Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009984.1 Kokia drynarioides strain JFW-HI SEQ_124736, 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: 36904
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:10 original size:4 final size:4
Alignment explanation
Indices: 2--67 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
1 C
* * * *
2 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
50 CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT CTTT C
68 CCGTTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.81
5 7 0.13
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:36 original size:17 final size:15
Alignment explanation
Indices: 2--68 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 15
1 C
2 CTTTCTTTCCTTCTT
1 CTTTCTTTCCTTCTT
17 CTTTCTTTCC-TC-T
1 CTTTCTTTCCTTCTT
*
30 CCTTC-TTCCTTTCTTT
1 CTTTCTTTCC-TTC-TT
46 CTTTCTTTCC-T-TT
1 CTTTCTTTCCTTCTT
59 CTTTCTTTCC
1 CTTTCTTTCC
69 CGTTTATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 4 0.09
13 17 0.38
14 4 0.09
15 11 0.24
16 5 0.11
17 4 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:48 original size:29 final size:27
Alignment explanation
Indices: 8--65 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
1 CCTTTCT
8 TTCCTTCTTCTTTCTTTCCTCTCCTTC
1 TTCCTTCTTCTTTCTTTCCTCTCCTTC
* *
35 TTCCTTTCTTTCTTTCTTTCCTTTCTTTC
1 TTCC-TTC-TTCTTTCTTTCCTCTCCTTC
64 TT
1 TT
66 TCCCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 20 0.74
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (27 bp):
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Found at i:1422 original size:23 final size:23
Alignment explanation
Indices: 1396--1451 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1386 TTATATGCCT
** *
1396 TTGTGGCATGCTTTTCTTTTGTC
1 TTGTGGCACACTTTTCCTTTGTC
1419 TTGTGGCACACTTTTCCTTTGTC
1 TTGTGGCACACTTTTCCTTTGTC
1442 TTGTGGCACA
1 TTGTGGCACA
1452 TTTCTGCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.48
Consensus pattern (23 bp):
TTGTGGCACACTTTTCCTTTGTC
Found at i:4166 original size:50 final size:52
Alignment explanation
Indices: 4081--4177 Score: 153
Period size: 50 Copynumber: 1.9 Consensus size: 52
4071 TCCTTGAGCC
*
4081 AAAAAAAAAATGTTTGAGTTTCAAAAAACAAATAATAATGTTTTATTTGAGT
1 AAAAAAAAAATGTTAGAGTTTCAAAAAACAAATAATAATGTTTTATTTGAGT
* *
4133 AAAAAAAAAAT-TTAGAGTTT-AAAGAATAAATAATAATGTTTTATT
1 AAAAAAAAAATGTTAGAGTTTCAAAAAACAAATAATAATGTTTTATT
4178 ATAAAACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
50 23 0.55
51 8 0.19
52 11 0.26
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (52 bp):
AAAAAAAAAATGTTAGAGTTTCAAAAAACAAATAATAATGTTTTATTTGAGT
Found at i:5813 original size:7 final size:7
Alignment explanation
Indices: 5801--5831 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5791 TTACTATCAC
5801 CAATTAA
1 CAATTAA
5808 CAATTAA
1 CAATTAA
5815 CAATTAA
1 CAATTAA
*
5822 CAATTGA
1 CAATTAA
5829 CAA
1 CAA
5832 CTTTAGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (7 bp):
CAATTAA
Found at i:9890 original size:17 final size:17
Alignment explanation
Indices: 9864--9926 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
