AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_mjan_reg_300.orf -o225_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 RMJ14632 144 M_jannaschii_chromosome #2 RMJ04589 300 M_jannaschii_chromosome #3 RMJ06354 111 M_jannaschii_chromosome #4 RMJ02789 36 M_jannaschii_chromosome #5 RMJ02161 56 M_jannaschii_chromosome Motif number 1 GAAACTTTATTAAATTTTCACGTGCATTTCCAA 1 71 0 TAAATTTCGT 0.823729 -74 TAAATTTTAATTTACACCTCCGA 1 132 0 TAAATTTTTT 0.986222 -13 AATCTTAACTTAATTTTTGGTTTC 2 2 0 TAATTTTTTT 0.979988 -299 AAAAACTATGAAAATTTTCTTTTAATCTTAACT 2 25 0 AAAATTTTTT 0.957075 -276 GTAAAGTTGTTAAATTTAGTTATGAAAAATTGA 2 59 1 TAAATTATAT 0.754535 -242 ATTGGCATCTAAATTATTGGTTTTTGCAAATAT 2 136 0 AAATTTTTTT 0.936338 -165 TGACAAGGCTTAATTTTTCTTTTGTTAATTAAT 2 167 0 TAATTTTTTT 0.979969 -134 ATGATACCTGAAATTTTTGATTTGCATATTTTT 2 209 0 AAATTTTTTT 0.935909 -92 TCAGGTATCATAATTATTATATGGTGAGTTCTA 2 231 1 TAATTTTATG 0.843461 -70 TGAGTTCTACTAAATATCTATTTTATTATTTTT 2 255 1 TAAATTCTTT 0.90566 -46 TTATTATTTTTAAATCTTACTATAAAAAGGATT 2 277 1 TAAATTTTAT 0.953212 -24 AAAATCACCAAAATGTTGGATTCCCCACATAA 3 10 1 AAAATTTATT 0.880802 -102 TAACATAACATAAATTTTTTAATGTATAAGTTA 3 40 0 TAAATTTAAT 0.868371 -72 TATGTTATATTATATATTATTTTTTAATTTGCC 3 66 1 TATATTTTTT 0.912451 -46 ATTAAATATATGATTATATAAATGG 3 97 0 TAAATTAATT 0.787318 -15 CTATTCAAAATAATTTTTTATGGTGATGATTT 4 15 1 TAATTTTTGG 0.875605 -22 TATTGACTTATATTTATTTATTTTTTG 5 5 0 TATTTTTTTT 0.873965 -52 CTCATCACCGTAAATTTTTTTGGTTATAATATT 5 34 0 TAAATTTTGG 0.915899 -23 ***** ** *** Masking position 7 Map Score: 25.4064 Number of sites scoring better than the average of aligned sites = 1743 Number in coding regions = 1270 Number in noncoding regions = 473 Number of orfs with sites within 600 bp upstream = 375 Fraction of orfs with sites within 600 bp upstream = 0.0602313 Motif number 2 TTCCACCTTATTTTGGTCTTTTTAAAAC 1 6 0 TTTTGTTTTT 0.910729 -139 TTGATGAAACTTTATTAAATTTTCACGTGCATT 1 76 0 TTTATAATTT 0.844275 -69 AAACCAAAAATTAAGTTAAGATTAAAAGAAAAT 2 12 1 TTAAGTAGTT 0.576658 -289 TTAAAAGAAAATTTTCATAGTTTTTCGTAAAGT 2 33 1 ATTTTAAGTT 0.618346 -268 AATTATTGGTTTTTGCAAATATTCTAAAGATAA 2 125 0 TTTTGAATTT 0.946169 -176 TTAATTTTTCTTTTGTTAATTAATTGGCATCTA 2 158 0 TTTTGTATAA 0.585356 -143 GAAATTTTTGATTTGCATATTTTTGATAGGATA 2 200 0 ATTTGAATTT 0.85056 -101 CTAAATATCTATTTTATTATTTTTAAATCTTAC 2 264 1 ATTTTTATTT 0.849662 -37 GAATCCAACATTTTGGTGATTTT 3 1 0 TTTTGTATTT 0.969235 -111 ATAACATAAATTTTTTAATGTATAAGTTATGTG 3 36 0 TTTTTATGAT 0.47477 -76 CATTAAAAAATTTATGTTATGTTATATTATATA 3 49 1 TTTATTATTT 0.906877 -63 GTTATGTTATATTATATATTATTTTTTAATTTG 3 64 1 ATTATTTTTT 0.504978 -48 TAATTTGCCATTTATATAATCATATATTTAAT 3 90 1 TTTATTATAT 0.843253 -22 TAAAAAATTATTTTGAATAGAATT 4 2 0 TTTTGAAGAT 0.834347 -35 AAATAATTTTTTATGGTGATGATTT 