Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003434.1 Kokia drynarioides strain JFW-HI SEQ_116211, 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: 49542
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:79 original size:16 final size:16
Alignment explanation
Indices: 34--83 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
24 TAAACCTAGC
*
34 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
50 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
64 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
80 TAAT
1 TAAT
84 AACCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:2113 original size:45 final size:45
Alignment explanation
Indices: 2049--2175 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 45
2039 TAAAGCTAAG
*
2049 GATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGCCAAA
1 GATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGACAAA
* * * * * *
2094 GATATCAACCTCAATTTGACGAGTCACCGCAATACTTAAGAGAAG
1 GATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGACAAA
* *
2139 GATATCAGGCTGAGTTTGACGAGCCACCGCAATACTC
1 GATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
2176 TACTTCTCCC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (45 bp):
GATATCAGCCTCAGTTTGACGAGCCACCGCAATACTCAAGACAAA
Found at i:2193 original size:21 final size:21
Alignment explanation
Indices: 2167--2212 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2157 ACGAGCCACC
*
2167 GCAATACTCTACTTCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
2188 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
2209 GCAA
1 GCAA
2213 ATGGACCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:6457 original size:4 final size:4
Alignment explanation
Indices: 6450--6480 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
6440 CCCTTCCTTC
6450 CTTT CTTT CTTT CTTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CT
6481 CGTTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:6469 original size:13 final size:13
Alignment explanation
Indices: 6451--6478 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6441 CCTTCCTTCC
6451 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
6464 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
6477 TT
1 TT
6479 CTCGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:9285 original size:14 final size:14
Alignment explanation
Indices: 9266--9296 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
9256 AAGACCTTGA
9266 TCAGTTTGAAAACT
1 TCAGTTTGAAAACT
9280 TCAGTTTGAAAACT
1 TCAGTTTGAAAACT
9294 TCA
1 TCA
9297 TTGTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (14 bp):
TCAGTTTGAAAACT
Found at i:16673 original size:2 final size:2
Alignment explanation
Indices: 16668--16718 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
16658 TTAAAAAAAC
16668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16710 AT AT AT AT A
1 AT AT AT AT A
16719 CACACTTGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21092 original size:58 final size:58
Alignment explanation
Indices: 21027--21141 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 58
21017 TTTTTTAAAG
* * *
21027 GACAAAAAAAAACTAAATTTTAATAGAAAAATAATTGTTAAATTCAAAGATTAATTTC
1 GACAAAAAAAAACTAAATTTCAATAGAAAAATAATTATCAAATTCAAAGATTAATTTC
* ** * * * *
21085 GACAAAAAATATTTAAGTTTCAATAGATAAATAATTATCAAATTTAAGGATTAATTT
1 GACAAAAAAAAACTAAATTTCAATAGAAAAATAATTATCAAATTCAAAGATTAATTT
21142 AAAGAAAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (58 bp):
GACAAAAAAAAACTAAATTTCAATAGAAAAATAATTATCAAATTCAAAGATTAATTTC
Found at i:29327 original size:2 final size:2
Alignment explanation
Indices: 29322--29349 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29312 TTTTTTTGTT
29322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29350 CATGAATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34123 original size:30 final size:27
Alignment explanation
Indices: 34055--34125 Score: 70
Period size: 30 Copynumber: 2.5 Consensus size: 27
34045 TCTTTCGTAA
* * *
34055 ATTTAAAGTTTAGTCTTTTATTTTTAT
1 ATTTAAAATTTAGTCTTTTACTTTCAT
*
34082 ATTTAGGAATTTAGTCTCTTTACCTTTCAT
1 ATTTA-AAATTTAGTCT-TTTA-CTTTCAT
34112 ATTTTAAAATTTAG
1 A-TTTAAAATTTAG
34126 ATCCAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.14
28 9 0.26
29 4 0.11
30 13 0.37
31 4 0.11
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (27 bp):
ATTTAAAATTTAGTCTTTTACTTTCAT
Found at i:38514 original size:2 final size:2
Alignment explanation
Indices: 38509--38534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38499 TATATATATA
38509 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
38535 CCTATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:46238 original size:14 final size:15
Alignment explanation
Indices: 46214--46247 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
46204 AAATAAACAG
*
46214 AAAAATGAAAAGAAA
1 AAAAATAAAAAGAAA
46229 AAAAATAAAAAGAAA
1 AAAAATAAAAAGAAA
46244 AAAA
1 AAAA
46248 GAAATGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAAATAAAAAGAAA
Done.