AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_pyro_reg_300.orf -o00910_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0066 227 328aa long hypothetical L-asparaginase #2 PH0067 59 184aa long hypothetical protein #3 PH0231 95 303aa long hypothetical protein #4 PH0232 53 305aa long hypothetical L-asparaginase #5 PH0359 300 443aa long hypothetical glutamine synthetase #6 PH1102 121 480aa long hypothetical asparagine synthetase #7 PH1103 23 127aa long hypothetical 30S ribosomal protein S8 #8 PH1463 40 438aa long hypothetical L-asparaginase #9 PH1593 275 422aa long hypothetical glutamate dehydrogenase #10 PH1595 272 172aa long hypothetical protein Motif number 1 CCTAGATCCCAGGGAAGGTGGGCTCTATGGTG 1 21 1 AGAAGGTGGG 0.949573 -207 ATCTTACTTATTAGAATTTGAGTTGGTGGTCA 1 205 1 TGAATTTGAG 0.942224 -23 TCGATATCCTTTCAATTTTGGGATGGGCA 4 35 1 TAATTTTGGG 0.730792 -19 CAAAAATCAGTTAAAATTTGGGGGTTATTGTG 5 162 0 TAAATTTGGG 0.96248 -139 GCAAACGGGATGAGAAAGTGGGCAATTCTGAA 6 31 0 TGAAAGTGGG 0.973001 -91 ACTAATTCATTTAGAAATTGGGAAGGTTTTTA 6 76 1 TGAAATTGGG 0.972502 -46 TGCCCAATAGCGAGGTGGGTTAA 7 8 1 TCGAGGTGGG 0.885101 -16 TTGGAAGTGGAGTGAGCTGATG 9 1 1 TGAAGTGGAG 0.803998 -275 TCGATGTATATAAAAATTTGAGATTTAAAGGG 9 97 1 TAAATTTGAG 0.880694 -179 TTTCTTTCGATTTGAAAGTGGGACACAGGAGT 9 146 0 TGAAAGTGGG 0.973001 -130 TGATTGGCGATACAAATTTGAGCAATAGCCTA 9 240 0 TAAATTTGAG 0.880512 -36 TTAAATATCTTCCGGAGGTGGGGAGATGAAAA 10 34 1 TGGAGGTGGG 0.978967 -239 TTCAGGAAAGAAGAGAGTTGGGGATATCCTTA 10 124 1 AAGAGTTGGG 0.808528 -149 * ********* Masking position 10 Map Score: 12.2113 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 232 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 TAGAGCCCACCTTCCCTGGGATCTAGGCTCTTCC 1 14 0 CTCCTGATCT 0.96078 -214 TTATAAATCTCTTTCATAGTATTTGCCAAAAATT 1 167 1 CTTCTGATTT 0.987657 -61 TTGATTATCGATATCATAGCGTTTATAAGATTAT 3 13 1 ATTCTGGTTT 0.824816 -83 TTTATATCCCCTCTCTTAACATTTTTCTGGGGGT 8 13 1 CTTCTAATTT 0.980563 -28 TTTATGAAAACTCCCTTTAAATCTCAAATTTTTA 9 107 0 CTCCTAATCT 0.93919 -169 AGGAGATGATCTTTCTTTCGATTTGAAAGTGGGA 9 155 0 CTTCTCATTT 0.976648 -121 AAGAAAGATCATCTCCTTGAATTTCCTTAACGAA 9 172 1 ATTCTGATTT 0.957587 -104 CAACTCTCTTCTTTCCTGAAATTTTAACCTCAAT 10 110 0 CTTCTAATTT 0.980563 -163 CTTCCCTTTGATGTCATCAAATCTAGGTATAGTT 10 160 0 ATTCTAATCT 0.910192 -113 TCTTCTGTAGCTATCTTACCATTTATAATAATTA 10 195 0 CTTCTCATTT 0.976638 -78 ** ** * * **** Masking position 7 Map Score: 11.3966 