COMMAND LINE: /usr/local/BEST/bin/consensus-v6c -f all_XD.cs -L 10 -q 1000 -A a:t c:g -c0 -pr2 -n 10 -pt 0 -pf 10 ***** PID: 27825 ***** L-mer Width: 10 Minimum distance between starting points of words: 10 Save the top alignments derived from each intermediate alignment Maximum number of matrices to save between cycles: 1000 Status of complementary sequence: IGNORE. Algorithim options: unlimited (0 or more) matches per sequence. Maximum number of cycles is 10. Stop only when the maximum number of cycles is reached. The number of matrices to print. Top Matrices saved from each cycle: NONE Matrices Saved from the last cycle: 10 ***** Sequence information from file "all_XD.cs". ***** sequence 1: CfDhoxD1 fragments: 1-501 sequence 2: CfDhoxD3 fragments: 1-501 sequence 3: CfDhoxD4 fragments: 1-501 sequence 4: CfDhoxD10 fragments: 1-501 sequence 5: CfDhoxD11 fragments: 1-501 sequence 6: CfDhoxD12 fragments: 1-501 sequence 7: CfDhoxD13 fragments: 1-501 sequence 8: HsDhoxD1 fragments: 1-501 sequence 9: HsDhoxD3 fragments: 1-501 sequence 10: HsDhoxD4 fragments: 1-501 sequence 11: HsDhoxD8 fragments: 1-501 sequence 12: HsDhoxD9 fragments: 1-501 sequence 13: HsDhoxD10 fragments: 1-501 sequence 14: HsDhoxD11 fragments: 1-501 Total number of sequences: 14. Total number of sequence fragments: 14. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 7014 A 0.191046; observed occurrence = 1340 (letter 1) C 0.295694; observed occurrence = 2074 (letter 2) G 0.317223; observed occurrence = 2225 (letter 3) T 0.196036; observed occurrence = 1375 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.191046 letter 2: C (complement: G) prior frequency = 0.295694 letter 3: G (complement: C) prior frequency = 0.317223 letter 4: T (complement: A) prior frequency = 0.196036 INFORMATION CONTENT IS CALCULATED USING NATURAL LOGARITHMS (i.e. BASE e). DIVIDE BY ln(2) = 0.693 TO CONVERT TO BASE 2, WHICH WAS USED IN PREVIOUS VERSIONS OF THIS PROGRAM. [] MATRICES SAVED FOR NEXT CYCLE [] []------------------------------------------------------[] [] total | top adjusted | ln top [] ln expected [] CYCLE [] number | information | p-value [] frequency [] ------[]----------|--------------|-------------[]-------------[] 1 [] 6888 | 2.9484 | 0.0000 [] 8.8375 [] 2 [] 592 | 7.8524 | -26.3777 [] -9.3959 [] 3 [] 908 | 9.8891 | -39.4709 [] -14.7504 [] 4 [] 748 | 10.5502 | -48.6902 [] -16.5190 [] 5 [] 877 | 10.9912 | -59.0456 [] -19.6468 [] 6 [] 806 | 11.5592 | -72.4851 [] -26.0413 [] 7 [] 864 | 11.5410 | -81.2657 [] -27.9312 [] 8 [] 850 | 11.3967 | -89.0145 [] -28.9229 [] 9 [] 870 | 11.3428 | -97.9592 [] -31.2285 [] 10 [] 878 | 11.2851 | -107.0026 [] -33.7382 [] INFORMATION CONTENT IS CALCULATED USING NATURAL LOGARITHMS (i.e. BASE e). DIVIDE BY ln(2) = 0.693 TO CONVERT TO BASE 2, WHICH WAS USED IN PREVIOUS VERSIONS OF THIS PROGRAM. THE