AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_rpxx_reg_100.orf -o00860_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP325 107 GLUTAMYL-TRNA SYNTHETASE (gltX1) #2 RP466 300 PORPHOBILINOGEN DEAMINASE (hemC) #3 RP539 300 DELTA-AMINOLEVULINIC ACID DEHYDRATASE (hemB) #4 RP623 114 GLUTAMYL-TRNA SYNTHETASE (gltX2) #5 RP847 300 POSSIBLE PROTOPORPHYRINOGEN OXIDASE (hemK) #6 RP881 300 PROLINE/BETAINE TRANSPORTER (proP7) #7 RP885 300 UROPORPHYRINOGEN DECARBOXYLASE (hemE) Motif number 1 ATCAAATTATTACTATAAACTAAAAATATACGGTGTT 1 21 1 TTTAAAAAAT 0.986706 -87 GCAAATATAACATTTAAAATTACAATTTTATAGTCA 2 10 1 ATTAAATAAT 0.940912 -291 GGAATTGAACATAATTAAATAAAAATTTTTTAGTGTA 2 175 0 AATAAAAAAT 0.745234 -126 AAGATAGAAAATATGTATACAAAAAATAACCAACCTA 3 99 0 ATTATAAAAT 0.924354 -202 TATAGTTTAATGATTTAAATGAAGATTTTTAAATTAG 3 139 0 TTTAAAAAAT 0.986703 -162 CAAATTTTTTTTGTCTAAAGCAATATTTTTACTATAA 3 218 1 TTTAAAAAAT 0.986706 -83 TATACTCAGAACTTTTTAAATTATAATTTGATTAGAG 4 53 0 ATTTAATAAT 0.74209 -62 TGAGTTATATATATTTAAAATAATAATAATAA 4 93 1 ATTAAAAAAT 0.979353 -22 AACAAGAAACATATCTATAAGAATATTAGACGCAAAC 5 101 1 ATTATAAAAT 0.924357 -200 TAGTTAGAGGAGCTATTAAAGTAGAGTGGTAGTTTGC 5 132 0 ATTTAATAAT 0.742198 -169 TACTACTTTTTTATATAAACTAAGTTTTGATTTTGTA 6 22 0 TTTAAAAATT 0.927127 -279 ATCTAAGCATTGCTATAAACATAAAATATTTATGATA 6 65 1 TTTAAATAAT 0.957926 -236 ACTTGTTAAATGTTTTATATTAAGATTCGTAACATCT 6 126 0 TTTATAAAAT 0.945723 -175 AGTGTAAATATCATTTTAACTAAGAATAAGAAAGTTT 6 216 0 TTTTAAAAAT 0.930638 -85 ATGATGTAAATTGTCTATAATAATAATTAGTAATTAA 6 259 1 TTTATAAAAT 0.94586 -42 TAGTACATTTTCTTTTAAAGAAACAGTTTGTGGATAA 7 29 1 TTTAAAAAAT 0.986705 -272 GAAAAGACTATCTTTTCAAAGAAAAGTGATATTTATT 7 73 0 TTTCAAAAAT 0.887042 -228 AAAGATAGTCTTTTCTAAACTAAAAATGAATCTTGCA 7 95 1 TTTAAAAAAT 0.986703 -206 AATTATCCACTTGTATAAATTAATTATAAATTTATGT 7 135 1 TTTAAAAATT 0.927126 -166 TTTTTTAAGAAAATTTAAATGAAAATTTTGTTGATAA 7 194 1 ATTAAAAAAT 0.968569 -107 ATAAACAGAATTATGTAAATTAAATGTTTCAAACATA 7 232 0 TTTAAAAATT 0.927104 -69 TTCTACTAAAAGATTTAAATATATATTATTTATATAT 7 273 0 ATTAAATAAT 0.9409 -28 * * **** ** * * Masking position 6 Map Score: 40.4603 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 132 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 TTTAGTTTATAGTAATAATTTGATATTAAAC 1 14 0 ATAATAATTT 0.892178 -94 ATTACTATAAACTAAAAATATACGGTGTTAC 1 29 1 ATAAAAATAT 0.940836 -79 CAAATATAACATTTAAAATTACAATTTTATA 2 12 1 ATTAAAATTA 0.85407 -289 AATCTAGTGCAATAAAAATGTCGGTATATTT 2 105 1 ATAAAAATGT 0.905767 -196 AACATAATTAAATAAAAATTTTTTAGTGTAT 2 174 0 ATAAAAATTT 0.935467 -127 AAACATTAATATTTATAATTAATCCCATATA 2 243 0 ATTATAATTA 0.769626 -58 AAATATGTATACAAAAAATAACCAACCTAAA 3 97 0 AAAAAAATAA 0.833824 -204 TTAGTACAAGATAGAAAATATGTATACAAAA 3 112 0 AAGAAAATAT 0.75204 -189 AGCTAACGAAAATAAAAATATAGTTTAATGA 3 163 0 ATAAAAATAT 0.940836 -138 TGCTTTAGACAAAAAAAATTTGCTTGCAATT 3 209 0 AAAAAAATTT 0.852664 -92 ACTATCTTATAGTAAAAATATTGCTTTAGAC 3 230 0 ATAAAAATAT 0.940836 -71 GAACTTTTTAAATTATAATTTGATTAGAGTA 4 51 0 ATTATAATTT 0.808678 -64 ATATATTTAAAATAATAATAATAA 4 101 1 ATAATAATAA 0.877663 -14 TAAAGCTTATAATAAAAATATTCAGATCAAT 5 205 1 ATAAAAATAT 0.940836 -96 AATATACCGTATAGATAATAAACGTTTCCTT 5 233 1 AAGATAATAA 0.577757 -68 ATTGCTATAAACATAAAATATTTATGATATA 6 73 1 AATAAAATAT 0.764195 -228 TCTTATTCTTAGTTAAAATGATATTTACACT 6 222 1 ATTAAAATGA 0.795112 -79 AATTGTCTATAATAATAATTAGTAATTAATT 6 267 1 ATAATAATTA 0.867371 -34 TGAATTTAAAATAAATTAATTACT 6 287 0 ATTAAAATAA 0.865234 -14 TGTTTCTTTAAAAGAAAATGTACTAGATTTT 7 23 0 AAGAAAATGT 0.647048 -278 TCTTTTCTAAACTAAAAATGAATCTTGCACT 7 103 1 ATAAAAATGA 0.883679 -198 ATTCACATAAATTTATAATTAATTTATACAA 7 145 0 ATTATAATTA 0.769626 -156 AATTTATGTGAATAATAATTAAAATACTGAT 7 163 1 ATAATAATTA 0.867371 -138 AGAAAATTTAAATGAAAATTTTGTTGATAAC 7 201 1 ATGAAAATTT 0.87382 -100 ATAACAATATATAAATAATATATATTTAAAT 7 267 1 AAAATAATAT 0.783728 -34 * ********* Masking position 9 Map Score: 32.2583 Number of sites scoring better than the average of aligned sites = 1552 Number in coding regions = 966 Number in noncoding regions = 586 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 3 ATATACGGTGTTACAATACAAGATTTCGTGGTTA 1 46 1 TTCAATAAAT 0.731159 -62 CACACACGTATAGCAATTAATAAAATTAGTTATT 1 83 1 TACAATATAA 0.694922 -25 GACTATAAAATTGTAATTTTAAATGTTATATTTG 2 12 0 TTTAATTAAT 0.537331 -289 TATTAACATCTATTACTCTTTGATAAACTCCATT 2 50 0 TATACTTTAT 0.729956 -251 GACATTTTTATTGCACTAGATTATAATGTGCTGC 2 93 0 TTCACTATAT 0.94202 -208 CTATTGTAGAATACACTAAAAAATTTTTATTTAA 2 164 1 ATCACTAAAT 0.596745 -137 AATTAATCCCATATACTATTTCATTAGCCTTATA 2 224 0 ATTACTTTAT 0.617646 -77 TAATTATAAATATTAATGTTTGAAATTTTACTAG 2 253 1 TATAATTTAA 0.494795 -48 GTGTTTTCTACTATTTTAACATGGCTAGT 2 282 0 TTTACTTTAA 0.834059 -19 TTAGCAAAAAATACACTGGATGAATATGATACAA 3 28 0 ATCACTATAA 0.76211 -273 ATTTTCTATCTTGTACTAATTTAAAAATCTTCAT 3 124 1 TTTACTTTAA 0.853353 -177 AAAAATTTGCTTGCAATTTATAAAATTTAGACAA 3 193 0 TTCAATATAA 0.854815 -108 AAAGCAATATTTTTACTATAAGATAGTTAAATGA 3 234 1 TTTACTAAAT 0.820542 -67 ATCACTTGGATTTTAATATATCATTTAACTATCT 3 254 0 TTTAATATAT 0.838773 -47 TCTAATCAAATTATAATTTAAAAAGTTCTGAGTA 4 54 1 TTTAATAAAA 0.627658 -61 TAACTAAGTAATTTAATAGATGATGTGTACTATT 5 163 1 ATTAATATAT 0.550483 -138 AGATAAACCATACTACTTTTTTATATAAACTAAG 6 35 0 TATACTTTAT 0.729956 -266 TAATCTAGTTTAGCACTTGTTAAATGTTTTATAT 6 143 0 TACACTTTAA 0.753552 -158 AAAATGATATTTACACTTTATAAATGATGTAAAT 6 236 1 TTCACTATAA 0.931553 -65 AAAATGAATCTTGCACTTAATTATCCACTTGTAT 7 117 1 TTCACTATAT 0.942029 -184 ATTCTGTTTATAACAATATATAAATAATATATAT 7 258 1 TACAATATAA 0.694922 -43 ATTCTACTAAAAGATTTAAATATAT 7 286 0 TTTACTAAAT 0.823072 -15 ** **** ** ** Masking position 7 Map Score: 18.3151 Number of sites scoring better than the average of aligned sites = 926 Number in coding regions = 617 