COMMAND LINE: PhyloCon-v3b -a alphabet -f LEU3.pcons -s 1 -o1 ***** PID: 23543 ***** Number of standard deviations to adjust before identifying matrix peaks: 1 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: 200 Status of complementary sequence: IGNORE. Algorithim options: one match per sequence. Stop only when the maximum number of cycles is reached. Do NOT permit terminal gaps. Matrices to print for each cycle: 4 ***** Sequence information from file "LEU3.pcons". ***** sequence 1: YGL125W Gene Index: 1 Ortholog Index: 1 fragments: 1-380 sequence 2: 4906 Gene Index: 1 Ortholog Index: 2 fragments: 1-411 sequence 3: 6553 Gene Index: 1 Ortholog Index: 3 fragments: 1-434 sequence 4: 4911 Gene Index: 1 Ortholog Index: 4 fragments: 1-358 sequence 5: YOR108W Gene Index: 2 Ortholog Index: 1 fragments: 1-744 sequence 6: 4906 Gene Index: 2 Ortholog Index: 2 fragments: 1-709 sequence 7: 6553 Gene Index: 2 Ortholog Index: 3 fragments: 1-729 sequence 8: 4911 Gene Index: 2 Ortholog Index: 4 fragments: 1-718 sequence 9: YMR108W Gene Index: 3 Ortholog Index: 1 fragments: 1-722 sequence 10: 4906 Gene Index: 3 Ortholog Index: 2 fragments: 1-711 sequence 11: 6553 Gene Index: 3 Ortholog Index: 3 fragments: 1-710 sequence 12: 4911 Gene Index: 3 Ortholog Index: 4 fragments: 1-725 Total number of sequences: 12. Total number of sequence fragments: 24. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 14702 A 0.324174; observed occurrence = 4766 (letter 1) C 0.175826; observed occurrence = 2585 (letter 2) G 0.175826; observed occurrence = 2585 (letter 3) T 0.324174; observed occurrence = 4766 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from file "alphabet". ***** letter 1: A (complement: T) prior frequency = 0.324174 letter 2: C (complement: G) prior frequency = 0.175826 letter 3: G (complement: C) prior frequency = 0.175826 letter 4: T (complement: A) prior frequency = 0.324174 STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.500 STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.528 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. [] PROFILES SAVED FROM W-CONSENSUS [] []-------------------------------------------------------------[] GENE [] sequence | matrix | saved [] shortest | longest [] Index [] number | number | matrices [] width | width [] ------[]----------|-------------|-------------[]----------|----------[] STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.528 1 [] 4 | 123 | 50 [] 40 | 113 [] STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.528 2 [] 4 | 157 | 50 [] 26 | 108 [] STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.528 3 [] 4 | 144 | 50 [] 29 | 137 [] [] PROFILES SAVED FROM P-CONSENSUS [] []-------------------------------------------------------------[] [] sequence | HSP | saved [] shortest | longest [] CYCLE [] number | number | matrices [] peak | peak [] ------[]----------|-------------|-------------[]----------|----------[] 1 [] 8 | 80351 | 200 [] 10 | 20 [] 2 [] 12 | 43574 | 200 [] 10 | 15 [] THE LIST OF MATRICES FROM EACH CYCLE (sorted by ALLR statistic): CYCLE 1: MATRIX 1-1: Gene groups included: 1 2 number of sequences = 8 width = 15 allr = 16.437 total llr = 131.498 crude_infomation = 12.487 unadjusted information = 18.265 sample size adjusted information = 14.953 ln(p-value) = -106.402 p-value = 6.16842E-47 A | 0 0 0 0 0 7 0 0 0 0 3 0 1 2 0 C | 7 8 0 0 0 0 3 7 0 0 0 7 7 0 1 G | 1 0 8 5 0 1 5 1 8 8 5 1 0 4 0 T | 0 0 0 3 8 0 0 0 0 0 0 0 0 2 7 1|4 : 1/59 CCGGTAGCGGGCCGT 2|2 : 2/59 CCGGTAGCGGGCCTT 3|3 : 3/66 CCGGTAGCGGGCCGT 4|1 : 4/49 CCGGTAGCGGGCCGT 5|5 : -5/463 CCGTTACCGGACCAT 6|8 : -6/449 CCGTTACCGGACCTT 7|7 : -7/451 CCGTTACCGGACCGT 8|6 : -8/23 GCGGTGGGGGGGAAC MATRIX 1-2: Gene groups included: 1 2 number of sequences = 8 width = 10 allr = 16.245 total llr = 129.958 crude_infomation = 11.308 unadjusted information = 15.160 sample size adjusted information = 12.953 ln(p-value) = -104.674 p-value = 3.47336E-46 A | 0 0 0 0 0 8 4 0 0 0 C | 8 8 0 0 0 0 0 8 0 0 G | 0 0 8 8 0 0 4 0 8 8 T | 0 0 0 0 8 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : 5/468 CCGGTAACGG 6|7 : 6/454 CCGGTAACGG 7|6 : 7/456 CCGGTAACGG 8|8 : 8/473 CCGGTAACGG MATRIX 1-3: Gene groups included: 1 3 number of sequences = 8 width = 10 allr = 16.245 total llr = 129.958 crude_infomation = 11.614 unadjusted information = 15.466 sample size adjusted information = 13.258 ln(p-value) = -108.343 p-value = 8.85749E-48 A | 0 0 0 0 0 8 0 0 0 0 C | 8 8 0 0 0 0 4 8 0 0 G | 0 0 8 8 0 0 4 0 8 8 T | 0 0 0 0 8 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : 9/255 CCGGTACCGG 6|6 : 10/261 CCGGTACCGG 7|7 : 11/255 CCGGTACCGG 8|8 : 12/266 CCGGTACCGG MATRIX 1-4: Gene groups included: 1 3 number of sequences = 8 width = 10 allr = 16.245 total llr = 129.958 crude_infomation = 11.614 unadjusted information = 15.466 sample size adjusted information = 13.258 ln(p-value) = -108.343 p-value = 8.8575E-48 A | 0 0 0 0 0 8 0 0 0 0 C | 8 8 0 0 0 0 4 8 0 0 G | 0 0 8 8 0 0 4 0 8 8 T | 0 0 0 0 8 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : -9/255 CCGGTACCGG 6|6 : -10/261 CCGGTACCGG 7|7 : -11/255 CCGGTACCGG 8|8 : -12/266 CCGGTACCGG CYCLE 2: MATRIX 2-1: Gene groups included: 1 2 3 number of sequences = 12 width = 10 allr = 17.510 total llr = 210.119 crude_infomation = 12.148 unadjusted information = 14.682 sample size adjusted information = 13.278 ln(p-value) = -155.925 p-value = 1.91769E-68 A | 0 0 0 0 0 12 0 0 0 0 C | 12 12 0 0 0 0 8 12 0 0 G | 0 0 12 8 0 0 4 0 12 12 T | 0 0 0 4 12 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : -5/468 CCGTTACCGG 6|7 : -6/454 CCGTTACCGG 7|6 : -7/456 CCGTTACCGG 8|8 : -8/473 CCGTTACCGG 9|9 : 9/255 CCGGTACCGG 10|10 : 10/261 CCGGTACCGG 11|11 : 11/255 CCGGTACCGG 12|12 : 12/266 CCGGTACCGG MATRIX 2-2: Gene groups included: 1 2 3 number of sequences = 12 width = 10 allr = 17.510 total llr = 210.119 crude_infomation = 12.148 unadjusted