COMMAND LINE: /usr/local/BEST/bin/consensus-v6c -f all_XX.cs -L 10 -q 1000 -A a:t c:g -c0 -pr2 -n 10 -pt 0 -pf 10 ***** PID: 27827 ***** 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_XX.cs". ***** sequence 1: CfAhoxA1 fragments: 1-501 sequence 2: CfAhoxA2 fragments: 1-501 sequence 3: CfAhoxA3 fragments: 1-501 sequence 4: CfAhoxA4 fragments: 1-501 sequence 5: CfAhoxA5 fragments: 1-501 sequence 6: CfAhoxA6 fragments: 1-501 sequence 7: CfAhoxA7 fragments: 1-501 sequence 8: CfAhoxA9 fragments: 1-501 sequence 9: CfAhoxA10 fragments: 1-501 sequence 10: HsA fragments: 1-501 sequence 11: HsAhoxa1 fragments: 1-501 sequence 12: HsAhoxa2 fragments: 1-501 sequence 13: HsAhoxa3 fragments: 1-501 sequence 14: HsAhoxa4 fragments: 1-501 sequence 15: HsAhoxa5 fragments: 1-501 sequence 16: HsAhoxa6 fragments: 1-501 sequence 17: HsAhoxa7 fragments: 1-501 sequence 18: HsAhoxa9 fragments: 1-501 sequence 19: HsAhoxa10 fragments: 1-501 sequence 20: HsAhoxa11 fragments: 1-501 sequence 21: HsAhoxa13 fragments: 1-501 sequence 22: CfBhoxB1 fragments: 1-501 sequence 23: CfBhoxB2 fragments: 1-501 sequence 24: CfBhoxB3 fragments: 1-501 sequence 25: CfBhoxB4 fragments: 1-501 sequence 26: CfBhoxB5 fragments: 1-501 sequence 27: CfBhoxB6 fragments: 1-501 sequence 28: CfBhoxB7 fragments: 1-501 sequence 29: CfBhoxB8 fragments: 1-501 sequence 30: CfBhoxB9 fragments: 1-501 sequence 31: CfBhoxB13 fragments: 1-501 sequence 32: HsBhoxB1 fragments: 1-501 sequence 33: HsBhoxB2 fragments: 1-501 sequence 34: HsBhoxB3 fragments: 1-501 sequence 35: HsBhoxB4 fragments: 1-501 sequence 36: HsBhoxB5 fragments: 1-501 sequence 37: HsBhoxB6 fragments: 1-501 sequence 38: HsBhoxB7 fragments: 1-501 sequence 39: HsBhoxB8 fragments: 1-501 sequence 40: HsBhoxB9 fragments: 1-501 sequence 41: CfChoxC4 fragments: 1-501 sequence 42: CfChoxC5 fragments: 1-501 sequence 43: CfChoxC6 fragments: 1-501 sequence 44: CfChoxC10 fragments: 1-501 sequence 45: CfChoxC11 fragments: 1-501 sequence 46: CfChoxC12 fragments: 1-501 sequence 47: CfChoxC13 fragments: 1-501 sequence 48: HsChoxC4 fragments: 1-501 sequence 49: HsChoxC5 fragments: 1-501 sequence 50: CfDhoxD1 fragments: 1-501 sequence 51: CfDhoxD3 fragments: 1-501 sequence 52: CfDhoxD4 fragments: 1-501 sequence 53: CfDhoxD10 fragments: 1-501 sequence 54: CfDhoxD11 fragments: 1-501 sequence 55: CfDhoxD12 fragments: 1-501 sequence 56: CfDhoxD13 fragments: 1-501 sequence 57: HsDhoxD1 fragments: 1-501 sequence 58: HsDhoxD3 fragments: 1-501 sequence 59: HsDhoxD4 fragments: 1-501 sequence 60: HsDhoxD8 fragments: 1-501 sequence 61: HsDhoxD9 fragments: 1-501 sequence 62: HsDhoxD10 fragments: 1-501 sequence 63: HsDhoxD11 fragments: 1-501 Total number of sequences: 63. Total number of sequence fragments: 63. