Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008311.1 Kokia drynarioides strain JFW-HI SEQ_122976, 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: 57782
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:3519 original size:90 final size:90
Alignment explanation
Indices: 3347--3523 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
3337 AAGTGCACAG
3347 ACTTTCCCATCTTAACATAACCCATCCCCTCCCCTGCTTCTTGCTCTCCCACAAAAAATTATTAT
1 ACTTTCCCATCTTAACATAACCCATCCCCTCCCCTGCTTCTTGCTCTCCCACAAAAAATTATTAT
3412 CTTCACAACCAAGGTATCCATACAC
66 CTTCACAACCAAGGTATCCATACAC
* * *
3437 ACTTTCCCATCTTAACATAGCCCATCCCCTCCCTTGCTTCTTGCTCTCCCACAAAAAACTTCTTA
1 ACTTTCCCATCTTAACATAACCCATCCCCTCCCCTGCTTCTTGCTCTCCCACAAAAAA-TTATTA
**
3502 TCTTTGCAACCAA-GTATCCATA
65 TCTTCACAACCAAGGTATCCATA
3524 GTTCCCTTAG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 65 0.80
91 16 0.20
ACGTcount: A:0.27, C:0.37, G:0.05, T:0.31
Consensus pattern (90 bp):
ACTTTCCCATCTTAACATAACCCATCCCCTCCCCTGCTTCTTGCTCTCCCACAAAAAATTATTAT
CTTCACAACCAAGGTATCCATACAC
Found at i:8307 original size:14 final size:14
Alignment explanation
Indices: 8288--8315 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8278 TTATCAAAGG
8288 TAAGATATTTTATA
1 TAAGATATTTTATA
8302 TAAGATATTTTATA
1 TAAGATATTTTATA
8316 CAAAATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TAAGATATTTTATA
Found at i:8981 original size:5 final size:5
Alignment explanation
Indices: 8971--8996 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
8961 TGAAAGTTAC
8971 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
8997 ATCATTTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:12850 original size:11 final size:11
Alignment explanation
Indices: 12826--12866 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12816 TTTTAAAATA
12826 TAAAATTA--T
1 TAAAATTATTT
12835 TAAAATTATTT
1 TAAAATTATTT
* *
12846 TAAAATAAATT
1 TAAAATTATTT
12857 TAAAATTATT
1 TAAAATTATT
12867 AAATAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:12888 original size:31 final size:32
Alignment explanation
Indices: 12794--12888 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 32
12784 AGCAAATAAT
*
12794 TTTAAAATTATTAAAATTATTTT--TTTAAAA
1 TTTAAAATTATTAAAATTATTTTAATTTTAAA
* **
12824 TATAAAATTATTAAAATTATTTTAA-AATAAA
1 TTTAAAATTATTAAAATTATTTTAATTTTAAA
* *
12855 TTTAAAATTATT-AAATAATTTTAATTTTCAA
1 TTTAAAATTATTAAAATTATTTTAATTTTAAA
12886 TTT
1 TTT
12889 CATCTTCTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
30 33 0.62
31 20 0.38
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAAAATTATTAAAATTATTTTAATTTTAAA
Found at i:12934 original size:18 final size:18
Alignment explanation
Indices: 12883--12934 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
12873 TTTTAATTTT
12883 CAATTTCATCTTCTTCCC
1 CAATTTCATCTTCTTCCC
*
12901 C-A-TT-AT-TTCTTTCC
1 CAATTTCATCTTCTTCCC
12915 CAATTTCATCTTCTTCCC
1 CAATTTCATCTTCTTCCC
12933 CA
1 CA
12935 TTTTTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.29
15 3 0.11
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (18 bp):
CAATTTCATCTTCTTCCC
Found at i:12937 original size:17 final size:17
