COMMAND LINE: /usr/local/BEST/bin/consensus-v6c -f all_XB.cs -L 10 -q 1000 -A a:t c:g -c0 -pr2 -n 10 -pt 0 -pf 10 ***** PID: 27820 ***** 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_XB.cs". ***** sequence 1: CfBhoxB1 fragments: 1-501 sequence 2: CfBhoxB2 fragments: 1-501 sequence 3: CfBhoxB3 fragments: 1-501 sequence 4: CfBhoxB4 fragments: 1-501 sequence 5: CfBhoxB5 fragments: 1-501 sequence 6: CfBhoxB6 fragments: 1-501 sequence 7: CfBhoxB7 fragments: 1-501 sequence 8: CfBhoxB8 fragments: 1-501 sequence 9: CfBhoxB9 fragments: 1-501 sequence 10: CfBhoxB13 fragments: 1-501 sequence 11: HsBhoxB1 fragments: 1-501 sequence 12: HsBhoxB2 fragments: 1-501 sequence 13: HsBhoxB3 fragments: 1-501 sequence 14: HsBhoxB4 fragments: 1-501 sequence 15: HsBhoxB5 fragments: 1-501 sequence 16: HsBhoxB6 fragments: 1-501 sequence 17: HsBhoxB7 fragments: 1-501 sequence 18: HsBhoxB8 fragments: 1-501 sequence 19: HsBhoxB9 fragments: 1-501 Total number of sequences: 19. Total number of sequence fragments: 19. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 9519 A 0.218405; observed occurrence = 2079 (letter 1) C 0.276815; observed occurrence = 2635 (letter 2) G 0.282488; observed occurrence = 2689 (letter 3) T 0.222292; observed occurrence = 2116 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.218405 letter 2: C (complement: G) prior frequency = 0.276815 letter 3: G (complement: C) prior frequency = 0.282488 letter 4: T (complement: A) prior frequency = 0.222292 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 [] 9348 | 1.4180 | 0.0000 [] 9.1429 [] 2 [] 518 | 6.5956 | -30.4281 [] -12.8355 [] 3 [] 984 | 9.0806 | -45.6421 [] -20.0054 [] 4 [] 638 | 9.9201 | -48.0269 [] -14.6339 [] 5 [] 935 | 10.6942 | -60.5742 [] -19.6482 [] 6 [] 723 | 10.4908 | -65.1089 [] -16.8323 [] 7 [] 898 | 10.6856 | -74.9888 [] -19.5158 [] 8 [] 807 | 10.7301 | -83.9260 [] -21.3903 [] 9 [] 889 | 10.7805 | -93.4090 [] -23.9284 [] 10 [] 835 | 10.6936 | -101.3426 [] -25.0226 [] 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 835): MATRIX 1 number of sequences = 10 unadjusted information = 12.4059 sample size adjusted information = 10.6936 ln(p-value) = -101.343 p-value = 9.71588E-45 ln(expected frequency) = -25.0226 expected frequency = 1.35773E-11 A | 0 0 2 0 0 0 0 0 0 0 C | 2 0 0 1 0 0 0 10 6 10 G | 0 0 0 0 0 0 0 0 0 0 T | 8 10 8 9 10 10 10 0 4 0 1|9 : 5/39 TTTCTTTCTC 2|2 : 7/138 TTATTTTCCC 3|7 : 8/334 CTTTTTTCCC 4|10 : 8/402 TTTTTTTCTC 5|3 : 10/50 TTTTTTTCCC 6|5 : 13/200 TTTTTTTCTC 7|8 : 15/193 CTTTTTTCCC 8|1 : 17/138 TTATTTTCCC 9|4 : 18/336 TTTTTTTCCC 10|6 : 18/402 TTTTTTTCTC MATRIX 2 number of sequences = 10 unadjusted information = 12.4059 sample size adjusted information = 10.6936 ln(p-value) = -101.343 p-value = 9.71588E-45 ln(expected frequency) = -25.0226 expected frequency = 1.35773E-11 A | 0 0 2 0 0 0 0 0 0 0 C | 0 0 0 1 0 0 2 10 6 10 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 8 9 10 10 8 0 4 0 1|10 : 5/39 TTTCTTTCTC 2|2 : 7/138 TTATTTTCCC 3|8 : 8/335 TTTTTTCCCC 4|5 : 8/402 TTTTTTTCTC 5|3 : 10/50 TTTTTTTCCC 6|7 : 13/200 TTTTTTTCTC 7|9 : 15/194 TTTTTTCCCC 8|1 : 17/138 TTATTTTCCC 9|4 : 18/336 TTTTTTTCCC 10|6 : 18/402 TTTTTTTCTC MATRIX 3 number of sequences = 10 unadjusted information = 12.4059 sample size adjusted information = 10.6936 ln(p-value) = -101.343 p-value = 9.71588E-45 ln(expected frequency) = -25.0226 expected frequency = 1.35773E-11 A | 0 0 2 0 0 0 0 0 0 0 C | 0 0 0 1 0 0 2 10 6 10 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 8 9 10 10 8 0 4 0 1|2 : 7/138 TTATTTTCCC 2|8 : 8/335 TTTTTTCCCC 3|5 : 8/402 TTTTTTTCTC 4|3 : 10/50 TTTTTTTCCC 5|7 : 13/200 TTTTTTTCTC 6|10 : 15/29 TTTCTTTCTC 7|9 : 15/194 TTTTTTCCCC 8|1 : 17/138 TTATTTTCCC 9|4 : 18/336 TTTTTTTCCC 10|6 : 18/402 TTTTTTTCTC MATRIX 4 number of sequences = 10 unadjusted information = 12.4059 sample size adjusted information = 10.6936 ln(p-value) = -101.343 p-value = 9.71588E-45 ln(expected frequency) = -25.0226 expected frequency = 1.35773E-11 A | 0 0 2 0 0 0 0 0 0 0 C | 2 0 0 1 0 0 0 10 6 10 G | 0 0 0 0 0 0 0 0 0 0 T | 8 10 8 9 10 10 10 0 4 0 1|2 : 7/138 TTATTTTCCC 2|7 : 8/334 CTTTTTTCCC 3|8 : 8/402 TTTTTTTCTC 4|3 : 10/50 TTTTTTTCCC 5|5 : 13/200 TTTTTTTCTC 6|10 : 15/29 TTTCTTTCTC 7|9 : 15/193 CTTTTTTCCC 8|1 : 17/138 TTATTTTCCC 9|4 : 18/336 TTTTTTTCCC 10|6 : 18/402 TTTTTTTCTC MATRIX 5 number of sequences = 10 unadjusted information = 12.3787 sample size adjusted information = 10.6664 ln(p-value) = -100.962 p-value = 1.42107E-44 ln(expected frequency) = -24.6424 expected frequency = 1.98586E-11 A | 0 0 1 0 0 0 0 0 2 0 C | 0 0 0 0 0 0 4 10 5 10 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 9 10 10 10 6 0 3 0 1|2 : 7/300 TTTTTTCCAC 2|4 : 8/335 TTTTTTCCCC 3|8 : 8/402 TTTTTTTCTC 4|5 : 10/50 TTTTTTTCCC 5|7 : 13/200 TTTTTTTCTC 6|3 : 15/194 TTTTTTCCCC 7|10 : 17/138 TTATTTTCCC 8|1 : 17/300 TTTTTTCCAC 9|6 : 18/336 TTTTTTTCCC 10|9 : 18/402 TTTTTTTCTC MATRIX 6 number of sequences = 10 unadjusted information = 12.3787 sample size adjusted information = 10.6664 ln(p-value) = -100.962 p-value = 1.42107E-44 ln(expected frequency) = -24.6424 expected frequency = 1.98586E-11 A | 0 0 1 0 0 0 0 0 2 0 C | 0 0 