AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_mjan_reg_100.orf -o00310_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 Purged sequences: MJ0086 36 unspecified methyltransferase MJ0806 81 X-pro aminopeptidase (pepQ) Input sequences: #1 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #2 MJ0087 23 hemin permease (hemU) #3 MJ0090 80 collagenase (prtC) #4 MJ0260 94 signal sequence peptidase I, SEC11 #5 MJ0261 161 conserved hypothetical protein #6 MJ0652 300 conserved hypothetical protein #7 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #8 MJ1597 226 serine hydroxymethyltransferase (glyA) Motif number 1 CTTTTTTCTATTTTTTATATAATTTTTATGAAT 1 11 1 TTTTTTATAT 0.924717 -124 TTTATATAATTTTTATGAATATTGATGTATTTT 1 24 1 TTTTATATAT 0.938861 -111 ATTGATGTATTTTTAACGATTATTTTTGATAAA 1 44 1 TTTTAAATTT 0.894821 -91 AACAAAAATTTTTAATATCTAATATATATTTTT 1 83 0 TTTAATCTAT 0.837397 -52 ACTATCACATTTTTTGAATTATT 2 2 0 TTTTTTATTT 0.8803 -22 TCTTTTTTATATAATGAGGTCATAT 3 3 1 TTTTTTATAT 0.924717 -78 TTTTTTAAATTTTAAATTATATTTGAAGTATAA 3 50 0 TTTAAAATAT 0.953448 -31 ACCTCATATATTTATTCCATAATGTTTTGAAAA 4 18 0 TTTATTATAT 0.946062 -77 TTTTTACTGATTTTTAGGTTAATGATTCCACCT 4 47 0 TTTTTATTAT 0.885497 -48 ATAACTTGAATTTATAAATTTATTGATATATTG 5 39 0 TTTATATTTT 0.868704 -123 TCAAGTTATCATTATATATTATTATTTGTGAAA 5 63 1 ATTATATTAT 0.645381 -99 AGCCTCATAGTTTATTATTTTTTATCAATATTT 6 142 1 TTTATTTTTT 0.877177 -159 AGTTAAGTTTTTTATTAAATATTGATAAAAAAT 6 158 0 TTTATTATAT 0.946426 -143 CATTAACTATTTTTAATCTTAATAATATATAAT 6 247 1 TTTTAATTAT 0.905822 -54 TTACTGTAAATTTATTATATATTATTAAGATTA 6 260 0 TTTATTATAT 0.946454 -41 AAATAGTTTTTAATTTTATTACTGTAAATT 6 281 0 TTTTAATTAT 0.905826 -20 TATAGAGTCTTTTAAAACATTTTGAAATACTAA 7 52 0 TTTAAAATTT 0.924635 -127 TTAGTATTATTTTAAATTCTTTTTATAGAGTCT 7 75 0 TTTAAACTTT 0.741158 -104 TTAAATTCTATTTTAATTTTAGTATTATTTTAA 7 93 0 TTTTAATTAT 0.905826 -86 TGTTGTGTAATTTATTAAATTCTATTTTAATTT 7 107 0 TTTATTATTT 0.913832 -72 CACCAAAAACTTTTTTATATAGTGTCTTTCAAA 8 17 1 TTTTTTATAT 0.925077 -210 AAGGAAGGCATTTAAATATTTATTGTCAAATAT 8 89 1 TTTAAATTTT 0.891715 -138 ATTAAAGTTTATTAATAAATATTTGACAATAAA 8 107 0 ATTAATATAT 0.784576 -120 ATTAATAAACTTTAATTAATTTTGAAGACAGTA 8 124 1 TTTAATATTT 0.929527 -103 TAAAAATATCTTTAAACTATACTGTCTTCAAAA 8 143 0 TTTAAAATAT 0.953448 -84 AATACGGTATATTTATTGTTTCTATTTCTATTA 8 182 1 ATTTATTTTT 0.532472 -45 TTCTATTTCTATTAAACGTTAATAAGAGGGATA 8 201 1 ATTAAATTAT 0.681871 -26 ****** *** * Masking position 10 Map Score: 41.0195 Number of sites scoring better than the average of aligned sites = 2121 Number in coding regions = 1470 Number in noncoding regions = 651 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 2 ATAAAAATTATATAAAAAATAGAAAAAAG 1 9 0 TATAAAAAAA 0.910485 -126 ATACATCAATATTCATAAAAATTATATAAAA 1 23 0 ATTCATAAAA 0.66152 -112 TTCGGTAGTTTATCAAAAATAATCGTTAAAA 1 54 0 TATCAAAAAA 0.800756 -81 ATATATTAGATATTAAAAATTTTTGTTCATA 1 89 1 TATTAAAAAT 0.762165 -46 AATAATTCAAAAAATGTGATAGT 2 5 1 ATTCAAAAAT 0.812471 -19 GACCTCATTATATAAAAAAGA 3 1 0 TATAAAAAAA 0.910541 -80 TAATTTAAAATTTAAAAAAATTTCTAA 3 64 1 TTTAAAAAAT 0.942127 -17 GATAACTTGAATTTATAAATTTATTGATATA 5 42 0 ATTTATAAAT 0.609107 -120 TTTCACAAATAATAATATATAATGATAACTT 5 65 0 AATAATATAA 0.531245 -97 ATAATTTGCAAATAAAATATATATAAGTTAA 5 115 0 AATAAAATAA 0.665092 -47 TCCTATTCCTTTTAAAAAGCTTCCTCTCTAC 6 83 1 TTTAAAAAGT 0.7141 -218 ATTGATAAAAAATAATAAACTATGAGGCTCA 6 140 0 AATAATAAAT 0.831941 -161 TTTATCAATATTTAATAAAAAACTTAACTTG 6 162 1 TTTAATAAAA 0.880133 -139 CTTAATAATATATAATAAATTTACAGTAATA 6 264 1 TATAATAAAT 0.880191 -37 ACAGTAATAAAATTAAAAACTATTT 6 286 1 AATTAAAAAT 0.683476 -15 TTCAAAATGTTTTAAAAGACTCTATAAAAAG 7 59 1 TTTAAAAGAT 0.760753 -120 TAAAAGACTCTATAAAAAGAATTTAAAATAA 7 71 1 TATAAAAAGA 0.609411 -108 ATAAAAAGAATTTAAAATAATACTAAAATTA 7 82 1 TTTAAAATAT 0.825163 -97 TAATACTAAAATTAAAATAGAATTTAATAAA 7 99 1 ATTAAAATAA 0.715504 -80 TAAAATAGAATTTAATAAATTACACAACATT 7 111 1 TTTAATAAAT 0.902855 -68 AAAGACACTATATAAAAAAGTTTTTGGTGCT 8 15 0 TATAAAAAAT 0.927944 -212 ATATAGTGTCTTTCAAAAACATTTTGAAGTA 8 33 1 TTTCAAAAAA 0.83569 -194 AAAGGAAGGCATTTAAATATTTATTGTCAAA 8 88 1 ATTTAAATAT 0.441739 -139 TCAAATATTTATTAATAAACTTTAATTAATT 8 114 1 ATTAATAAAT 0.862323 -113 CTTATTAACGTTTAATAGAAATAGAAACAAT 8 196 0 TTTAATAGAA 0.589118 -31 ********* * Masking position 3 Map Score: 24.5995 Number of sites scoring better than the average of aligned sites = 3571 Number in coding regions = 2612 Number in noncoding regions = 959 Number of orfs with sites within 600 bp upstream = 587 Fraction of orfs with sites within 600 bp upstream = 0.094282 Motif number 3 TTATATAAAAAATAGAAAAAAG 1 3 0 AATAGAAAAA 0.793177 -132 TGAAGTATAAAATAGCAATAACCAATATGA 3 30 0 AATAGCAATA 0.679218 -51 