Alignment explanation
Indices: 12885--12937 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
12875 TTAATTTTCA
12885 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
*
12902 A-TT-AT-TTCTTTCCCA
1 ATTTCATCTTC-TTCCCC
12917 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
12934 ATTT
1 ATTT
12938 TTCTATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.27
16 4 0.13
17 12 0.40
18 3 0.10
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTCATCTTCTTCCCC
Found at i:13169 original size:98 final size:99
Alignment explanation
Indices: 13022--13218 Score: 324
Period size: 98 Copynumber: 2.0 Consensus size: 99
13012 TTTCGAACCA
**
13022 AACCATGGTTACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCATCACTCT
1 AACCATGGCCACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCATCACTCT
*
13087 CCCAACCCTTCAA-GTTCTCTATTTTAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
* *
13120 AACCATGGCCACTTCTCCACTTGGATTTTGAATCAAACCATGGCTTCTTCTTCTTCCATCACTCT
1 AACCATGGCCACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCATCACTCT
**
13185 CTTAACCCTTCAAGGTTCTCTATTTCAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
13219 TTCTTAGGAA
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 72 0.79
99 19 0.21
ACGTcount: A:0.22, C:0.32, G:0.09, T:0.37
Consensus pattern (99 bp):
AACCATGGCCACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCATCACTCT
CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
Found at i:13847 original size:21 final size:22
Alignment explanation
Indices: 13823--13865 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13813 AAATAATTTT
*
13823 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
13844 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
13866 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:15128 original size:6 final size:6
Alignment explanation
Indices: 15119--15155 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
15109 GTGCCTATGC
15119 CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA C
1 CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA CTGCGA C
15156 GGCGGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGCGA
Found at i:27825 original size:21 final size:21
Alignment explanation
Indices: 27788--27848 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
27778 AATATTTTTC
*
27788 TCATAAAAATGA-T-TAAAATA
1 TCATAAAAAT-ATTATAAAAAA
27808 TCATAAAAATATTATAAAAAA
1 TCATAAAAATATTATAAAAAA
*
27829 TCAGAAAAA-ACTTATAAAAA
1 TCATAAAAATA-TTATAAAAA
27849 TTATTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 12 0.33
21 23 0.64
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (21 bp):
TCATAAAAATATTATAAAAAA
Found at i:27847 original size:10 final size:9
Alignment explanation
Indices: 27834--28055 Score: 107
Period size: 9 Copynumber: 23.6 Consensus size: 9
27824 AAAAATCAGA
27834 AAAAACTTAT
1 AAAAA-TTAT
27844 AAAAATTAT
1 AAAAATTAT
**
27853 -TTAATTA-
1 AAAAATTAT
27860 AAAAA-T-T
1 AAAAATTAT
*
27867 GAAAATTGAT
1 AAAAATT-AT
*
27877 AAGAACTTAT
1 AA-AAATTAT
*
27887 AAAAAATAT
1 AAAAATTAT
* *
27896 AGATATTAT
1 AAAAATTAT
27905 AAAAAAATT-T
1 --AAAAATTAT
27915 AATAAATTAT
1 AA-AAATTAT