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 TTATTACTATAAACTAAAAATATACGGTGT 1 27 1 AAACTAAAAA 0.970253 -81 ATTGTAGAATACACTAAAAAATTTTTATTT 2 166 1 ACACTAAAAA 0.859991 -135 AAAAATAACCAACCTAAAAATACTAAACAC 3 85 0 AACCTAAAAA 0.837251 -216 GAAAATATGTATACAAAAAATAACCAACCT 3 100 0 ATACAAAAAA 0.844713 -201 ATCTTGTACTAATTTAAAAATCTTCATTTA 3 131 1 AATTTAAAAA 0.59098 -170 CAAGCTAACGAAAATAAAAATATAGTTTAA 3 166 0 AAAATAAAAA 0.855351 -135 ATATTGCTTTAGACAAAAAAAATTTGCTTG 3 214 0 AGACAAAAAA 0.66544 -87 TAACTATCTTATAGTAAAAATATTGCTTTA 3 233 0 ATAGTAAAAA 0.641121 -68 ATCAAATTATAATTTAAAAAGTTCTGAGTA 4 58 1 AATTTAAAAA 0.59098 -57 CATGAAAATTAATCTAGAAAAATGGGCTTT 5 34 1 AATCTAGAAA 0.727161 -267 TTCTGGCTTAAATCTTAAAATCTGTAGTAA 5 62 1 AATCTTAAAA 0.78714 -239 AAGGTTGATAAAACAAGAAACATATCTATA 5 90 1 AAACAAGAAA 0.711399 -211 GTTAAAGCTTATAATAAAAATATTCAGATC 5 203 1 ATAATAAAAA 0.752815 -98 GCATTGCTATAAACATAAAATATTTATGAT 6 71 1 AAACATAAAA 0.773761 -230 TAGATTATAAATACTTAAAACCATTATCCT 6 170 1 ATACTTAAAA 0.844713 -131 AGTCTTTTCTAAACTAAAAATGAATCTTGC 7 101 1 AAACTAAAAA 0.970253 -200 TATGTGAATAATAATTAAAATACTGATTTT 7 167 1 ATAATTAAAA 0.496526 -134 ********** Masking position 8 Map Score: 11.6431 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 494 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 5 GTATAGCAATTAATAAAATTAGTTATTT 1 90 1 TAATAAAATT 0.951963 -18 TATTCTACAATAGTAAAATCACGGACAATT 2 147 0 TAGTAAAATC 0.834526 -154 TTAACATGGCTAGTAAAATTTCAAACATTA 2 266 0 TAGTAAAATT 0.935699 -35 TGCTTGCAATTTATAAAATTTAGACAAGCT 3 190 0 TTATAAAATT 0.696543 -111 AACTATCTTATAGTAAAAATATTGCTTTAG 3 232 0 TAGTAAAAAT 0.748245 -69 TTAGAGTATCTAGGAAAATAATTTGCAATA 4 29 0 TAGGAAAATA 0.718668 -86 CTAGATACTCTAATCAAATTATAATTTAAA 4 46 1 TAATCAAATT 0.757614 -69 CAAGTTCTAATGAGAAAATTT 5 2 0 TGAGAAAATT 0.824568 -299 AACATATCTATAAGAATATTAGACGCAAAC 5 108 1 TAAGAATATT 0.744484 -193 TTAAAGCTTATAATAAAAATATTCAGATCA 5 204 1 TAATAAAAAT 0.801884 -97 TAACTAAGAATAAGAAAGTTTTATTAGGAA 6 207 0 TAAGAAAGTT 0.811973 -94 TATAAAATTAAGAAAATCTAGTACATTT 7 9 1 TAAGAAAATC 0.904661 -292 CTGATTTTTTTAAGAAAATTTAAATGAAAA 7 189 1 TAAGAAAATT 0.964763 -112 ********** Masking position 6 Map Score: 9.03909 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 231 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TATCAAATTATTACTATAAACTAAAAATATAC 1 20 1 TTCTATAACT 0.825571 -88 GCTGCATAGTTTTTTATTAACATCTATTACTC 2 66 0 TTTTATAACA 0.957185 -235 TATATGGGATTAATTATAAATATTAATGTTTG 2 243 1 TATTATAATA 0.564943 -58 TATCTCATTTTAGTTAATCACTTGGATTTTAA 3 272 0 TATTAACACT 0.493137 -29 CTGAATATTTTTATTATAAGCTTTAACACGGA 5 198 0 TTTTATAGCT 0.705158 -103 ATACTACTTTTTTATATAAACTAAGTTTTGAT 6 28 0 TTATATAACT 0.634401 -273 TATCTAAGCATTGCTATAAACATAAAATATTT 6 64 1 TTCTATAACA 0.857685 -237 TGGTTTTAAGTATTTATAATCTAGTTTAGCAC 6 161 0 TATTATATCT 0.555451 -140 TTACTAATTATTATTATAGACAATTTACATCA 6 260 0 TTTTATGACA 0.808556 -41 