Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001399.1 Kokia drynarioides strain JFW-HI SEQ_112887, 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: 65319
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:931 original size:17 final size:17
Alignment explanation
Indices: 905--951 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
895 ACTTTGATTT
*
905 AAATAGATTTAAACTTA
1 AAATAAATTTAAACTTA
**
922 AAATAAATTTAATTTTA
1 AAATAAATTTAAACTTA
939 AAATAAATTTAAA
1 AAATAAATTTAAA
952 TCCTGTTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATAAATTTAAACTTA
Found at i:1432 original size:18 final size:17
Alignment explanation
Indices: 1400--1439 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1390 TGCATTTAAA
1400 TTATTACATTTATAATT
1 TTATTACATTTATAATT
*
1417 TTATTAGATATTATAATT
1 TTATTACAT-TTATAATT
*
1435 GTATT
1 TTATT
1440 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
TTATTACATTTATAATT
Found at i:5345 original size:25 final size:25
Alignment explanation
Indices: 5311--5361 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5301 TATGCTAAAG
5311 AATGTAGTAATAAACTCATCAACTC
1 AATGTAGTAATAAACTCATCAACTC
5336 AATGTAGTAATAAACTCATCAACTC
1 AATGTAGTAATAAACTCATCAACTC
5361 A
1 A
5362 GCTGTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
AATGTAGTAATAAACTCATCAACTC
Found at i:13840 original size:22 final size:22
Alignment explanation
Indices: 13787--13840 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
13777 TTTAGCGGTC
*
13787 AAAAATTAAATTATAATTTATA
1 AAAAATTAAAATATAATTTATA
** *
13809 TGAAAGTAAAATATAAATTT-TA
1 AAAAATTAAAATAT-AATTTATA
13831 AAAAATTAAA
1 AAAAATTAAA
13841 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAATTAAAATATAATTTATA
Found at i:14727 original size:31 final size:31
Alignment explanation
Indices: 14692--14768 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
14682 GGTTCATGAT
* * *
14692 TAAAATTTTA-AAATTCAAAGAGTATAGAGAC
1 TAAAATTTGACAAATTCAAAAAGTA-AAAGAC
*
14723 TAAAA-TTGACGAATTCAAAAAGTAAAAGAC
1 TAAAATTTGACAAATTCAAAAAGTAAAAGAC
14753 TAAAA-TTGATCAAATT
1 TAAAATTTGA-CAAATT
14769 AAAGGGACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (31 bp):
TAAAATTTGACAAATTCAAAAAGTAAAAGAC
Found at i:14755 original size:30 final size:31
Alignment explanation
Indices: 14703--14761 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
14693 AAAATTTTAA
* *
14703 AATTCAAAGAGTATAGAGACTAAAATTGACG
1 AATTCAAAAAGTATAAAGACTAAAATTGACG
14734 AATTCAAAAAGTA-AAAGACTAAAATTGA
1 AATTCAAAAAGTATAAAGACTAAAATTGA
14762 TCAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.22
Consensus pattern (31 bp):
AATTCAAAAAGTATAAAGACTAAAATTGACG
Found at i:27903 original size:20 final size:20
Alignment explanation
Indices: 27878--27915 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27868 TTTCAATTTT
27878 TAAAAA-AATTATAAATTTCA
1 TAAAAATAATTA-AAATTTCA
27898 TAAAAATAATTAAAATTT
1 TAAAAATAATTAAAATTT
27916 ATTAGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATAATTAAAATTTCA
Found at i:29682 original size:22 final size:21
Alignment explanation
Indices: 29607--29683 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
29597 TCCCCTGTTG
* *
29607 TTTGTTGTCATTTGCTACCAT
1 TTTGTTGTTATTTGCTACTAT
* * *
29628 TTTGTTGTTGTTTTCTTCTCAT
1 TTTGTTGTTATTTGCTACT-AT
* *
29650 TGTGTTATTATATTGCTACTAT
1 TTTGTTGTTAT-TTGCTACTAT
29672 TTTGTTGTTATT
1 TTTGTTGTTATT
29684 GTTTGAATAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
21 15 0.36
22 21 0.50
23 6 0.14
ACGTcount: A:0.13, C:0.12, G:0.14, T:0.61
Consensus pattern (21 bp):
TTTGTTGTTATTTGCTACTAT
Found at i:29888 original size:14 final size:14
Alignment explanation
Indices: 29865--29900 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29855 TATATTTTTA
29865 AAAAAAAATTAAAT
1 AAAAAAAATTAAAT
* *
29879 AAAAATAATTATAT
1 AAAAAAAATTAAAT
29893 AAAAAAAA
