AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i104_Cobalt_Transport_mjan_reg_300.orf -o104_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 RMJ08709 49 M_jannaschii_chromosome #2 RMJ15425 296 M_jannaschii_chromosome Motif number 1 TTCTTTAATTTTTTACTTTTTT 1 3 1 CTTTAATTTT 0.982626 -47 TTTTTTACTTTTTTAAATTTTAAAATTTAA 1 19 1 TTTTAAATTT 0.969083 -31 AAAACCCACCTTTAAATTTTAAAATTTAA 1 31 0 CTTTAAATTT 0.984685 -19 AATAACTACTTTTTATATATCTTTATTTTT 2 17 1 TTTTATATAT 0.773454 -280 TTTTATATATCTTTATTTTTAGTAATACTT 2 27 1 CTTTATTTTT 0.986307 -270 TTTAGTAATACTTAATATTACCTAAGTTGC 2 44 1 CTTAATATTA 0.861222 -253 CCTAAGTTGCCTTACTATTTAAATAGTTTA 2 64 1 CTTACTATTT 0.806801 -233 AATGATTAATTTTTCTTTTTTAGTAATAAA 2 90 0 TTTTCTTTTT 0.917316 -207 TTAAAAATGTCTTTAATTTAAATAAGTAAT 2 121 1 CTTTAATTTA 0.963706 -176 TTTTTTCATATTTTTTATTACTTATTTAAA 2 137 0 TTTTTTATTA 0.684601 -160 TAATGAGTTATTTTGTTTTTTTCATATTTT 2 153 0 TTTTGTTTTT 0.917316 -144 ATAAAATAAACTTTAATTTTGTTACTATTA 2 181 0 CTTTAATTTT 0.982626 -116 TTTAACGGTATTTTATTATTAATAAAATAA 2 202 0 TTTTATTATT 0.750281 -95 AATAAAATACCGTTAAATTTATATAAGATA 2 215 1 CGTTAAATTT 0.890753 -82 TTATAGTACTCTTTATCTTATATAAATTTA 2 228 0 CTTTATCTTA 0.899822 -69 TGTTAAGTTTTTTTGAATTATATTCAGGGG 2 261 1 TTTTGAATTA 0.822985 -36 ********** Masking position 3 Map Score: 24.1766 Number of sites scoring better than the average of aligned sites = 2824 Number in coding regions = 2189 Number in noncoding regions = 635 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 2 TTCTTTAATTTTTTACTTTTTTAAATTTTA 1 9 1 TTTTTTATTT 0.984414 -41 TACTTTTTTAAATTTTAAAATTTAAAGGTGGG 1 24 1 AATTTTAAAT 0.489717 -26 AATAACTACTTTTTATATATCTTTATTTTTAG 2 17 1 TTTTATAATT 0.724876 -280 ATATATCTTTATTTTTAGTAATACTTAATATT 2 31 1 ATTTTTATAT 0.975804 -266 AGTAATAAACTATTTAAATAGTAAGGCAACTT 2 67 0 TATTTAATAT 0.879755 -230 TTAATTTTTCTTTTTTAGTAATAAACTATTTA 2 83 0 TTTTTTATAT 0.992519 -214 AATTAAAGACATTTTTAATAATGATTAATTTT 2 107 0 ATTTTTATAT 0.791151 -190 TTTTTTCATATTTTTTATTACTTATTTAAATT 2 135 0 TTTTTTATAT 0.992674 -162 ATTAATGAGTTATTTTGTTTTTTTCATATTTT 2 153 0 TATTTTGTTT 0.821826 -144 AAACTTTAATTTTGTTACTATTAATGAGTTAT 2 172 0 TTTGTTATAT 0.955586 -125 AATTAAAGTTTATTTTATTAATAATAAAATAC 2 193 1 TATTTTATAT 0.9829 -104 AACTTAACACATTTATAGTACTCTTTATCTTA 2 238 0 ATTTATATAT 0.927793 -59 GTGTTAAGTTTTTTTGAATTATATTCAGGGGT 2 260 1 TTTTTGATTT 0.915567 -37 ******* ** * Masking position 3 Map Score: 22.7155 Number of sites scoring better than the average of aligned sites = 1990 Number in coding regions = 1367 Number in noncoding regions = 623 Number of orfs with sites within 600 bp upstream = 444 Fraction of orfs with sites within 600 bp upstream = 0.0713138 Motif number 3 CCATAATAACTACTTTTTATATATCTTTAT 2 13 1 TACTTTTTAT 0.807158 -284 TAATATTAAGTATTACTAAAAATAAAGATA 2 34 0 TATTACTAAA 0.977548 -263 TAATACTTAATATTACCTAAGTTGCCTTAC 2 49 1 TATTACCTAA 0.874215 -248 TAAGTTGCCTTACTATTTAAATAGTTTATT 2 66 1 TACTATTTAA 0.967476 -231 TTAAATAGTTTATTACTAAAAAAGAAAAAT 2 82 1 TATTACTAAA 0.977548 -215 AAAAATTAATCATTATTAAAAATGTCTTTA 2 106 1 CATTATTAAA 0.893416 -191 TCATATTTTTTATTACTTATTTAAATTAAA 2 132 0 TATTACTTAT 0.967476 -165 TTAATTTTGTTACTATTAATGAGTTATTTT 2 169 0 TACTATTAAT 0.977553 -128 AACGGTATTTTATTATTAATAAAATAAACT 2 199 0 TATTATTAAT 0.975721 -98 AGATAAAGAGTACTATAAATGTGTTAAGTT 2 240 1 TACTATAAAT 0.872851 -57 ********** Masking position 4 Map Score: 15.4043 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 257 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 ********** No masking Map Score: -2.60469e-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 5 ********** No masking Map Score: -2.60469e-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 6 ********** No masking Map Score: -2.60469e-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