AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -idnaA_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP029 300 RECF PROTEIN (recF) #2 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #3 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #4 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #5 RP513 300 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA) #6 RP600 195 unknown Motif number 1 GGAGTTCTATAAAATTTTTGTAATACTTGAATTTT 1 72 0 AAATTTTAAA 0.914459 -229 ATTTCTATACAGAATAAATGCAATATATCAATAAT 1 254 1 AAATAATAAA 0.919958 -47 TAATTTTTTTAAATAAAATCAAACA 2 1 0 AATAAATAAA 0.914015 -89 TTTTATTTAAAAAAATTATAGAAAAAGTTTATTTT 2 18 1 AAAATATAAA 0.982519 -72 ATACTAACATATATATGATCTAAAATAAACTTTTT 2 39 0 AATATATAAA 0.963827 -51 ATTTTATCTCAACATTGTTACAACATAACTTTGCT 3 63 0 ACATTTTAAA 0.688153 -44 AACAATGTTGAGATAAAATCTAAAAACAAAAAATA 3 79 1 AATAAATAAA 0.914015 -28 ATATAGTTACATAAATCATATACCAAATCGTAATT 4 13 1 AAAATATACA 0.856317 -152 ATTTGGTGTAAGATTACATGCAAAAAATTATTCTA 4 83 1 AATTAATAAA 0.844933 -82 CGTGAGCTAGAGAAATTATAGAATAATTTTTTGCA 4 101 0 AAAATATAAA 0.982519 -64 GCTCACGATAAAAAACCTTTAAACAATGTAATATT 4 129 1 AAAACTTAAA 0.752613 -36 TATTGTTGAAAAAAATAATACAAAAG 5 2 0 AAAATATAAA 0.982519 -299 ACGAGATATCAAAATTTTTTAAAAAAACTGTTTAA 5 46 0 AAATTTTAAA 0.914459 -255 TCTCGTATCTAGATCTAATAAAATACCAATCTTTA 5 75 1 AATCTATAAA 0.807786 -226 CAAAAATCTAAAAAAAAATAAAATATTTATATTGA 5 169 1 AAAAAATAAA 0.957306 -132 CACGAGAATAATAATTTATTCAATATAAATATTTT 5 188 0 AAATTATAAA 0.966454 -113 ATTATTATAAAAAAATTTTGCAAGATGTTATAG 6 9 0 AAAATTTAAA 0.954245 -187 TATCTAGGCTCTATATCATTGAAAATGATGTTCAT 6 66 0 CATATATAAA 0.73859 -130 AACTTTTATTATCAATAATAGAAAAAAACGTAAAT 6 171 1 ACAATATAAA 0.920645 -25 * **** ** ** * Masking position 9 Map Score: 26.1818 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 446 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 TAGAGCATTTAATGTTTATTATCACTCCTGAG 1 28 1 AATGTTTTAT 0.921263 -273 AAGTATTACAAAAATTTTATAGAACTCCATAT 1 79 1 AAAATTATAG 0.727552 -222 AGGACTTTACAATTTTTCATTGTTCATAGTAC 1 114 1 AATTTTATTG 0.804045 -187 ATAATAGTATAATTATTGATATATTGCATTTA 1 268 0 AATTTTATAT 0.854908 -33 AATTATAGAAAAAGTTTATTTTAGATCATATA 2 31 1 AAAGTTTTTT 0.877446 -59 AATTATTTTTTGTTTTTAGATT 3 95 0 AATTTTTTTG 0.870202 -12 GAAATTATAGAATAATTTTTTGCATGTAATCT 4 93 0 AATATTTTTG 0.727552 -72 ACATTGTTTAAAGGTTTTTTATCGTGAGCTAG 4 126 0 AAGGTTTTAT 0.732172 -39 TTTTTTTAAAAAATTTTGATATCTCGTATCTA 5 54 1 AAATTTATAT 0.85489 -247 ATTTCTCCATAAAGATTGGTATTTTATTAGAT 