Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011626.1 Kokia drynarioides strain JFW-HI SEQ_126617, 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: 41142
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:150 original size:20 final size:20
Alignment explanation
Indices: 120--174 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
110 CAGCCCGAAT
* *
120 ACACCGGCACAAAGCCTGAT
1 ACACCGACACAAAGCCTGAA
*
140 ACATCGACACAAAGCCTGAA
1 ACACCGACACAAAGCCTGAA
*
160 ACACCGGCACAAAGC
1 ACACCGACACAAAGC
175 TTGGATACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.35, G:0.18, T:0.07
Consensus pattern (20 bp):
ACACCGACACAAAGCCTGAA
Found at i:3698 original size:18 final size:18
Alignment explanation
Indices: 3675--3739 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
3665 GATAATATAT
*
3675 ATGTGATGAAAAATGTAC
1 ATGTGATGAAAAATGTAA
* *
3693 ATGTGAAGAGAAATGTAA
1 ATGTGATGAAAAATGTAA
*
3711 ATGTGATGAATAAATTGTGA
1 ATGTGATGAA-AAA-TGTAA
3731 ATGATGATG
1 ATG-TGATG
3740 TTAAATGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 23 0.61
19 3 0.08
20 7 0.18
21 5 0.13
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.29
Consensus pattern (18 bp):
ATGTGATGAAAAATGTAA
Found at i:4521 original size:18 final size:18
Alignment explanation
Indices: 4498--4551 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
4488 TATGATAATA
4498 TATATGTGATGAAAAATG
1 TATATGTGATGAAAAATG
* *
4516 TATATGTGAAGAGAAATG
1 TATATGTGATGAAAAATG
*
4534 TAAATGTGATGAATAAAT
1 TATATGTGATGAA-AAAT
4552 TGTGAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.31
Consensus pattern (18 bp):
TATATGTGATGAAAAATG
Found at i:4673 original size:23 final size:22
Alignment explanation
Indices: 4643--4794 Score: 169
Period size: 23 Copynumber: 6.5 Consensus size: 22
4633 ACACTAGCGC
*
4643 GCCCTCTGTTTAGCACGTTTTGT
1 GCCCTCTGTTTAGCAC-TTGTGT
4666 GCCCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGTTTAGCACT-TGTGT
4689 GCCCTCTGTTATTAGCACTTCGTGT
1 GCCCTCTG-T-TTAGCACTT-GTGT
*
4714 GCCCTCTGATTAGCACTTCGTGT
1 GCCCTCTGTTTAGCACTT-GTGT
*
4737 GCCCTCTGATTAGCACTTTGTGT
1 GCCCTCTGTTTAGCAC-TTGTGT
* *
4760 GCCCTCTGTTACCCAGCACTTATGT
1 GCCCTCTGTT---TAGCACTTGTGT
4785 GCCCTCTGTT
1 GCCCTCTGTT
4795 AAGTACTTCG
Statistics
Matches: 116, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
22 1 0.01
23 71 0.61
24 4 0.03
25 35 0.30
26 5 0.04
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (22 bp):
GCCCTCTGTTTAGCACTTGTGT
Found at i:4715 original size:48 final size:45
Alignment explanation
Indices: 4643--4793 Score: 171
Period size: 48 Copynumber: 3.2 Consensus size: 45
4633 ACACTAGCGC
*
4643 GCCCTCTGT-TTAGCACGTTTTGTGCCCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGTATTAGCAC-TTGTGTGCCCTCTGTTTAGCACT-TGTGT
*
4689 GCCCTCTGTTATTAGCACTTCGTGTGCCCTCTGATTAGCACTTCGTGT
1 GCCCTCTG-TATTAGCACTT-GTGTGCCCTCTGTTTAGCACTT-GTGT
* *
4737 GCCCTCTG-ATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATGT
1 GCCCTCTGTATTAGCAC-TTGTGTGCCCTCTGTT---TAGCACTTGTGT
4785 GCCCTCTGT
1 GCCCTCTGT
4794 TAAGTACTTC
Statistics
Matches: 91, Mismatches: 5, Indels: 15
0.82 0.05 0.14
Matches are distributed among these distances:
46 29 0.32
47 6 0.07
48 49 0.54
49 7 0.08
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (45 bp):
GCCCTCTGTATTAGCACTTGTGTGCCCTCTGTTTAGCACTTGTGT
Found at i:4804 original size:71 final size:71
Alignment explanation
Indices: 4643--4792 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 71
4633 ACACTAGCGC
* * * **
4643 GCCCTCTGTTTAGCACGTT-TTGTGCCCTCTGTTTAGCACTGTGTGTGCCCTCTGTTATTAGCAC
1 GCCCTCTGATTAGCAC-TTCGTGTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTTACCAGCAC
*
4707 TTCGTGT
65 TTCATGT
*
4714 GCCCTCTGATTAGCACTTCGTGTGCCCTCTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCAC
1 GCCCTCTGATTAGCACTTCGTGTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTTA-CCAGCAC
4779 TT-ATGT
65 TTCATGT
4785 GCCCTCTG
1 GCCCTCTG
4793 TTAAGTACTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
70 2 0.03
71 61 0.87
72 7 0.10
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.37
Consensus pattern (71 bp):
GCCCTCTGATTAGCACTTCGTGTGCCCTCTGATTAGCACTGTGTGTGCCCTCTGTTACCAGCACT
TCATGT
Found at i:7034 original size:6 final size:6
Alignment explanation
Indices: 7009--7053 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
6999 GCAATTCATA
* * *
7009 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
7054 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:12283 original size:19 final size:19
Alignment explanation
Indices: 12259--12301 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12249 TTTACTTAAA
*
12259 AAATAT-AAAATAAATATAT
1 AAATATGAAAA-AAAGATAT