4 22 1 TTATGTATAT 0.726182 -15 TTGACTTATATTTATTTATTTTTTG 5 3 0 TTTATTTTTT 0.759288 -54 CCGTAAATTTTTTTGGTTATAATATTGACTTAT 5 27 0 TTTTGTATAT 0.94613 -30 ***** * ** ** Masking position 2 Map Score: 13.1549 Number of sites scoring better than the average of aligned sites = 3856 Number in coding regions = 3046 Number in noncoding regions = 810 Number of orfs with sites within 600 bp upstream = 515 Fraction of orfs with sites within 600 bp upstream = 0.0827176 Motif number 3 ATAAAGTTTCATCAAAACTAACACCTCCTC 1 94 1 ATCAAAACTA 0.958443 -51 GGAGGTGTAAATTAAAATTTA 1 134 1 ATTAAAATTT 0.70194 -11 GAAACCAAAAATTAAGTTAAGAT 2 4 1 ACCAAAAATT 0.882519 -297 TTTTCTTTTAATCTTAACTTAATTTTTGGT 2 14 0 ATCTTAACTT 0.824814 -287 ACGAAAAACTATGAAAATTTTCTTTTAATC 2 31 0 ATGAAAATTT 0.777305 -270 TGTTCAATTTTTCATAACTAAATTTAACAA 2 65 0 TTCATAACTA 0.61064 -236 ATTAATTGGCATCTAAATTATTGGTTTTTG 2 143 0 ATCTAAATTA 0.795952 -158 GTCATATCCTATCAAAAATATGCAAATCAA 2 196 1 ATCAAAAATA 0.965471 -105 AAATATGCAAATCAAAAATTTCAGGTATCA 2 211 1 ATCAAAAATT 0.977658 -90 AATTTCAGGTATCATAATTATTATATGGTG 2 227 1 ATCATAATTA 0.924264 -74 AATATAACATAACATAAATTTTTTAATGTA 3 47 0 AACATAAATT 0.763869 -65 CATTTATATAATCATATATTTAAT 3 98 1 ATCATATATT 0.748441 -14 AATCATCACCATAAAAAATTATTTTGAATA 4 16 0 ATAAAAAATT 0.775173 -21 ********** Masking position 6 Map Score: 10.9125 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 797 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 GTTTTAAAAAGACCAAAATA 1 1 1 GTTTTAAAAA 0.844855 -144 TGCACGTGAAAATTTAATAAAGTTTCATCA 1 78 1 AATTTAATAA 0.850612 -67 ATTAAGTTAAGATTAAAAGAAAATTTTCAT 2 21 1 GATTAAAAGA 0.897936 -280 TTCATAACTAAATTTAACAACTTTACGAAA 2 55 0 AATTTAACAA 0.894053 -246 GATGCCAATTAATTAACAAAAGAAAAATTA 2 160 1 AATTAACAAA 0.87931 -141 TTTATAGTAAGATTTAAAAATAATAAAATA 2 273 0 GATTTAAAAA 0.970154 -28 ATAACTTATACATTAAAAAATTTATGTTAT 3 39 1 CATTAAAAAA 0.925114 -73 ATAAATGGCAAATTAAAAAATAATATATAA 3 75 0 AATTAAAAAA 0.964807 -37 ********** Masking position 6 Map Score: 5.95944 Number of sites scoring better than the average of aligned sites = 757 Number in coding regions = 610 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 5 TATTTAGTAGAACTCACCATATAATAATTA 2 241 0 AACTCACCAT 0.96586 -60 AAAATCACCAAAATGTTGGAT 3 2 1 AAATCACCAA 0.95022 -110 AAATCATCACCATAAAAAATTAT 4 24 0 TCATCACCAT 0.986773 -13 CTCATCACCGTAAATTTTTTT 5 46 0 TCATCACCGT 0.977659 -11 ********** Masking position 6 Map Score: 0.581871 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ********** No masking Map Score: -1.31207e-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 7 ********** No masking Map Score: -1.31207e-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: -1.31207e-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