COMMAND LINE: PhyloCon-v3b -f LEU3_2.pcons -a alphabet -s 1 -o1 -u2 ***** PID: 5643 ***** 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_2.pcons". ***** sequence 1: YGL125W Gene Index: 1 Ortholog Index: 1 fragments: 1-58 69-380 sequence 2: 4906 Gene Index: 1 Ortholog Index: 2 fragments: 1-58 69-411 sequence 3: 6553 Gene Index: 1 Ortholog Index: 3 fragments: 1-65 76-434 sequence 4: 4911 Gene Index: 1 Ortholog Index: 4 fragments: 1-48 59-358 sequence 5: YOR108W Gene Index: 2 Ortholog Index: 1 fragments: 1-467 478-744 sequence 6: 4906 Gene Index: 2 Ortholog Index: 2 fragments: 1-453 464-709 sequence 7: 6553 Gene Index: 2 Ortholog Index: 3 fragments: 1-455 466-729 sequence 8: 4911 Gene Index: 2 Ortholog Index: 4 fragments: 1-472 483-718 sequence 9: YMR108W Gene Index: 3 Ortholog Index: 1 fragments: 1-254 265-722 sequence 10: 4906 Gene Index: 3 Ortholog Index: 2 fragments: 1-260 271-711 sequence 11: 6553 Gene Index: 3 Ortholog Index: 3 fragments: 1-254 265-710 sequence 12: 4911 Gene Index: 3 Ortholog Index: 4 fragments: 1-265 276-725 Total number of sequences: 12. Total number of sequence fragments: 48. #**** Information on observed frequency and occurrence of each letter. ****# #Total number of letters in the input sequences = 14462 A 0.327617; observed occurrence = 4738 (letter 1) C 0.172383; observed occurrence = 2493 (letter 2) G 0.172383; observed occurrence = 2493 (letter 3) T 0.327617; observed occurrence = 4738 (letter 4) PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. ***** Information for the alphabet from file "alphabet". ***** letter 1: A (complement: T) prior frequency = 0.327617 letter 2: C (complement: G) prior frequency = 0.172383 letter 3: G (complement: C) prior frequency = 0.172383 letter 4: T (complement: A) prior frequency = 0.327617 STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.500 STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.511 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 0.511 1 [] 4 | 148 | 50 [] 28 | 113 [] STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.511 2 [] 4 | 168 | 50 [] 23 | 104 [] STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO 0.511 3 [] 4 | 142 | 50 [] 17 | 119 [] [] PROFILES SAVED FROM P-CONSENSUS [] []-------------------------------------------------------------[] [] sequence | HSP | saved [] shortest | longest [] CYCLE [] number | number | matrices [] peak | peak [] ------[]----------|-------------|-------------[]----------|----------[] 1 [] 8 | 51282 | 200 [] 9 | 38 [] 