AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_hsp60_hsp10_synecho_reg_300.orf -o257_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY34400 122 Synechocystis #2 RCY25319 96 Synechocystis #3 RCY52064 162 Synechocystis #4 RCY53893 62 Synechocystis #5 RCY48792 300 Synechocystis Motif number 1 ATTGCTTGACCCAGTGCAACACCCCGGTGA 1 11 0 CCAGTGCAAC 0.968049 -112 TCCCACCTCACGAGTGCTAATTTAGCTAAA 1 40 0 CGAGTGCTAA 0.992657 -83 TCGTGAGGTGGGAGTGCTAAACCCTCTCCC 1 57 1 GGAGTGCTAA 0.979515 -66 AGTAAAACCTCGTGGGCAAATTAATGCAAT 2 74 0 CGTGGGCAAA 0.888893 -23 CCATTTAAATCCAGGGCGATCGCCAAGCTC 3 33 1 CCAGGGCGAT 0.929793 -130 TCTTGGCAGTGGAGTGCTAAGTCAGGTAAG 3 82 0 GGAGTGCTAA 0.979515 -81 TCCACTGCCAAGAGTGCTAAAGTGCTTTAT 3 99 1 AGAGTGCTAA 0.968669 -64 GTGCTCTTGTCCGGTGCGATA 5 2 0 CCGGTGCGAT 0.937715 -299 ATCAAAAAGAAGGGTGCGACCAAAATTTTT 5 84 0 AGGGTGCGAC 0.911784 -217 TTAACCCTATCTAGTGCAAACCATAGCATT 5 241 0 CTAGTGCAAA 0.930875 -60 ********** Masking position 9 Map Score: 12.5042 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 210 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 GTTTAGCACTCCCACCTCACGAGTGCTAATTTAGCT 1 43 0 CCCTCAGTGC 0.994404 -80 CAAATTACTACTGACCTTGCAAGACTATCATCTGGA 1 86 1 CCCTCAGACT 0.991026 -37 TAATTTTTACCGATCCTGACCTGTGTTAAAACTTGC 2 17 1 CCCTCTGTGT 0.968728 -80 ACCGGGAAACCGAACCTTACCTGACTTAGCACTCCA 3 67 1 CCCTCTGACT 0.968453 -96 TGACTTAGCACTCCACTGCCAAGAGTGCTAAAGTGC 3 88 1 CACTCAGAGT 0.954878 -75 TAACGTCAAAGGTGGCGGACAAGTCCATAAAGCACT 3 119 0 GGCGCAGTCC 0.836715 -44 CCTGAAAAAATCCTGCTCCCAAGAGCGAGTCACTAA 4 23 0 TGCTCAGAGC 0.97775 -40 TATCGCACCGGACAAGAGCACGGATGCAG 5 4 1 CCCGCAGAGC 0.99114 -297 CAATTAAGATTAACCCTATCTAGTGCAAACCATAGC 5 244 0 TCCTCAGTGC 0.98312 -57 CGAAAATTTTTCCGCTGCCGAGACTGCCGGTCAAT 5 276 0 TGCTCAGACT 0.949116 -25 * *** * ***** Masking position 10 Map Score: 11.9677 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 269 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 AGTGCTAAACCCTCTCCCAAATTACTACTGAC 1 69 1 CCTCTCCCAT 0.96524 -54 AGAAGTCATCCTCCAGATGATAGTCTTG 1 105 0 CATCCTCCAT 0.996219 -18 AATGGGTAAAAATCCTGCAAGTTTTAACACAG 2 37 0 AATCCTGCAT 0.960815 -60 AACGTCCGTTACTCCCCCATTTAAATCCAGGG 3 17 1 ACTCCCCCAT 0.990445 -146 GAAAGTTCCAAATCCTCCAAATACCAATACTT 5 123 1 AATCCTCCAT 0.992221 -178 GGTTAGCTTCCATACTCCAGCTAAGTCCCTCC 5 156 0 CATACTCCAT 0.976052 -145 GAAGCTAACCCCTGCTCCATATTTGCAAGGTA 5 178 1 CCTGCTCCAT 0.986477 -123 ********* * Masking position 9 Map Score: 8.38378 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 307 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 CGGGGTGTTGCACTGGGTCAAGCAATTTAGC 1 15 1 CATGGGTCAA 0.935642 -108 