Assignment: GS 540 HW2
Name: Conor Camplisson
Email: concamp@uw.edu
Language: Python
Runtime: 33.1 sec

Fasta 1: CP003913.fna
Non-alphabetic characters: 681
>gi|440453185|gb|CP003913.1| Mycoplasma pneumoniae M129-B7, complete genome
*=816373
A=249201
C=162924
G=163697
T=240551
N=0

Nucleotide Frequencies:
A=0.3053
C=0.1996
G=0.2005
T=0.2947

Dinucleotide Count Matrix:
A=98512 50763 47914 52012
C=53047 36681 26746 46450
G=40870 37148 36764 48915
T=56772 38332 52273 93173

Dinucleotide Frequency Matrix:
A=0.1207 0.0622 0.0587 0.0637
C=0.0650 0.0449 0.0328 0.0569
G=0.0501 0.0455 0.0450 0.0599
T=0.0695 0.0470 0.0640 0.1141

Conditional Frequency Matrix:
A=0.3953 0.2037 0.1923 0.2087
C=0.3256 0.2251 0.1642 0.2851
G=0.2497 0.2269 0.2246 0.2988
T=0.2360 0.1594 0.2173 0.3873

Fasta 2: simulated_equal_freq.fa
Non-alphabetic characters: 0
>simulated_equal_freq
*=816373
A=204496
C=203794
G=204159
T=203924
N=0

Nucleotide Frequencies:
A=0.2505
C=0.2496
G=0.2501
T=0.2498

Dinucleotide Count Matrix:
A=51122 51212 51114 51048
C=50998 50966 50784 51045
G=51138 50840 51232 50949
T=51238 50775 51029 50882

Dinucleotide Frequency Matrix:
A=0.0626 0.0627 0.0626 0.0625
C=0.0625 0.0624 0.0622 0.0625
G=0.0626 0.0623 0.0628 0.0624
T=0.0628 0.0622 0.0625 0.0623

Conditional Frequency Matrix:
A=0.2500 0.2504 0.2500 0.2496
C=0.2502 0.2501 0.2492 0.2505
G=0.2505 0.2490 0.2509 0.2496
T=0.2513 0.2490 0.2502 0.2495

Fasta 3: simulated_markov_0.fa
Non-alphabetic characters: 0
>simulated_markov_0
*=816373
A=248748
C=162830
G=164026
T=240769
N=0

Nucleotide Frequencies:
A=0.3047
C=0.1995
G=0.2009
T=0.2949

Dinucleotide Count Matrix:
A=75320 49910 50241 73276
C=49626 32300 32789 48115
G=50322 32668 32614 48422
T=73480 47952 48382 70955

Dinucleotide Frequency Matrix:
A=0.0923 0.0611 0.0615 0.0898
C=0.0608 0.0396 0.0402 0.0589
G=0.0616 0.0400 0.0399 0.0593
T=0.0900 0.0587 0.0593 0.0869

Conditional Frequency Matrix:
A=0.3028 0.2006 0.2020 0.2946
C=0.3048 0.1984 0.2014 0.2955
G=0.3068 0.1992 0.1988 0.2952
T=0.3052 0.1992 0.2009 0.2947

Fasta 4: simulated_markov_1.fa
Non-alphabetic characters: 0
>simulated_markov_1
*=816373
A=249747
C=162576
G=163642
T=240408
N=0

Nucleotide Frequencies:
A=0.3059
C=0.1991
G=0.2005
T=0.2945

Dinucleotide Count Matrix:
A=99263 50746 47775 51963
C=52971 36546 26807 46252
G=40731 37256 36898 48757
T=56782 38028 52161 93436

Dinucleotide Frequency Matrix:
A=0.1216 0.0622 0.0585 0.0637
C=0.0649 0.0448 0.0328 0.0567
G=0.0499 0.0456 0.0452 0.0597
T=0.0696 0.0466 0.0639 0.1145

Conditional Frequency Matrix:
A=0.3975 0.2032 0.1913 0.2081
C=0.3258 0.2248 0.1649 0.2845
G=0.2489 0.2277 0.2255 0.2979
T=0.2362 0.1582 0.2170 0.3887

Run 1:

Fasta 1: CP001872.fna
Non-alphabetic characters: 851
>gi|284930242|gb|CP001872.1| Mycoplasma gallisepticum str. R(high), complete genome
*=1012027
A=349322
C=159094
G=159365
T=344246
N=0

Fasta 2: simulated_equal_freq.fa
Non-alphabetic characters: 0
>simulated_equal_freq
*=816373
A=204496
C=203794
G=204159
T=203924
N=0

Match Length Histogram:
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 2096
9 208383
10 473117
11 233873
12 69924
13 18424
14 4674
15 1174
16 277
17 57
18 13
19 6
20 1

The longest match length: 20
Number of match strings: 1

Match string: TAATTTTCTAAATAAAATTA

Fasta: CP001872.fna
Position: 18193
Strand: forward

Fasta: simulated_equal_freq.fa
Position: 704510
Strand: forward

Run 2:

Fasta 1: CP001872.fna
Non-alphabetic characters: 851
>gi|284930242|gb|CP001872.1| Mycoplasma gallisepticum str. R(high), complete genome
*=1012027
A=349322
C=159094
G=159365
T=344246
N=0

Fasta 2: simulated_markov_0.fa
Non-alphabetic characters: 0
>simulated_markov_0
*=816373
A=249008
C=163032
G=163723
T=240610
N=0

Match Length Histogram:
1 1
2 1
3 1
4 1
5 1
6 1
7 12
8 3443
9 105638
10 374008
11 330929
12 138605
13 42853
14 12099
15 3257
16 865
17 227
18 62
19 22
20 1

The longest match length: 20
Number of match strings: 1

Match string: AAATTACAATAACTACACAA

Fasta: simulated_markov_0.fa
Position: 193796
Strand: forward

Fasta: CP001872.fna
Position: 903456
Strand: forward

Run 3:

Fasta 1: CP001872.fna
Non-alphabetic characters: 851
>gi|284930242|gb|CP001872.1| Mycoplasma gallisepticum str. R(high), complete genome
*=1012027
A=349322
C=159094
G=159365
T=344246
N=0

Fasta 2: simulated_markov_1.fa
Non-alphabetic characters: 0
>simulated_markov_1
*=816373
A=248913
C=162513
G=163996
T=240951
N=0

Match Length Histogram:
1 1
2 1
3 1
4 1
5 1
6 1
7 29
8 10637
9 136998
10 336808
11 302824
12 149037
13 53277
14 16046
15 4604
16 1274
17 351
18 100
19 28
20 6
21 1
22 1

The longest match length: 22
Number of match strings: 1

Match string: TATCATTAAACTCAAACAACTC

Fasta: CP001872.fna
Position: 173650
Strand: forward

Fasta: simulated_markov_1.fa
Position: 384424
Strand: forward

Question 4-A:

[ TODO ]

Question 4-B:

[ TODO ]

Question 4-C:

[ TODO ]

Program:

int main() {
	do_analysis();
	return 0;
}