COMMAND LINE: /usr/local/BEST/bin/consensus-v6c -f all_XA.cs -L 10 -q 1000 -A a:t c:g -c0 -pr2 -n 10 -pt 0 -pf 10 ***** PID: 27815 ***** 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_XA.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 Total number of sequences: 21. Total number of sequence fragments: 21. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 10521 A 0.204068; observed occurrence = 2147 (letter 1) C 0.298261; observed occurrence = 3138 (letter 2) G 0.306910; observed occurrence = 3229 (letter 3) T 0.190761; observed occurrence = 2007 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.204068 letter 2: C (complement: G) prior frequency = 0.298261 letter 3: G (complement: C) prior frequency = 0.306910 letter 4: T (complement: A) prior frequency = 0.190761 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 [] 10332 | 2.9328 | 0.0000 [] 9.2430 [] 2 [] 538 | 7.7824 | -27.3245 [] -9.5318 [] 3 [] 930 | 10.2299 | -43.6990 [] -17.7620 [] 4 [] 596 | 10.5761 | -49.5579 [] -15.7645 [] 5 [] 896 | 11.3100 | -62.5608 [] -21.1343 [] 6 [] 672 | 11.3960 | -71.3847 [] -22.5074 [] 7 [] 861 | 11.7421 | -83.9814 [] -27.8075 [] 8 [] 713 | 11.7081 | -93.1317 [] -29.7951 [] 9 [] 839 | 11.6157 | -101.8250 [] -31.4433 [] 10 [] 742 | 11.4784 | -110.0045 [] -32.6832 [] 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 742): MATRIX 1 number of sequences = 10 unadjusted information = 13.195 sample size adjusted information = 11.4784 ln(p-value) = -110.004 p-value = 1.68137E-48 ln(expected frequency) = -32.6832 expected frequency = 6.39518E-15 A | 0 0 0 0 0 0 0 0 0 0 C | 0 0 1 1 0 9 5 0 6 0 G | 0 0 0 0 0 1 0 0 0 0 T | 10 10 9 9 10 0 5 10 4 10 1|10 : 1/417 TTTTTCTTCT 2|1 : 2/404 TTTTTCCTCT 3|7 : 3/94 TTCTTCTTCT 4|5 : 3/289 TTTTTCTTTT 5|3 : 11/417 TTTTTCTTCT 6|8 : 12/132 TTTTTGCTCT 7|2 : 12/404 TTTTTCCTCT 8|4 : 13/72 TTTTTCCTTT 9|9 : 13/97 TTTCTCCTTT 10|6 : 13/289 TTTTTCTTTT MATRIX 2 number of sequences = 10 unadjusted information = 13.1481 sample size adjusted information = 11.4315 ln(p-value) = -109.363 p-value = 3.19263E-48 ln(expected frequency) = -32.042 expected frequency = 1.21433E-14 A | 0 0 1 0 0 0 0 0 0 0 C | 0 0 1 0 0 8 4 0 7 0 G | 0 0 0 0 0 2 0 0 0 0 T | 10 10 8 10 10 0 6 10 3 10 1|3 : 1/417 TTTTTCTTCT 2|1 : 2/404 TTTTTCCTCT 3|7 : 3/94 TTCTTCTTCT 4|8 : 3/289 