2 [] 12 | 18929 | 200 [] 7 | 24 [] THE LIST OF MATRICES FROM EACH CYCLE (sorted by ALLR statistic): CYCLE 1: MATRIX 1-1: Gene groups included: 1 3 number of sequences = 8 width = 20 allr = 14.660 total llr = 117.279 crude_infomation = 8.086 unadjusted information = 15.775 sample size adjusted information = 11.361 ln(p-value) = -62.3064 p-value = 8.7235E-28 A | 3 6 8 8 8 7 6 6 2 5 8 8 7 8 6 7 7 7 4 4 C | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 G | 4 2 0 0 0 1 1 2 5 3 0 0 1 0 0 1 0 0 3 3 T | 1 0 0 0 0 0 1 0 1 0 0 0 0 0 2 0 1 0 0 1 1|4 : 1/218 GAAAAGTAGAAAAAAAAAGG 2|1 : 2/238 GAAAAAAGTAAAAAAAAAAG 3|2 : 3/266 GAAAAAGAAGAAAATAAAAA 4|3 : 4/213 TGAAAAAGGGAAAATAAAAA 5|7 : -9/322 AAAAAAAAAGAAAAAATACG 6|6 : -10/328 AAAAAAAAGAAAAAAGACGA 7|5 : -11/325 AGAAAAAAGAAAGAAAAAGT 8|8 : -12/342 GAAAAAAAGAAAAAAAAAAA MATRIX 1-2: Gene groups included: 1 3 number of sequences = 8 width = 19 allr = 14.533 total llr = 116.267 crude_infomation = 8.605 unadjusted information = 15.910 sample size adjusted information = 11.716 ln(p-value) = -66.8858 p-value = 8.95083E-30 A | 5 7 8 8 8 6 5 6 2 7 8 8 7 6 8 7 7 7 3 C | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 G | 3 1 0 0 0 2 2 1 6 1 0 0 1 0 0 1 0 0 4 T | 0 0 0 0 0 0 1 1 0 0 0 0 0 2 0 0 1 0 0 1|1 : 1/218 GAAAAGTAGAAAAAAAAAG 2|4 : 2/239 AAAAAAGTAAAAAAAAAAG 3|2 : 3/267 AAAAAGAAGAAAATAAAAA 4|3 : 4/214 GAAAAAGGGAAAATAAAAA 5|7 : -9/323 AAAAAAAAAGAAAAAATAC 6|6 : -10/329 AAAAAAAAGAAAAAAGACG 7|5 : -11/326 AGAAAAAAGAAAGAAAAAG 8|8 : -12/343 GAAAAAAAGAAAAAAAAAA MATRIX 1-3: Gene groups included: 1 3 number of sequences = 8 width = 18 allr = 14.330 total llr = 114.641 crude_infomation = 12.380 unadjusted information = 19.299 sample size adjusted information = 15.327 ln(p-value) = -101.064 p-value = 1.2832E-44 A | 0 0 1 0 0 7 8 8 5 6 0 0 7 3 0 0 1 0 C | 7 1 6 0 0 0 0 0 1 0 4 4 0 0 5 0 7 7 G | 0 7 0 8 8 1 0 0 0 2 0 1 1 5 0 8 0 0 T | 1 0 1 0 0 0 0 0 2 0 4 3 0 0 3 0 0 1 1|1 : 1/2 TCAGGAAAAGTTGGCGAT 2|2 : 2/270 CGTGGGAAAGCTAATGCC 3|4 : 3/299 CGCGGAAAAACTAATGCC 4|3 : 4/246 CGCGGAAAAACGAATGCC 5|6 : 9/289 CGCGGAAAAATCAGCGCC 6|8 : 10/295 CGCGGAAATATCAGCGCC 7|7 : 11/290 CGCGGAAACATCAGCGCC 8|5 : 12/299 CGCGGAAATACCAGCGCC MATRIX 1-4: Gene groups included: 1 3 number of sequences = 8 width = 19 allr = 14.229 total llr = 113.830 crude_infomation = 8.738 unadjusted information = 16.043 sample size adjusted information = 11.849 ln(p-value) = -67.9916 p-value = 2.96229E-30 A | 4 7 8 8 8 6 6 6 1 7 8 8 7 6 8 7 7 7 4 C | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 