aekimura / bioinformaticshw2

BioinformaticsHW2

Results are also stored in calculations.txt

random_kmers.py was used to generate the random k-mers that were used for this assignment

random k-mers that were generated are stored in rkmers.txt

kmer_calc.py contains the python code written for this assignment

Sequence Lenth = 9193

1-mer calculations: Random = 2298 ( 0.25 ) A count = 2770 ( 0.30131621886217774 ) T count = 2389 ( 0.25987164146633307 ) C count = 1995 ( 0.21701294463178505 ) G count = 2038 ( 0.2216904166213423 ) N count = 1 ( 0.00010877841836179702 )

2-mer calculations: Random = 574 ( 0.0625 ) GC count = 421 ( 0.045805679469045804 ) CC count = 497 ( 0.05407463823305408 ) CC count = 497 ( 0.05407463823305408 ) CG count = 279 ( 0.030355782831030357 ) CA count = 672 ( 0.07311500380807312 )

3-mer calculations: Random = 143 ( 0.015625 ) GTG count = 144 ( 0.015669205658324265 ) AGA count = 234 ( 0.02546245919477693 ) CTC count = 157 ( 0.01708378672470076 ) TTC count = 163 ( 0.017736670293797607 ) TTA count = 146 ( 0.01588683351468988 )

4-mer calculations: Random = 35 ( 0.00390625 ) GATA count = 23 ( 0.0025029927086734137 ) CCCT count = 21 ( 0.002285341168788769 ) TCTG count = 15 ( 0.001632386549134835 ) CAGG count = 25 ( 0.0027206442485580586 ) AGTG count = 41 ( 0.004461856567635216 )

5-mer calculations: Random = 8 ( 0.0009765625 ) ACCAA count = 34 ( 0.0037004788855028296 ) TCGCA count = 2 ( 0.00021767522855898998 ) GGCTA count = 7 ( 0.0007618632999564649 ) TGGTT count = 9 ( 0.000979538528515455 ) TCCCG count = 6 ( 0.00065302568567697 )

6-mer calculations: Random = 2 ( 0.000244140625 ) TACCCG count = 0 ( 0.0 ) AATCAT count = 1 ( 0.00010884946119516709 ) CTTGCC count = 5 ( 0.0005442473059758355 ) GGTTCT count = 0 ( 0.0 ) ACTTAA count = 1 ( 0.00010884946119516709 )

7-mer calculations: Random = 0 ( 6.103515625e-05 ) GACTACT count = 0 ( 0.0 ) CTTAATT count = 2 ( 0.00021772262138036142 ) CCTCCCT count = 0 ( 0.0 ) CGAATGT count = 0 ( 0.0 ) GAGTACA count = 2 ( 0.00021772262138036142 )

8-mer calculations: Random = 0 ( 1.52587890625e-05 ) CTTATGAT count = 0 ( 0.0 ) GTGTTGAA count = 0 ( 0.0 ) AATCTGAT count = 0 ( 0.0 ) TCGCCTGT count = 0 ( 0.0 ) TTGCGGTG count = 0 ( 0.0 )

9-mer calculations: Random = 0 ( 3.814697265625e-06 ) CGGCCCGTC count = 0 ( 0.0 ) GGTTCCTTT count = 0 ( 0.0 ) ACCCACGTT count = 0 ( 0.0 ) CGTTTATCT count = 0 ( 0.0 ) CAAGTCTGG count = 0 ( 0.0 )

10-mer calculations: Random = 0 ( 9.5367431640625e-07 ) CTACTGCACG count = 0 ( 0.0 ) TGAGTCTTAA count = 0 ( 0.0 ) GCGTAGCCCG count = 0 ( 0.0 ) GAGTGAGTAC count = 0 ( 0.0 ) TGCAATGCTC count = 0 ( 0.0 )