AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_mjan_reg_100.orf -o00220_mjan_100.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 MJ0069 145 acetylglutamate kinase (argB) #2 MJ0188 300 inosine-5'-monophosphate dehydrogenase, putative #3 MJ0313 142 spermidine synthase (speE) #4 MJ0429 167 argininosuccinate synthetase (argG) #5 MJ0721 194 acetylornithine aminotransferase (argD) #6 MJ0791 300 argininosuccinate lyase (argH) #7 MJ0881 300 ornithine carbamoyltransferase (argF) #8 MJ1096 221 N-acetyl-gamma-glutamyl-phosphate reductase (argC) Motif number 1 ATCTTAATTTTTATTAATTACCTTAGTTACG 1 50 1 TATTAATTAC 0.473066 -96 AGTTATTGTTTGATAAATTTTAAATAATTCC 1 96 1 TATAAATTTT 0.898496 -50 GTGTTTCATTTTTTATATATTCTTTTTATAT 2 13 1 TTTATATATT 0.746797 -288 TATATATTCTTTTTATATATTCCCACAATAC 2 26 1 TTTATATATT 0.746797 -275 TACCATATTATATATTATTTTCGGTTTTTAG 2 77 1 TTATTATTTT 0.878559 -224 CAACATCAAATTAATAACTATCCTTTAACCT 2 110 0 TAATAACTAT 0.50244 -191 AGTTCCATTGTAAATTATTTTAAGGATTAGA 2 152 0 TAATTATTTT 0.829006 -149 CTTTCGCAGTTTGTATATTTTATTAAAGGCA 2 233 0 TGTATATTTT 0.525081 -68 CAGCATAAATTTTTAAATTTTTATATTGTAA 2 269 0 TTTAAATTTT 0.929546 -32 ACAAAAGGTTTAATTAACATTACTCCATTTA 3 77 1 TATTAACATT 0.581539 -66 CATTACTCCATTTATAACTATTATATTTACA 3 94 1 TTATAACTAT 0.600818 -49 CTACATCACCTTATTTATTTTAGGAGGTGTA 3 121 0 TATTTATTTT 0.936496 -22 TATTAGCAGTTTATATATAATAGGTGAGTTA 4 55 1 TATATATAAT 0.481955 -113 TCCTTAAACTTTTTGTATTTTATTGCTTATA 4 101 0 TTTGTATTTT 0.763639 -67 AGTTTAAGGATTTATAATTTTATGTAAGATA 4 122 1 TTATAATTTT 0.873366 -46 GAAAGTATTTTTATTAATATTGCTATAATTA 5 29 0 TATTAATATT 0.74966 -166 AAAAGTTTTATTTTTAATTTTAAAATCATTT 5 164 1 TTTTAATTTT 0.95444 -31 CGCCAACTATTCTTTAATTTTTTGTATGGTG 6 36 1 TTTTAATTTT 0.954441 -265 TATATAGAGGTTTTGTATTATTACATTTGTG 6 90 0 TTTGTATTAT 0.603013 -211 TATAATTTACTATTTAACTTTAAATCATAAT 6 122 0 TTTTAACTTT 0.906734 -179 TTCTAATAAGTTAAAAATTTTAACATATATA 6 149 0 TAAAAATTTT 0.744558 -152 AAGTTATAATTGTTTTATTATTAAAAATTCT 6 176 0 TTTTTATTAT 0.911773 -125 TAGTTAAAAATAATTTACTTTTTTAAAGTTA 6 201 0 TATTTACTTT 0.872512 -100 AAGTAAATTATTTTTAACTATTTTATAATTT 6 212 1 TTTTAACTAT 0.820494 -89 TTTTAACTATTTTATAATTTTATATCAAAAA 6 223 1 TTATAATTTT 0.873366 -78 ATATTGATTATGTTATATTTCATTTTTTGAT 6 246 0 TTTATATTTC 0.652864 -55 