COMMAND LINE: /home/njones/profiles/extern/bin/consensus-v6c -A A:T G:C -L 16 -c0 ***** PID: 15692 ***** L-mer Width: 16 Minimum distance between starting points of words: not relevant 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: one match per sequence. Stop only when the maximum number of cycles is reached. The number of matrices to print. Top Matrices saved from each cycle: 4 Matrices Saved from the last cycle: 4 ***** Sequence information from the standard input. ***** sequence 1: 1041553598-28-0 fragments: 1-1501 sequence 2: 1041553598-28-1 fragments: 1-1501 sequence 3: 1041553598-28-10 fragments: 1-1501 sequence 4: 1041553598-28-11 fragments: 1-1501 sequence 5: 1041553598-28-12 fragments: 1-1501 sequence 6: 1041553598-28-13 fragments: 1-1501 sequence 7: 1041553598-28-14 fragments: 1-1501 sequence 8: 1041553598-28-15 fragments: 1-1501 sequence 9: 1041553598-28-16 fragments: 1-1501 sequence 10: 1041553598-28-17 fragments: 1-1501 sequence 11: 1041553598-28-18 fragments: 1-1501 sequence 12: 1041553598-28-19 fragments: 1-1501 sequence 13: 1041553598-28-2 fragments: 1-1501 sequence 14: 1041553598-28-3 fragments: 1-1501 sequence 15: 1041553598-28-4 fragments: 1-1501 sequence 16: 1041553598-28-5 fragments: 1-1501 sequence 17: 1041553598-28-6 fragments: 1-1501 sequence 18: 1041553598-28-7 fragments: 1-1501 sequence 19: 1041553598-28-8 fragments: 1-1501 sequence 20: 1041553598-28-9 fragments: 1-1501 Total number of sequences: 20. Total number of sequence fragments: 20. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 30020 A 0.249933; observed occurrence = 7503 (letter 1) G 0.245003; observed occurrence = 7355 (letter 2) C 0.252298; observed occurrence = 7574 (letter 3) T 0.252765; observed occurrence = 7588 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from the command line. ***** letter 1: A (complement: T) prior frequency = 0.249933 letter 2: G (complement: C) prior frequency = 0.245003 letter 3: C (complement: G) prior frequency = 0.252298 letter 4: T (complement: A) prior frequency = 0.252765 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 [] 29720 | 0.1995 | 0.0000 [] 10.2996 [] 2 [] 516 | 7.7135 | -19.9338 [] -0.0791 [] 3 [] 973 | 9.7310 | -28.8188 [] 0.1315 [] 4 [] 875 | 10.6984 | -37.8727 [] -0.1716 [] 5 [] 948 | 10.8940 | -44.7456 [] 1.4224 [] 6 [] 923 | 11.2349 | -53.9821 [] 0.4061 [] 7 [] 947 | 11.2213 | -61.4507 [] 0.9345 [] 8 [] 938 | 11.4407 | -71.5891 [] -1.4146 [] 9 [] 950 | 11.4858 | -80.7174 [] -2.9513 [] 10 [] 948 | 11.4882 | -89.7613 [] -4.5961 [] 11 [] 948 | 11.5020 | -99.2138 [] -6.8400 [] 12 [] 950 | 11.5363 | -109.1869 [] -9.7970 [] 13 [] 952 | 11.5484 | -119.0925 [] -12.8842 [] 14 [] 938 | 11.4955 | -128.1758 [] -15.3569 [] 15 [] 938 | 11.4426 | -137.2863 [] -18.0798 [] 16 [] 939 | 11.3937 | -146.4738 [] -21.1266 [] 17 [] 943 | 11.2931 | -154.7161 [] -23.5120 [] 18 [] 925 | 11.1873 | -162.7463 [] -26.0301 [] 19 [] 955 | 11.0495 | -169.9946 [] -28.2258 [] 20 [] 943 | 10.9031 | -176.8594 [] -30.7825 [] 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 TOP MATRICES FROM EACH CYCLE--sorted by expected frequency (total of 19): MATRIX 1 number of sequences = 20 unadjusted information = 12.1676 sample size adjusted information = 10.9031 ln(p-value) = -176.859 p-value = 1.55224E-77 ln(expected frequency) = -30.7825 expected frequency = 4.27892E-14 A | 20 0 15 0 7 9 19 5 13 0 8 0 0 0 16 0 G | 0 13 0 3 0 4 0 5 0 5 0 0 3 0 0 12 C | 0 7 0 17 0 2 0 2 0 15 12 6 16 12 0 8 T | 0 0 5 0 13 5 1 8 7 0 0 14 1 8 4 0 1|10 : 1/1248 AGACTCATAGATCCTC 2|12 : 2/1218 AGACATAGACATCCAG 3|13 : 3/324 AGACAGAAACACCTAG 4|7 : 4/128 ACTCTGATACCTCTAG 5|19 : 5/1151 AGTCATAGTCATGTTG 6|18 : 6/1431 AGTCTAAGTCCTCCAC 7|5 : 7/133 AGACTAATACCCGCAG 8|1 : 8/827 ACACTTATTGCCCTAC 9|16 : 9/1117 AGAGTTATTCATCCTG 10|15 : 10/519 AGAGATAAACCTCTAG 11|8 : 11/301 ACTCTGACTCCTGCAG 12|17 : 12/1383 AGAGAAATACCTTCAG 13|14 : 13/628 AGTCAAACACCCCTAC 14|11 : 14/440 AGACACAAACCTCCAC 15|2 : 15/1313 ACACTAATAGCCCTAC 16|9 : 16/1429 ACACTAAGACATCCTG 17|20 : 17/563 AGACTATGACACCTAC 18|6 : 18/235 ACACTGATACATCCAG 19|4 : 19/1029 AGACTAAATGCTCCAG 20|3 : 20/70 ACACTAAATGCTCCAC MATRIX 2 number of sequences = 19 unadjusted information = 12.3857 sample size adjusted information = 11.0495 ln(p-value) = -169.995 p-value = 1.48696E-74 ln(expected frequency) = -28.2258 expected frequency = 5.51679E-13 A | 19 0 15 0 6 9 18 5 13 0 7 0 0 0 16 0 G | 0 12 0 3 0 4 0 4 0 5 0 0 2 0 0 11 C | 0 7 0 16 0 2 0 2 0 14 12 6 16 12 0 8 T | 0 0 4 0 13 4 1 8 6 0 0 13 1 7 3 0 1|6 : 1/1248 AGACTCATAGATCCTC 2|12 : 2/1218 AGACATAGACATCCAG 3|11 : 3/324 AGACAGAAACACCTAG 4|8 : 4/128 ACTCTGATACCTCTAG 5|3 : 6/1431 AGTCTAAGTCCTCCAC 6|10 : 7/133 AGACTAATACCCGCAG 7|19 : 8/827 ACACTTATTGCCCTAC 8|17 : 9/1117 AGAGTTATTCATCCTG 9|15 : 10/519 AGAGATAAACCTCTAG 10|18 : 11/301 ACTCTGACTCCTGCAG 11|16 : 12/1383 AGAGAAATACCTTCAG 12|14 : 13/628 AGTCAAACACCCCTAC 13|4 : 14/440 AGACACAAACCTCCAC 14|9 : 15/1313 ACACTAATAGCCCTAC 15|5 : 16/1429 ACACTAAGACATCCTG 16|13 : 17/563 AGACTATGACACCTAC 17|7 : 18/235 ACACTGATACATCCAG 18|2 : 19/1029 AGACTAAATGCTCCAG 19|1 : 20/70 ACACTAAATGCTCCAC MATRIX 3 number of sequences = 18 unadjusted information = 12.6039 sample size adjusted information = 11.1873 ln(p-value) = -162.746 p-value = 2.09009E-71 ln(expected frequency) = -26.0301 expected frequency = 4.95743E-12 A | 18 0 15 0 6 9 17 5 13 0 7 0 0 0 15 0 G | 0 12 0 3 0 3 0 4 0 5 0 0 1 0 0 10 C | 0 6 0 15 0 2 0 1 0 13 11 6 16 11 0 8 T | 0 0 3 0 12 4 1 8 5 0 0 12 1 7 3 0 1|8 : 1/1248 