[Computer:~/be490] user% more motifs.txt 

AGCTGAC

GACTAAT

GGCTAAT

CATTAAC

CTCTAAC

TTTTAAC

TACTAAC

TACTAAT

TACTAAC

TGCTAAC

TATTAAC

TTCTAAC

TTCTAAC

TGCTAAC

TTCTAAC

CACTAAC

TGCTAAC

GACTAAC

TATTAAC

CGCTAAC

AACTAAC

TACTAAT

AACTAAC

TACTAAC

TACTTAC

TACTAAT

TACTAAT

TTCTAAC

TTCTAAC

CGCTGAC

TACTAAT

TACTAAT

TACTGAC

TACTAAC

TACTGAC

TGCTAAC

AACTAAC

TTCTAAC

GACTAAC

AACTAAC

TTCTAAT

TTCTAAC

TATTAAC

TACTGAC

TTCTAAC

TACTAAT

TCCTAAC

TACTAAC

TACTAAC

TTCTAAC

GACTAAC

TATTAAC

TACTGAC

TGCTAAC

TACTAAC

TTTTAAC

TTCTAAC

TACTAAC

TTCTAAC

TACTAAC

TTCTAAC

TACTAAC

TACTAAC

TACTAAC

TACTAAC

TATTAAC

TACTAAC

GACTAAC

GACTAAC

TACTAAC

TACTTAC

TTCTAAC

TACTAAC

TACTAAC

TTTTAAC

[Computer:~/be490] user% python motif.py motifs.txt 

Frequency Matrix:

A 0.067 0.627 0.000 0.000 0.893 1.000 0.000

T 0.773 0.240 0.120 1.000 0.027 0.000 0.133

G 0.093 0.120 0.000 0.000 0.080 0.000 0.000

C 0.067 0.013 0.880 0.000 0.000 0.000 0.867



Position 1: entropy = 1.127, information = 0.873

Position 2: entropy = 1.367, information = 0.633

Position 3: entropy = 0.529, information = 1.471

Position 4: entropy = 0.000, information = 2.000

Position 5: entropy = 0.576, information = 1.424

Position 6: entropy = 0.000, information = 2.000

Position 7: entropy = 0.567, information = 1.433



Total Information Content = 9.834



Sequence AGCTGAC has score s = 2.999

Sequence GACTAAT has score s = 6.650

Sequence GGCTAAT has score s = 4.266

Sequence CATTAAC has score s = 5.991

Sequence CTCTAAC has score s = 7.481

Sequence TTTTAAC has score s = 8.142

Sequence TACTAAC has score s = 12.401

Sequence TACTAAT has score s = 9.701

Sequence TACTAAC has score s = 12.401

Sequence TGCTAAC has score s = 10.017

Sequence TATTAAC has score s = 9.527

Sequence TTCTAAC has score s = 11.017

Sequence TTCTAAC has score s = 11.017

Sequence TGCTAAC has score s = 10.017

Sequence TTCTAAC has score s = 11.017

Sequence CACTAAC has score s = 8.865

Sequence TGCTAAC has score s = 10.017

Sequence GACTAAC has score s = 9.351

Sequence TATTAAC has score s = 9.527

Sequence CGCTAAC has score s = 6.481

Sequence AACTAAC has score s = 8.865

Sequence TACTAAT has score s = 9.701

Sequence AACTAAC has score s = 8.865

Sequence TACTAAC has score s = 12.401

Sequence TACTTAC has score s = 7.335

Sequence TACTAAT has score s = 9.701

Sequence TACTAAT has score s = 9.701

Sequence TTCTAAC has score s = 11.017

Sequence TTCTAAC has score s = 11.017

Sequence CGCTGAC has score s = 2.999

Sequence TACTAAT has score s = 9.701

Sequence TACTAAT has score s = 9.701

Sequence TACTGAC has score s = 8.920

Sequence TACTAAC has score s = 12.401

Sequence TACTGAC has score s = 8.920

Sequence TGCTAAC has score s = 10.017

Sequence AACTAAC has score s = 8.865

Sequence TTCTAAC has score s = 11.017

Sequence GACTAAC has score s = 9.351

Sequence AACTAAC has score s = 8.865

Sequence TTCTAAT has score s = 8.316

Sequence TTCTAAC has score s = 11.017

Sequence TATTAAC has score s = 9.527

Sequence TACTGAC has score s = 8.920

Sequence TTCTAAC has score s = 11.017

Sequence TACTAAT has score s = 9.701

Sequence TCCTAAC has score s = 6.847

Sequence TACTAAC has score s = 12.401

Sequence TACTAAC has score s = 12.401

Sequence TTCTAAC has score s = 11.017

Sequence GACTAAC has score s = 9.351

Sequence TATTAAC has score s = 9.527

Sequence TACTGAC has score s = 8.920

Sequence TGCTAAC has score s = 10.017

Sequence TACTAAC has score s = 12.401

Sequence TTTTAAC has score s = 8.142

Sequence TTCTAAC has score s = 11.017

Sequence TACTAAC has score s = 12.401

Sequence TTCTAAC has score s = 11.017

Sequence TACTAAC has score s = 12.401

Sequence TTCTAAC has score s = 11.017

Sequence TACTAAC has score s = 12.401

Sequence TACTAAC has score s = 12.401

Sequence TACTAAC has score s = 12.401

Sequence TACTAAC has score s = 12.401

Sequence TATTAAC has score s = 9.527

Sequence TACTAAC has score s = 12.401

Sequence GACTAAC has score s = 9.351

Sequence GACTAAC has score s = 9.351

Sequence TACTAAC has score s = 12.401

Sequence TACTTAC has score s = 7.335

Sequence TTCTAAC has score s = 11.017

Sequence TACTAAC has score s = 12.401

Sequence TACTAAC has score s = 12.401

Sequence TTTTAAC has score s = 8.142

Mean score = 9.834

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