Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011209.1 Kokia drynarioides strain JFW-HI SEQ_126186, 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: 42240
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:2199 original size:69 final size:69
Alignment explanation
Indices: 2117--2258 Score: 284
Period size: 69 Copynumber: 2.1 Consensus size: 69
2107 GGGTGGCCGA
2117 CGCCCCAAGCCCCTAACTCAAACTATCCGAATGCCATCTACCACCACCACCACCAACCTCCTCCT
1 CGCCCCAAGCCCCTAACTCAAACTATCCGAATGCCATCTACCACCACCACCACCAACCTCCTCCT
2182 CCGG
66 CCGG
2186 CGCCCCAAGCCCCTAACTCAAACTATCCGAATGCCATCTACCACCACCACCACCAACCTCCTCCT
1 CGCCCCAAGCCCCTAACTCAAACTATCCGAATGCCATCTACCACCACCACCACCAACCTCCTCCT
2251 CCGG
66 CCGG
2255 CGCC
1 CGCC
2259 AAGTTATCCT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.25, C:0.51, G:0.09, T:0.14
Consensus pattern (69 bp):
CGCCCCAAGCCCCTAACTCAAACTATCCGAATGCCATCTACCACCACCACCACCAACCTCCTCCT
CCGG
Found at i:7925 original size:48 final size:48
Alignment explanation
Indices: 7854--7955 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 48
7844 GTTGTATAAA
7854 AAGAACTATTATAGGTCCCTCTTAATCTGAACATGAAACAGGATAGGG
1 AAGAACTATTATAGGTCCCTCTTAATCTGAACATGAAACAGGATAGGG
*
7902 AAGAACTATTATAGGTCCCTCTTAATCTGAACATGATACAGGATAGGG
1 AAGAACTATTATAGGTCCCTCTTAATCTGAACATGAAACAGGATAGGG
7950 AAGAAC
1 AAGAAC
7956 AGAACGATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (48 bp):
AAGAACTATTATAGGTCCCTCTTAATCTGAACATGAAACAGGATAGGG
Found at i:13555 original size:27 final size:27
Alignment explanation
Indices: 13524--13577 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
13514 CTAAACTATT
13524 AGTTAGTTTAGCTGTTCCTGAAACATA
1 AGTTAGTTTAGCTGTTCCTGAAACATA
13551 AGTTAGTTTAGCTGTTCCTGAAACATA
1 AGTTAGTTTAGCTGTTCCTGAAACATA
13578 CCCAAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (27 bp):
AGTTAGTTTAGCTGTTCCTGAAACATA
Found at i:20115 original size:16 final size:15
Alignment explanation
Indices: 20086--20128 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
20076 AGATATTCAC
20086 ATAAAATAAATGAAGAA
1 ATAAAAT-AATGAA-AA
20103 ATAAAATAATGAAAA
1 ATAAAATAATGAAAA
20118 ATAACAATAAT
1 ATAA-AATAAT
20129 TACTGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (15 bp):
ATAAAATAATGAAAA
Found at i:23952 original size:2 final size:2
Alignment explanation
Indices: 23945--23976 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23935 AAATTCTCGT
23945 TA TA 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 TA TA
23977 AGAGTAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25691 original size:33 final size:34
Alignment explanation
Indices: 25645--25712 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
25635 ATATGATAAA
**
25645 TATTTTAATTTTTTTA-AAAGGTGTTTTTAATTTT
1 TATTTTAA-TTTTTTAGAAACATGTTTTTAATTTT
25679 TATTTT-ATTTTTTAGAAACATGTTTTTAATTTT
1 TATTTTAATTTTTTAGAAACATGTTTTTAATTTT
25712 T
1 T
25713 TTAAGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 7 0.23
33 18 0.58
34 6 0.19
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.65
Consensus pattern (34 bp):
TATTTTAATTTTTTAGAAACATGTTTTTAATTTT
Found at i:25721 original size:15 final size:14
Alignment explanation
Indices: 25703--25740 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
25693 GAAACATGTT
25703 TTTAATTTTTTTAA
1 TTTAATTTTTTTAA
*
25717 GTTTAATTTTATTAA
1 -TTTAATTTTTTTAA
25732 TTT-ATTTTT
1 TTTAATTTTT
25741 AAAATATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.24
14 3 0.14
15 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTAATTTTTTTAA
Found at i:26237 original size:33 final size:33
Alignment explanation
Indices: 26173--26239 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