9854 GGTCCAACAG
* *
9864 AATTTGAATTTATTTTA
1 AATTTAAATTTATTATA
**
9881 AATTTAAATTTATTGGA
1 AATTTAAATTTATTATA
*
9898 AATTTAAATTTATCATA
1 AATTTAAATTTATTATA
9915 AATTTAAATTTA
1 AATTTAAATTTA
9927 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:10175 original size:18 final size:19
Alignment explanation
Indices: 10148--10192 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
10138 CATGCTGCCA
* *
10148 CGTCAGCATCAATAGCC-C
1 CGTCACCATCAATAACCAC
*
10166 CGTCACCATCATTAACCAC
1 CGTCACCATCAATAACCAC
10185 CGTCACCA
1 CGTCACCA
10193 GTAAGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.18
Consensus pattern (19 bp):
CGTCACCATCAATAACCAC
Found at i:20388 original size:18 final size:18
Alignment explanation
Indices: 20365--20400 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20355 GCATCTAATA
*
20365 TTGTTCCTTATAATTATT
1 TTGTTCCTTATAAATATT
20383 TTGTTCCTTATAAATATT
1 TTGTTCCTTATAAATATT
20401 CGACAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (18 bp):
TTGTTCCTTATAAATATT
Found at i:20893 original size:49 final size:49
Alignment explanation
Indices: 20807--21093 Score: 294
Period size: 49 Copynumber: 5.9 Consensus size: 49
20797 TACAGGTTTC
* **
20807 AGTACCACGAAG-CATGAAAGGAAAGATTTAAACCGCAATGGCGAATCT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCT
* * * ** *
20855 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAACCT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCT
* * * *
20904 AGTACCTC-AGAGACATGAAGGGAAAGATTTAAGTCGTAAAGGCGAATCC
1 AGTACCACGA-AGACATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCT
** * * * *
20953 AGTACCACGAAGACACAAAAGGAAAGGTTTGAGTCGCAATGGCGAACCT
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCT
* *
21002 AGTACCTC-AGAGACATGAAGGGAAAGATTTAAG-CTGCAATGGCGAATCC
1 AGTACCACGA-AGACATGAAGGGAAAGATTTAAGTC-GCAATGGCGAATCT
** * *
21051 AGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCACAATGGC
1 AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGGC
21094 CAGAGCATGG
Statistics
Matches: 191, Mismatches: 41, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
48 15 0.08
49 173 0.91
50 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.16
Consensus pattern (49 bp):
AGTACCACGAAGACATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCT
Found at i:21055 original size:147 final size:146
Alignment explanation
Indices: 20806--21085 Score: 334
Period size: 147 Copynumber: 1.9 Consensus size: 146
20796 CTACAGGTTT
** * *
20806 CAGTACCACGAAGCATGAAAGGAAAGATTTAAACCGCAATGGCGAATCTAGTACCACGAAGATAT
1 CAGTACCACGAAGCACAAAAGGAAAGATTTAAACCGCAATGGCGAACCTAGTACCACGAAGACAT
* * * **
20871 GGAGGGAAAGGTTTAAGTCGCAACAGCGAACCTAGTACCTC-AGAGACATGAAGGGAAAGATTTA
66 GAAGGGAAAGATTTAAGTCGCAACAGCGAACCTAGTACCACGA-AGACACAAAGGGAAAGATTTA
20935 AGTCGTAAAGGCGAATC
130 AGTCGTAAAGGCGAATC
* * ** *
20952 CAGTACCACGAAGACACAAAAGGAAAGGTTTGAGTCGCAATGGCGAACCTAGTACCTC-AGAGAC
1 CAGTACCACGAAG-CACAAAAGGAAAGATTTAAACCGCAATGGCGAACCTAGTACCACGA-AGAC
** *
21016 ATGAAGGGAAAGATTTAAG-CTGCAATGGCGAATCC-AGTACCACGAAGACACAAAGGGAAAGGT
64 ATGAAGGGAAAGATTTAAGTC-GCAACAGCGAA-CCTAGTACCACGAAGACACAAAGGGAAAGAT