TTTTTCTTTT 5|10 : 8/327 TTATTGTTCT 6|5 : 11/417 TTTTTCTTCT 7|9 : 12/132 TTTTTGCTCT 8|2 : 12/404 TTTTTCCTCT 9|4 : 13/72 TTTTTCCTTT 10|6 : 13/289 TTTTTCTTTT MATRIX 3 number of sequences = 10 unadjusted information = 13.0854 sample size adjusted information = 11.3688 ln(p-value) = -108.509 p-value = 7.50495E-48 ln(expected frequency) = -31.1873 expected frequency = 2.85454E-14 A | 0 0 2 0 0 0 0 0 0 0 C | 0 0 1 0 0 8 3 0 7 0 G | 0 0 0 0 0 2 0 0 0 0 T | 10 10 7 10 10 0 7 10 3 10 1|4 : 1/417 TTTTTCTTCT 2|8 : 2/404 TTTTTCCTCT 3|7 : 3/94 TTCTTCTTCT 4|6 : 3/289 TTTTTCTTTT 5|2 : 8/327 TTATTGTTCT 6|3 : 11/417 TTTTTCTTCT 7|9 : 12/404 TTTTTCCTCT 8|10 : 13/72 TTTTTCCTTT 9|5 : 13/289 TTTTTCTTTT 10|1 : 18/330 TTATTGTTCT MATRIX 4 number of sequences = 10 unadjusted information = 13.0582 sample size adjusted information = 11.3416 ln(p-value) = -108.139 p-value = 1.0864E-47 ln(expected frequency) = -30.8174 expected frequency = 4.13217E-14 A | 0 0 2 0 0 0 0 0 0 0 C | 0 0 0 0 0 6 3 0 6 0 G | 0 0 0 0 0 3 0 0 0 0 T | 10 10 8 10 10 1 7 10 4 10 1|4 : 1/417 TTTTTCTTCT 2|7 : 2/399 TTTTTTTTTT 3|6 : 3/289 TTTTTCTTTT 4|2 : 8/327 TTATTGTTCT 5|3 : 11/417 TTTTTCTTCT 6|9 : 12/132 TTTTTGCTCT 7|10 : 12/404 TTTTTCCTCT 8|8 : 13/72 TTTTTCCTTT 9|5 : 13/289 TTTTTCTTTT 10|1 : 18/330 TTATTGTTCT MATRIX 5 number of sequences = 10 unadjusted information = 13.0548 sample size adjusted information = 11.3382 ln(p-value) = -108.092 p-value = 1.13777E-47 ln(expected frequency) = -30.7712 expected frequency = 4.32755E-14 A | 0 0 1 0 0 0 0 0 0 0 C | 0 0 0 1 0 8 5 0 6 0 G | 0 0 0 0 0 2 0 0 0 0 T | 10 10 9 9 10 0 5 10 4 10 1|4 : 1/417 TTTTTCTTCT 2|6 : 2/404 TTTTTCCTCT 3|2 : 3/289 TTTTTCTTTT 4|10 : 8/327 TTATTGTTCT 5|5 : 11/417 TTTTTCTTCT 6|8 : 12/132 TTTTTGCTCT 7|7 : 12/404 TTTTTCCTCT 8|1 : 13/72 TTTTTCCTTT 9|9 : 13/97 TTTCTCCTTT 10|3 : 13/289 TTTTTCTTTT MATRIX 6 number of sequences = 10 unadjusted information = 13.0378 sample size adjusted information = 11.3212 ln(p-value) = -107.862 p-value = 1.43323E-47 ln(expected frequency) = -30.5403 expected frequency = 5.45138E-14 A | 0 0 2 0 0 0 0 0 0 0 C | 0 0 1 0 0 7 3 0 8 0 G | 0 0 0 0 0 3 0 0 0 0 T | 10 10 7 10 10 0 7 10 2 10 1|4 : 1/417 TTTTTCTTCT 2|8 : 2/404 TTTTTCCTCT 3|7 : 3/94 TTCTTCTTCT 4|6 : 3/289 TTTTTCTTTT 5|2 : 8/327 TTATTGTTCT 6|3 : 11/417 TTTTTCTTCT 7|10 : 12/132 