0 0 0 0 4 10 5 10 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 9 10 10 10 6 0 3 0 1|9 : 7/138 TTATTTTCCC 2|2 : 7/300 TTTTTTCCAC 3|4 : 8/335 TTTTTTCCCC 4|10 : 8/402 TTTTTTTCTC 5|5 : 10/50 TTTTTTTCCC 6|7 : 13/200 TTTTTTTCTC 7|3 : 15/194 TTTTTTCCCC 8|1 : 17/300 TTTTTTCCAC 9|6 : 18/336 TTTTTTTCCC 10|8 : 18/402 TTTTTTTCTC MATRIX 7 number of sequences = 10 unadjusted information = 12.3648 sample size adjusted information = 10.6525 ln(p-value) = -100.768 p-value = 1.72537E-44 ln(expected frequency) = -24.4484 expected frequency = 2.4111E-11 A | 0 0 0 0 0 0 0 1 0 0 C | 0 0 0 4 0 0 0 8 0 6 G | 0 0 0 1 0 0 0 0 0 0 T | 10 10 10 5 10 10 10 1 10 4 1|5 : 5/39 TTTCTTTCTC 2|9 : 7/61 TTTGTTTCTT 3|7 : 8/322 TTTCTTTCTT 4|2 : 8/402 TTTTTTTCTC 5|3 : 10/48 TTTTTTTTTC 6|10 : 13/162 TTTTTTTATT 7|4 : 13/200 TTTTTTTCTC 8|6 : 15/29 TTTCTTTCTC 9|8 : 18/323 TTTCTTTCTT 10|1 : 18/402 TTTTTTTCTC MATRIX 8 number of sequences = 10 unadjusted information = 12.3523 sample size adjusted information = 10.64 ln(p-value) = -100.594 p-value = 2.05396E-44 ln(expected frequency) = -24.274 expected frequency = 2.87028E-11 A | 0 0 0 0 0 0 0 1 0 0 C | 0 0 0 4 0 0 0 8 1 7 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 10 6 10 10 10 1 9 3 1|5 : 5/39 TTTCTTTCTC 2|9 : 8/322 TTTCTTTCTT 3|2 : 8/402 TTTTTTTCTC 4|3 : 10/48 TTTTTTTTTC 5|10 : 13/162 TTTTTTTATT 6|4 : 13/200 TTTTTTTCTC 7|7 : 15/29 TTTCTTTCTC 8|8 : 18/323 TTTCTTTCTT 9|6 : 18/336 TTTTTTTCCC 10|1 : 18/402 TTTTTTTCTC MATRIX 9 number of sequences = 10 unadjusted information = 12.3483 sample size adjusted information = 10.636 ln(p-value) = -100.538 p-value = 2.17172E-44 ln(expected frequency) = -24.2183 expected frequency = 3.03485E-11 A | 0 0 0 0 0 0 0 0 0 0 C | 0 0 0 4 0 0 0 9 1 7 G | 0 0 0 1 0 0 0 0 0 0 T | 10 10 10 5 10 10 10 1 9 3 1|5 : 5/39 TTTCTTTCTC 2|9 : 7/61 TTTGTTTCTT 3|7 : 8/322 TTTCTTTCTT 4|2 : 8/402 TTTTTTTCTC 5|3 : 10/48 TTTTTTTTTC 6|4 : 13/200 TTTTTTTCTC 7|6 : 15/29 TTTCTTTCTC 8|8 : 18/323 TTTCTTTCTT 9|10 : 18/336 TTTTTTTCCC 10|1 : 18/402 TTTTTTTCTC MATRIX 10 number of sequences = 10 unadjusted information = 12.3421 sample size adjusted information = 10.6298 ln(p-value) = -100.452 p-value = 2.36767E-44 ln(expected frequency) = -24.1319 expected frequency = 3.30868E-11 A | 0 0 0 0 0 0 0 0 0 0 C | 0 0 0 5 0 1 0 9 1 8 G | 0 0 0 0 0 0 0 0 0 0 T | 10 10 10 5 10 9 10 1 9 2 1|9 : 4/164 TTTCTCTCTC 2|5 : 5/39 TTTCTTTCTC 3|8 : 8/322 TTTCTTTCTT 4|2 : 8/402 TTTTTTTCTC 5|3 : 10/48 TTTTTTTTTC 6|4 : 13/200 TTTTTTTCTC 7|7 : 15/29 TTTCTTTCTC 8|10 : 18/323 TTTCTTTCTT 9|6 : 18/336 TTTTTTTCCC 10|1 : 18/402 TTTTTTTCTC