21079 TTAAGTC
127 TTAAGTC
21086 ACAATGGCCA
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
146 15 0.13
147 94 0.84
148 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (146 bp):
CAGTACCACGAAGCACAAAAGGAAAGATTTAAACCGCAATGGCGAACCTAGTACCACGAAGACAT
GAAGGGAAAGATTTAAGTCGCAACAGCGAACCTAGTACCACGAAGACACAAAGGGAAAGATTTAA
GTCGTAAAGGCGAATC
Found at i:21091 original size:98 final size:98
Alignment explanation
Indices: 20819--21093 Score: 399
Period size: 98 Copynumber: 2.8 Consensus size: 98
20809 TACCACGAAG
* * * * * ***
20819 CATGAAAGGAAAGATTTAAACCGCAATGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTT
**
20884 TAAGTCGCAACAGCGAACCTAGTACCTCAGAGA
66 TAAGTCGCAATGGCGAACCTAGTACCTCAGAGA
* * *
20917 CATGAAGGGAAAGATTTAAG-TCGTAAAGGCGAATCCAGTACCACGAAGACACAAAAGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCT-GCAATGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGT
*
20981 TTGAGTCGCAATGGCGAACCTAGTACCTCAGAGA
65 TTAAGTCGCAATGGCGAACCTAGTACCTCAGAGA
21015 CATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTT
*
21080 TAAGTCACAATGGC
66 TAAGTCGCAATGGC
21094 CAGAGCATGG
Statistics
Matches: 156, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
98 155 0.99
99 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (98 bp):
CATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTT
TAAGTCGCAATGGCGAACCTAGTACCTCAGAGA
Found at i:21746 original size:29 final size:28
Alignment explanation
Indices: 21714--22036 Score: 201
Period size: 29 Copynumber: 11.2 Consensus size: 28
21704 CAGAAATCAT
*
21714 ATTTTGACCTCAAATTCTCCAAAAATTAC
1 ATTTTTACCTCAAATT-TCCAAAAATTAC
* *
21743 ATTTTTTCC-CTAAACTTTCC-AAAATTCC
1 ATTTTTACCTC-AAA-TTTCCAAAAATTAC
21771 ATTTTTTACCTCAAATTTTCCAAAAATTAC
1 A-TTTTTACCTCAAA-TTTCCAAAAATTAC
* * *
21801 ATTTTTACCCCGAACTTTCC-AAAATTCC
1 ATTTTTACCTC-AAATTTCCAAAAATTAC
* * *
21829 CTTTTTAACCTTGAATTTTCCAAAAATTAC
1 ATTTTT-ACC-TCAAATTTCCAAAAATTAC
**
21859 ATTTTTACC-CTAAACTTTTTAAAAATTAC
1 ATTTTTACCTC-AAA-TTTCCAAAAATTAC
* *
21888 ATTTTTACCCCTAAACTTTCC-AAAATTTC
1 ATTTTTACCTC-AAA-TTTCCAAAAATTAC
** * *
21917 ATTTTGGCATCGAATTTTCCAAAAATTAC
1 ATTTTTACCTC-AAATTTCCAAAAATTAC
* * *
21946 ATTTTTCCCCCAAACTTTCC-AAAATTCC
1 ATTTTTACCTCAAA-TTTCCAAAAATTAC
* * ** *
21974 ATTTTGACCT-TAATTTTAAAAAAATAC
1 ATTTTTACCTCAAATTTCCAAAAATTAC
**
22001 ATTTTTACCCTCGAACCTTCCAAAAATTAC
1 ATTTTTA-CCTC-AAATTTCCAAAAATTAC
22031 TATTTT
1 -ATTTT
22037 ACCCTCGAAT
Statistics
Matches: 225, Mismatches: 50, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
26 3 0.01
27 14 0.06
28 47 0.21
29 111 0.49
30 45 0.20
31 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTTTTACCTCAAATTTCCAAAAATTAC
Found at i:21784 original size:58 final size:58
Alignment explanation
Indices: 21694--21921 Score: 248
Period size: 58 Copynumber: 3.9 Consensus size: 58
21684 TTGTAGGTCT
* * * *
21694 CTAAACTGTCCAGAAA-T-CATATTTTGACCTCAAATTCTCCAAAAATTACATTTTTTCC
1 CTAAACTTTCCA-AAATTCCAT-TTTTAACCTCAAATTTTCCAAAAATTACATTTTTACC
*
21752 CTAAACTTTCCAAAATTCCATTTTTTACCTCAAATTTTCCAAAAATTACATTTTTACC
1 CTAAACTTTCCAAAATTCCATTTTTAACCTCAAATTTTCCAAAAATTACATTTTTACC