12278 AAATATGAAAAAAAGATAT
1 AAATATGAAAAAAAGATAT
*
12297 CAATA
1 AAATA
12302 ATAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATATGAAAAAAAGATAT
Found at i:20391 original size:16 final size:17
Alignment explanation
Indices: 20367--20407 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
20357 TCAAATATAT
20367 TATTAAAAATATTAATA
1 TATTAAAAATATTAATA
20384 TATT-AAAATATTAAT-
1 TATTAAAAATATTAATA
*
20399 TTTTAAAAA
1 TATTAAAAA
20408 CTTATTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAAAATATTAATA
Found at i:32513 original size:12 final size:12
Alignment explanation
Indices: 32480--32513 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32470 ATATATTGTG
*
32480 TTTTAAAATTAT
1 TTTTAAAAATAT
*
32492 TTTTATAAATAT
1 TTTTAAAAATAT
32504 TTTTAAAAAT
1 TTTTAAAAAT
32514 TAATATTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:32823 original size:19 final size:20
Alignment explanation
Indices: 32772--32826 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
32762 AGTAAAATTA
32772 TAAAAATATTTT-TTTATAAT
1 TAAAAATATTTTATTT-TAAT
**
32792 T-AAAATAAATTATTTT-AT
1 TAAAAATATTTTATTTTAAT
32810 TAAAAATATTTTATTTT
1 TAAAAATATTTTATTTT
32827 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 3 0.10
19 22 0.76
20 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAATATTTTATTTTAAT
Found at i:32828 original size:21 final size:21
Alignment explanation
Indices: 32772--32837 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 21
32762 AGTAAAATTA
* *
32772 TAAAAATATTTT-TTTATAAT
1 TAAAAATATTTTATTTTTTAT
**
32792 T-AAAATAAATTA--TTTTAT
1 TAAAAATATTTTATTTTTTAT
32810 TAAAAATATTTTATTTTTTATT
1 TAAAAATATTTTATTTTTTA-T
32832 TAAAAA
1 TAAAAA
32838 ATAATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 5 0.14
19 17 0.49
20 1 0.03
21 5 0.14
22 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAAATATTTTATTTTTTAT
Found at i:33796 original size:27 final size:27
Alignment explanation
Indices: 33778--33830 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
33768 AATAGTATAA
33778 ATTTAGTTTAATTTTGTAAAAATAAAT
1 ATTTAGTTTAATTTTGTAAAAATAAAT
*
33805 ATTTAGTTTAATTTTGAAAAAATAAA
1 ATTTAGTTTAATTTTGTAAAAATAAA
33831 ATAAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (27 bp):
ATTTAGTTTAATTTTGTAAAAATAAAT
Found at i:38844 original size:10 final size:10
Alignment explanation
Indices: 38831--38874 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
38821 AAAAACCATA
38831 AAAATTTATT
1 AAAATTTATT
38841 AAAA-TTATT
1 AAAATTTATT
*
38850 AAAAATTATT
1 AAAATTTATT
*
38860 AGAAATTAATT
1 A-AAATTTATT
38871 AAAA
1 AAAA
38875 ATCAAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.30
10 13 0.43
11 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAATTTATT
Found at i:38852 original size:20 final size:22
Alignment explanation
Indices: 38829--38876 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
38819 TAAAAAACCA
38829 TAAAAATTTATTA-AAATT-AT
1 TAAAAATTTATTAGAAATTAAT
38849 TAAAAA-TTATTAGAAATTAAT
1 TAAAAATTTATTAGAAATTAAT
38870 TAAAAAT
1 TAAAAAT
38877 CAAGAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 11 0.44
21 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAAATTTATTAGAAATTAAT
Found at i:39238 original size:18 final size:18
Alignment explanation
Indices: 39197--39266 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
39187 AATCTGATTA
*
39197 TTTTTAATTAATTTCTAAT
1 TTTTTTATTAATTT-TAAT
*
39216 GTTTTTATTAATTTTAAT
1 TTTTTTATTAATTTTAAT
39234 TTTTTT-TATAATTTTAAT
1 TTTTTTAT-TAATTTTAAT
* *
39252 TATTTTAATAATTTT
1 TTTTTTATTAATTTT
39267 TTATGTGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.02
18 31 0.70
19 12 0.27
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTTTTATTAATTTTAAT
Found at i:39248 original size:8 final size:9
Alignment explanation
Indices: 39198--39266 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
39188 ATCTGATTAT
39198 TTTTAATTAA
1 TTTTAA-TAA
**
39208 TTTCTAATGT
1 TTT-TAATAA
*
39218 TTTTATTAA
1 TTTTAATAA
**
39227 TTTTAATTT
1 TTTTAATAA
*
39236 TTTTTATAA
1 TTTTAATAA
*
39245 TTTTAATTA
1 TTTTAATAA
39254 TTTTAATAA
1 TTTTAATAA
39263 TTTT
1 TTTT
39267 TTATGTGTTT
Statistics
Matches: 44, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
9 34 0.77
10 7 0.16
11 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTAATAA
Found at i:39266 original size:28 final size:28
Alignment explanation
Indices: 39217--39270 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
39207 ATTTCTAATG
* *
39217 TTTTTATTAATTTTAATTTTTTTTATAA
1 TTTTAATTAATTTTAATATTTTTTATAA
39245 TTTTAATT-ATTTTAATAATTTTTTAT
1 TTTTAATTAATTTTAAT-ATTTTTTAT
39271 GTGTTTTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTAATTAATTTTAATATTTTTTATAA
Done.