Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012603.1 Kokia drynarioides strain JFW-HI SEQ_127612, 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: 28448
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2157 original size:19 final size:19
Alignment explanation
Indices: 2130--2166 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2120 TGCACCACGC
* *
2130 AATACAAATATAAAATTAT
1 AATAAAAATAGAAAATTAT
2149 AATAAAAATAGAAAATTA
1 AATAAAAATAGAAAATTA
2167 AAACAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAAAAATAGAAAATTAT
Found at i:2174 original size:19 final size:19
Alignment explanation
Indices: 2135--2174 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2125 CACGCAATAC
* * *
2135 AAATATAAAATTATAATAA
1 AAATAGAAAATTAAAACAA
2154 AAATAGAAAATTAAAACAA
1 AAATAGAAAATTAAAACAA
2173 AA
1 AA
2175 GGGAATGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATAGAAAATTAAAACAA
Found at i:14406 original size:19 final size:19
Alignment explanation
Indices: 14382--14427 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
14372 ATACAATAAG
14382 TTTTAATATAATTAA-TTTA
1 TTTTAATATAA-TAATTTTA
*
14401 TTTTAATATTATAATTTTA
1 TTTTAATATAATAATTTTA
*
14420 TTTGAATA
1 TTTTAATA
14428 ATAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAATATAATAATTTTA
Found at i:14434 original size:18 final size:19
Alignment explanation
Indices: 14389--14437 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
14379 AAGTTTTAAT
*
14389 ATAAT-TAA-TTTATTTTA
1 ATAATATAATTTTATTTGA
*
14406 ATATTATAATTTTATTTGA
1 ATAATATAATTTTATTTGA
14425 ATAATA-AATTTTA
1 ATAATATAATTTTA
14438 ATAGTAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 13 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATAATATAATTTTATTTGA
Found at i:14568 original size:23 final size:24
Alignment explanation
Indices: 14538--14590 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
14528 TTCAATAATA
14538 AATATTTTGTAA-TATA-AAATATG
1 AATATTTT-TAATTATATAAATATG
14561 AATA-TTTTAATTATATAAATATG
1 AATATTTTTAATTATATAAATATG
*
14584 AGTATTT
1 AATATTT
14591 CTTTAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 7 0.27
23 14 0.54
24 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (24 bp):
AATATTTTTAATTATATAAATATG
Found at i:14763 original size:18 final size:17
Alignment explanation
Indices: 14718--14769 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
14708 ATTATATTAA
**
14718 TTATTATAAAATATTATT
1 TTATTATAAAA-AAAATT
*
14736 TTATTATAAAATAAATT
1 TTATTATAAAAAAAATT
*
14753 TTGATTGTAAAAAAAAT
1 TT-ATTATAAAAAAAAT
14770 GCTACTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TTATTATAAAAAAAATT
Found at i:27420 original size:6 final size:6
Alignment explanation
Indices: 27399--27481 Score: 73
Period size: 6 Copynumber: 13.8 Consensus size: 6
27389 TAAAATTAGG
** *
27399 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATATT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-A-A
**
27448 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
27482 TCAAATTTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 46 0.75
7 4 0.07
8 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:27434 original size:17 final size:18
Alignment explanation
Indices: 27399--27480 Score: 96
Period size: 17 Copynumber: 4.6 Consensus size: 18
27389 TAAAATTAGG
*
27399 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTCTTAAA
27417 TTTAAATTTA-TCTTAAA
1 TTTAAATTTATTCTTAAA
*
27434 TTTAAATTTATATTTTTAAA
1 TTTAAA-TT-TATTCTTAAA
**
27454 TTTAAATTTGCT-TTAAA
1 TTTAAATTTATTCTTAAA
27471 TTTAAATTTA
1 TTTAAATTTA
27481 ATCAAATTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
17 26 0.46
18 14 0.25
19 4 0.07
20 12 0.21
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTCTTAAA
Found at i:27454 original size:37 final size:37
Alignment explanation
Indices: 27399--27480 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
27389 TAAAATTAGG
*
