AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i176_cobalamin_biosynthesis_1_synecho_reg_100.orf -o176_synecho_100.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 RCY32260 300 Synechocystis #2 RCY35846 218 Synechocystis #3 RCY33500 23 Synechocystis #4 RCY29821 289 Synechocystis #5 RCY44275 57 Synechocystis #6 RCY33343 128 Synechocystis Motif number 1 ACCCAGGGGTGGAGGATGGATTTCTGACCT 2 31 1 GGAGGATGGA 0.887382 -188 GGAAGAAAGCAGGGGAAGATTGTCAACCCA 2 105 0 AGGGGAAGAT 0.942762 -114 GCAAATGGGAGGGGGAAAAACGTTGAGGGA 2 179 0 GGGGGAAAAA 0.983638 -40 TCAGGAGCCTAGGGGATGGTTGGTAACTGG 4 14 1 AGGGGATGGT 0.927745 -276 GGGGAGCCAGGGGGGCTTTTCAAACACTCT 4 159 0 GGGGGCTTTT 0.898335 -131 CCCCAAGTTTGGGGGAAGTTAAGTAAAAGT 4 185 1 GGGGGAAGTT 0.987801 -105 ACCCATTATTGGGGGATTTAGGGGGCAAAA 4 216 1 GGGGGATTTA 0.968049 -74 GGGGGATTTAGGGGGCAAAATAAAACTTTT 4 226 1 GGGGGCAAAA 0.954202 -64 ACAAAAAATAGGGCGATGATCATAGAGCAA 5 16 0 GGGCGATGAT 0.945519 -42 GGGGGATGAGGGGGGATAAAACTAA 6 6 0 GGGGGATAAA 0.988061 -123 CCCTTTCAAAGGGGGATGAGGGGGGATAAA 6 16 0 GGGGGATGAG 0.983518 -113 CCTTTGAAAGGGGGGAAATAATTGTTATTT 6 34 1 GGGGGAAATA 0.976226 -95 ********** Masking position 5 Map Score: 19.305 Number of sites scoring better than the average of aligned sites = 2448 Number in coding regions = 2101 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 306 Fraction of orfs with sites within 600 bp upstream = 0.0491487 Motif number 2 ATTATCATAGAAAATTTTATTATTAGTCTTTG 1 137 0 AAATTTTTTA 0.726295 -164 GACCATTTTAAATATTTAGTTTAAATGCCTAA 1 187 0 AAATTTATTT 0.83969 -114 AATTTTACGCAATTTATAGTTATCGATAAATG 1 230 1 AATTATATTA 0.644236 -71 ACGGACCATCGACATTTATATATTCTCTGTAA 4 111 1 GAATTTAATA 0.861466 -179 AATAATGGGTGACTTTTACTTAACTTCCCCCA 4 194 0 GATTTTATTA 0.967936 -96 TCTGTTTGAAAAGTTTTATTTTGCCCCCTAAA 4 232 0 AATTTTATTT 0.781137 -58 CAGATTCTTAGACATTTATTCATCTTTTTTTC 4 260 1 GAATTTATCA 0.911708 -30 TTGTTTGGAAGAGATTTACTTACAATGCCTTC 6 63 1 GAATTTATTA 0.977874 -66 AAGCTTGGCCGATTTTTAGTGAGGAAATTTAA 6 103 1 GATTTTATGA 0.875825 -26 TTTTAGTGAGGAAATTTAATTAA 6 116 1 GAATTTATTA 0.977731 -13 ** ***** *** Masking position 7 Map Score: 6.05344 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 132 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 GAACGTCCAAAACCCAGGGGTGGAGGATGG 2 20 1 AACCCAGGGG 0.958613 -199 ATGGATTTCTGACCTTAGCGACCCAAACAG 2 46 1 GACCTTAGCG 0.892661 -173 GCTAACAGGCAAGCTTAGGGAAGAAAGCAG 2 123 0 AAGCTTAGGG 0.972315 -96 TTTTCAGGAGCCTAGGGGATGGTTGGT 4 8 1 GAGCCTAGGG 0.982015 -282 CAAACTTGGGGAGCCAGGGGGGCTTTTCAA 4 166 0 GAGCCAGGGG 0.988646 -124 CTGGCTCCCCAAGTTTGGGGGAAGTTAAGT 4 179 1 AAGTTTGGGG 0.953598 -111 ATTATTGGGGGATTTAGGGGGCAAAATAAA 4 220 1 GATTTAGGGG 0.758652 -70 TCTAAAATTTAAGCTTGGCCGATTTTTAGT 6 93 1 AAGCTTGGCC 0.840286 -36 ********** Masking position 2 Map Score: 4.94291 Number of sites scoring better than the average of aligned