27925 AAAAAATTAT
1 -AAAAATTAT
27935 -AAAATTAAT
1 AAAAATT-AT
27944 AAAACGTATT-T
1 AAAA---ATTAT
27955 AAAATATTAT
1 AAAA-ATTAT
*
27965 AAAAACGTAT
1 AAAAA-TTAT
* *
27975 TAAATTCTAT
1 AAAAAT-TAT
*
27985 AAAAATCAT
1 AAAAATTAT
27994 AAAAATTAT
1 AAAAATTAT
28003 AGAAAATTAT
1 A-AAAATTAT
* *
28013 TAAAAGTAT
1 AAAAATTAT
*
28022 TAAAATTAAT
1 AAAAATT-AT
*
28032 ATAAACTTAT
1 A-AAAATTAT
28042 AAAAATTAT
1 AAAAATTAT
28051 AAAAA
1 AAAAA
28056 CTTGAATTGG
Statistics
Matches: 162, Mismatches: 28, Indels: 45
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.03
8 16 0.10
9 63 0.39
10 54 0.33
11 21 0.13
13 3 0.02
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27847 original size:11 final size:10
Alignment explanation
Indices: 27810--28055 Score: 72
Period size: 10 Copynumber: 24.7 Consensus size: 10
27800 TTAAAATATC
27810 ATAAAAATATT
1 ATAAAAA-ATT
*
27821 ATAAAAAATC
1 ATAAAAAATT
*
27831 AGAAAAAACTT
1 ATAAAAAA-TT
27842 ATAAAAATTATTT
1 ATAAAAA--A-TT
27855 AATTAAAAAA-T
1 -A-TAAAAAATT
*
27866 -T-GAAAATT
1 ATAAAAAATT
* *
27874 GATAAGAACTT
1 -ATAAAAAATT
27885 ATAAAAAA-T
1 ATAAAAAATT
* *
27894 AT-AGATATT
1 ATAAAAAATT
27903 ATAAAAAAATT
1 AT-AAAAAATT
*
27914 -TAATAAATT
1 ATAAAAAATT
27923 ATAAAAAATT
1 ATAAAAAATT
27933 AT--AAAATT
1 ATAAAAAATT
*
27941 AATAAAACGTATT
1 -ATAAAA--AATT
*
27954 -TAAAATATT
1 ATAAAAAATT
**
27963 ATAAAAACGT
1 ATAAAAAATT
*
27973 AT--TAAATT
1 ATAAAAAATT
* *
27981 CTATAAAAATC
1 ATA-AAAAATT
27992 AT-AAAAATT
1 ATAAAAAATT
*
28001 ATAGAAAATT
1 ATAAAAAATT
* *
28011 AT-TAAAAGT
1 ATAAAAAATT
*
28020 AT-TAAAATT
1 ATAAAAAATT
* *
28029 AATATAAACTT
1 -ATAAAAAATT
28040 AT-AAAAATT
1 ATAAAAAATT
28049 ATAAAAA
1 ATAAAAA
28056 CTTGAATTGG
Statistics
Matches: 173, Mismatches: 36, Indels: 53
0.66 0.14 0.20
Matches are distributed among these distances:
7 4 0.02
8 15 0.09
9 47 0.27
10 51 0.29
11 42 0.24
13 7 0.04
14 1 0.01
15 6 0.03
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:28016 original size:20 final size:19
Alignment explanation
Indices: 27900--28055 Score: 83
Period size: 20 Copynumber: 8.1 Consensus size: 19
27890 AAATATAGAT
*
27900 ATTATAAAAA-AATTTAATAA
1 ATTATAAAAATTA-TTAA-AA
27920 ATTATAAAAA--ATTATAAA
1 ATTATAAAAATTATTA-AAA
**
27938 ATTAATAAAACGTATTTAAAA
1 ATT-ATAAAAATTA-TTAAAA
*
27959 TATTATAAAAACGTATT-AAA
1 -ATTATAAAAA-TTATTAAAA
* *
27979 TTCTATAAAAATCA-TAAAA
1 AT-TATAAAAATTATTAAAA
27998 ATTATAGAAAATTATT-AAA
1 ATTATA-AAAATTATTAAAA
* * *
28017 AGTATTAAAATTAATATAAA
1 ATTATAAAAATTATTA-AAA
*
28037 CTTATAAAAATTA-TAAAA
1 ATTATAAAAATTATTAAAA
28055 A
1 A
28056 CTTGAATTGG
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
18 24 0.22
19 29 0.27
20 35 0.32
21 12 0.11
22 9 0.08
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTATAAAAATTATTAAAA
Found at i:28016 original size:29 final size:28
Alignment explanation
Indices: 27982--28055 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
27972 TATTAAATTC
27982 TATAAAAATCATAAAAATT-ATAGAAAAT
1 TATAAAAAT-ATAAAAATTAATAGAAAAT
* * * *
28010 TATTAAAAGTATTAAAATTAATATAAACT
1 TA-TAAAAATATAAAAATTAATAGAAAAT
28039 TATAAAAATTATAAAAA
1 TATAAAAA-TATAAAAA