TAATCGTGTTTAAATAATATTGATTATGTTA 6 262 0 TAATAATATT 0.496278 -39 CTTAAACAGTTAATTTATTATAAAAAATACA 7 13 1 TATTTATTAT 0.87395 -288 TTTTAAGAACTGTTTTATTATTGTATTTTTT 7 34 0 TTTTTATTAT 0.911773 -267 ATTAACTTTGTGTTATATTTTTCAGTGCTAT 7 70 0 TTTATATTTT 0.932629 -231 TTCTTTTTATTTATTAACTTTGTGTTATATT 7 82 0 TATTAACTTT 0.867069 -219 TACAAAAACATCAAATATTATTAATAGTTAA 7 114 1 TAAATATTAT 0.589805 -187 TGCCCTTATTTATTTAATTTCATTCAATAAC 7 165 1 TTTTAATTTC 0.74 -136 TCATGAGCCATTATTTATATTGTTGTAGTTT 7 241 0 TATTTATATT 0.758572 -60 TTAAAAACTATTTTATATTATCATGAGCCAT 7 261 0 TTTATATTAT 0.866816 -40 TTTATCACCTTTTATACTATTAAAAACTAT 7 281 0 TTTATACTAT 0.751267 -20 TCCAATCTTTAATTTTTTATCTATTC 8 6 1 TTTTAATTTT 0.954441 -216 TTTTATCTATTCTTTTATTTTTTAAACTGAA 8 25 1 TTTTTATTTT 0.956486 -197 AGATGCTCTTTATAATATTTTCAGTTTAAAA 8 44 0 TTAATATTTT 0.820091 -178 TATTAGTTTTTAATAAACTTTTTGTAAAAAA 8 109 0 TATAAACTTT 0.804224 -113 TTATAAAAAATCTTAAATTATACA 8 208 1 TTTAAATTAT 0.861169 -14 * ********* Masking position 7 Map Score: 45.1774 Number of sites scoring better than the average of aligned sites = 3705 Number in coding regions = 2653 Number in noncoding regions = 1052 Number of orfs with sites within 600 bp upstream = 614 Fraction of orfs with sites within 600 bp upstream = 0.0986187 Motif number 2 AAACAATAACTTTAAATAATAGAAGCCGTAA 1 76 0 TTTAAATATA 0.605302 -70 TTTGATAAATTTTAAATAATTCCTTTATCCA 1 104 1 TTTAAATATT 0.865656 -42 ACTCATAAACTTAAAAGGTTTT 1 134 1 TTAAAAGTTT 0.797317 -12 TGGGAATATATAAAAAGAATATATAAAAAAT 2 20 0 TAAAAAGATA 0.621242 -281 AAGGATTAGATATAAATACTTCAACATCAAA 2 131 0 TATAAATCTT 0.905995 -170 TATCTAATCCTTAAAATAATTTACAATGGAA 2 150 1 TTAAAATATT 0.9342 -151 AGCATAAATTTTTAAATTTTTATATTGTAAT 2 268 0 TTTAAATTTT 0.841368 -33 CTTTTGTCTATAAAAATTTTTGCATGGTGCT 3 53 0 TAAAAATTTT 0.943483 -90 TCAATCTAAATAGAAATTTTTGGGGATAAA 4 10 0 TAGAAATTTT 0.640777 -158 TACATAAAATTATAAATCCTTAAACTTTTTG 4 117 0 TATAAATCTT 0.905998 -51 ATGTAAGATATAAAAATATTTTGTGAGGGAT 4 143 1 TAAAAATTTT 0.943964 -25 GCAATATTAATAAAAATACTTTCACATAAAA 5 37 1 TAAAAATCTT 0.955026 -158 TACTTTCACATAAAAATGTTTTGTTGGTGAC 5 53 1 TAAAAATTTT 0.943983 -142 TAAACCATATCAAAAATGATTAAAATACTCA 5 85 1 CAAAAATATT 0.601739 -110 CAACACAAAATATAAATACTTATAATGCATT 5 124 1 TATAAATCTT 0.905995 -71 ATTACTTCCCTTAAAAGTTTTATTTTTAATT 