information = 14.682 sample size adjusted information = 13.278 ln(p-value) = -155.925 p-value = 1.91769E-68 A | 0 0 0 0 0 12 0 0 0 0 C | 12 12 0 0 0 0 8 12 0 0 G | 0 0 12 8 0 0 4 0 12 12 T | 0 0 0 4 12 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : -5/468 CCGTTACCGG 6|7 : -6/454 CCGTTACCGG 7|6 : -7/456 CCGTTACCGG 8|8 : -8/473 CCGTTACCGG 9|9 : -9/255 CCGGTACCGG 10|10 : -10/261 CCGGTACCGG 11|11 : -11/255 CCGGTACCGG 12|12 : -12/266 CCGGTACCGG MATRIX 2-3: Gene groups included: 1 2 3 number of sequences = 12 width = 10 allr = 16.310 total llr = 195.717 crude_infomation = 12.322 unadjusted information = 14.857 sample size adjusted information = 13.453 ln(p-value) = -158.721 p-value = 1.16985E-69 A | 0 0 0 0 0 12 4 0 0 0 C | 12 12 0 0 0 0 4 12 0 0 G | 0 0 12 12 0 0 4 0 12 12 T | 0 0 0 0 12 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : 5/468 CCGGTAACGG 6|7 : 6/454 CCGGTAACGG 7|6 : 7/456 CCGGTAACGG 8|8 : 8/473 CCGGTAACGG 9|9 : 9/255 CCGGTACCGG 10|10 : 10/261 CCGGTACCGG 11|11 : 11/255 CCGGTACCGG 12|12 : 12/266 CCGGTACCGG MATRIX 2-4: Gene groups included: 1 2 3 number of sequences = 12 width = 10 allr = 16.310 total llr = 195.717 crude_infomation = 12.322 unadjusted information = 14.857 sample size adjusted information = 13.453 ln(p-value) = -158.721 p-value = 1.16985E-69 A | 0 0 0 0 0 12 4 0 0 0 C | 12 12 0 0 0 0 4 12 0 0 G | 0 0 12 12 0 0 4 0 12 12 T | 0 0 0 0 12 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : 5/468 CCGGTAACGG 6|7 : 6/454 CCGGTAACGG 7|6 : 7/456 CCGGTAACGG 8|8 : 8/473 CCGGTAACGG 9|9 : -9/255 CCGGTACCGG 10|10 : -10/261 CCGGTACCGG 11|11 : -11/255 CCGGTACCGG 12|12 : -12/266 CCGGTACCGG THE LIST OF TOP MATRICES IN ALL CYCLES (sorted by total LLR): MATRIX 1: Gene groups included: 1 2 3 number of sequences = 12 width = 10 allr = 17.510 total llr = 210.119 crude_infomation = 12.148 unadjusted information = 14.682 sample size adjusted information = 13.278 ln(p-value) = -155.925 p-value = 1.91769E-68 A | 0 0 0 0 0 12 0 0 0 0 C | 12 12 0 0 0 0 8 12 0 0 G | 0 0 12 8 0 0 4 0 12 12 T | 0 0 0 4 12 0 0 0 0 0 1|4 : 1/59 CCGGTAGCGG 2|2 : 2/59 CCGGTAGCGG 3|3 : 3/66 CCGGTAGCGG 4|1 : 4/49 CCGGTAGCGG 5|5 : -5/468 CCGTTACCGG 6|7 : -6/454 CCGTTACCGG 7|6 : -7/456 CCGTTACCGG 8|8 : -8/473 CCGTTACCGG 9|9 : 9/255 CCGGTACCGG 10|10 : 10/261 CCGGTACCGG 11|11 : 11/255 CCGGTACCGG 12|12 : 12/266 CCGGTACCGG MATRIX 2: Gene groups included: 1 2 number of sequences = 8 width = 15 allr = 16.437 total llr = 131.498 crude_infomation = 12.487 unadjusted information = 18.265 sample size adjusted information = 14.953 ln(p-value) = -106.402 p-value = 6.16842E-47 A | 0 0 0 0 0 7 0 0 0 0 3 0 1 2 0 C | 7 8 0 0 0 0 3 7 0 0 0 7 7 0 1 G | 1 0 8 5 0 1 5 1 8 8 5 1 0 4 0 T | 0 0 0 3 8 0 0 0 0 0 0 0 0 2 7 1|4 : 1/59 CCGGTAGCGGGCCGT 2|2 : 2/59 CCGGTAGCGGGCCTT 3|3 : 3/66 CCGGTAGCGGGCCGT 4|1 : 4/49 CCGGTAGCGGGCCGT 5|5 : -5/463 CCGTTACCGGACCAT 6|8 : -6/449 CCGTTACCGGACCTT 7|7 : -7/451 CCGTTACCGGACCGT 8|6 : -8/23 GCGGTGGGGGGGAAC