LIST OF MATRICES FROM FINAL CYCLE--sorted by information (total of 878): MATRIX 1 number of sequences = 10 unadjusted information = 13.0027 sample size adjusted information = 11.2851 ln(p-value) = -107.003 p-value = 3.3834E-47 ln(expected frequency) = -33.7382 expected frequency = 2.22681E-15 A | 8 0 0 0 0 0 10 10 10 0 C | 2 6 0 6 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 0 0 T | 0 4 10 4 10 0 0 0 0 10 1|2 : 3/489 CTTCTGAAAT 2|8 : 4/373 ATTTTCAAAT 3|3 : 9/29 ACTCTGAAAT 4|4 : 9/39 ACTCTGAAAT 5|10 : 9/76 ACTTTGAAAT 6|6 : 9/86 ACTCTGAAAT 7|7 : 9/123 ACTTTGAAAT 8|5 : 9/133 ACTCTGAAAT 9|1 : 10/489 CTTCTGAAAT 10|9 : 13/373 ATTTTCAAAT MATRIX 2 number of sequences = 10 unadjusted information = 12.8878 sample size adjusted information = 11.1702 ln(p-value) = -105.466 p-value = 1.57345E-46 ln(expected frequency) = -32.2012 expected frequency = 1.03558E-14 A | 9 0 0 0 0 0 10 10 9 0 C | 1 7 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 3 10 5 10 0 0 0 0 10 1|9 : 3/489 CTTCTGAAAT 2|7 : 4/373 ATTTTCAAAT 3|6 : 7/274 ACTTTGAAGT 4|10 : 9/29 ACTCTGAAAT 5|3 : 9/39 ACTCTGAAAT 6|2 : 9/76 ACTTTGAAAT 7|4 : 9/86 ACTCTGAAAT 8|1 : 9/123 ACTTTGAAAT 9|5 : 9/133 ACTCTGAAAT 10|8 : 13/373 ATTTTCAAAT MATRIX 3 number of sequences = 10 unadjusted information = 12.8878 sample size adjusted information = 11.1702 ln(p-value) = -105.466 p-value = 1.57345E-46 ln(expected frequency) = -32.2012 expected frequency = 1.03558E-14 A | 9 0 0 0 0 0 10 10 9 0 C | 1 7 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 3 10 5 10 0 0 0 0 10 1|7 : 4/373 ATTTTCAAAT 2|6 : 7/274 ACTTTGAAGT 3|3 : 9/29 ACTCTGAAAT 4|9 : 9/39 ACTCTGAAAT 5|2 : 9/76 ACTTTGAAAT 6|4 : 9/86 ACTCTGAAAT 7|1 : 9/123 ACTTTGAAAT 8|5 : 9/133 ACTCTGAAAT 9|10 : 10/489 CTTCTGAAAT 10|8 : 13/373 ATTTTCAAAT MATRIX 4 number of sequences = 10 unadjusted information = 12.8161 sample size adjusted information = 11.0985 ln(p-value) = -104.511 p-value = 4.08735E-46 ln(expected frequency) = -31.2466 expected frequency = 2.69012E-14 A | 8 0 0 0 0 0 10 10 9 0 C | 2 7 0 6 0 1 0 0 0 0 G | 0 0 0 0 0 9 0 0 1 0 T | 0 3 10 4 10 0 0 0 0 10 1|2 : 3/489 CTTCTGAAAT 2|9 : 4/373 ATTTTCAAAT 3|10 : 7/274 ACTTTGAAGT 4|3 : 9/29 ACTCTGAAAT 5|4 : 9/39 ACTCTGAAAT 6|6 : 9/76 ACTTTGAAAT 7|5 : 9/86 ACTCTGAAAT 8|7 : 9/123 ACTTTGAAAT 9|8 : 9/133 ACTCTGAAAT 10|1 : 10/489 CTTCTGAAAT MATRIX 5 number of sequences = 10 unadjusted information = 12.8161 sample size adjusted information = 11.0985 ln(p-value) = -104.511 p-value = 4.08735E-46 ln(expected frequency) = -31.2466 expected frequency = 2.69012E-14 A | 8 0 0 0 0 0 10 10 9 0 C | 2 7 0 6 0 1 0 0 0 0 G | 0 0 0 0 0 9 0 0 1 0 T | 0 3 10 4 10 0 0 0 0 10 1|2 : 3/489 CTTCTGAAAT 2|10 : 7/274 ACTTTGAAGT 3|3 : 9/29 ACTCTGAAAT 4|4 : 9/39 ACTCTGAAAT 5|6 : 9/76 ACTTTGAAAT 6|5 : 9/86 ACTCTGAAAT 7|7 : 9/123 ACTTTGAAAT 8|8 : 9/133 ACTCTGAAAT 9|1 : 10/489 