5 152 1 TTAAAAGTTT 0.797317 -43 ATTTTTAATTTTAAAATCATTTTGGTGATTA 5 173 1 TTAAAATATT 0.9342 -22 ACTATTTAACTTTAAATCATAATATATATAG 6 114 0 TTTAAATATA 0.605308 -187 ATTATATATGTTAAAATTTTTAACTTATTAG 6 147 1 TTAAAATTTT 0.921173 -154 GTTTTATTATTAAAAATTCTAATAAGTTAAA 6 165 0 TAAAAATCTA 0.830844 -136 ATAAAATAGTTAAAAATAATTTACTTTTTTA 6 207 0 TAAAAATATT 0.953421 -94 TTTAATCGTGTTTAAATAATATTGATTATGT 6 264 0 TTTAAATATA 0.605302 -37 AAAACAGTTCTTAAAAAACTTATAGCACTGA 7 49 1 TTAAAAACTT 0.626155 -252 AGTTAATAAATAAAAAGAATTACAAAAACAT 7 94 1 TAAAAAGATT 0.873282 -207 AATTAACTATTAATAATATTTGATGTTTTTG 7 116 0 TAATAATTTT 0.456261 -185 TTTATACTATTAAAAACTATTTTATATTATC 7 270 0 TAAAAACATT 0.661849 -31 AAAGGTTTTATAAAAAATCTTAAATTATACA 8 201 1 TAAAAAACTT 0.707205 -21 ******* *** Masking position 6 Map Score: 32.5238 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 870 Number in noncoding regions = 362 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 3 AAAATTAAGATTTTAGATAAAACGAGATTTTT 1 29 0 TTTTAGTAAA 0.466782 -117 TATTTAAAGTTATTGTTTGATAAATTTTAAAT 1 89 1 TATTGTTATA 0.615325 -57 ACGTGTTTCATTTTTTATATATTCTTT 2 6 1 TTTCATTTTA 0.701361 -295 ATGGATACCATATTATATATTATTTTCGGTTT 2 72 1 TATTATTTTA 0.788541 -229 TATATATTATTTTCGGTTTTTAGTAAGGTTAA 2 85 1 TTTCGGTTTA 0.711864 -216 ATTTTTAAATTTTTATATTGTAATAGAACTTT 2 260 0 TTTTATTGTA 0.75686 -41 TAATTAAACCTTTTGTCTATAAAAATTTTTGC 3 61 0 TTTTGTTTAA 0.912501 -82 AAATAGAAATTTTTGGGGATAAA 4 2 0 TTTTGGGTAA 0.827739 -166 ATAACTCACCTATTATATATAAACTGCTAATA 4 55 0 TATTATTTAA 0.6998 -113 TTGCTTATAGTTTTGGAGTATATATAACTCAC 4 78 0 TTTTGGGATA 0.704366 -90 TCCTTAAACTTTTTGTATTTTATTGCTTATAG 4 100 0 TTTTGTTTTA 0.937646 -68 CACAAAATATTTTTATATCTTACATAAAATTA 4 136 0 TTTTATTTTA 0.930114 -32 TAATTAATCTTTTTGGTGATAAGT 5 3 0 TTTTGGGTAA 0.827739 -192 AACAAAACATTTTTATGTGAAAGTATTTTTAT 5 46 0 TTTTATTAAA 0.7549 -149 TTGTGTTGTTTTTTGTTGAGTATTTTAATCAT 5 100 0 TTTTGTGGTA 0.631941 -95 CCCTTAAAAGTTTTATTTTTAATTTTAAAATC 5 159 1 TTTTATTTAA 0.903251 -36 TTTAAAATCATTTTGGTGATTAA 5 182 1 TTTTGGGTTA 0.87293 -13 TATTTTATAATTTTATATCAAAAAATGAAATA 6 230 1 TTTTATTAAA 0.73017 -71 TTGTAATTCTTTTTATTTATTAACTTTGTGTT 7 87 0 TTTTATTTTA 0.930032 -214 TTATCTATTCTTTTATTTTTTAAACTGAAAAT 8 27 1 TTTTATTTTA 0.930306 -195 AAAGAGCATCTATTAGATTTAAAAGGAATCCA 8 64 1 