1 AAAAAAAA
29901 GTTTAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAAAATTAAAT
Found at i:32880 original size:23 final size:23
Alignment explanation
Indices: 32850--32926 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
32840 ACGCTAGCGC
32850 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
32873 GCTTACTGTTTCGTACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
32896 GCTTACTGTTTCGCATTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
32919 GCCTACTG
1 GCTTACTG
32927 ATTTGCGCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:32966 original size:23 final size:23
Alignment explanation
Indices: 32933--32985 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
32923 ACTGATTTGC
32933 GCCTACT-GATTGCACTGTGTGT
1 GCCTACTGGATTGCACTGTGTGT
32955 GCCTACTGGATTGCACTGTGTGT
1 GCCTACTGGATTGCACTGTGTGT
*
32978 GCTTACTG
1 GCCTACTG
32986 TTTCCCCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (23 bp):
GCCTACTGGATTGCACTGTGTGT
Found at i:41113 original size:15 final size:16
Alignment explanation
Indices: 41095--41124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41085 AACAACAGAT
41095 GAAGAA-GAAGAAAAA
1 GAAGAAGGAAGAAAAA
41110 GAAGAAGGAAGAAAA
1 GAAGAAGGAAGAAAA
41125 GGAGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
GAAGAAGGAAGAAAAA
Found at i:43520 original size:15 final size:15
Alignment explanation
Indices: 43500--43528 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43490 CGTCAGTAAG
43500 CTTTACTAAAGAGCA
1 CTTTACTAAAGAGCA
43515 CTTTACTAAAGAGC
1 CTTTACTAAAGAGC
43529 GTTGATGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (15 bp):
CTTTACTAAAGAGCA
Found at i:43637 original size:17 final size:18
Alignment explanation
Indices: 43605--43639 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43595 TAAGGAAAAT
*
43605 AATAAAAATTATAATTTA
1 AATAAAAATTAAAATTTA
43623 AATAAAAA-TAAAATTTA
1 AATAAAAATTAAAATTTA
43640 GGAAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAAAATTAAAATTTA
Found at i:43673 original size:42 final size:42
Alignment explanation
Indices: 43571--43673 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 42
43561 TGCTTTCTTG
43571 AAAA-TATAA-TTTTATG--AATAAAATTAAGGAAAATAATA
1 AAAATTATAATTTTTATGAAAATAAAATTAAGGAAAATAATA
** * * * *
43609 AAAATTATAATTTAAATAAAAATAAAATTTAGGAAAA-ATTC
1 AAAATTATAATTTTTATGAAAATAAAATTAAGGAAAATAATA
*
43650 AAAATTATGTATTTTTATGAAAAT
1 AAAATTAT-AATTTTTATGAAAAT
43674 TGAAATGTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
38 4 0.08
39 5 0.10
40 4 0.08
41 10 0.20
42 27 0.54
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (42 bp):
AAAATTATAATTTTTATGAAAATAAAATTAAGGAAAATAATA
Found at i:46382 original size:3 final size:3
Alignment explanation
Indices: 46376--46407 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
46366 AAGAGAGGAG
46376 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
46408 GGCAATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:63342 original size:17 final size:18
Alignment explanation
Indices: 63308--63348 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
63298 TAAAAAAATA
**
63308 TTTTATTAGTTTATTTAT
1 TTTTATTAAATTATTTAT
63326 TTTTATTAAATTA-TTAT
1 TTTTATTAAATTATTTAT
63343 TTTTAT
1 TTTTAT
63349 ATATGGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTATTAAATTATTTAT
Found at i:65261 original size:36 final size:36
Alignment explanation
Indices: 65185--65263 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
65175 ATGGGGTGGT
* *
65185 GGTGGTGGAGGAGACTTATATTTGTAGACTGGAGTG
1 GGTGGTGGAGGAGACTTATACTTGTAGACTGGAGTA
* * * *
65221 GGTGGTGGGGGAGACTTGTACTTGTA-AGTGTGCGTA
1 GGTGGTGGAGGAGACTTATACTTGTAGACTG-GAGTA
65257 GGTGGTG
1 GGTGGTG
65264 AGGGTAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.18, C:0.06, G:0.46, T:0.30
Consensus pattern (36 bp):
GGTGGTGGAGGAGACTTATACTTGTAGACTGGAGTA
Done.