G | 4 1 0 0 0 2 1 2 6 1 0 0 1 0 0 1 0 0 3 T | 0 0 0 0 0 0 1 0 1 0 0 0 0 2 0 0 1 0 0 1|2 : 1/218 GAAAAGTAGAAAAAAAAAG 2|1 : 2/238 GAAAAAAGTAAAAAAAAAA 3|4 : 3/267 AAAAAGAAGAAAATAAAAA 4|3 : 4/214 GAAAAAGGGAAAATAAAAA 5|7 : -9/323 AAAAAAAAAGAAAAAATAC 6|6 : -10/329 AAAAAAAAGAAAAAAGACG 7|5 : -11/326 AGAAAAAAGAAAGAAAAAG 8|8 : -12/343 GAAAAAAAGAAAAAAAAAA CYCLE 2: MATRIX 2-1: Gene groups included: 1 2 3 number of sequences = 12 width = 17 allr = 10.569 total llr = 126.831 crude_infomation = 7.104 unadjusted information = 11.409 sample size adjusted information = 9.021 ln(p-value) = -75.4436 p-value = 1.71899E-33 A | 9 6 2 5 0 0 6 1 0 0 0 0 0 5 3 0 1 C | 1 3 3 0 0 4 0 7 0 1 0 2 1 0 1 2 0 G | 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 T | 0 3 7 7 12 8 6 2 12 11 12 10 11 7 8 10 11 1|10 : -1/222 ACCTTTTTTTTTCTACT 2|12 : -2/248 AATATCACTTTTTTTTT 3|9 : -3/277 AATATCACTTTTTATTT 4|11 : -4/224 AATATCACTTTTTATTT 5|1 : 5/253 AACTTTAGTTTTTATTT 6|4 : 6/375 GCAATTTCTCTTTTCCA 7|2 : 7/254 ATTTTTAGTTTCTAATT 8|3 : 8/275 AACTTTAATTTTTAATT 9|5 : 9/325 ATTTTTTCTTTTTTTTT 10|7 : 10/332 CTTTTTTCTTTTTTTTT 11|6 : 11/325 ACTTTTTCTTTCTTTTT 12|8 : 12/335 GAAATCTTTTTTTTTTT MATRIX 2-2: Gene groups included: 1 2 3 number of sequences = 12 width = 9 allr = 10.379 total llr = 124.551 crude_infomation = 6.868 unadjusted information = 9.148 sample size adjusted information = 7.883 ln(p-value) = -80.8063 p-value = 8.0584E-36 A | 8 0 0 12 0 0 0 12 4 C | 0 0 0 0 4 0 11 0 1 G | 0 0 12 0 0 0 1 0 0 T | 4 12 0 0 8 12 0 0 7 1|9 : 1/128 TTGACTCAA 2|11 : 2/133 TTGACTCAA 3|10 : 3/137 TTGATTCAA 4|12 : 4/299 TTGATTGAA 5|1 : 5/487 ATGACTCAT 6|3 : 6/473 ATGACTCAC 7|2 : 7/475 ATGATTCAT 8|4 : 8/493 ATGATTCAT 9|8 : 9/367 ATGATTCAT 10|5 : 10/373 ATGATTCAT 11|6 : 11/369 ATGATTCAT 12|7 : 12/387 ATGATTCAT MATRIX 2-3: Gene groups included: 1 2 3 number of sequences = 12 width = 20 allr = 10.279 total llr = 123.344 crude_infomation = 8.391 unadjusted information = 13.456 sample size adjusted information = 10.646 ln(p-value) = -88.5555 p-value = 3.47398E-39 A | 1 0 2 8 6 2 5 0 0 7 1 0 0 0 0 0 5 2 0 1 C | 4 0 0 1 2 2 0 0 4 0 8 1 1 0 2 0 0 2 2 0 G | 0 11 1 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 T | 7 1 9 1 4 8 7 12 8 5 1 11 11 12 10 12 7 8 10 10 1|11 : -1/228 CGAAATATCACCTTTTTTTT 2|10 : -2/236 TTTTTTTTTACTTTTTTCCG 3|9 : -3/277 CGAAATATCACTTTTTATTT 4|12 : -4/224 TGTAATATCACTTTTTATTT 5|1 : 5/250 TGTAACTTTAGTTTTTATTT 6|4 : 6/372 AGTGCAATTTCTCTTTTCCA 7|2 : 7/251 TGTATTTTTAGTTTCTAATT 8|3 : 8/272 TGTAACTTTAATTTTTAATT 