AACATTATGGAATAAATATATGAGGTGGAA 4 25 1 AATAAATATA 0.96356 -70 ACAATATATCAATAAATTTATAAATTCAAG 5 38 1 AATAAATTTA 0.927087 -124 TAATTTCACAAATAATAATATATAATGATA 5 69 0 AATAATAATA 0.691859 -93 TTGCAAATAAAATATATATAAGTTAAACAT 5 111 0 AATATATATA 0.720394 -51 TTATTTAGCGAATAGAATTCTTATAATATA 5 142 1 AATAGAATTC 0.765181 -20 ATCAATATTTAATAAAAAACTTAACTTGAC 6 165 1 AATAAAAAAC 0.686769 -136 TCAGGATAACATTAGATATATATACCTTTA 6 204 1 ATTAGATATA 0.775828 -97 TATTATTAAGATTAAAAATAGTTAATGTAA 6 244 0 ATTAAAAATA 0.857712 -57 AATAATATATAATAAATTTACAGTAATAAA 6 267 1 AATAAATTTA 0.927087 -34 AATTTACAGTAATAAAATTAAAAACTATTT 6 281 1 AATAAAATTA 0.933697 -20 ATAATACTAAAATTAAAATAGAATTTAATA 7 98 1 AATTAAAATA 0.679996 -81 AATAGAATTTAATAAATTACACAACATTCA 7 114 1 AATAAATTAC 0.484174 -65 ACATTCATTGATTAAAATTATTCAAAGGCT 7 137 1 ATTAAAATTA 0.740792 -42 AATATTTGACAATAAATATTTAAATGCCTT 8 93 0 AATAAATATT 0.78794 -134 AAAGTTTATTAATAAATATTTGACAATAAA 8 107 0 AATAAATATT 0.78794 -120 AAATAGAAACAATAAATATACCGTATTAAT 8 179 0 AATAAATATA 0.96356 -48 ATTAACGTTTAATAGAAATAGAAACAATAA 8 194 0 AATAGAAATA 0.949692 -33 ********** Masking position 3 Map Score: 18.7884 Number of sites scoring better than the average of aligned sites = 1590 Number in coding regions = 1084 Number in noncoding regions = 506 Number of orfs with sites within 600 bp upstream = 407 Fraction of orfs with sites within 600 bp upstream = 0.065371 Motif number 4 AATATTCATAAAAATTATATAAAAAATAGA 1 17 0 AAAATTATAT 0.644673 -118 AATAATCGTTAAAAATACATCAATATTCAT 1 38 0 AAAAATACAT 0.728342 -97 TAAACTACCGAAAAATATATATTAGATATT 1 73 1 AAAAATATAT 0.836545 -62 ATTAGATATTAAAAATTTTTGTTCATATCA 1 93 1 AAAAATTTTT 0.493207 -42 TAAAATTTAAAAAAATTTCTAA 3 69 1 AAAAATTTCT 0.716616 -12 ACATTATGGAATAAATATATGAGGTGGAAT 4 26 1 ATAAATATAT 0.791714 -69 TTATCCACTCAACAACATCTTTTTTACTGA 4 70 0 AACAACATCT 0.59552 -25 CAATATATCAATAAATTTATAAATTCAAGT 5 39 1 ATAAATTTAT 0.45535 -123 TTTCACAAATAATAATATATAATGATAACT 5 66 0 AATAATATAT 0.781474 -96 TTTGCAAATAAAATATATATAAGTTAAACA 5 112 0 AAATATATAT 0.478206 -50 ATTATTTTTTATCAATATTTAATAAAAAAC 6 155 1 ATCAATATTT 0.655673 -146 TATTAAGATTAAAAATAGTTAATGTAAGGT 6 241 0 AAAAATAGTT 0.685404 -60 TTTTAATCTTAATAATATATAATAAATTTA 6 257 1 AATAATATAT 0.781474 -44 AATAAAATTAAAAACTATTT 6 291 1 AAAACTATTT 0.745368 -10 TAGAGTCTTTTAAAACATTTTGAAATACTA 7 53 0 TAAAACATTT 0.449149 -126 