Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010846.1 Kokia drynarioides strain JFW-HI SEQ_125813, 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: 69634
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:5995 original size:13 final size:13
Alignment explanation
Indices: 5979--6005 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5969 AATATCTTTA
5979 TAAAATTTCATAT
1 TAAAATTTCATAT
5992 TAAAATTTCATAT
1 TAAAATTTCATAT
6005 T
1 T
6006 TATTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAAATTTCATAT
Found at i:8624 original size:24 final size:25
Alignment explanation
Indices: 8573--8646 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
8563 AAACAAAGGG
**
8573 AGAAGCAAAAG-AGAATGAAAAAAAAA
1 AGAA-CAAAAGAAGAA-GAAAAATTAA
8599 AGAA-AAAAGAAGAAGAAAAATTAA
1 AGAACAAAAGAAGAAGAAAAATTAA
*
8623 AGAACATAA-AAGAA-AAAAATTAA
1 AGAACAAAAGAAGAAGAAAAATTAA
8646 A
1 A
8647 TTGCTCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 10 0.23
24 22 0.51
25 7 0.16
26 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (25 bp):
AGAACAAAAGAAGAAGAAAAATTAA
Found at i:27127 original size:23 final size:25
Alignment explanation
Indices: 27101--27146 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
27091 CAGAAAATTG
27101 TATTTTATTA-TTTT-AATAATTTA
1 TATTTTATTATTTTTAAATAATTTA
27124 TATTTTATTATTTTTAAATAATT
1 TATTTTATTATTTTTAAATAATT
27147 AAATTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTATTATTTTTAAATAATTTA
Found at i:28108 original size:21 final size:20
Alignment explanation
Indices: 28069--28108 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28059 TCCATCTTTA
* *
28069 ACCGTTACAGTGTTGACATT
1 ACCGTTACAATGCTGACATT
28089 ACCGTTAACAATGCTGACAT
1 ACCGTT-ACAATGCTGACAT
28109 AACGCTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (20 bp):
ACCGTTACAATGCTGACATT
Found at i:28192 original size:20 final size:21
Alignment explanation
Indices: 28164--28202 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28154 AGTTGTCATG
* *
28164 TTAACAAAA-AAAATATTTTT
1 TTAAAAAAATAAAAAATTTTT
28184 TTAAAAAAATAAAAAATTT
1 TTAAAAAAATAAAAAATTT
28203 AATGAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAAAATAAAAAATTTTT
Found at i:31952 original size:18 final size:18
Alignment explanation
Indices: 31929--31971 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31919 GAATATGTTT
31929 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
31947 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
31965 TTAATTA
1 TTAATTA
31972 CATATTGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:36834 original size:23 final size:22
Alignment explanation
Indices: 36808--36870 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 22
36798 TTTAAACAAT
36808 ATAAATTCAAATTTAAAAAATAA
1 ATAAATT-AAATTTAAAAAATAA
36831 AT--A--AAATTTAAAAAATAA
1 ATAAATTAAATTTAAAAAATAA
*
36849 A-AATATTAAAATTTATAAAATA
1 ATAA-ATT-AAATTTAAAAAATA
36871 TATGAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 16 0.48
20 1 0.03
21 1 0.03
23 15 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAATTAAATTTAAAAAATAA
Found at i:38421 original size:12 final size:11
Alignment explanation
Indices: 38393--38427 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
38383 TCATTAATAA
38393 ATAAACGAGTC
1 ATAAACGAGTC
*
38404 ATAAACGAGCTT
