AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -isoxS_synecho_opreg_300.orf -g0.48 -x5 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 = 0 Input sequences: #1 1652528 300 hypothetical protein #2 cysK 69 cysteine synthase #3 zwf 106 glucose 6-phosphate dehydrogenase #4 sodB 300 superoxide dismutase #5 murZ 300 UDP-N-acetylglucosamine 1-carboxyvinyltransferase #6 fumC 104 fumarase Motif number 1 TAGGCTAAGCAAGGCCATTGGTCTGTTTTG 1 154 0 AAGGCCATTG 0.979815 -147 CTATACTCAGTAACACATTGTACACGTTTT 1 236 0 TAACACATTG 0.857012 -65 TTACTGAGTATAGGACTTGGTTCCCGTAGT 1 253 1 TAGGACTTGG 0.701448 -48 AAAGAGCGACAAAGCCTTGGTAATCATCGC 4 146 0 AAAGCCTTGG 0.950823 -155 GCTCTTTTTCTTGCCCATGGCCACCGGCAA 4 169 1 TTGCCCATGG 0.799852 -132 GGGTAAAGTGAGAGCCATGGAATCCCCTAT 4 259 1 AGAGCCATGG 0.910097 -42 ATAACTGTTAAAACCCATTGTCTAGGCAAT 5 93 0 AAACCCATTG 0.98163 -208 ATTGCTGCACAAGCCCATCGAATGCTAAAA 5 121 1 AAGCCCATCG 0.946848 -180 CGAATGCTAAAAACACATTGGTTAATGAAC 5 139 1 AAACACATTG 0.929758 -162 GGAGAATTGTCAACCCATTGTTGCTTAGAT 5 217 0 CAACCCATTG 0.934175 -84 GACTGTTGATAATGCCTTTGCCACCGGAGT 6 69 1 AATGCCTTTG 0.787459 -36 ********** Masking position 8 Map Score: 8.03788 Number of sites scoring better than the average of aligned sites = 1724 Number in coding regions = 1570 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 GTCCTGGCTCCCTGAGCTAGCCCGCAAAACAG 1 130 1 CCGACTAGCC 0.959721 -171 GAGCTAGCCCGCAAAACAGACCAATGGCCTTG 1 143 1 GCAACAGACC 0.898498 -158 TAGATGCTAGGCTAAGCAAGGCCATTGGTCTG 1 159 0 GCAACAAGGC 0.958268 -142 TTATTTTAAAGCGTAAGTGGCCACACAATACG 3 75 1 GCTAGTGGCC 0.905026 -32 TTGCTATCGCCCATTTCAAGCCCACCCGCTTA 4 41 0 CCTTCAAGCC 0.904534 -260 AATCATCGCCGCCAACCAAGCCTGACAGTTTT 4 123 0 GCAACAAGCC 0.987747 -178 TGGCGGCGATGATTACCAAGGCTTTGTCGCTC 4 141 1 GATACAAGGC 0.781057 -160 GATACGGACCGCCAAGCTGGGC 5 1 0 GCAACTGGGC 0.902433 -300 GCTTGGCGGTCCGTATCTGGCCGATTTGTAAA 5 16 1 CCTACTGGCC 0.979406 -285 AACAGTTATTGCTGCACAAGCCCATCGAATGC 5 114 1 GCGCCAAGCC 0.967577 -187 CCACCAACGTCCATCCCAGGACAACCCAGACA 5 184 0 CCTCCAGGAC 0.794786 -117 ** ** ****** Masking position 12 Map Score: 7.62115 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 1191 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 AAACATTGCTATCGCCCATTTCAAGCCCAC 4 48 0 ATCGCCCATT 0.984555 -253 CAGTTTTTTAATCCCTTGTTAATCTCTCGG 4 100 0 ATCCCTTGTT 0.832884 -201 CCAAGGCTTTGTCGCTCTTTTTCTTGCCCA 4 156 1 GTCGCTCTTT 0.91843 -145 GAGCCATGGAATCCCCTATTGAGTAGAGAA 4 270 1 ATCCCCTATT 0.975936 -31 GTTAACTTTTGTCCCCTTTTGTTGGAGGTT 5 271 1 GTCCCCTTTT 0.963301 -30 TCGCCCATTAGTCCCCCAATCAAATCAACG 6 17 0 GTCCCCCAAT 0.954544 -88 CTAACAGGCGATCGCCCATTAGTCCCCCAA 6 28 0 ATCGCCCATT 0.984555 -77 ********** Masking position 2 Map Score: 5.46712 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 358 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 GAAGCTGTAGGCGGTTTTTCTTTACCAACACTG 1 91 1 GTTTTTCTTT 0.9882 -210 GGGAGAAGTTGACAATTTTCTTTAGATTCATGG 1 191 0 GATTTTCTTT 0.962199 -110 AACTGAGAAAGAAATTTTTCCTGAAAACTTTGC 3 12 1 GTTTTTCCTG 0.979654 -95 CACAATTCCCGAAAGTTTTCTTTTTCTGGCAAA 3 40 0 GGTTTTCTTT 0.974178 -67 AGGCTTTGTCGCTCTTTTTCTTGCCCATGGCCA 4 159 1 GTTTTTCTTG 0.992463 -142 TCGCCTGTTAGTCTTTTTTCTTGACTGTTGATA 6 47 1 GTTTTTCTTG 0.992463 -58 * ********* Masking position 7 Map Score: 5.37987 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 73 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 GGAACGATGATGTTGATGGTTAATAACAGA 1 54 0 TGTTGATGGT 0.899925 -247 GAGCAGAAGCTGTAGGCGGTTTTTCTTTAC 1 86 1 TGTAGGCGGT 0.972762 -215 TGTCAGGCTTGGTTGGCGGCGATGATTACC 4 128 1 GGTTGGCGGC 0.972692 -173 AAAGACAAAATATTGCCGGTGGCCATGGGC 4 181 0 TATTGCCGGT 