** * **
21810 CCGAACTTTCCAAAATTCCCTTTTTAACCTTGAATTTTCCAAAAATTACATTTTTACC
1 CTAAACTTTCCAAAATTCCATTTTTAACCTCAAATTTTCCAAAAATTACATTTTTACC
** * * * *
21868 CTAAACTTTTTAAAAATTACATTTTT-ACCCCTAAACTTTCC-AAAATTTCATTTT
1 CTAAAC-TTTCCAAAATTCCATTTTTAACCTC-AAATTTTCCAAAAATTACATTTT
21922 GGCATCGAAT
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
57 3 0.02
58 117 0.81
59 25 0.17
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (58 bp):
CTAAACTTTCCAAAATTCCATTTTTAACCTCAAATTTTCCAAAAATTACATTTTTACC
Found at i:21864 original size:87 final size:86
Alignment explanation
Indices: 21758--21978 Score: 252
Period size: 87 Copynumber: 2.5 Consensus size: 86
21748 TTCCCTAAAC
* *
21758 TTTCC-AAAATTCCATTTTTTACCTCAAATTTTCCAAAAATTACATTTTTACCCC-GAACTTTCC
1 TTTCCAAAAATTACA-TTTTTACC-CAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCC
* * *
21821 AAAATTCCCTTTTTAACCTTGAAT
64 AAAATT-CCATTTTAACATCGAAT
*
21845 TTTCCAAAAATTACATTTTTACCCTAAACTTTT-TAAAAATTACATTTTTACCCCTAAACTTTCC
1 TTTCCAAAAATTACATTTTTACCC-AAA-TTTTCCAAAAATTACATTTTTACCCCTAAACTTTCC
* **
21909 AAAATTTCATTTTGGCATCGAAT
64 AAAATTCCATTTTAACATCGAAT
* * *
21932 TTTCCAAAAATTACATTTTTCCCCCAAACTTTCC-AAAATTCCATTTT
1 TTTCCAAAAATTACATTTTT-ACCCAAATTTTCCAAAAATTACATTTT
21979 GACCTTAATT
Statistics
Matches: 115, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
86 16 0.14
87 70 0.61
88 29 0.25
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (86 bp):
TTTCCAAAAATTACATTTTTACCCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAA
AATTCCATTTTAACATCGAAT
Found at i:34134 original size:16 final size:17
Alignment explanation
Indices: 34113--34144 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34103 ATTAAAAGAC
34113 ATAAAAATATA-AAATA
1 ATAAAAATATATAAATA
34129 ATAAAAATATATAAAT
1 ATAAAAATATATAAAT
34145 TTGCATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATATATAAATA
Found at i:36778 original size:4 final size:4
Alignment explanation
Indices: 36757--36810 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
36747 GGGGACCAAC
* *
36757 GAAA GAAG GAAA -AAA GAAA GAAA -AAA AAAA GAAA GAAA GAAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
36804 GAAA GAA
1 GAAA GAA
36811 GGAGAAGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.14
4 34 0.77
5 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:36802 original size:9 final size:9
Alignment explanation
Indices: 36768--36807 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
36758 AAAGAAGGAA
36768 AAAAGAAAG
1 AAAAGAAAG
* *
36777 AAAAAAAAA
1 AAAAGAAAG
36786 AGAAAGAAAG
1 A-AAAGAAAG
36796 AAAAGAAAG
1 AAAAGAAAG
36805 AAA
1 AAA
36808 GAAGGAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:36808 original size:13 final size:12
Alignment explanation
Indices: 36765--36810 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
36755 ACGAAAGAAG
36765 GAAAAAAG-AAA
1 GAAAAAAGAAAA
36776 GAAAAAA-AAAA
1 GAAAAAAGAAAA
36787 GAAAGAAAGAAAA
1 GAAA-AAAGAAAA
36800 GAAAGAAAGAA
1 GAAA-AAAGAA
36811 GGAGAAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.44
12 3 0.09
13 15 0.47
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAAAA
Done.