AGACTCATAGATCCTC 2|6 : 2/1218 AGACATAGACATCCAG 3|12 : 3/324 AGACAGAAACACCTAG 4|16 : 4/128 ACTCTGATACCTCTAG 5|3 : 6/1431 AGTCTAAGTCCTCCAC 6|9 : 7/133 AGACTAATACCCGCAG 7|11 : 8/827 ACACTTATTGCCCTAC 8|15 : 9/1117 AGAGTTATTCATCCTG 9|14 : 10/519 AGAGATAAACCTCTAG 10|17 : 12/1383 AGAGAAATACCTTCAG 11|18 : 13/628 AGTCAAACACCCCTAC 12|4 : 14/440 AGACACAAACCTCCAC 13|10 : 15/1313 ACACTAATAGCCCTAC 14|5 : 16/1429 ACACTAAGACATCCTG 15|13 : 17/563 AGACTATGACACCTAC 16|7 : 18/235 ACACTGATACATCCAG 17|2 : 19/1029 AGACTAAATGCTCCAG 18|1 : 20/70 ACACTAAATGCTCCAC MATRIX 4 number of sequences = 17 unadjusted information = 12.8005 sample size adjusted information = 11.2931 ln(p-value) = -154.716 p-value = 6.42173E-68 ln(expected frequency) = -23.512 expected frequency = 6.15002E-11 A | 17 0 15 0 5 8 16 5 12 0 7 0 0 0 14 0 G | 0 11 0 3 0 3 0 4 0 5 0 0 1 0 0 10 C | 0 6 0 14 0 2 0 0 0 12 10 5 15 11 0 7 T | 0 0 2 0 12 4 1 8 5 0 0 12 1 6 3 0 1|8 : 1/1248 AGACTCATAGATCCTC 2|6 : 2/1218 AGACATAGACATCCAG 3|12 : 3/324 AGACAGAAACACCTAG 4|16 : 4/128 ACTCTGATACCTCTAG 5|3 : 6/1431 AGTCTAAGTCCTCCAC 6|9 : 7/133 AGACTAATACCCGCAG 7|11 : 8/827 ACACTTATTGCCCTAC 8|15 : 9/1117 AGAGTTATTCATCCTG 9|14 : 10/519 AGAGATAAACCTCTAG 10|17 : 12/1383 AGAGAAATACCTTCAG 11|4 : 14/440 AGACACAAACCTCCAC 12|10 : 15/1313 ACACTAATAGCCCTAC 13|5 : 16/1429 ACACTAAGACATCCTG 14|13 : 17/563 AGACTATGACACCTAC 15|7 : 18/235 ACACTGATACATCCAG 16|2 : 19/1029 AGACTAAATGCTCCAG 17|1 : 20/70 ACACTAAATGCTCCAC 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 943): MATRIX 1 number of sequences = 20 unadjusted information = 12.1676 sample size adjusted information = 10.9031 ln(p-value) = -176.859 p-value = 1.55224E-77 ln(expected frequency) = -30.7825 expected frequency = 4.27892E-14 A | 20 0 15 0 7 9 19 5 13 0 8 0 0 0 16 0 G | 0 13 0 3 0 4 0 5 0 5 0 0 3 0 0 12 C | 0 7 0 17 0 2 0 2 0 15 12 6 16 12 0 8 T | 0 0 5 0 13 5 1 8 7 0 0 14 1 8 4 0 1|10 : 1/1248 AGACTCATAGATCCTC 2|12 : 2/1218 AGACATAGACATCCAG 3|13 : 3/324 AGACAGAAACACCTAG 4|7 : 4/128 ACTCTGATACCTCTAG 5|19 : 5/1151 AGTCATAGTCATGTTG 6|18 : 6/1431 AGTCTAAGTCCTCCAC 7|5 : 7/133 AGACTAATACCCGCAG 8|1 : 8/827 ACACTTATTGCCCTAC 9|16 : 9/1117 AGAGTTATTCATCCTG 10|15 : 10/519 AGAGATAAACCTCTAG 11|8 : 11/301 ACTCTGACTCCTGCAG 12|17 : 12/1383 AGAGAAATACCTTCAG 13|14 : 13/628 AGTCAAACACCCCTAC 14|11 : 14/440 AGACACAAACCTCCAC 15|2 : 15/1313 ACACTAATAGCCCTAC 16|9 : 16/1429 ACACTAAGACATCCTG 17|20 : 17/563 AGACTATGACACCTAC 18|6 : 18/235 ACACTGATACATCCAG 19|4 : 19/1029 AGACTAAATGCTCCAG 20|3 : 20/70 ACACTAAATGCTCCAC MATRIX 2 number of sequences = 20 unadjusted information = 12.1125 sample size adjusted information = 10.848 ln(p-value) = -175.695 p-value = 4.97142E-77 ln(expected frequency) = -29.6185 expected frequency = 1.37043E-13 A | 19 0 15 0 6 8 19 5 13 