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 31563 A 0.208472; observed occurrence = 6580 (letter 1) C 0.291702; observed occurrence = 9207 (letter 2) G 0.296043; observed occurrence = 9344 (letter 3) T 0.203783; observed occurrence = 6432 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.208472 letter 2: C (complement: G) prior frequency = 0.291702 letter 3: G (complement: C) prior frequency = 0.296043 letter 4: T (complement: A) prior frequency = 0.203783 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 [] 30996 | 2.2023 | 0.0000 [] 10.3416 [] 2 [] 578 | 7.3459 | -31.8140 [] -11.8240 [] 3 [] 912 | 9.8093 | -47.7210 [] -18.4880 [] 4 [] 678 | 11.2610 | -63.6280 [] -25.4398 [] 5 [] 883 | 11.9795 | -71.9121 [] -24.9918 [] 6 [] 744 | 12.6354 | -87.6406 [] -32.1706 [] 7 [] 858 | 13.1122 | -103.3644 [] -39.4990 [] 8 [] 795 | 13.4698 | -119.0659 [] -46.9385 [] 9 [] 944 | 13.4005 | -128.9316 [] -48.6600 [] 10 [] 942 | 13.3968 | -140.3383 [] -52.0280 [] 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 942): MATRIX 1 number of sequences = 10 unadjusted information = 15.1115 sample size adjusted information = 13.3968 ln(p-value) = -140.338 p-value = 1.12681E-61 ln(expected frequency) = -52.028 expected frequency = 2.53813E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 2 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|3 : 20/275 AAAAAAAAAA 2|4 : 23/321 AAAAAAAAAA 3|6 : 27/232 AAAAAAAAAA 4|5 : 37/232 AAAAAAAAAA 5|2 : 41/313 ACAAAAAAAA 6|7 : 44/438 AAAAAAAAAA 7|8 : 46/254 AAAAAAAAAA 8|9 : 46/265 AAAAAAAAAA 9|1 : 56/72 ACAAAAAAAA 10|10 : 56/172 AAAAAAAAAA MATRIX 2 number of sequences = 10 unadjusted information = 15.1115 sample size adjusted information = 13.3968 ln(p-value) = -140.338 p-value = 1.12681E-61 ln(expected frequency) = -52.028 expected frequency = 2.53813E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 2 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|3 : 20/275 AAAAAAAAAA 2|4 : 23/321 AAAAAAAAAA 3|6 : 27/232 AAAAAAAAAA 4|5 : 37/232 AAAAAAAAAA 5|2 : 41/313 ACAAAAAAAA 6|7 : 44/438 AAAAAAAAAA 7|8 : 46/254 AAAAAAAAAA 8|9 : 46/264 AAAAAAAAAA 9|1 : 56/72 ACAAAAAAAA 10|10 : 56/173 AAAAAAAAAA MATRIX 3 number of sequences = 10 unadjusted information = 15.1115 sample size adjusted information = 13.3968 ln(p-value) = -140.338 p-value = 1.12681E-61 ln(expected frequency) = -52.028 expected frequency = 2.53812E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 2 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|3 : 20/275 AAAAAAAAAA 2|4 : 23/321 AAAAAAAAAA 3|6 : 27/232 AAAAAAAAAA 4|5 : 37/232 AAAAAAAAAA 5|2 : 41/313 ACAAAAAAAA 6|7 : 44/438 AAAAAAAAAA 7|8 : 46/254 AAAAAAAAAA 8|9 : 46/264 AAAAAAAAAA 9|1 : 56/72 ACAAAAAAAA 10|10 : 56/172 AAAAAAAAAA MATRIX 4 number of sequences = 10 unadjusted information = 15.1115 sample size adjusted information = 13.3968 ln(p-value) = -140.338 p-value = 1.12681E-61 ln(expected frequency) = -52.028 expected frequency = 2.53812E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 2 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|3 : 20/275 AAAAAAAAAA 2|4 : 23/321 AAAAAAAAAA 3|6 : 27/232 AAAAAAAAAA 4|5 : 37/232 AAAAAAAAAA 5|2 : 41/313 ACAAAAAAAA 6|7 : 44/438 AAAAAAAAAA 7|8 : 46/254 AAAAAAAAAA 8|9 : 46/265 AAAAAAAAAA 9|1 : 56/72 ACAAAAAAAA 10|10 : 56/173 AAAAAAAAAA MATRIX 5 number of sequences = 10 unadjusted information = 15.1086 sample size adjusted information = 13.3939 ln(p-value) = -140.289 p-value = 1.18347E-61 ln(expected frequency) = -51.979 expected frequency = 2.66575E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 