26163 AAATATTACA
*
26173 TTTTCATTTTAATATAATTATTTAATGAAATAT
1 TTTTCATTTTAATATAAGTATTTAATGAAATAT
*
26206 TTTTCATTTTAAATTTAAGT-TTTAGAT-AAATAT
1 TTTTCATTTT-AATATAAGTATTTA-ATGAAATAT
26239 T
1 T
26240 ATTAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 21 0.70
34 9 0.30
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.55
Consensus pattern (33 bp):
TTTTCATTTTAATATAAGTATTTAATGAAATAT
Found at i:28760 original size:41 final size:41
Alignment explanation
Indices: 28715--28796 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
28705 AAACCTGTTG
28715 CTAAATGAAAAGAGGGAAGCCAATGACTCAGGGATCCTAGT
1 CTAAATGAAAAGAGGGAAGCCAATGACTCAGGGATCCTAGT
28756 CTAAATGAAAAGAGGGAAGCCAATGACTCAGGGATCCTAGT
1 CTAAATGAAAAGAGGGAAGCCAATGACTCAGGGATCCTAGT
28797 GCCACACTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (41 bp):
CTAAATGAAAAGAGGGAAGCCAATGACTCAGGGATCCTAGT
Found at i:40195 original size:30 final size:30
Alignment explanation
Indices: 40161--40233 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
40151 ACATTAATTG
* *
40161 AAAGGTTTGATTGATTAATTTATCATTTTT
1 AAAGGTTTAATTGATTAATTTATCATCTTT
* * * *
40191 AAAGGCTCAATTAATTAATTTTTCATCTTT
1 AAAGGTTTAATTGATTAATTTATCATCTTT
*
40221 AAGGGTTTAATTG
1 AAAGGTTTAATTG
40234 GGTGTAAAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (30 bp):
AAAGGTTTAATTGATTAATTTATCATCTTT
Found at i:41240 original size:17 final size:17
Alignment explanation
Indices: 41187--41258 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
41177 AATTTTTAAA
41187 TAAGTTTGAATTTATTT
1 TAAGTTTGAATTTATTT
* ** *
41204 TAAATTCAAAATTCATTT
1 TAAGTT-TGAATTTATTT
*
41222 TAAGTTTGAATTTACTT
1 TAAGTTTGAATTTATTT
*
41239 TAAATTT-AAGTTTATTT
1 TAAGTTTGAA-TTTATTT
41256 TAA
1 TAA
41259 ATTAAATTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 2 0.05
17 27 0.64
18 13 0.31
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (17 bp):
TAAGTTTGAATTTATTT
Found at i:41259 original size:17 final size:16
Alignment explanation
Indices: 41195--41266 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
41185 AATAAGTTTG
*
41195 AATTTATTTTAAATTCAA
1 AATTTATTTTAAATT--T
* *
41213 AATTCATTTTAAGTTT
1 AATTTATTTTAAATTT
*
41229 GAATTTACTTTAAATTT
1 -AATTTATTTTAAATTT
*
41246 AAGTTTATTTTAAATTA
1 AA-TTTATTTTAAATTT
41263 AATT
1 AATT
41267 AAAAGACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.09
17 27 0.61
18 13 0.30
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
AATTTATTTTAAATTT
Found at i:41352 original size:39 final size:39
Alignment explanation
Indices: 41298--41375 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
41288 TATCCATCTT
41298 TCAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAA
1 TCAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAA
41337 TCAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAA
1 TCAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAA
41376 ACCCGAGCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (39 bp):
TCAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAA
Found at i:41387 original size:40 final size:39
Alignment explanation
Indices: 41299--41389 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
41289 ATCCATCTTT
*
41299 CAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAAT
1 CAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAAC
41338 CAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAAAC
1 CAAAGCCCAAATTGGACTTGATCCTAACATACC-AAAAAC
**
41378 CCGAGCCCAAAT
1 CAAAGCCCAAAT
41390 ACAATTCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.18
Consensus pattern (39 bp):
CAAAGCCCAAATTGGACTTGATCCTAACATACCAAAAAC
Done.