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TCCCACTTAATTCCCTGAGGAACTTCGGTTTTCA 1 56 0 TTCTAGGAAT 0.985849 -172 CTTAAGCATTTTCATTAACAAATTAGTATTAG 2 9 0 TTCTACAAAT 0.810518 -51 AATTTTTAAGTCCGATTAGATAATCTTATAAACG 3 32 0 TCCTAGATAT 0.802646 -64 AAGTGGGCAATTCTGAAAGGATGTAAAAGAAAAG 6 14 0 TTCAAGGATT 0.810926 -108 TGCATACTAATTCATTTAGAAATTGGGAAGGTTT 6 71 1 TTCTAGAAAT 0.973425 -51 GGTTTTTACATTCCATTAGGTAGATAAGGGCG 6 100 1 TTCTAGGTAA 0.910648 -22 AAAGGGAGTTTTCATAAAGATATACTCCTGTGTC 9 123 1 TTCAAGATAA 0.570733 -153 TGATCTTTCTTTCGATTTGAAAGTGGGACACAGG 9 149 0 TTCTTGAAAT 0.823137 -127 TGGAAATCCTTTCGTTAAGGAAATTCAAGGAGAT 9 182 0 TTCTAGGAAT 0.985849 -94 TAGGTATAGTTTCCCTAAGGATATCCCCAACTCT 10 137 0 TTCTAGGATT 0.945313 -136 GGATAAAGATTTCGTTAAGGTAATGCCAGTAGTA 10 241 1 TTCTAGGTAT 0.976233 -32 *** * ***** * Masking position 1 Map Score: 8.95599 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 213 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CTAATACTAATTTGTTAATGAAA 2 4 1 ATACTAATTT 0.942594 -56 AGAACAGTAAATAATAATTTTTAAGTCCGA 3 51 0 ATAATAATTT 0.958432 -45 AACCCTGTTAATGATAATTTCTCTAATAGT 5 30 1 ATGATAATTT 0.918551 -271 TGGGGCTTTTATCATAATTTTGTCAATTTA 5 129 1 ATCATAATTT 0.859708 -172 TTCAGATTGCATACTAATTCATTTAGAAAT 6 64 1 ATACTAATTC 0.813543 -58 ATCGATGTATATAAAAATTTGAGATTTAAA 9 96 1 ATAAAAATTT 0.94033 -180 TTGATTGGCGATACAAATTTGAGCAATAGC 9 243 0 ATACAAATTT 0.91817 -33 AGGTGGGGAGATGAAAATTAAGCTCATGGG 10 49 1 ATGAAAATTA 0.708814 -224 CTTACCATTTATAATAATTATCTTCCCTTT 10 185 0 ATAATAATTA 0.879385 -88 GAGGTAACGGATAAAGATTTCGTTAAGGTA 10 233 1 ATAAAGATTT 0.766711 -40 ********** Masking position 7 Map Score: 7.70509 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 26 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GAGATTTATAAAAGGGTGGTTAAAGTGTCAAGA 1 145 0 AAAGGGGGAA 0.98362 -83 TTAGAATTTGAGTTGGTGGTCAA 1 215 1 AGTTGGGGAA 0.834076 -13 CCCAAAATTGAAAGGATATCGAAAGGTTAAAAG 4 24 0 AAAGGAATAA 0.789421 -30 AGGGTTCCATAAAGGAAGGCGAATA 5 3 0 AAAGGAGGAA 0.964515 -298 ACAGTATATTAGTGGGTAGAAGATTTCTTCGTC 5 194 1 AGTGGGAGGA 0.844809 -107 GGCAATTCTGAAAGGATGTAAAAGAAAAGTAT 6 10 0 AAAGGAGTAA 0.857146 -112 AAATGTTAAGAGAGGGGATATAAACC 8 4 0 AGAGGGATAA 0.905606 -37 AAAAGCCCTCAGAGGGAAGTCGGTCATCATGCA 9 31 0 AGAGGGAGGG 0.806611 -245 AGCTTTCGGTAAATGAGGGTGGAAATCCTTTCG 9 202 0 AAATGAGGGA 0.83054 -74 GGAACCGGCTAAATGAGAGAAAACTCCCATGAG 10 71 0 AAATGAAGAA 0.845617 -202 GGTTCCCAGGAGATTGAGGTTAAAATTTCAGGA 