1 ATAAACGAG-TC
38416 ATAAACGAGTC
1 ATAAACGAGTC
38427 A
1 A
38428 ACAAATGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (11 bp):
ATAAACGAGTC
Found at i:38423 original size:23 final size:24
Alignment explanation
Indices: 38393--38447 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
38383 TCATTAATAA
*
38393 ATAAACGAGTC-ATAAACGAGCTT
1 ATAAACGAGTCAACAAACGAGCTT
*
38416 ATAAACGAGTCAACAAATGAGCTT
1 ATAAACGAGTCAACAAACGAGCTT
*
38440 TTAAACGA
1 ATAAACGA
38448 ACGAACACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (24 bp):
ATAAACGAGTCAACAAACGAGCTT
Found at i:41153 original size:5 final size:5
Alignment explanation
Indices: 41143--41172 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
41133 TAAAAAAACT
41143 TAAAA TAAAA TAAAA TAAAA TAAATA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TAAA
41173 TATGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:50305 original size:38 final size:38
Alignment explanation
Indices: 50253--50332 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
50243 TGACTATCAC
50253 CCCACCGCGCGCTTTCAATCCTTTCACACAGCCATTGG
1 CCCACCGCGCGCTTTCAATCCTTTCACACAGCCATTGG
*
50291 CCCACCGCGTGCTTTCAATCCTTTCACACAGCCATTGG
1 CCCACCGCGCGCTTTCAATCCTTTCACACAGCCATTGG
50329 CCCA
1 CCCA
50333 TTTATCCTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.19, C:0.42, G:0.15, T:0.24
Consensus pattern (38 bp):
CCCACCGCGCGCTTTCAATCCTTTCACACAGCCATTGG
Found at i:51585 original size:33 final size:34
Alignment explanation
Indices: 51513--51587 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
51503 TTTCAAGCTC
51513 AGTATGTACTGTAAGTTTTCAAACTCAAGAAATT
1 AGTATGTACTGTAAGTTTTCAAACTCAAGAAATT
* * *
51547 AGTATGTATTTTAAGTTTTCAAACTGAAG-AATT
1 AGTATGTACTGTAAGTTTTCAAACTCAAGAAATT
51580 AGTATGTA
1 AGTATGTA
51588 AAAATGACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 12 0.32
34 26 0.68
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (34 bp):
AGTATGTACTGTAAGTTTTCAAACTCAAGAAATT
Found at i:52826 original size:25 final size:20
Alignment explanation
Indices: 52800--52956 Score: 215
Period size: 20 Copynumber: 7.8 Consensus size: 20
52790 ACTCGCCGTT
*
52800 CCGTTCCGTTCCATTAATCG
1 CCGTTCCGTTCCGTTAATCG
52820 CCGTTCCGTTCCGTTAATCG
1 CCGTTCCGTTCCGTTAATCG
52840 CCGTTCCGTTCCGTTAATCG
1 CCGTTCCGTTCCGTTAATCG
52860 CCGTTCCGTTCCGTTAATCG
1 CCGTTCCGTTCCGTTAATCG
*
52880 CTGTTCCGTTCCGTTAATCG
1 CCGTTCCGTTCCGTTAATCG
* **
52900 CCGTTCAGTTCATTTAATCG
1 CCGTTCCGTTCCGTTAATCG
* ** *
52920 CCGTTCAGTTCATTTAATCT
1 CCGTTCCGTTCCGTTAATCG
* *
52940 TCGTTCAGTTCCGTTAA
1 CCGTTCCGTTCCGTTAA
52957 CATAAAAAAG
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 127 1.00
ACGTcount: A:0.14, C:0.31, G:0.17, T:0.38
Consensus pattern (20 bp):
CCGTTCCGTTCCGTTAATCG
Found at i:55172 original size:6 final size:6
Alignment explanation
Indices: 55161--55232 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
55151 ACCCCAACAG
* * *
55161 AATTTA AATTT- -ATTTA AGTTTA AATTT- ACTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
55205 -ATTATA AATTTA AGTTTA AATTTA AATT
1 AATT-TA AATTTA AATTTA AATTTA AATT
55233 AATGTCCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 7 0.13
5 4 0.08
6 38 0.73
7 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:55184 original size:16 final size:16