0.903496 -120 GCCCAGCTTGGCGGTCCGTATCTGG 5 6 1 GCTTGGCGGT 0.983741 -295 TGTCCCCTTTTGTTGGAGGTTGTGAAAACC 5 280 1 TGTTGGAGGT 0.963785 -21 TAGTCTTTTTTCTTGACTGTTGATAATGCC 6 55 1 TCTTGACTGT 0.797605 -50 ********** Masking position 3 Map Score: 2.989 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 697 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 AAACTGGCCCTGCCCCTAGCCATCACCAAA 1 11 1 TGCCCCTAGC 0.94014 -290 AACATCATCGTTCCGTGAGCAGAAGCTGTA 1 70 1 TTCCGTGAGC 0.962307 -231 GTGGTCCTGGCTCCCTGAGCTAGCCCGCAA 1 127 1 CTCCCTGAGC 0.9759 -174 TAGGACTTGGTTCCCGTAGTCATTATTAGG 1 263 1 TTCCCGTAGT 0.914234 -38 CCTTGTTAATCTCTCGGAGCTACTTAACAA 4 87 0 CTCTCGGAGC 0.939558 -214 GACAAAATATTGCCGGTGGCCATGGGCAAG 4 178 0 TGCCGGTGGC 0.965904 -123 TTTGCAAATACTCCGGTGGCAAAGGCATTA 6 78 0 CTCCGGTGGC 0.980709 -27 ********** Masking position 3 Map Score: 2.33454 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 924 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 AGACCAATGGCCTTGCTTAGCCTAGCATCT 1 160 1 CCTTGCTTAG 0.952372 -141 TTTTGACCTACTTTGATTTGG 4 2 0 CTTTGATTTG 0.947221 -299 CAATGTTTCCCGTTGAATTGTTAAGTAGCT 4 70 1 CGTTGAATTG 0.955884 -231 GTCAACCCATTGTTGCTTAGATTCCACCAA 5 209 0 TGTTGCTTAG 0.911464 -92 AAATTCCGTTGATTTGATTGGGGGAC 6 7 1 CGTTGATTTG 0.986171 -98 ********** Masking position 4 Map Score: 0.783097 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 116 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TTTTAGCTTTTCCTCACACC 1 291 0 TTTTAGCTTT 0.956802 -10 AGTTATTAGAGTTTAACTTTCAAACAAGTG 2 33 0 GTTTAACTTT 0.90714 -37 ATAAGTCAATTTGTAACATTCAGTTTACAA 5 41 0 TTGTAACATT 0.90714 -260 AGACAATGGGTTTTAACAGTTATTGCTGCA 5 100 1 TTTTAACAGT 0.90714 -201 ACCAATGTGTTTTTAGCATTCGATGGGCTT 5 131 0 TTTTAGCATT 0.956802 -170 AAAGGACTGGTGTTAACTTTTGTCCCCTTT 5 260 1 TGTTAACTTT 0.90714 -41 ********** Masking position 5 Map Score: 0.660662 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 74 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 ********** No masking Map Score: -4.38104e-13 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 AAGGCCATTGGTCTGTTTTGCGGGCTAGCTCA 1 142 0 GTCTTTTGCG 0.964397 -159 GTATTGTGTGGCCACTTACGCTTTAAAATAAC 3 74 0 GCCATTAGCT 0.976203 -33 GTCAAAACGAGCCTATTAAGCGGGTGGGCTTG 4 25 1 GCCTTTAGCG 0.991291 -276 TGATTACCAAGGCTTTGTCGCTCTTTTTCTTG 4 150 1 GGCTTGTGCT 0.914342 -151 GCAATATTTTGTCTTTTGTGCGGTTCTCCACC 4 195 1 GTCTTTGGCG 0.957923 -106 CCATTGTCTAGGCAATTATGCTTAACATCCTA 5 77 0 GGCATTAGCT 0.965652 -224 ATGGGCGATCGCCTGTTAGTCTTTTTTCTTGA 6 39 1 GCCTTTATCT 0.924422 -66 **** *** *** Masking position 6 Map Score: 1.80024 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 143 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 CCTGCCCCTAGCCATCACCAAAATAGCAACTAT 1 19 1 GCAACCAAAA 0.98146 -282 TAGGCGGTTTTTCTTTACCAACACTGATTGTGG 1 98 1 TCTACCAACA 0.915906 -203 AGCTCAGGGAGCCAGGACCACAATCAGTGTTGG 1 115 0 GCAACCACAA 0.94216 -186 GGACAACCCAGACAAGATCAACAAATTATGTTC 5 165 0 GCAATCAACA 0.96756 -136 TTGTTGCTTAGATTCCACCAACGTCCATCCCAG 5 197 0 GTTACCAACG 0.879938 -104 TTCTCCCGATGACTAAACCAAAGGACTGGTGTT 5 241 1 GCTACCAAAG 0.964736 -60 CGGTGGCAAAGGCATTATCAACAGTCAAGAAAA 6 62 0 GCAATCAACA 0.96756 -43 * ** ******* Masking position 7 Map Score: 1.30881 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 589 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 12 ********** No masking Map Score: -4.38104e-13 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 13 ********** No masking Map Score: -4.38104e-13 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 14 ********** No masking Map Score: -4.38104e-13 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