5 87 0 AAAGTTGTAT 0.687834 -214 TATAGTAACTAAATCTTATTTTTGTCAAGTCA 5 139 1 AAATTTTTTT 0.854514 -162 AAAAAAAATAAAATATTTATATTGAATAAATT 5 179 1 AAATTTATAT 0.85489 -122 ATATTGAATAAATTATTATTCTCGTGTCTACT 5 197 1 AATTTTTTCT 0.644509 -104 TCGTTATTATAATGCTTTTTTGCAAAAATGAC 5 257 0 AATGTTTTTG 0.890687 -44 ACATCTTGCAAAATTTTTTTATAATAATATTA 6 16 1 AAATTTTTAT 0.905895 -180 CCCAATGTAGAATGGTTATTAGAGTGCTTAAT 6 128 0 AATGTTTTAG 0.930134 -68 TATTGATAATAAAAGTTAATAGAACTTTCCCA 6 156 0 AAAATTATAG 0.727552 -40 **** ** **** Masking position 6 Map Score: 14.1301 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 542 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 3 GTTCAATGTACAATTTTTAGAGCA 1 4 1 CAATGTAAAT 0.943794 -297 GTAATACTTGAATTTTAGAGTCTGTTATCTC 1 57 0 AATTTTAAGT 0.861817 -244 AACAATGAAAAATTGTAAAGTCCTATAATAT 1 107 0 AATTGTAAGT 0.944367 -194 TTTCATTGTTCATAGTACAGTATATCAATTG 1 128 1 CATAGTAAGT 0.930235 -173 ATGAAAGAATAATAGTATAATTATTGATATA 1 277 0 AATAGTAAAT 0.838974 -24 GAGCTAGAGAAATTATAGAATAATTTTTTGC 4 102 0 AATTATAAAT 0.620708 -63 AACCTTTAAACAATGTAATATTAGTAATAAA 4 142 1 CAATGTATAT 0.856528 -23 TTTTAATTACCAATGTATAGTAACTAAATCT 5 124 1 CAATGTAAGT 0.951104 -177 AAAATGACACCATTTTAGTGTATAGAACTTC 5 234 0 CATTTTATGT 0.830477 -67 TTATTTTAATAATATTATTATAAAAAAATTT 6 26 0 AATATTATAT 0.404955 -170 ATACCGAAATCATTTTAAAATACTTGAATAA 6 98 1 CATTTTAAAT 0.922447 -98 AGAACTTTCCCAATGTAGAATGGTTATTAGA 6 137 0 CAATGTAAAT 0.943794 -59 ******* *** Masking position 7 Map Score: 9.97448 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 83 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 ACAAAAATTTTATAGAACTCCATATTATAG 1 86 1 TATAGAACTC 0.894657 -215 AACTCCATATTATAGGACTTTACAATTTTT 1 101 1 TATAGGACTT 0.913321 -200 ATTTATTCTGTATAGAAATTGCAATAGTAG 1 243 0 TATAGAAATT 0.943081 -58 TATCGTGAGCTAGAGAAATTATAGAATAAT 4 109 0 TAGAGAAATT 0.864114 -56 ATTACCAATGTATAGTAACTAAATCTTATT 5 129 1 TATAGTAACT 0.811582 -172 CATTTTAGTGTATAGAACTTCAATTAAGTA 5 225 0 TATAGAACTT 0.978307 -76 TATAGATACTAATTGGTTAT 5 291 0 TATAGATACT 0.70953 -10 AAATGATGTTCATAGAACCTTATTATTTTA 6 49 0 CATAGAACCT 0.897913 -147 TTTTCAATGATATAGAGCCTAGATACCGAA 6 76 1 TATAGAGCCT 0.947739 -120 GAATGGTTATTAGAGTGCTTAATTATTCAA 6 121 0 TAGAGTGCTT 0.67414 -75 AATAAAAGTTAATAGAACTTTCCCAATGTA 6 151 0 AATAGAACTT 0.863863 -45 ********** Masking position 4 Map Score: 9.64701 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 154 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 