0 9 0 0 0 15 0 G | 0 13 0 2 0 5 0 5 0 5 0 0 3 0 0 12 C | 0 7 0 18 0 2 0 3 0 15 11 6 17 11 0 8 T | 1 0 5 0 14 5 1 7 7 0 0 14 0 9 5 0 1|8 : 1/1248 AGACTCATAGATCCTC 2|6 : 2/1218 AGACATAGACATCCAG 3|16 : 3/324 AGACAGAAACACCTAG 4|11 : 4/128 ACTCTGATACCTCTAG 5|20 : 5/1151 AGTCATAGTCATGTTG 6|3 : 6/1431 AGTCTAAGTCCTCCAC 7|9 : 7/133 AGACTAATACCCGCAG 8|12 : 8/827 ACACTTATTGCCCTAC 9|17 : 9/1117 AGAGTTATTCATCCTG 10|15 : 10/519 AGAGATAAACCTCTAG 11|18 : 11/301 ACTCTGACTCCTGCAG 12|19 : 12/997 TGACTGACACATCTTG 13|14 : 13/628 AGTCAAACACCCCTAC 14|4 : 14/440 AGACACAAACCTCCAC 15|10 : 15/1313 ACACTAATAGCCCTAC 16|5 : 16/1429 ACACTAAGACATCCTG 17|13 : 17/563 AGACTATGACACCTAC 18|7 : 18/235 ACACTGATACATCCAG 19|2 : 19/1029 AGACTAAATGCTCCAG 20|1 : 20/70 ACACTAAATGCTCCAC MATRIX 3 number of sequences = 20 unadjusted information = 12.0588 sample size adjusted information = 10.7942 ln(p-value) = -174.561 p-value = 1.54509E-76 ln(expected frequency) = -28.4845 expected frequency = 4.25923E-13 A | 20 0 14 0 8 10 19 5 13 1 8 0 0 0 16 0 G | 0 13 0 3 0 4 0 6 0 4 0 0 3 0 0 13 C | 0 7 0 17 0 1 0 2 0 15 12 6 16 11 0 7 T | 0 0 6 0 12 5 1 7 7 0 0 14 1 9 4 0 1|20 : 1/671 AGTCAAAGAAATCTTG 2|12 : 2/1218 AGACATAGACATCCAG 3|11 : 3/324 AGACAGAAACACCTAG 4|7 : 4/128 ACTCTGATACCTCTAG 5|19 : 5/1151 AGTCATAGTCATGTTG 6|5 : 6/1431 AGTCTAAGTCCTCCAC 7|6 : 7/133 AGACTAATACCCGCAG 8|1 : 8/827 ACACTTATTGCCCTAC 9|16 : 9/1117 AGAGTTATTCATCCTG 10|15 : 10/519 AGAGATAAACCTCTAG 11|8 : 11/301 ACTCTGACTCCTGCAG 12|18 : 12/1383 AGAGAAATACCTTCAG 13|9 : 13/628 AGTCAAACACCCCTAC 14|17 : 14/440 AGACACAAACCTCCAC 15|2 : 15/1313 ACACTAATAGCCCTAC 16|13 : 16/1429 ACACTAAGACATCCTG 17|14 : 17/563 AGACTATGACACCTAC 18|10 : 18/235 ACACTGATACATCCAG 19|4 : 19/1029 AGACTAAATGCTCCAG 20|3 : 20/70 ACACTAAATGCTCCAC MATRIX 4 number of sequences = 20 unadjusted information = 11.984 sample size adjusted information = 10.7195 ln(p-value) = -172.987 p-value = 7.46015E-76 ln(expected frequency) = -26.91 expected frequency = 2.05648E-12 A | 20 0 14 0 7 8 19 5 13 0 7 0 0 1 15 0 G | 0 13 0 3 0 4 0 5 0 5 0 0 3 0 0 13 C | 0 7 0 17 0 2 0 2 0 15 13 5 16 12 0 7 T | 0 0 6 0 13 6 1 8 7 0 0 15 1 7 5 0 1|10 : 1/1248 AGACTCATAGATCCTC 2|12 : 2/1218 AGACATAGACATCCAG 3|13 : 3/324 AGACAGAAACACCTAG 4|7 : 4/128 ACTCTGATACCTCTAG 5|19 : 5/1151 AGTCATAGTCATGTTG 6|18 : 6/1431 AGTCTAAGTCCTCCAC 7|5 : 7/133 AGACTAATACCCGCAG 8|1 : 8/827 ACACTTATTGCCCTAC 9|16 : 9/1117 AGAGTTATTCATCCTG 10|15 : 10/519 AGAGATAAACCTCTAG 11|8 : 11/301 ACTCTGACTCCTGCAG 12|17 : 12/1383 AGAGAAATACCTTCAG 13|14 : 13/628 AGTCAAACACCCCTAC 14|11 : 14/440 AGACACAAACCTCCAC 15|2 : 15/1313 ACACTAATAGCCCTAC 16|9 : 16/1429 ACACTAAGACATCCTG 17|20 : 17/23 AGTCTTTGACCTCATG 18|6 : 18/235 ACACTGATACATCCAG 19|4 : 19/1029 AGACTAAATGCTCCAG 20|3 : 20/70 ACACTAAATGCTCCAC