10 98 1 AGATTGGGAA 0.616832 -175 TGATGACATCAAAGGGAAGATAATTATTATAAA 10 175 1 AAAGGGAGAA 0.974038 -98 ****** ** ** Masking position 1 Map Score: 5.89849 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 1009 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 TCTTGACACTTTAACCACCCTTTTATAAATCT 1 145 1 TTACCACCTT 0.948469 -83 TTAAGTCCGATTAGATAATCTTATAAACGCTA 3 29 0 TTGATATCTT 0.727656 -67 CTTTTAACCTTTCGATATCCTTTCAATTTTGG 4 24 1 TTGATACCTT 0.964606 -30 TATTCGCCTTCCTTTATGGAACCC 5 3 1 TTGCCTCCTT 0.959169 -298 TAAACTTAGTTTATATAGCCTTGACTCTCGGA 5 71 0 TTTATACCTT 0.945452 -230 ATAAACTAAGTTTACTTGCCTTCCTAACCCTC 5 89 1 TTACTTCCTT 0.947677 -212 ATACTTTTCTTTTACATCCTTTCAGAATTGC 6 10 1 TTTACACCTT 0.934625 -112 GATCATCTCCTTGAATTTCCTTAACGAAAGGA 9 178 1 TTAATTCCTT 0.933635 -98 TTTATAATAATTATCTTCCCTTTGATGTCATC 10 176 0 TTTCTTCCTT 0.947677 -97 ** **** **** Masking position 2 Map Score: 7.46644 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 291 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 GGGGATTTGGATAGAGCTCCCACTTAATTCC 1 76 0 ATAGACTCCC 0.938486 -152 TTCGAACACCATAAACCTTCTAACGAGGGGA 1 102 0 ATAAACTTCT 0.935688 -126 CCACCCTTTTATAAATCTCTTTCATAGTATT 1 159 1 ATAAACTCTT 0.787545 -69 CATTAGACGAAGAAATCTTCTACCCACTAAT 5 201 0 AGAAACTTCT 0.935179 -100 AATGGAATGTAAAAACCTTCCCAATTTCTAA 6 86 0 AAAAACTTCC 0.959773 -36 TATATCTTTATGAAAACTCCCTTTAAATCTC 9 116 0 TGAAACTCCC 0.916209 -160 AATAGCCTATATAAAGCTTTCGGTAAATGAG 9 218 0 ATAAACTTTC 0.897802 -58 TTAAGTAGTTAAATATCTTCCGGAGGTGGGG 10 26 1 AAATACTTCC 0.810791 -247 GCTAAATGAGAGAAAACTCCCATGAGCTTAA 10 66 0 AGAAACTCCC 0.985773 -207 ***** ***** Masking position 5 Map Score: 5.30505 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 213 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 AAACCGAAGTTCCTCAGGGAATTAAGTGGG 1 59 1 TCCTCAGGGA 0.906359 -169 ATTTCTCTAATAGTCAGGGAGCACTTCCGA 5 46 1 TAGTCAGGGA 0.950155 -255 GGAAATCCTTTCGTTAAGGAAATTCAAGGA 9 185 0 TCGTTAAGGA 0.650223 -91 GTTGGGGATATCCTTAGGGAAACTATACCT 10 140 1 TCCTTAGGGA 0.609331 -133 GATAAAGATTTCGTTAAGGTAATGCCAGTA 10 242 1 TCGTTAAGGT 0.876223 -31 ********** Masking position 6 Map Score: 2.43711 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 77 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 TAGAGCCCACCTTCCCTGGGATCTAGGCTC 1 18 0 CTTCCCTGGG 0.959198 -210 GTTATTAACGCTTTCTGGGGG 2 49 1 CTTTCTGGGG 0.992655 -11 AACCCTCTTACTTGCTGGGGCTTTTATCAT 5 114 1 CTTGCTGGGG 