CTTCTGAAAT 10|9 : 13/373 ATTTTCAAAT MATRIX 6 number of sequences = 10 unadjusted information = 12.6478 sample size adjusted information = 10.9302 ln(p-value) = -102.284 p-value = 3.79174E-45 ln(expected frequency) = -29.0191 expected frequency = 2.49556E-13 A | 8 0 0 0 0 0 10 10 9 0 C | 2 6 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 4 10 5 10 0 0 0 0 10 1|2 : 3/489 CTTCTGAAAT 2|8 : 4/373 ATTTTCAAAT 3|10 : 7/274 ACTTTGAAGT 4|3 : 9/29 ACTCTGAAAT 5|4 : 9/39 ACTCTGAAAT 6|6 : 9/76 ACTTTGAAAT 7|7 : 9/123 ACTTTGAAAT 8|5 : 9/133 ACTCTGAAAT 9|1 : 10/489 CTTCTGAAAT 10|9 : 13/373 ATTTTCAAAT MATRIX 7 number of sequences = 10 unadjusted information = 12.6478 sample size adjusted information = 10.9302 ln(p-value) = -102.284 p-value = 3.79174E-45 ln(expected frequency) = -29.0191 expected frequency = 2.49556E-13 A | 8 0 0 0 0 0 10 10 9 0 C | 2 6 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 4 10 5 10 0 0 0 0 10 1|9 : 3/489 CTTCTGAAAT 2|7 : 4/373 ATTTTCAAAT 3|6 : 7/274 ACTTTGAAGT 4|3 : 9/29 ACTCTGAAAT 5|2 : 9/76 ACTTTGAAAT 6|4 : 9/86 ACTCTGAAAT 7|1 : 9/123 ACTTTGAAAT 8|5 : 9/133 ACTCTGAAAT 9|10 : 10/489 CTTCTGAAAT 10|8 : 13/373 ATTTTCAAAT MATRIX 8 number of sequences = 10 unadjusted information = 12.6478 sample size adjusted information = 10.9302 ln(p-value) = -102.284 p-value = 3.79174E-45 ln(expected frequency) = -29.0191 expected frequency = 2.49556E-13 A | 8 0 0 0 0 0 10 10 9 0 C | 2 6 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 4 10 5 10 0 0 0 0 10 1|2 : 3/489 CTTCTGAAAT 2|8 : 4/373 ATTTTCAAAT 3|10 : 7/274 ACTTTGAAGT 4|3 : 9/29 ACTCTGAAAT 5|4 : 9/39 ACTCTGAAAT 6|6 : 9/76 ACTTTGAAAT 7|5 : 9/86 ACTCTGAAAT 8|7 : 9/123 ACTTTGAAAT 9|1 : 10/489 CTTCTGAAAT 10|9 : 13/373 ATTTTCAAAT MATRIX 9 number of sequences = 10 unadjusted information = 12.6478 sample size adjusted information = 10.9302 ln(p-value) = -102.284 p-value = 3.79174E-45 ln(expected frequency) = -29.0191 expected frequency = 2.49556E-13 A | 8 0 0 0 0 0 10 10 9 0 C | 2 6 0 5 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 4 10 5 10 0 0 0 0 10 1|9 : 3/489 CTTCTGAAAT 2|7 : 4/373 ATTTTCAAAT 3|6 : 7/274 ACTTTGAAGT 4|3 : 9/39 ACTCTGAAAT 5|2 : 9/76 ACTTTGAAAT 6|4 : 9/86 ACTCTGAAAT 7|1 : 9/123 ACTTTGAAAT 8|5 : 9/133 ACTCTGAAAT 9|10 : 10/489 CTTCTGAAAT 10|8 : 13/373 ATTTTCAAAT MATRIX 10 number of sequences = 10 unadjusted information = 12.6269 sample size adjusted information = 10.9093 ln(p-value) = -102.008 p-value = 4.99364E-45 ln(expected frequency) = -28.7438 expected frequency = 3.2866E-13 A | 8 0 0 0 0 0 10 10 9 0 C | 2 6 0 6 0 2 0 0 0 0 G | 0 0 0 0 0 8 0 0 1 0 T | 0 4 10 4 10 0 0 0 0 10 1|9 : 3/489 CTTCTGAAAT 2|7 : 4/373 ATTTTCAAAT 3|6 : 7/274 ACTTTGAAGT 4|2 : 9/29 ACTCTGAAAT 5|3 : 9/39 ACTCTGAAAT 6|1 : 9/86 ACTCTGAAAT 7|5 : 9/123 ACTTTGAAAT 8|4 : 9/133 ACTCTGAAAT 9|10 : 10/489 CTTCTGAAAT 10|8 : 13/373 ATTTTCAAAT