TTTATTCACAATTTTATCCACAAACTGTTTCT 7 47 0 ATTTATCACA 0.612119 -254 AGAAAAGTGATATTTATTCACAATTTTATCCA 7 59 0 TATTATCACA 0.935376 -242 ATCTTGCACTTAATTATCCACTTGTATAAATT 7 124 1 TATTATCACT 0.919163 -177 TTGTATAAATTAATTATAAATTTATGTGAATA 7 145 1 TATTATAATT 0.572356 -156 AGTATTTTAATTATTATTCACATAAATTTATA 7 159 0 TTTTATCACA 0.948569 -142 GTTTCAAACATAGTTATCAACAAAATTTTCAT 7 212 0 TATTATAACA 0.946299 -89 TATTTATATATTGTTATAAACAGAATTATGTA 7 252 0 TTTTATAACA 0.957159 -49 ** **** **** Masking position 6 Map Score: 11.0497 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 165 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 CTTAAAATCTGTAGTAAGGTTGATAAAACA 5 75 1 GTAGTAAGGT 0.91839 -226 AGCTATTAAAGTAGAGTGGTAGTTTGCGTC 5 129 0 GTAGAGTGGT 0.970129 -172 GCTTTAACACGGATAATAGTACACATCATC 5 181 0 GGATAATAGT 0.763039 -120 TGGAGAGAGGTTTTTTGCCTA 5 290 0 GGAGAGAGGT 0.964753 -11 ATATAAAAAAGTAGTATGGTTTATCTAAGC 6 43 1 GTAGTATGGT 0.954538 -258 AATGATTACAGGATAATGGTTTTAAGTATT 6 179 0 GGATAATGGT 0.95416 -122 ********** Masking position 3 Map Score: 0.811823 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 GCAAATATAACATTTAAAATTACAATTT 2 9 1 AACATTTAAA 0.910363 -292 CTTCATTTAAATCATTAAACTATATTTTTA 3 152 1 ATCATTAAAC 0.842157 -149 ATTTTAATATATCATTTAACTATCTTATAG 3 249 0 ATCATTTAAC 0.955803 -52 GTTTCCTTAGCACATTTAATTATACAACAA 5 256 1 CACATTTAAT 0.86752 -45 CTTAATATAAAACATTTAACAAGTGCTAAA 6 139 1 AACATTTAAC 0.975817 -162 CTATGTTTGAAACATTTAATTTACATAATT 7 231 1 AACATTTAAT 0.947113 -70 ********** Masking position 5 Map Score: 2.42799 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 30 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: 3.92463e-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: 3.92463e-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 11 ACTATAAACTAAAAATATACGGTGTTACAA 1 32 1 AAAAATATAC 0.731628 -76 TCTTACGTACTAAAATATACCGACATTTTT 2 118 0 TAAAATATAC 0.899691 -183 TTTACTATTGTAGAATACACTAAAAAATTT 2 160 1 TAGAATACAC 0.826084 -141 GTTAAAATAGTAGAAAACAC 2 291 1 TAGAAAACAC 0.826085 -10 CTATTTTTAGCAAAAAATACACTGGATGAA 3 38 0 CAAAAAATAC 0.9463 -263 AATAACCAACCTAAAAATACTAAACACGCT 3 82 0 CTAAAAATAC 0.712609 -219 AATATGTATACAAAAAATAACCAACCTAAA 3 97 0 CAAAAAATAA 0.606235 -204 AAATAATTTGCAATATATACTGTTGAGATT 4 14 0 CAATATATAC 0.712604 -101 ATATATAACTCAGAATATACTCAGAACTTT 4 75 0 CAGAATATAC 0.950229 -40 ATTTTTAGTTTAGAAAAGACTATCTTTTCA 7 92 0 TAGAAAAGAC 0.720749 -209 ********** Masking position 5 Map Score: 2.5111 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 143 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 ********** No masking Map Score: 3.92463e-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 13 ********** No masking Map Score: 3.92463e-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 14 ********** No masking Map Score: 3.92463e-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