27399 TTTAAA-TT-TATTTTTAAATTTAAATTT-ATCTTAAA
1 TTTAAATTTATATTTTTAAATTTAAATTTGCT-TTAAA
27434 TTTAAATTTATATTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTATATTTTTAAATTTAAATTTGCTTTAAA
27471 TTTAAATTTA
1 TTTAAATTTA
27481 ATCAAATTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 6 0.14
36 2 0.05
37 34 0.79
38 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTAAATTTATATTTTTAAATTTAAATTTGCTTTAAA
Found at i:27539 original size:18 final size:18
Alignment explanation
Indices: 27516--27570 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
27506 GTAATATTTA
*
27516 AAATTAAAAGCCCAAATT
1 AAATTAAAAGTCCAAATT
*
27534 AAATTAAAAGTCCAAAAT
1 AAATTAAAAGTCCAAATT
27552 AAA-TACAAAGTCCAAATT
1 AAATTA-AAAGTCCAAATT
27570 A
1 A
27571 CAATCTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 2 0.06
18 31 0.94
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATTAAAAGTCCAAATT
Found at i:27769 original size:25 final size:26
Alignment explanation
Indices: 27737--27795 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
27727 ACCAGAGGCC
27737 GCCA-CATCATCAG-CAACTTGCACT
1 GCCACCATCATCAGCCAACTTGCACT
* *
27761 GCCACCATCTTCAGCCTCAACTTGCATT
1 GCCACCATCATCAG-C-CAACTTGCACT
27789 GCCACCA
1 GCCACCA
27796 GCTGCTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 8 0.28
28 17 0.59
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (26 bp):
GCCACCATCATCAGCCAACTTGCACT
Found at i:28226 original size:3 final size:3
Alignment explanation
Indices: 28220--28301 Score: 67
Period size: 3 Copynumber: 27.3 Consensus size: 3
28210 ATTATTATGG
* * * * *
28220 TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA TAA TAT TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
** * *
28265 CGA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28302 GACATTAATT
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:28244 original size:18 final size:18
Alignment explanation
Indices: 28220--28301 Score: 83
Period size: 18 Copynumber: 4.4 Consensus size: 18
28210 ATTATTATGG
28220 TAATAATAATAATAATAT
1 TAATAATAATAATAATAT
*
28238 TACTAATATCATTAATAATAT
1 TAATAATA--A-TAATAATAT
* ** *
28259 TAATGACGATAATAATAA
1 TAATAATAATAATAATAT
*
28277 TAATATTAATAATAATAT
1 TAATAATAATAATAATAT
28295 TAATAAT
1 TAATAAT
28302 GACATTAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
18 34 0.69
19 1 0.02
20 1 0.02
21 13 0.27
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (18 bp):
TAATAATAATAATAATAT
Found at i:28300 original size:9 final size:9
Alignment explanation
Indices: 28194--28301 Score: 60
Period size: 9 Copynumber: 12.0 Consensus size: 9
28184 TCAAAATGTC
28194 ATTAATAAT
1 ATTAATAAT
*
28203 ATTATTAATT
1 ATTAATAA-T
**
28213 ATT-ATGGT
1 ATTAATAAT
*
28221 AATAATAAT
1 ATTAATAAT
* *
28230 AATAATATT
1 ATTAATAAT
*
28239 ACTAAT-AT
1 ATTAATAAT
28247 CATTAATAAT
1 -ATTAATAAT
**
28257 ATTAATGACG
1 ATTAAT-AAT
28267 A-TAATAAT
1 ATTAATAAT
* *
28275 AATAATATT
1 ATTAATAAT
*
28284 AATAATAAT
1 ATTAATAAT
28293 ATTAATAAT
1 ATTAATAAT
28302 GACATTAATT
Statistics
Matches: 75, Mismatches: 18, Indels: 12
0.71 0.17 0.11
Matches are distributed among these distances:
8 6 0.08
9 61 0.81
10 8 0.11
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (9 bp):
ATTAATAAT
Found at i:28310 original size:12 final size:12
Alignment explanation
Indices: 28194--28301 Score: 81
Period size: 12 Copynumber: 8.8 Consensus size: 12
28184 TCAAAATGTC
*
28194 ATTAATAATATT
1 ATTAATAATAAT
* *
28206 ATTAATTATTAT
1 ATTAATAATAAT
**
28218 GGTAATAATAAT
1 ATTAATAATAAT
*
28230 AATAATATTACTAAT
1 ATTAATA--A-TAAT
* *
28245 ATCATTAATAAT
1 ATTAATAATAAT
* **
28257 ATTAATGACGAT
1 ATTAATAATAAT
*
28269 AATAATAATAAT
1 ATTAATAATAAT
28281 ATTAATAATAAT
1 ATTAATAATAAT
28293 ATTAATAAT
1 ATTAATAAT
28302 GACATTAATT
Statistics
Matches: 71, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
12 61 0.86
13 1 0.01
14 1 0.01
15 8 0.11
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (12 bp):
ATTAATAATAAT
Done.