COMMAND LINE: /usr/local/BEST/bin/consensus-v6c -f all_XC.cs -L 10 -q 1000 -A a:t c:g -c0 -pr2 -n 10 -pt 0 -pf 10 ***** PID: 27823 ***** 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_XC.cs". ***** sequence 1: CfChoxC4 fragments: 1-501 sequence 2: CfChoxC5 fragments: 1-501 sequence 3: CfChoxC6 fragments: 1-501 sequence 4: CfChoxC10 fragments: 1-501 sequence 5: CfChoxC11 fragments: 1-501 sequence 6: CfChoxC12 fragments: 1-501 sequence 7: CfChoxC13 fragments: 1-501 sequence 8: HsChoxC4 fragments: 1-501 sequence 9: HsChoxC5 fragments: 1-501 Total number of sequences: 9. Total number of sequence fragments: 9. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 4509 A 0.224884; observed occurrence = 1014 (letter 1) C 0.301619; observed occurrence = 1360 (letter 2) G 0.266356; observed occurrence = 1201 (letter 3) T 0.207141; observed occurrence = 934 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.224884 letter 2: C (complement: G) prior frequency = 0.301619 letter 3: G (complement: C) prior frequency = 0.266356 letter 4: T (complement: A) prior frequency = 0.207141 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 [] 4428 | 1.9844 | 0.0000 [] 8.3957 [] 2 [] 556 | 7.1491 | -31.4871 [] -15.3891 [] 3 [] 966 | 8.8020 | -35.2741 [] -11.8794 [] 4 [] 778 | 10.1046 | -48.6562 [] -18.2528 [] 5 [] 928 | 10.1709 | -54.4471 [] -17.2584 [] 6 [] 883 | 10.5310 | -64.8538 [] -21.0623 [] 7 [] 937 | 10.5891 | -73.3102 [] -23.0702 [] 8 [] 948 | 10.5270 | -80.9794 [] -24.4247 [] 9 [] 959 | 10.3200 | -87.0513 [] -24.2999 [] 10 [] 938 | 10.2224 | -94.4821 [] -25.6397 [] 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 938): MATRIX 1 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|10 : 2/412 AGAACAAAAA 3|7 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|3 : 6/254 AAAAAAAAAA 8|1 : 6/266 AAAAAAAAAA 9|6 : 8/314 ACAAAAAAAT 10|9 : 9/416 AGAACAAAAA MATRIX 2 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|7 : 1/313 ACAAAAAAAA 2|1 : 2/412 AGAACAAAAA 3|9 : 3/252 AAAAAGAAAT 4|10 : 3/452 AGAAATAAAT 5|3 : 4/438 AAAAAAAAAA 6|6 : 5/102 AAAAAAAAAT 7|4 : 6/254 AAAAAAAAAA 8|5 : 6/264 AAAAAAAAAA 9|8 : 8/314 ACAAAAAAAT 10|2 : 9/416 AGAACAAAAA MATRIX 3 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|9 : 2/412 AGAACAAAAA 3|7 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|1 : 6/256 AAAAAAAAAA 8|3 : 6/266 AAAAAAAAAA 9|6 : 8/314 ACAAAAAAAT 10|10 : 9/416 AGAACAAAAA MATRIX 4 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|9 : 2/412 AGAACAAAAA 3|7 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|3 : 6/255 AAAAAAAAAA 8|1 : 6/267 AAAAAAAAAA 9|6 : 8/314 ACAAAAAAAT 10|10 : 9/416 AGAACAAAAA MATRIX 5 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|1 : 1/313 ACAAAAAAAA 2|9 : 2/412 AGAACAAAAA 3|6 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|5 : 5/102 AAAAAAAAAT 7|3 : 6/255 AAAAAAAAAA 8|4 : 6/266 AAAAAAAAAA 9|7 : 8/314 ACAAAAAAAT 10|10 : 9/416 AGAACAAAAA MATRIX 6 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|9 : 2/412 AGAACAAAAA 3|6 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|3 : 5/102 AAAAAAAAAT 7|1 : 6/257 AAAAAAAAAA 8|4 : 6/267 AAAAAAAAAA 9|7 : 8/314 ACAAAAAAAT 10|10 : 9/416 AGAACAAAAA MATRIX 7 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|6 : 1/313 ACAAAAAAAA 2|10 : 2/412 AGAACAAAAA 3|1 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|3 : 4/438 AAAAAAAAAA 6|2 : 5/102 AAAAAAAAAT 7|4 : 6/254 AAAAAAAAAA 8|5 : 6/265 AAAAAAAAAA 9|7 : 8/314 ACAAAAAAAT 10|9 : 9/416 AGAACAAAAA MATRIX 8 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|10 : 2/412 AGAACAAAAA 3|7 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|1 : 6/255 AAAAAAAAAA 8|3 : 6/265 AAAAAAAAAA 9|6 : 8/314 ACAAAAAAAT 10|9 : 9/416 AGAACAAAAA MATRIX 9 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|9 : 2/412 AGAACAAAAA 3|7 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|3 : 6/254 AAAAAAAAAA 8|1 : 6/267 AAAAAAAAAA 9|6 : 8/314 ACAAAAAAAT 10|10 : 9/416 AGAACAAAAA MATRIX 10 number of sequences = 10 unadjusted information = 11.9358 sample size adjusted information = 10.2224 ln(p-value) = -94.4821 p-value = 9.2667E-42 ln(expected frequency) = -25.6397 expected frequency = 7.32523E-12 A | 10 5 10 10 8 8 10 10 10 6 C | 0 2 0 0 2 0 0 0 0 0 G | 0 3 0 0 0 1 0 0 0 0 T | 0 0 0 0 0 1 0 0 0 4 1|5 : 1/313 ACAAAAAAAA 2|10 : 2/412 AGAACAAAAA 3|6 : 3/252 AAAAAGAAAT 4|8 : 3/452 AGAAATAAAT 5|2 : 4/438 AAAAAAAAAA 6|4 : 5/102 AAAAAAAAAT 7|1 : 6/256 AAAAAAAAAA 8|3 : 6/267 AAAAAAAAAA 9|7 : 8/314 ACAAAAAAAT 10|9 : 9/416 AGAACAAAAA