28056 CTTGAATTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
TATAAAAATATAAAAATTAATAGAAAAT
Found at i:31876 original size:14 final size:13
Alignment explanation
Indices: 31844--31883 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
31834 AAAAACCCAT
31844 AAAAA-TTATAAA
1 AAAAATTTATAAA
*
31856 CAAAATTTATAACA
1 AAAAATTTATAA-A
31870 AAAAATTTATAAA
1 AAAAATTTATAAA
31883 A
1 A
31884 TTATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATTTATAAA
Found at i:45531 original size:34 final size:34
Alignment explanation
Indices: 45493--45561 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
45483 TTAATAAGAT
45493 TGGTTTCTGTCAATTCCCCTGTTAGAACTCATAC
1 TGGTTTCTGTCAATTCCCCTGTTAGAACTCATAC
45527 TGGTTTCTGTCAATTCCCCTGTTAGAACTCATAC
1 TGGTTTCTGTCAATTCCCCTGTTAGAACTCATAC
45561 T
1 T
45562 ATGATCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.39
Consensus pattern (34 bp):
TGGTTTCTGTCAATTCCCCTGTTAGAACTCATAC
Found at i:47706 original size:183 final size:185
Alignment explanation
Indices: 47396--47763 Score: 668
Period size: 183 Copynumber: 2.0 Consensus size: 185
47386 AACAAGGAAC
* *
47396 CTTGGTCACTTTAAAGACTGTTTCAATAAATGTTATGTGCAATTGGTTAGATTATGCCACATAAA
1 CTTGGTCACTTTAAAGACTGTTTCAATAAATGTTACGTGAAATTGGTTAGATTATGCCACATAAA
* *
47461 AAAGCACAGTTTGCAACTATTCCTACTATATTTGATATCATGCTTTAGAATAGGAAAACAAACTC
66 AAAGAACAGTTTGCAACTATTCCTACTATATGTGATATCATGCTTTAGAATAGGAAAACAAACTC
*
47526 AAGAGAGTAAAATCAAGTAATTAAACTTCTGCAGAATACGAGCAATTAACCAGAG
131 AAGAGAGTAAAATCAAGCAATTAAACTTCTGCAGAATACGAGCAATTAACCAGAG
*
47581 CTTGGTCACTTTAAGGACTGTTTCAATAAATGTTACGTGAAATTGGTTAGATTATGCCACA-AAA
1 CTTGGTCACTTTAAAGACTGTTTCAATAAATGTTACGTGAAATTGGTTAGATTATGCCACATAAA
47645 AAA-AACAGTTTGCAACTATTCCTACTATATGTGATATCATGCTTTAGAATAGGAAAACAAACTC
66 AAAGAACAGTTTGCAACTATTCCTACTATATGTGATATCATGCTTTAGAATAGGAAAACAAACTC
47709 AAGAGAGTAAAATCAAGCAATTAAACTTCTGCAGAATACGAGCAATTAACCAGAG
131 AAGAGAGTAAAATCAAGCAATTAAACTTCTGCAGAATACGAGCAATTAACCAGAG
47764 GGTCAATTTA
Statistics
Matches: 177, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 113 0.64
184 6 0.03
185 58 0.33
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (185 bp):
CTTGGTCACTTTAAAGACTGTTTCAATAAATGTTACGTGAAATTGGTTAGATTATGCCACATAAA
AAAGAACAGTTTGCAACTATTCCTACTATATGTGATATCATGCTTTAGAATAGGAAAACAAACTC
AAGAGAGTAAAATCAAGCAATTAAACTTCTGCAGAATACGAGCAATTAACCAGAG
Found at i:54930 original size:22 final size:23
Alignment explanation
Indices: 54905--54947 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
54895 AAAAAATTAC
54905 AAAATAATCATT-AAATTATTTG
1 AAAATAATCATTAAAATTATTTG
**
54927 AAAATTTTCATTAAAATTATT
1 AAAATAATCATTAAAATTATT
54948 GAATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAATAATCATTAAAATTATTTG
Found at i:54954 original size:31 final size:31
Alignment explanation
Indices: 54910--54979 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
54900 ATTACAAAAT
*
54910 AATCATTAAATTATTTGAAAATTTTCATTAA
1 AATCATTGAATTATTTGAAAATTTTCATTAA
* * * *
54941 AATTATTGAATTATTTTAAAATTTTTATTTA
1 AATCATTGAATTATTTGAAAATTTTCATTAA
54972 AATCATTG
1 AATCATTG
54980 GGATTTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (31 bp):
AATCATTGAATTATTTGAAAATTTTCATTAA
Done.