CACAGGTCAGGATCGGTAAAAATTAATCGAC 2 11 0 GACGGTAAAA 0.910695 -86 TGCAATAGATGAATGGGTAAAAATCCTGCAA 2 49 0 GATGGGTAAA 0.983888 -48 CAAGCTCTAAGACCGGGAAACCGAACCTTAC 3 56 1 GACGGGAAAC 0.987189 -107 CTGCTCCCAAGAGCGAGTCACTAAATATACT 4 16 0 GACGAGTCAC 0.902813 -47 CCATAGCATTGAGTGGGTAACTTGTTGTCAA 5 220 0 GATGGGTAAC 0.983567 -81 GTTTGCACTAGATAGGGTTAATCTTAATTGA 5 250 1 GAAGGGTTAA 0.85637 -51 GCAGTCTCGGCAGCGGAAAAATTTTCG 5 284 1 CACGGAAAAA 0.78298 -17 ** ******** Masking position 2 Map Score: 3.67024 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1070 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 5 GTAATTTGGGAGAGGGTTTAGCACTCCCAC 1 64 0 AGAGGGTTTA 0.923492 -59 GTTAAAACTTGCAGGATTTTTACCCATTCA 2 41 1 GCAGGATTTT 0.981648 -56 AATTTGCCCACGAGGTTTTACTTTT 2 82 1 CGAGGTTTTA 0.923492 -15 TGGCGATCGCCCTGGATTTAAATGGGGGAG 3 28 0 CCTGGATTTA 0.915464 -135 GCTCTTGGGAGCAGGATTTTTTCAGGGAGG 4 33 1 GCAGGATTTT 0.981648 -30 ATTGGTATTTGGAGGATTTGGAACTTTCCC 5 121 0 GGAGGATTTG 0.971613 -180 CAAATATGGAGCAGGGGTTAGCTTCCATAC 5 173 0 GCAGGGGTTA 0.962204 -128 ********** Masking position 8 Map Score: 4.44873 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 455 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 CACTGGGTCAAGCAATTTAGCTAAATTAGC 1 25 1 AGCAATTTAG 0.954484 -98 AAGTCCATAAAGCACTTTAGCACTCTTGGC 3 105 0 AGCACTTTAG 0.865835 -58 AGACTAAAAAGTTACAAATAACGTC 3 148 0 AAAAAGTTAC 0.927092 -15 CACGGATGCAGAAAATTTAGAAAGTTTTGA 5 29 1 GAAAATTTAG 0.867471 -272 CCTCCTAGAAAAAAATTTTGGTCGCACCCT 5 74 1 AAAAATTTTG 0.896396 -227 AAGGGTTGACAACAAGTTACCCACTCAATG 5 215 1 AACAAGTTAC 0.940955 -86 TCGGCAGCGGAAAAATTTTCG 5 290 1 AAAAATTTTC 0.789945 -11 ********** Masking position 4 Map Score: 1.49461 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 306 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 GGTTTAGCACTCCCACCTCACGAGTGCTAA 1 50 0 TCCCACCTCA 0.875046 -73 AGAAGTCATCCTCCAGATGATAGT 1 109 0 GTCATCCTCC 0.940237 -14 CAGGGCGATCGCCAAGCTCTAAGACCGGGA 3 44 1 GCCAAGCTCT 0.941927 -119 CCCTGAAAAAATCCTGCTCCCAAGAGCGAG 4 30 0 ATCCTGCTCC 0.945512 -33 ATTTTCTGCATCCGTGCTCTTGTCCGGTGC 5 15 0 TCCGTGCTCT 0.952962 -286 GGGGTTAGCTTCCATACTCCAGCTAAGTCC 5 160 0 TCCATACTCC 0.951425 -141 TGGAAGCTAACCCCTGCTCCATATTTGCAA 5 176 1 CCCCTGCTCC 0.989504 -125 ********** Masking position 8 Map Score: 1.33759 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 954 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 ********** No masking Map Score: 1.20325e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.20325e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 1.20325e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0