AATGTGCAAATTTGATTAATAATTCAAACTCAA 1 170 1 TTTTAATAAT 0.737127 -131 AATAAATGCAATATATCAATAATTATACTATTA 1 266 1 ATATAATAAT 0.829442 -35 TTATACTATTATTCTTTCATAAA 1 288 1 ATTTCATAAA 0.93841 -13 TTTCTATAATTTTTTTAAATAAAATCAAACA 2 9 0 TTTTAATAAA 0.509717 -81 ATATATAGTTACATAAATCATATACCA 4 5 1 ATATCATAAA 0.87194 -160 TGGTGTAAGATTACATGCAAAAAATTATTCTAT 4 86 1 TTATCAAAAA 0.551656 -79 CATGCAAAAAATTATTCTATAATTTCTCTAGCT 4 99 1 ATTTTATAAT 0.636061 -66 ACAATGTAATATTAGTAATAAATT 4 151 1 ATTTATAAAT 0.53049 -14 GTATCGCATTATTGTTGAAAAAAATAATACAAA 5 13 0 ATTTAAAAAA 0.826416 -288 AGATATCAAAATTTTTTAAAAAAACTGTTTAAG 5 45 0 ATTTAAAAAA 0.548731 -256 TAAAAGCTGCATTTCTCCATAAAGATTGGTATT 5 96 0 ATTTCATAAA 0.939542 -205 GTTACTATACATTGGTAATTAAAAGCTGCATTT 5 115 0 ATTTATTAAA 0.814276 -186 AAATGGTGTCATTTTTGCAAAAAAGCATTATAA 5 250 1 ATTTCAAAAA 0.861827 -51 ATCTTGCAAAATTTTTTTATAATAATATTATTA 6 18 1 ATTTTATAAT 0.675425 -178 TAGAACCTTATTATTTTAATAATATTATTATAA 6 34 0 TTATAATAAT 0.570834 -162 TCATTTTAAAATACTTGAATAATTAAGCACTCT 6 107 1 ATATAATAAT 0.849006 -89 TTTTTCTATTATTGATAATAAAAGTTAATAGAA 6 164 0 ATTTATAAAA 0.694029 -32 *** * ****** Masking position 6 Map Score: 16.9666 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 619 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 6 TAAACATTAAATGCTCTAAAAATTGTACATT 1 15 0 ATGCTCAAAA 0.918615 -286 CTGAGATAACAGACTCTAAAATTCAAGTATT 1 55 1 AGACTCAAAA 0.922531 -246 TTAATAATTCAAACTCAAAAGAACAAATATA 1 185 1 AAACTCAAAG 0.869176 -116 TTTTTTAAATAAAATCAAACA 2 1 0 AAAATCAACA 0.851531 -89 TAACATATATATGATCTAAAATAAACTTTTT 2 39 0 ATGATCAAAA 0.906923 -51 ATATGTTAGTATAAACGAAAATAGTTTTTCA 2 62 1 ATAAACAAAA 0.909056 -28 ATGTTGAGATAAAATCTAAAAACAAAAAATA 3 83 1 AAAATCAAAA 0.970938 -24 ACTGCATGTTAAACTCAAAAATTTGGTGTAA 4 63 1 AAACTCAAAA 0.974812 -102 GTTGAAAAAAATAATACAAAAG 5 2 0 ATAATAAAAA 0.668577 -299 TGTCAAGTCAAAAATCTAAAAAAAAATAAAA 5 161 1 AAAATCAAAA 0.970938 -140 TTGAAGTTCTATACACTAAAATGGTGTCATT 5 232 1 ATACACAAAA 0.920503 -69 AATAATAGAAAAAAACGTAAAT 6 184 1 AAAAACTAAA 0.579091 -12 ****** **** Masking position 9 Map Score: 12.6918 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 209 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 ********** No masking Map Score: 4.00336e-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 8 ********** No masking Map Score: 4.00336e-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 9 ********** No masking Map Score: 4.00336e-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