2 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|1 : 2/361 AGAAAAAAAA 2|2 : 12/363 AGAAAAAAAA 3|3 : 20/275 AAAAAAAAAA 4|4 : 23/321 AAAAAAAAAA 5|6 : 27/232 AAAAAAAAAA 6|5 : 37/232 AAAAAAAAAA 7|8 : 44/438 AAAAAAAAAA 8|7 : 46/254 AAAAAAAAAA 9|9 : 46/264 AAAAAAAAAA 10|10 : 56/172 AAAAAAAAAA MATRIX 6 number of sequences = 10 unadjusted information = 15.1086 sample size adjusted information = 13.3939 ln(p-value) = -140.289 p-value = 1.18347E-61 ln(expected frequency) = -51.979 expected frequency = 2.66576E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 2 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|1 : 2/361 AGAAAAAAAA 2|2 : 12/363 AGAAAAAAAA 3|3 : 20/275 AAAAAAAAAA 4|4 : 23/321 AAAAAAAAAA 5|6 : 27/232 AAAAAAAAAA 6|5 : 37/232 AAAAAAAAAA 7|8 : 44/438 AAAAAAAAAA 8|7 : 46/254 AAAAAAAAAA 9|9 : 46/265 AAAAAAAAAA 10|10 : 56/173 AAAAAAAAAA MATRIX 7 number of sequences = 10 unadjusted information = 15.1086 sample size adjusted information = 13.3939 ln(p-value) = -140.289 p-value = 1.18347E-61 ln(expected frequency) = -51.979 expected frequency = 2.66576E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 2 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|1 : 2/361 AGAAAAAAAA 2|2 : 12/363 AGAAAAAAAA 3|3 : 20/275 AAAAAAAAAA 4|4 : 23/321 AAAAAAAAAA 5|6 : 27/232 AAAAAAAAAA 6|5 : 37/232 AAAAAAAAAA 7|8 : 44/438 AAAAAAAAAA 8|7 : 46/254 AAAAAAAAAA 9|9 : 46/264 AAAAAAAAAA 10|10 : 56/173 AAAAAAAAAA MATRIX 8 number of sequences = 10 unadjusted information = 15.1086 sample size adjusted information = 13.3939 ln(p-value) = -140.289 p-value = 1.18347E-61 ln(expected frequency) = -51.979 expected frequency = 2.66576E-23 A | 10 8 10 10 10 10 10 10 10 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 2 0 0 0 0 0 0 0 0 T | 0 0 0 0 0 0 0 0 0 0 1|1 : 2/361 AGAAAAAAAA 2|2 : 12/363 AGAAAAAAAA 3|3 : 20/275 AAAAAAAAAA 4|4 : 23/321 AAAAAAAAAA 5|6 : 27/232 AAAAAAAAAA 6|5 : 37/232 AAAAAAAAAA 7|8 : 44/438 AAAAAAAAAA 8|7 : 46/254 AAAAAAAAAA 9|9 : 46/265 AAAAAAAAAA 10|10 : 56/172 AAAAAAAAAA MATRIX 9 number of sequences = 10 unadjusted information = 15.0337 sample size adjusted information = 13.319 ln(p-value) = -139.03 p-value = 4.17066E-61 ln(expected frequency) = -50.7193 expected frequency = 9.39438E-23 A | 10 10 9 10 10 10 10 10 9 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 0 1 0 0 0 0 0 1 0 1|2 : 20/275 AAAAAAAAAA 2|3 : 23/321 AAAAAAAAAA 3|6 : 27/232 AAAAAAAAAA 4|4 : 37/232 AAAAAAAAAA 5|5 : 44/438 AAAAAAAAAA 6|9 : 45/103 AAAAAAAATA 7|7 : 46/255 AAAAAAAAAA 8|8 : 46/265 AAAAAAAAAA 9|10 : 56/169 AATAAAAAAA 10|1 : 56/180 AAAAAAAAAA MATRIX 10 number of sequences = 10 unadjusted information = 15.0337 sample size adjusted information = 13.319 ln(p-value) = -139.03 p-value = 4.17066E-61 ln(expected frequency) = -50.7193 expected frequency = 9.39438E-23 A | 10 9 10 10 10 10 10 10 9 10 C | 0 0 0 0 0 0 0 0 0 0 G | 0 0 0 0 0 0 0 0 0 0 T | 0 1 0 0 0 0 0 0 1 0 1|2 : 20/275 AAAAAAAAAA 2|3 : 23/322 AAAAAAAAAA 3|4 : 27/232 AAAAAAAAAA 4|6 : 37/232 AAAAAAAAAA 5|5 : 44/438 AAAAAAAAAA 6|9 : 45/103 AAAAAAAATA 7|7 : 46/255 AAAAAAAAAA 8|8 : 46/265 AAAAAAAAAA 9|10 : 56/170 ATAAAAAAAA 10|1 : 56/180 AAAAAAAAAA