Alignment explanation
Indices: 55161--55232 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
55151 ACCCCAACAG
55161 AATTTAAATTTATTTA
1 AATTTAAATTTATTTA
* *
55177 AGTTTAAATTTACTTAA
1 AATTTAAATTTA-TTTA
55194 AATTTAAATTTATTATA
1 AATTTAAATTTATT-TA
*
55211 AATTTAAGTTTAAATTTA
1 AATTTAAATTT--ATTTA
55229 AATT
1 AATT
55233 AATGTCCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
16 13 0.28
17 25 0.53
18 6 0.13
19 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:55226 original size:12 final size:11
Alignment explanation
Indices: 55161--55234 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
55151 ACCCCAACAG
55161 AATTTAAATTT
1 AATTTAAATTT
*
55172 -ATTTAAGTTT
1 AATTTAAATTT
* *
55182 AAATTT-ACTTAA
1 -AATTTAAATT-T
55194 AATTTAAATTT
1 AATTTAAATTT
55205 -ATTATAAATTT
1 AATT-TAAATTT
55216 AAGTTTAAATTT
1 AA-TTTAAATTT
*
55228 AAATTAA
1 AATTTAA
55235 TGTCCAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
10 12 0.24
11 19 0.38
12 17 0.34
13 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:57165 original size:30 final size:29
Alignment explanation
Indices: 57093--57320 Score: 132
Period size: 29 Copynumber: 7.8 Consensus size: 29
57083 GGAGACCTCG
* *
57093 AAACTTCCAAAAATTACATTTTTACCC-A
1 AAACTTCTAAAAATTCCATTTTTACCCTA
57121 TAAACTTCTAAAAATTCCATTTTTAACCCTA
1 -AAACTTCTAAAAATTCCATTTTT-ACCCTA
* * * *
57152 AAACTTTTGAAAATTACCATTATTA-CCTC
1 AAACTTCTAAAAATT-CCATTTTTACCCTA
* *
57181 GAACTTCTAAAAATTCCATTTTTGA-CCTCG
1 AAACTTCTAAAAATTCCATTTTT-ACCCT-A
*
57211 AAACATTC-AAAAATTACCA-TTTTACCCTC
1 AAAC-TTCTAAAAATT-CCATTTTTACCCTA
** * * **
57240 GGA-TGTCCAAAAATTCCATTTTGACCCCG
1 AAACT-TCTAAAAATTCCATTTTTACCCTA
*
57269 AAACTT-TCAAAAATTACCA-TTTTACCCTC
1 AAACTTCT-AAAAATT-CCATTTTTACCCTA
* *
57298 AGA-TGTCTAAAAATTCCGTTTTT
1 AAACT-TCTAAAAATTCCATTTTT
57321 GATCCCGATT
Statistics
Matches: 156, Mismatches: 26, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.01
28 15 0.10
29 86 0.55
30 40 0.26
31 14 0.09
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (29 bp):
AAACTTCTAAAAATTCCATTTTTACCCTA
Found at i:57186 original size:59 final size:59
Alignment explanation
Indices: 57092--57410 Score: 248
Period size: 59 Copynumber: 5.4 Consensus size: 59
57082 TGGAGACCTC
* * *
57092 GAAACTTCCAAAAATTA-CATTTTTACCCAT-AAACT-TCTAAAAATTCCATTTTTAACCCT
1 GAAACTTTCAAAAATTACCA-TTTTACCC-TCGAA-TGTCTAAAAATTCCATTTTTGACCCT
* **
57151 AAAACTTTTGAAAATTACCATTATTA-CCTCGAACT-TCTAAAAATTCCATTTTTGA-CCT
1 GAAACTTTCAAAAATTACCATT-TTACCCTCGAA-TGTCTAAAAATTCCATTTTTGACCCT
* * * *
57209 CGAAACATTCAAAAATTACCATTTTACCCTCGGATGTCCAAAAATTCCA-TTTTGACCCC
1 -GAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCT
*
57268 GAAACTTTCAAAAATTACCATTTTACCCTC-AGATGTCTAAAAATTCCGTTTTTGATCCC-
1 GAAACTTTCAAAAATTACCATTTTACCCTCGA-ATGTCTAAAAATTCCATTTTTGA-CCCT
*** *** * *
57327 GATTTTTTTCTAAAAATTATTGTTTTACCCTCAAATGTCT-AAAATGT-CATTTTTAACCC-
1 GA-AACTTTC-AAAAATTACCATTTTACCCTCGAATGTCTAAAAAT-TCCATTTTTGACCCT
* * *
57386 CAAATTTTTCCAAAATTACCATTTT
1 GAAA-CTTTCAAAAATTACCATTTT
57411 GCCCCCTCGA
Statistics
Matches: 213, Mismatches: 32, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
58 68 0.32
59 95 0.45
60 24 0.11
61 25 0.12
62 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (59 bp):
GAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCT
Done.