TTTTTGCTCT 8|9 : 12/404 TTTTTCCTCT 9|5 : 13/289 TTTTTCTTTT 10|1 : 18/330 TTATTGTTCT MATRIX 7 number of sequences = 10 unadjusted information = 13.0152 sample size adjusted information = 11.2986 ln(p-value) = -107.555 p-value = 1.94746E-47 ln(expected frequency) = -30.2337 expected frequency = 7.40727E-14 A | 0 0 0 0 0 0 0 0 0 0 C | 0 0 1 1 0 8 4 0 5 0 G | 0 0 0 0 0 1 0 0 0 0 T | 10 10 9 9 10 1 6 10 5 10 1|2 : 1/417 TTTTTCTTCT 2|4 : 2/399 TTTTTTTTTT 3|7 : 3/94 TTCTTCTTCT 4|10 : 3/289 TTTTTCTTTT 5|1 : 11/417 TTTTTCTTCT 6|8 : 12/132 TTTTTGCTCT 7|6 : 12/404 TTTTTCCTCT 8|5 : 13/72 TTTTTCCTTT 9|9 : 13/97 TTTCTCCTTT 10|3 : 13/289 TTTTTCTTTT MATRIX 8 number of sequences = 10 unadjusted information = 13.0061 sample size adjusted information = 11.2895 ln(p-value) = -107.432 p-value = 2.20312E-47 ln(expected frequency) = -30.1104 expected frequency = 8.37967E-14 A | 0 0 0 0 0 0 0 0 0 0 C | 0 0 1 2 0 10 4 0 6 0 G | 0 0 1 0 0 0 0 0 0 0 T | 10 10 8 8 10 0 6 10 4 10 1|3 : 1/417 TTTTTCTTCT 2|1 : 2/404 TTTTTCCTCT 3|7 : 3/94 TTCTTCTTCT 4|8 : 3/289 TTTTTCTTTT 5|10 : 11/151 TTGCTCTTCT 6|5 : 11/417 TTTTTCTTCT 7|2 : 12/404 TTTTTCCTCT 8|4 : 13/72 TTTTTCCTTT 9|9 : 13/97 TTTCTCCTTT 10|6 : 13/289 TTTTTCTTTT MATRIX 9 number of sequences = 10 unadjusted information = 13.0031 sample size adjusted information = 11.2865 ln(p-value) = -107.391 p-value = 2.29452E-47 ln(expected frequency) = -30.0697 expected frequency = 8.72733E-14 A | 0 0 0 2 0 0 0 0 0 0 C | 0 0 1 0 0 10 3 0 5 0 G | 0 0 2 0 0 0 0 0 0 0 T | 10 10 7 8 10 0 7 10 5 10 1|5 : 1/417 TTTTTCTTCT 2|8 : 2/404 TTTTTCCTCT 3|10 : 3/94 TTCTTCTTCT 4|3 : 3/289 TTTTTCTTTT 5|2 : 8/179 TTGATCTTTT 6|6 : 11/417 TTTTTCTTCT 7|9 : 12/404 TTTTTCCTCT 8|7 : 13/72 TTTTTCCTTT 9|4 : 13/289 TTTTTCTTTT 10|1 : 18/182 TTGATCTTTT MATRIX 10 number of sequences = 10 unadjusted information = 12.9807 sample size adjusted information = 11.2641 ln(p-value) = -107.088 p-value = 3.10759E-47 ln(expected frequency) = -29.7664 expected frequency = 1.18199E-13 A | 0 0 1 0 0 0 0 0 0 0 C | 0 0 1 0 0 7 3 0 6 0 G | 0 0 0 0 0 2 0 0 0 0 T | 10 10 8 10 10 1 7 10 4 10 1|2 : 1/417 TTTTTCTTCT 2|4 : 2/399 TTTTTTTTTT 3|6 : 3/94 TTCTTCTTCT 4|3 : 3/289 TTTTTCTTTT 5|10 : 8/327 TTATTGTTCT 6|1 : 11/417 TTTTTCTTCT 7|8 : 12/132 TTTTTGCTCT 8|7 : 12/404 TTTTTCCTCT 9|9 : 13/72 TTTTTCCTTT 10|5 : 13/289 TTTTTCTTTT