0.991275 -187 CTCTTAACATTTTTCTGGGGGTATTC 8 25 1 TTTTCTGGGG 0.962846 -16 AGTTAAATATCTTCCGGAGGTGGGGAGATG 10 32 1 CTTCCGGAGG 0.915489 -241 ********** Masking position 3 Map Score: 2.16976 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 65 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 TATTTGCCAAAAATTCTAAATCTTACTTAT 1 186 1 AAATTCTAAA 0.914407 -42 CCACCAACTCAAATTCTAATAAGTAAGATT 1 204 0 AAATTCTAAT 0.914407 -24 AGTAAATAATAATTTTTAAGTCCGATTAGA 3 46 0 AATTTTTAAG 0.763859 -50 AATAACCCCCAAATTTTAACTGATTTTTGA 5 165 1 AAATTTTAAC 0.9319 -136 AAACCTTCCCAATTTCTAAATGAATTAGTA 6 75 0 AATTTCTAAA 0.822931 -47 TTTAAATCTCAAATTTTTATATACATCGAT 9 96 0 AAATTTTTAT 0.64747 -180 TTCTTTCCTGAAATTTTAACCTCAATCTCC 10 106 0 AAATTTTAAC 0.9319 -167 ********** Masking position 2 Map Score: 1.0845 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 63 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 ACCTTCTAACGAGGGGATTTGGATAGAGCT 1 89 0 GAGGGGATTT 0.966221 -139 TCTATATGATCTGGTGATTTAAT 3 83 1 CTGGTGATTT 0.891007 -13 CTCTTACTTGCTGGGGCTTTTATCATAATT 5 118 1 CTGGGGCTTT 0.938195 -183 CAGTTAAAATTTGGGGGTTATTGTGCTTTA 5 157 0 TTGGGGGTTA 0.74006 -144 GCCCAATAGCGAGGTGGGTTAA 7 12 1 GAGGTGGGTT 0.729629 -12 AATGTTAAGAGAGGGGATATAAACC 8 6 0 GAGGGGATAT 0.958707 -35 TAACATTTTTCTGGGGGTATTC 8 29 1 CTGGGGGTAT 0.970613 -12 TCTTCCGGAGGTGGGGAGATGAAAATTAAG 10 41 1 GTGGGGAGAT 0.95582 -232 AAGAAGAGAGTTGGGGATATCCTTAGGGAA 10 131 1 TTGGGGATAT 0.937326 -142 ********** Masking position 6 Map Score: 6.29397 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 303 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 AGTCCGATTAGATAATCTTATAAACGCTAT 3 28 0 GATAATCTTA 0.775704 -68 AGTCTTTACTCATGAACATTGAACATTAGA 5 225 0 CATGAACATT 0.886708 -76 ACTAAAAGCGGATGATCATTAGATAACTAT 5 274 1 GATGATCATT 0.881064 -27 TATATACATCGATGAACATATTAAAACTCT 9 79 0 GATGAACATA 0.935456 -197 AATTCAAGGAGATGATCTTTCTTTCGATTT 9 165 0 GATGATCTTT 0.952784 -111 AGAAAACTCCCATGAGCTTAATTTTCATCT 10 57 0 CATGAGCTTA 0.872545 -216 ********** Masking position 5 Map Score: 0.205169 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 96 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 8.55083e-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 14 ********** No masking Map Score: 8.55083e-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 15 ********** No masking Map Score: 8.55083e-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