9|5 : 9/322 CGTATTTTTTCTTTTTTTTT 10|7 : 10/329 CGTCTTTTTTCTTTTTTTTT 11|6 : 11/322 TGTACTTTTTCTTTCTTTTT 12|8 : 12/332 TGGGAAATCTTTTTTTTTTT MATRIX 2-4: Gene groups included: 1 2 3 number of sequences = 12 width = 20 allr = 9.875 total llr = 118.503 crude_infomation = 7.906 unadjusted information = 12.971 sample size adjusted information = 10.161 ln(p-value) = -82.9667 p-value = 9.29041E-37 A | 1 2 1 7 7 2 4 0 0 5 1 0 0 0 0 0 6 2 1 1 C | 3 0 0 3 2 4 1 0 3 0 6 0 1 0 2 0 1 2 1 1 G | 0 10 1 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 T | 8 0 10 0 3 6 7 12 9 7 3 12 11 12 10 12 5 8 10 10 1|9 : -1/223 TATCACCTTTTTTTTTCTAC 2|12 : -2/243 TATCACTTTTTTTTTTACTT 3|11 : -3/277 CGAAATATCACTTTTTATTT 4|10 : -4/224 TGTAATATCACTTTTTATTT 5|1 : 5/250 TGTAACTTTAGTTTTTATTT 6|4 : 6/372 AGTGCAATTTCTCTTTTCCA 7|2 : 7/251 TGTATTTTTAGTTTCTAATT 8|3 : 8/272 TGTAACTTTAATTTTTAATT 9|5 : 9/322 CGTATTTTTTCTTTTTTTTT 10|7 : 10/329 CGTCTTTTTTCTTTTTTTTT 11|6 : 11/322 TGTACTTTTTCTTTCTTTTT 12|8 : 12/332 TGGGAAATCTTTTTTTTTTT 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 = 17 allr = 10.569 total llr = 126.831 crude_infomation = 7.104 unadjusted information = 11.409 sample size adjusted information = 9.021 ln(p-value) = -75.4436 p-value = 1.71899E-33 A | 9 6 2 5 0 0 6 1 0 0 0 0 0 5 3 0 1 C | 1 3 3 0 0 4 0 7 0 1 0 2 1 0 1 2 0 G | 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 T | 0 3 7 7 12 8 6 2 12 11 12 10 11 7 8 10 11 1|10 : -1/222 ACCTTTTTTTTTCTACT 2|12 : -2/248 AATATCACTTTTTTTTT 3|9 : -3/277 AATATCACTTTTTATTT 4|11 : -4/224 AATATCACTTTTTATTT 5|1 : 5/253 AACTTTAGTTTTTATTT 6|4 : 6/375 GCAATTTCTCTTTTCCA 7|2 : 7/254 ATTTTTAGTTTCTAATT 8|3 : 8/275 AACTTTAATTTTTAATT 9|5 : 9/325 ATTTTTTCTTTTTTTTT 10|7 : 10/332 CTTTTTTCTTTTTTTTT 11|6 : 11/325 ACTTTTTCTTTCTTTTT 12|8 : 12/335 GAAATCTTTTTTTTTTT MATRIX 2: Gene groups included: 1 3 number of sequences = 8 width = 20 allr = 14.660 total llr = 117.279 crude_infomation = 8.086 unadjusted information = 15.775 sample size adjusted information = 11.361 ln(p-value) = -62.3064 p-value = 8.7235E-28 A | 3 6 8 8 8 7 6 6 2 5 8 8 7 8 6 7 7 7 4 4 C | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 G | 4 2 0 0 0 1 1 2 5 3 0 0 1 0 0 1 0 0 3 3 T | 1 0 0 0 0 0 1 0 1 0 0 0 0 0 2 0 1 0 0 1 1|4 : 1/218 GAAAAGTAGAAAAAAAAAGG 2|1 : 2/238 GAAAAAAGTAAAAAAAAAAG 3|2 : 3/266 GAAAAAGAAGAAAATAAAAA 4|3 : 4/213 TGAAAAAGGGAAAATAAAAA 5|7 : -9/322 AAAAAAAAAGAAAAAATACG 6|6 : -10/328 AAAAAAAAGAAAAAAGACGA 7|5 : -11/325 AGAAAAAAGAAAGAAAAAGT 8|8 : -12/342 GAAAAAAAGAAAAAAAAAAA