TATTAGTTAA 0.727158 -158 GTTTAGATTTTATTAGTTTTTAATAAACTTTT 8 118 0 TATTAGTTTA 0.792694 -104 ****** * *** Masking position 3 Map Score: 23.0637 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 677 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 4 AAGCCGTAACTAAGGTAATTAATAAAAATTA 1 54 0 TAAGGTAATA 0.740663 -92 TATGAGTGGATAAAGGAATTATTTAAAATTT 1 110 0 TAAAGGAATA 0.953383 -36 TTTAAATGCCTAAAGGCATTATTATTCCATA 2 202 0 TAAAGGCATA 0.969034 -99 TATATTTTATTAAAGGCATTTAAATGCCTAA 2 220 0 TAAAGGCATT 0.820675 -81 ATAATAGTTATAAATGGAGTAATGTTAATTA 3 87 0 TAAATGGATA 0.655018 -56 ACTCCAAAACTATAAGCAATAAAATACAAAA 4 91 1 TATAAGCATA 0.640363 -77 ATAAAACTTTTAAGGGAAGTAATGCATTATA 5 144 0 TAAGGGAATA 0.970327 -51 GGGCAATATTTATGGGAATTAACAATTAACT 7 139 0 TATGGGAATA 0.900789 -162 ATTAAATAAATAAGGGCAATATTTATGGGAA 7 152 0 TAAGGGCATA 0.980766 -149 AACCTTATAGTAAGAGGAATATAATGAATGG 8 165 0 TAAGAGGATA 0.842252 -57 ******** ** Masking position 8 Map Score: 6.81681 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 181 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 TTTTGGTAGTTGGTGAGATAAG 1 3 0 TGGTGAGATA 0.946818 -143 GCCGTAACTAAGGTAATTAATAAAAATTAA 1 53 0 AGGTAATTAA 0.655366 -93 TTGAGTATTGTGGGAATATATAAAAAGAAT 2 31 0 TGGGAATATA 0.682897 -270 AAAATAAATAAGGTGATGTAGA 3 131 1 AGGTGATGTA 0.868554 -12 TAGAAATTTTTGGGGATAAA 4 1 0 TGGGGATAAA 0.921651 -167 TATATATAATAGGTGAGTTATATATACTCC 4 66 1 AGGTGAGTTA 0.877598 -102 TTAATCTTTTTGGTGATAAGT 5 2 0 TGGTGATAAG 0.852333 -193 AATGTTTTGTTGGTGACTTAAACCATATCA 5 67 1 TGGTGACTTA 0.868554 -128 AAAATCATTTTGGTGATTAA 5 185 1 TGGTGATTAA 0.954411 -10 TAAAATGCATTGGTGAAATA 6 291 1 TGGTGAAATA 0.867146 -10 ATAGTATAAAAGGTGATAAA 7 291 1 AGGTGATAAA 0.947565 -10 ********** Masking position 6 Map Score: 5.19652 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 193 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 TAAAATTTATCAAACAATAACTTTAAATAA 1 88 0 CAAACAATAA 0.616399 -58 ATCCTTTAACCTTACTAAAAACCGAAAATA 2 92 0 CTTACTAAAA 0.866772 -209 ATATCTAATCCTTAAAATAATTTACAATGG 2 149 1 CTTAAAATAA 0.535353 -152 TAAATAGCACCATGCAAAAATTTTTATAGA 3 48 1 CATGCAAAAA 0.858407 -95 TAAGCAATAAAATACAAAAAGTTTAAGGAT 4 103 1 AATACAAAAA 0.849446 -65 ATTTTTATATCTTACATAAAATTATAAATC 4 130 0 CTTACATAAA 0.683197 -38 TTTTATTAATATTGCTATAATTAATCTTTT 