AGACAGCACCAAAAACTTTTTTATATAGTG 8 11 1 AAAAACTTTT 0.685336 -216 AGTGTCTTTCAAAAACATTTTGAAGTAACC 8 37 1 AAAAACATTT 0.915312 -190 ATATTTGACAATAAATATTTAAATGCCTTC 8 92 0 ATAAATATTT 0.696324 -135 AAGTTTATTAATAAATATTTGACAATAAAT 8 106 0 ATAAATATTT 0.696324 -121 ATTAATACTTAAAAATATCTTTAAACTATA 8 155 0 AAAAATATCT 0.931701 -72 ********** Masking position 10 Map Score: 19.4468 Number of sites scoring better than the average of aligned sites = 1220 Number in coding regions = 882 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 5 TATTGCTATTTTATACTTCAAATATAATTTAAA 3 40 1 TATACTTCAT 0.852968 -41 AGGTTAATGATTCCACCTCATATATTTATTCCA 4 32 0 TCCACCTCAT 0.907909 -63 AATAATCCCTCTTAATGTGTTTTAA 5 3 1 TATCCCTCAA 0.900223 -159 TAATATATAATGATAACTTGAATTTATAAATTT 5 51 0 TATAACTTAT 0.878018 -111 GTGAAATTACTACTTCCTTTGATGTTTAACTTA 5 90 1 TCTTCCTTAT 0.841594 -72 AGGGCTTTTATACTACCTCGGATTATCATTGAG 6 26 0 TCTACCTCAT 0.979286 -275 ATTTTCTTCTTTATAACTTCTATCATGAGCCTC 6 115 1 TATAACTTAT 0.87785 -186 CATTAGATATATATACCTTTAAAATCATACCTT 6 213 1 AATACCTTAA 0.619572 -88 ACCTTTAAAATCATACCTTACATTAACTATTTT 6 227 1 TATACCTTAT 0.976547 -74 TTTTATCCCTCTTATTAACGTTTAA 8 212 0 TATCCCTCAT 0.970111 -15 * ******* ** Masking position 8 Map Score: 4.27067 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 195 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 TTAGATATTAAAAATTTTTGTTCATATCAT 1 94 1 AAAATTTTTG 0.699824 -41 TTAGAAATTTTTTTAAATTTTAAA 3 67 0 AAATTTTTTT 0.832858 -14 ATAGTTCTTTTCAAAACATT 4 1 1 ATAGTTCTTT 0.782803 -94 TAACTTATATATATTTTATTTGCAAATTAT 5 116 1 ATATTTTATT 0.606598 -46 CATGAGCCTCATAGTTTATTATTTTTTATC 6 138 1 ATAGTTTATT 0.886754 -163 ACTGTCAAGTTAAGTTTTTTATTAAATATT 6 168 0 TAAGTTTTTT 0.780735 -133 AAATAGTTTTTAATTTTATTAC 6 289 0 ATAGTTTTTA 0.782144 -12 ACTATATAAAAAAGTTTTTGGTGCTGTCT 8 10 0 AAAGTTTTTG 0.954286 -217 GTTACTTCAAAATGTTTTTGAAAGACACTA 8 36 0 AATGTTTTTG 0.746089 -191 AAAATTAATTAAAGTTTATTAATAAATATT 8 117 0 AAAGTTTATT 0.919701 -110 ********** Masking position 5 Map Score: 4.21332 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 580 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 7 ********** No masking Map Score: -3.34422e-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: -3.34422e-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: -3.34422e-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