AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_mjan_reg_300.orf -o00271_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ1260 300 SSU ribosomal protein S6E #2 MJ1261 205 translation initiation factor aIF-2, subunit gamma (aif2G) #3 MJ1262 163 conserved hypothetical protein #4 MJ1263 130 methionyl-tRNA synthetase (metS) #5 MJ1388 300 adenosylhomocysteinase (ahcY) Motif number 1 TTAAAACCAAAAATTATTTAAAATATTATGT 1 40 1 AATTATTTAA 0.813974 -261 TGAAATAAAGATATTTATAAAAATGCCCTTA 1 195 1 AATTTATAAA 0.966225 -106 TTGATAAAACAGATTTTTTAAGGGCATTTTT 1 213 0 AATTTTTTAA 0.813974 -88 GTTTGGTTTCTAATTTTTAAATTAACTTTTA 1 248 0 TATTTTTAAA 0.706951 -53 CAAACAAATAACAAAAATAAAAATAGGAGGG 1 274 1 AAAAAATAAA 0.873877 -27 GATAAATAAAATAAAAATAAAATTAGGAGCT 2 20 0 AAAAAATAAA 0.87379 -186 ATTTAAACACAGATAAATAAAATAAAAATAA 2 31 0 AATAAATAAA 0.940168 -175 AATCACCACTACAATATTTAAACACAGATAA 2 46 0 AAATATTTAA 0.658566 -160 TTTATAAGCTAAAATTATAAAAATGTGAAAA 2 116 1 AAATTATAAA 0.926554 -90 GTGTTTTTCAAAGTTAATAAAAATTAAGGAA 2 155 1 AGTTAATAAA 0.895862 -51 AAATTAAGGAATAAATATAAAAGCCCGTAGG 2 175 1 AAAATATAAA 0.87379 -31 TTTGATACTCATATTATTAAAA 3 2 0 AATTATTAAA 0.926555 -162 AAAGGTATTAAAGTTTATTAAGGAAATTTGA 4 22 1 AGTTTATTAA 0.748975 -109 TTAAAAATTAAGATTAATTAAGTAAGTAAAT 5 21 1 AATTAATTAA 0.908449 -280 AATTAATAAAAAGAAAATAAACCTTAAATTT 5 165 0 AGAAAATAAA 0.675677 -136 TATATAAATTAAATTAATAAAAAGAAAATAA 5 176 0 AATTAATAAA 0.966229 -125 TTATAAATTCAAATATATAAATTAAATTAAT 5 189 0 AATATATAAA 0.940168 -112 AAAGCTTTTATTATTTATAAATTCAAATATA 5 203 0 TATTTATAAA 0.84527 -98 AGGGTAGCAGAGATATATAAATTACTATTTT 5 244 0 AATATATAAA 0.940168 -57 GCTACCCTACTAATTTTTAAAATTAATTCTT 5 267 1 TATTTTTAAA 0.706951 -34 * ********* Masking position 8 Map Score: 26.1609 Number of sites scoring better than the average of aligned sites = 1557 Number in coding regions = 1054 Number in noncoding regions = 503 Number of orfs with sites within 600 bp upstream = 404 Fraction of orfs with sites within 600 bp upstream = 0.0648892 Motif number 2 TGTTTTATCAAAACTTAAAAGTTAATTTAA 1 233 1 AAACTTAAAA 0.776575 -68 AGTTAATTTAAAAATTAGAAACCAAACAAA 1 252 1 AAAATTAGAA 0.957367 -49 TAACAAAAATAAAAATAGGAGGGAATACT 1 282 1 AAAAATAGGA 0.844361 -19 AAATAAAAATAAAATTAGGAGCTATATTTT 2 13 0 AAAATTAGGA 0.966567 -193 ACAGATAAATAAAATAAAAATAAAATTAGG 2 24 0 AAAATAAAAA 0.684437 -182 TTTATAAGCTAAAATTATAAAAATGTGAAA 2 116 1 AAAATTATAA 0.776484 -90 AGTGTTTTTCAAAGTTAATAAAAATTAAGG 2 154 1 AAAGTTAATA 0.776575 -52 AAAGTTAATAAAAATTAAGGAATAAATATA 2 164 1 AAAATTAAGG 0.817347 -42 CACACACTTAAAAATTAAGATTAATTAAGT 5 14 1 AAAATTAAGA 0.965953 -287 TGGAAACTACAAGATTAAAATCAGACCGAT 5 126 1 AAGATTAAAA 0.762731 -175 ATATATAAATTAAATTAATAAAAAGAAAAT 5 178 0 TAAATTAATA 0.684437 -123 TTCTTCACTAAAAAATAGTAATTTATATAT 5 233 1 AAAAATAGTA 0.808204 -68 ATTAATTTTAAAAATTAGTAGGGTAGCAGA 5 264 0 AAAATTAGTA 0.957367 -37 ACTAATTTTTAAAATTAATTCTTTAAGGTG 5 275 1 AAAATTAATT 0.701058 -26 ********** Masking position 7 Map Score: 11.0286 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 