5 22 0 ATTGCTATAA 0.385665 -173 ATAGGGGCACCATACAAAAAATTAAAGAAT 6 44 0 CATACAAAAA 0.945925 -257 TATTATAAAAAATACAATAATAAAACAGTT 7 28 1 AATACAATAA 0.829651 -273 AATAAAAAGAATTACAAAAACATCAAATAT 7 102 1 ATTACAAAAA 0.867308 -199 TATTTAATTTCATTCAATAACCACATAAAC 7 175 1 CATTCAATAA 0.657369 -126 ATCCTGTTTTTTTACAAAAAGTTTATTAAA 8 102 1 TTTACAAAAA 0.66517 -120 TTATATTCCTCTTACTATAAGGTTCGTTCA 8 172 1 CTTACTATAA 0.848851 -50 ********** Masking position 9 Map Score: 6.60865 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 488 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 TAACTAAGGTAATTAATAAAAATTAAGATT 1 49 0 AATTAATAAA 0.582027 -97 CAATAACTTTAAATAATAGAAGCCGTAACT 1 74 0 AAATAATAGA 0.673614 -72 TATATTCCCACAATACTCAACGTTATGATT 2 41 1 CAATACTCAA 0.779261 -260 TAAAAACCGAAAATAATATATAATATGGTA 2 77 0 AAATAATATA 0.582027 -224 AATTTCAAATCATCAATTTTAGGATT 3 7 1 AAATCATCAA 0.905697 -136 TGGGTAAGAAAAATCCTAAAATTGATGATT 3 18 0 AAATCCTAAA 0.889534 -125 TAATAACTGTCAATAATCAATCTAAATAGA 4 27 0 CAATAATCAA 0.836921 -141 ATAAGCAATAAAATACAAAAAGTTTAAGGA 4 102 1 AAATACAAAA 0.475222 -66 ATAAAATTATAAATCCTTAAACTTTTTGTA 4 115 0 AAATCCTTAA 0.461479 -53 AAAATGATTAAAATACTCAACAAAAAACAA 5 97 1 AAATACTCAA 0.91216 -98 ATTTAAAGTTAAATAGTAAATTATATATGT 6 128 1 AAATAGTAAA 0.74373 -173 TTAGAATTTTTAATAATAAAACAATTATAA 6 174 1 TAATAATAAA 0.611561 -127 TTTTGATATAAAATTATAAAATAGTTAAAA 6 223 0 AAATTATAAA 0.644253 -78 ATGAAATATAACATAATCAATATTATTTAA 6 254 1 ACATAATCAA 0.615498 -47 ATAAAAAATACAATAATAAAACAGTTCTTA 7 32 1 CAATAATAAA 0.862169 -269 AAGAATTACAAAAACATCAAATATTATTAA 7 108 1 AAAACATCAA 0.561723 -193 TTTTCAGTTTAAAAAATAAAAGAATAGATA 8 28 0 AAAAAATAAA 0.710605 -194 GTTTATTAAAAACTAATAAAATCTAAACGC 8 122 1 AACTAATAAA 0.673614 -100 GTTTTATAAAAAATCTTAAATTATACA 8 205 1 AAATCTTAAA 0.554715 -17 ********** Masking position 10 Map Score: 6.75396 Number of sites scoring better than the average of aligned sites = 1248 Number in coding regions = 912 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 8 ********** No masking Map Score: 2.35433e-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: 2.35433e-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 10 ********** No masking Map Score: 2.35433e-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