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1 COMMAND LINE: patser-v3e -A a:t 0.25 c:g 0.25 -m /tmp/tmpE8Kxfh/files/000/dataset_2.dat -b 1 -c -d1 -ls 7.0 -f special.fa -p
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2
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3 File containing the matrix: /tmp/tmpE8Kxfh/files/000/dataset_2.dat
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4 File containing the sequence information: special.fa
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5 Type of matrix: alignment
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6 Total pseudo-counts added to the elements of the alignment matrix: 1
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7
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8 Range for approximating a weight matrix with integers: 10000
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9 Minimum score for calculating p-values: 0
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10 Also score the complementary strands
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11 Treat unrecognized symbols as discontinuities in the sequence.
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12 Print scores greater than or equal to 7.00
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13
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14 ***** Information for the alphabet from the command line. *****
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15 letter 1: A (complement: T) prior frequency = 0.250000
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16 letter 2: C (complement: G) prior frequency = 0.250000
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17 letter 3: G (complement: C) prior frequency = 0.250000
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18 letter 4: T (complement: A) prior frequency = 0.250000
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19
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20 width of the alignment matrix: 13
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21 A | 3 0 0 0 0 7 6 0 1 4 7 1 0
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22 C | 2 0 0 0 7 1 0 1 1 3 3 5 1
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23 G | 5 8 7 0 2 1 2 1 8 3 0 0 5
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24 T | 0 2 3 10 1 1 2 8 0 0 0 4 4
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25
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26 width of the matrix in file "/tmp/tmpE8Kxfh/files/000/dataset_2.dat": 13
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27 A C G T
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28 0.17 -0.20 0.65 -2.40
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29 -2.40 -2.40 1.10 -0.20
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30 -2.40 -2.40 0.97 0.17
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31 -2.40 -2.40 -2.40 1.32
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32 -2.40 0.97 -0.20 -0.79
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33 0.97 -0.79 -0.79 -0.79
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34 0.82 -2.40 -0.20 -0.20
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35 -2.40 -0.79 -0.79 1.10
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36 -0.79 -0.79 1.10 -2.40
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37 0.44 0.17 0.17 -2.40
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38 0.97 0.17 -2.40 -2.40
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39 -0.79 0.65 -2.40 0.44
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40 -2.40 -0.79 0.65 0.44
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41
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42 Information content (base e): 8.324
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43 Sample size adjusted information content
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44 (information content minus the average information
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45 expected from an arbitrary alignment of random sequences): 6.101
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46 Information content after adding pseudo-counts: 6.370
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47
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48 maximum score: 11.685
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49 minimum score: -29.563
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50 range of scores: 11.685 - -29.563 = 41.248
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51
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52 minimum score for calculating p-values: 0.000
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53 maximum ln(numerically calculated p-value): -3.681
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54 minimum ln(numerically calculated p-value): -18.022
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55
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56 ln(cutoff p-value) based on sample size adjusted information content: -6.101
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57 numerically calculated cutoff score: 3.835
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58 ln(numerically calculated cutoff p-value): -6.102
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59 average score above numerically calculated cutoff: 4.996
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60
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61 >3L:3245372,3251371 position= 2004 score= 7.87 ln(p-value)= -10.00
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62 >3L:3245372,3251371 position= 2062C score= 7.14 ln(p-value)= -9.15
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63 >3L:3245372,3251371 position= 2535 score= 8.69 ln(p-value)= -11.09
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64 >3L:3245372,3251371 position= 3092 score= 7.73 ln(p-value)= -9.82
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65 >3L:3245372,3251371 position= 4690C score= 7.02 ln(p-value)= -9.01
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