503 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 3 ACACGTCCCAACTCCATTGGGAGTCAGGACA 1 92 0 ACTCCTTGGG 0.996697 -209 AAGGGGCAGAACTCCACTGGGTCATTGACAC 1 119 0 ACTCCCTGGG 0.99102 -182 TCATTTCACTACCCCTTTGGGGTAAAGGGGC 1 143 0 ACCCCTTGGG 0.997894 -158 TAAATATAAAAGCCCGTAGGGCTTTTATAA 2 186 1 AGCCCTAGGG 0.986347 -20 TATCGCAATCGCCCCGTAGGGGCGAGTAATG 3 71 1 GCCCCTAGGG 0.98936 -93 CGAGTAATGAAATCCTTTAGGATTTCATCTG 3 93 1 AATCCTTAGG 0.899477 -71 ***** ***** Masking position 5 Map Score: 6.35315 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 12 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CTTTCAATGCTATTGTGATAATATAATA 1 6 0 TATGTGATAA 0.851714 -295 TGGGGAGGCATAGGGTGAAATAAAGATATTTAT 1 180 1 TAGGTGAAAA 0.848733 -121 GTTAATTTAAAAATTAGAAACCAAACAAATAAC 1 253 1 AATTAGAAAA 0.695156 -48 GTTTTTTGACTATTTTGATACTCCGAGTATAAC 2 83 1 TATTTGATAC 0.917542 -123 AAAATTATAAAAATGTGAAAATACCATAAGTGT 2 126 1 AATGTGAAAA 0.941378 -80 AATTTTTATTAACTTTGAAAAACACTTATGGTA 2 147 0 AATTTGAAAC 0.969082 -59 TCGGAGGTGTAAATTTGATACTCATATTATTAA 3 13 0 AATTTGATAC 0.918032 -151 CTTTAATACCTTTTTTGAAAGACA 4 2 0 TTTTTGAAAC 0.873 -129 TTTATTAAGGAAATTTGAATGCCTTCTATAAGA 4 35 1 AATTTGAATC 0.875937 -96 TATTACAAAATATTTTGAAAGACACTATTAGTC 4 93 1 TATTTGAAAC 0.965991 -38 TTTAATTTATATATTTGAATTTATAAATAATAA 5 194 1 ATTTTGAATA 0.49685 -107 ATTAATTCTTTAAGGTGAAATGA 5 288 1 TAGGTGAAAA 0.848784 -13 ** ******* * Masking position 8 Map Score: 6.81166 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 254 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 ACTGGGTCATTGACACGTCCCAACTCCATT 1 105 0 TGACACGTCC 0.986654 -196 AGTATCAAATTTACACCTCCGAGCGTTAGC 3 24 1 TTACACCTCC 0.989686 -140 CGATACTCCCTAACACCTCCTCGCTAACGC 3 46 0 TAACACCTCC 0.981956 -118 AAGGATTTCATTACTCGCCCCTACGGGGCG 3 80 0 TTACTCGCCC 0.957042 -84 ********** Masking position 3 Map Score: 0.923539 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 1 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 GATAAAACAGATTTTTTAAGGGCATTTTTA 1 212 0 ATTTTTTAAG 0.821445 -89 TTTTAAATTAACTTTTAAGTTTTGATAAAA 1 235 0 ACTTTTAAGT 0.772904 -66 TTGGTTTCTAATTTTTAAATTAACTTTTAA 1 247 0 ATTTTTAAAT 0.87153 -54 CTGTGTTTAAATATTGTAGTGGTGATTTCT 2 50 1 ATATTGTAGT 0.810124 -156 CTTTCAAAATATTTTGTAATAACTATTAAT 4 84 0 ATTTTGTAAT 0.923314 -47 ATTACAAAATATTTTGAAAGACACTATTAG 4 94 1 ATTTTGAAAG 0.827412 -37 ATTAATCTTAATTTTTAAGTGTGTGACA 5 9 0 ATTTTTAAGT 0.93431 -292 TCTGATTTTAATCTTGTAGTTTCCAAAGAA 5 121 0 ATCTTGTAGT 0.863455 -180 ATAAATTACTATTTTTTAGTGAAGAAAAGC 5 229 0 ATTTTTTAGT 0.94859 -72 ********** Masking position 5 Map Score: 5.7298 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 348 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 ********** No masking Map Score: -3.14527e-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 8 ********** No masking Map Score: -3.14527e-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: -3.14527e-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