sites = 1849 Number in coding regions = 1574 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 4 TGATGCTAAAAGATACACTCTCAAC 1 2 1 GTGTAAAGTA 0.907708 -299 TTGCACCAATGATCTTTACAGGAAGCTTGAATGC 1 54 0 GTCTTAAGAA 0.762151 -247 TGCAATTATAGCTGATTAGTACGACTATAAGGTA 1 83 1 GTGTTATAGA 0.840716 -218 AATTTTCTATGATAATAAAAGCGAAAATGACAAT 1 153 1 GTATAAAGGA 0.962436 -148 TATTTAAAATGGTCTTAATTGTGAAAATTTTACG 1 205 1 GTCTAATGGA 0.975389 -96 CCAGTGACGAGATAGCAAATGGGAGGGGGAAAAA 2 189 0 GTACAATGGA 0.87188 -30 CTAGGGGATGGTTGGTAACTGGGATTAATGATTT 4 22 1 GTGTAATGGA 0.986983 -268 TAAATTTAAGGCTGTTTACAGAGAATATATAAAT 4 124 0 GTGTTAAGGA 0.979258 -166 * ** *** ** ** Masking position 8 Map Score: 2.09168 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 131 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 CTCTCAACCATCCTTCAAAGCCTTCTGCAT 1 28 1 TCCTTCAAAG 0.943599 -273 GCCAGGGGGGCTTTTCAAACACTCTCTAAA 4 154 0 CTTTTCAAAC 0.952182 -136 TTACTTAACTTCCCCCAAACTTGGGGAGCC 4 181 0 TCCCCCAAAC 0.906575 -109 CAAAATAAAACTTTTCAAACAGATTCTTAG 4 241 1 CTTTTCAAAC 0.952182 -49 TTATTTCCCCCCTTTCAAAGGGGGATGAGG 6 25 0 CCTTTCAAAG 0.968326 -104 TAAGTAAATCTCTTCCAAACAAAATAACAA 6 55 0 TCTTCCAAAC 0.969702 -74 ********** Masking position 7 Map Score: 2.22252 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 164 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 AGGCAAGCTTAGGGAAGAAAGCAGGGGAAG 2 117 0 AGGGAAGAAA 0.977526 -102 AGCAAATGGGAGGGGGAAAAACGTTGAGGG 2 180 0 AGGGGGAAAA 0.993199 -39 TGGGGGATTTAGGGGGCAAAATAAAACTTT 4 225 1 AGGGGGCAAA 0.988461 -65 GGTGCAGGGAAAAAAAGATGAATAA 4 275 0 AGGGAAAAAA 0.954668 -15 ATTAATCAGTAGCGAGAAAAT 5 47 1 AGCGAGAAAA 0.946526 -11 AAGGGGGATGAGGGGGGATAAAACTAA 6 8 0 AGGGGGGATA 0.981836 -121 CCCCTTTGAAAGGGGGGAAATAATTGTTAT 6 32 1 AGGGGGGAAA 0.996696 -97 GCCGATTTTTAGTGAGGAAATTTAATTAA 6 110 1 AGTGAGGAAA 0.961038 -19 ********** Masking position 8 Map Score: 16.2241 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 526 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 7 GTAAAGATCATTGGTGCAATTATAGCTGAT 1 69 1 TTGGTGCAAT 0.954011 -232 AAAATGACAATTTAGGCATTTAAACTAAAT 1 176 1 TTTAGGCATT 0.885163 -125 TTGTGAAAATTTTACGCAATTTATAGTTAT 1 223 1 TTTACGCAAT 0.801839 -78 GTGTAGCGAATTGGGGCAATCTGTTTGGGT 2 66 0 TTGGGGCAAT 0.992581 -153 GGGAAAAACGTTGAGGGAATACCATGAGCA 2 167 0 TTGAGGGAAT 0.980178 -52 CTCCCCAAGTTTGGGGGAAGTTAAGTAAAA 4 183 1 TTGGGGGAAG 0.96916 -107 TCACCCATTATTGGGGGATTTAGGGGGCAA 4 214 1 TTGGGGGATT 0.977988 -76 ********** Masking position 8 Map Score: 6.62738 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 898 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 8 ********** No masking Map Score: -2.59896e-14 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: -2.59896e-14 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: -2.59896e-14 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