCCACCTATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
66 GCTGCCGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
36044 CATGTTAT
131 CATGTTAT
*
36052 CATCGAATCTTGACGATCTATTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTA
1 CATCGAATCTTGACGATCTACTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTA
* *
36117 GCTTCGGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
66 GCTGCCGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
36182 CATGTTAT
131 CATGTTAT
36190 CA
1 CA
36192 CCTATAAACA
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (138 bp):
CATCGAATCTTGACGATCTACTTTCTGCTGAGAACTCATCTCTGCAGTACTCCGATCAAGCATTA
GCTGCCGCAGTTTACTCTCCCACCCATAAATCTGCTGTTTTAAATCAATTTCAGCAGCAGCAAAG
CATGTTAT
Found at i:39218 original size:16 final size:18
Alignment explanation
Indices: 39194--39247 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
39184 CTGTTAAGTT
*
39194 TATT-TTATTTTAAAAAA
1 TATTATTATTTAAAAAAA
*
39211 TA-TA-TATTTGAAATAAAT
1 TATTATTATTT-AAA-AAAA
39229 TATTATTATTTAAAAAAA
1 TATTATTATTTAAAAAAA
39247 T
1 T
39248 GAAAATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 9 0.31
19 5 0.17
20 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTATTATTTAAAAAAA
Found at i:40897 original size:95 final size:94
Alignment explanation
Indices: 40734--40951 Score: 287
Period size: 95 Copynumber: 2.3 Consensus size: 94
40724 TCTAGGTCTA
* * ** *
40734 TATGTGTCGAGACAAA-GGTTTGAATGTCTCGAGACAATGTCATGTTCCTGTACAACTTTAGCTT
1 TATGTCTCGAGACAAAGGGCTT--ATGTCTTAAGATAATGTCATGTTCCTGTACAACTTTAGCTT
*
40798 CAAAGTTGTCTTGT-TTCAGGACAAATGAGTG
64 CAAAGTTGTCTTGTCTT-AAGACAAATGAGTG
* * *
40829 TATGTCTCGAGACAAAAGGGCTTATGTCTTAAGATAATGTCTTGTTTCTGTAGAACTTTAGCTTC
1 TATGTCTCGAGAC-AAAGGGCTTATGTCTTAAGATAATGTCATGTTCCTGTACAACTTTAGCTTC
*
40894 AAAGTTGTCTTGTCTTAAGACAAATGGGTG
65 AAAGTTGTCTTGTCTTAAGACAAATGAGTG
*
40924 TATGTCTCGAGACAAAGGGGTTATGTCT
1 TATGTCTCGAGACAAAGGGCTTATGTCT
40952 CGGGACATGA
Statistics
Matches: 109, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
94 14 0.13
95 86 0.79
96 5 0.05
97 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (94 bp):
TATGTCTCGAGACAAAGGGCTTATGTCTTAAGATAATGTCATGTTCCTGTACAACTTTAGCTTCA
AAGTTGTCTTGTCTTAAGACAAATGAGTG
Found at i:40929 original size:22 final size:21
Alignment explanation
Indices: 40904--40952 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
40894 AAAGTTGTCT
* *
40904 TGTCTTAAGACAAATGGGTGTA
1 TGTCTCAAGACAAAGGGGT-TA
*
40926 TGTCTCGAGACAAAGGGGTTA
1 TGTCTCAAGACAAAGGGGTTA
40947 TGTCTC
1 TGTCTC
40953 GGGACATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGACAAAGGGGTTA
Found at i:40950 original size:21 final size:22
Alignment explanation
Indices: 40911--40958 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
40901 TCTTGTCTTA
*
40911 AGACAAATGGGTGTATGTCTCG
1 AGACAAAGGGGTGTATGTCTCG
40933 AGACAAAGGGGT-TATGTCTCG
1 AGACAAAGGGGTGTATGTCTCG
*
40954 GGACA
1 AGACA
40959 TGATCCTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.23
Consensus pattern (22 bp):
AGACAAAGGGGTGTATGTCTCG
Found at i:45790 original size:25 final size:23
Alignment explanation
Indices: 45753--45863 Score: 98
Period size: 23 Copynumber: 4.7 Consensus size: 23
45743 ACACTAGCGC
45753 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
45776 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
** * *
45801 GCTCTCTGACTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * * *
45824 GCTCTCTGATTAGTACTTTTTGT
1 GCTCTCTGTTTAGCACTGTCTGT
*
45847 ACTCTCTGTTTAGCACT
1 GCTCTCTGTTTAGCACT
45864 ATGTGTGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 54 0.72
24 1 0.01
25 17 0.23
26 3 0.04
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:45861 original size:46 final size:47
Alignment explanation
Indices: 45754--45870 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 47
45744 CACTAGCGCG
* * *
45754 CTCTCTGTTTAGCACGTCT-CGTGCTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCAC-TATGTGTGCTCTCTG-TATTAGCACTGTGTGTA
** * * * *
45802 CTCTCTGACTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTTTGTA
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTATTAGCACTGTGTGTA
45848 CTCTCTGTTTAGCACTATGTGTG
1 CTCTCTGTTTAGCACTATGTGTG
45871 TTATCTGTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
46 32 0.56
47 2 0.04
48 23 0.40
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (47 bp):
CTCTCTGTTTAGCACTATGTGTGCTCTCTGTATTAGCACTGTGTGTA
Done.