Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010330.1 Kokia drynarioides strain JFW-HI SEQ_125195, 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: 21207
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:589 original size:40 final size:38
Alignment explanation
Indices: 545--680 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 38
535 TTGATAATGA
545 GATTAAATTGTAAAAGAAACTATAAGTTTTGTGATAGAGG
1 GATTAAATTG--AAAGAAACTATAAGTTTTGTGATAGAGG
* * * *
585 GATTAAATTGAAAG-AATTTTAAG-TTAGAATTGATA-ATGA
1 GATTAAATTGAAAGAAACTATAAGTTTTG---TGATAGA-GG
*
624 GATTAAATTGTAAAAGAAGCTATAAGTTTTGTGATAGAGG
1 GATTAAATTG--AAAGAAACTATAAGTTTTGTGATAGAGG
664 GATTAAATTGAAAGAAA
1 GATTAAATTGAAAGAAA
681 TTTTAAATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
36 3 0.04
37 7 0.09
38 11 0.14
39 16 0.21
40 26 0.34
41 5 0.06
42 6 0.08
43 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.21, T:0.32
Consensus pattern (38 bp):
GATTAAATTGAAAGAAACTATAAGTTTTGTGATAGAGG
Found at i:628 original size:39 final size:39
Alignment explanation
Indices: 511--633 Score: 137
Period size: 39 Copynumber: 3.1 Consensus size: 39
501 TTAGGGAATT
511 AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTA
1 AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTA
* * * *
550 AATTGTAAAAGAAACTATAAGTT---TTGTGATAGA-GGGATTA
1 AATTG--AAAG-AATTTTAAGTTAGAAT-TGATA-ATGAGATTA
590 AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTA
1 AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTA
629 AATTG
1 AATTG
634 TAAAAGAAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
37 9 0.13
38 5 0.07
39 22 0.33
40 17 0.25
41 5 0.07
42 9 0.13
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.35
Consensus pattern (39 bp):
AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTA
Found at i:634 original size:79 final size:79
Alignment explanation
Indices: 503--691 Score: 335
Period size: 79 Copynumber: 2.4 Consensus size: 79
493 ATAGTGAATT
503 AGGGAATT-AATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTAAATTGTAAAAGAAACTA
1 AGGG-ATTAAATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTAAATTGTAAAAGAAACTA
567 TAAGTTTTGTGATAG
65 TAAGTTTTGTGATAG
*
582 AGGGATTAAATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTAAATTGTAAAAGAAGCTAT
1 AGGGATTAAATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTAAATTGTAAAAGAAACTAT
647 AAGTTTTGTGATAG
66 AAGTTTTGTGATAG
*
661 AGGGATTAAATTGAAAGAAATTTTAAATTAG
1 AGGGATTAAATTGAAAG-AATTTTAAGTTAG
692 GGTTTTATTA
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
78 3 0.03
79 91 0.86
80 12 0.11
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (79 bp):
AGGGATTAAATTGAAAGAATTTTAAGTTAGAATTGATAATGAGATTAAATTGTAAAAGAAACTAT
AAGTTTTGTGATAG
Found at i:806 original size:17 final size:18
Alignment explanation
Indices: 784--819 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
774 TAAATGAGTT
784 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
801 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
819 A
1 A
820 TAGGAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:907 original size:42 final size:42
Alignment explanation
Indices: 854--939 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
844 TTAGTGCTGT
854 AATTAATAGCCTAAATTATTATTATTTTCGTAGCTAGCAAAG
1 AATTAATAGCCTAAATTATTATTATTTTCGTAGCTAGCAAAG
896 AATTAATAGCCTAAATTATTATTATTTTCGTAGCTAGCAAAG
1 AATTAATAGCCTAAATTATTATTATTTTCGTAGCTAGCAAAG
938 AA
1 AA
940 CCCGAAGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (42 bp):
AATTAATAGCCTAAATTATTATTATTTTCGTAGCTAGCAAAG
Found at i:13636 original size:7 final size:7
Alignment explanation
Indices: 13624--13651 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13614 CATTTAATAT
13624 TCAACAC
1 TCAACAC
13631 TCAACAC
1 TCAACAC
13638 TCAACAC
1 TCAACAC
13645 TCAACAC
1 TCAACAC
13652 AATTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
TCAACAC
Done.