AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_mpneu_reg_300.orf -o00252_mpneu_300.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 B01_orf414o 26 hisS; histidyl-tRNA synthetase (histidine--tRNA ligase) (hisRS). #2 B01_orf191 46 tdk; thymidine kinase. [EC:2.7.1.21] [SP:KITH_MYCPN] #3 B01_orf264 300 glpF; glycerol uptake facilitator protein. [SP:GLPF_MYCPN] #4 A05_orf900 300 alaS; alanyl-tRNA synthetase (alanine--tRNA ligase) (alaRS). #5 K04_orf430 21 pgi; glucose-6-phosphate isomerase (GPI) (phosphoglucose isomerase) #6 K04_orf726 273 vacB; vacB protein homolog. [SP:VACB_MYCPN] #7 G07_orf479 197 hypothetical protein. #8 G07_orf240 24 ung; uracil-DNA glycosylase. [EC:3.2.2.-] [SP:UNG_MYCPN] #9 G07_orf417 300 hypothetical protein. Motif number 1 AAGAAAAAGCTGTAATAAATGAAAAAAGCCTAGAAGCTC 3 17 0 TGAATAAAGC 0.942514 -284 GTTTGTAAATTTATCAGCCAAGAAAAAGCTGTAATAAAT 3 36 0 TTTCAGAAGC 0.580972 -265 TTTAGCACTTTTGTAAAATGGGCAAATGCAGTTGTTTGT 3 69 0 TTTAAGAAGC 0.766313 -232 TTTTTAACGGGTCAATTTTCAAATAAAGCCCTTGATTTA 3 104 0 GTAATAAAGC 0.973673 -197 AATTGACCCGTTAAAAAGTTAATTAATGGGAGGATAAGC 3 126 1 TTAAAAAAGG 0.85911 -175 TAAGCAAGCTTTAAAAAGCGCAAAATAGCGTTTAAAAAA 3 160 1 TTAAAAATGC 0.773319 -141 CTCTCAAAAAGTTATTTTTTAAGAAAAGCTATCAGTAAA 3 250 0 GTATTAAAGC 0.908607 -51 ATCAATGAGTGTTACTGGTACATTAAAGCGGGTTTTTAT 4 27 1 GTACTAAAGC 0.939893 -274 ACCAGCTTGCTTTAAATCCTTAAAAAGGGTATTAACGGC 4 153 1 TTAAAAAAGG 0.85911 -148 ACCAATTCTCTTCAAACCAAAATCAATGCCTAAAATGTA 4 267 1 TTAAAAAAGC 0.978298 -34 TTTAATGTGTGTTAATTTTAAACTAATGCT 6 2 0 GTAATAAAGC 0.973673 -272 AGTTTTGTCTTTAATTCAACAAACAAAGCTTTAGCATTT 7 23 1 TTATTAAAGC 0.923786 -175 AAAATCATAAGAAAAATAATGAAAAATGCTAAAGCTTTG 7 46 0 GAAAAAAAGC 0.771984 -152 TTATTCCGCTTGTACTCAAACAGAAAAGCACAGCGAGCA 7 84 1 TGACTAAAGC 0.873931 -114 TTCATTGAGCCGCAAAGGCAGCAA 8 1 1 TTATTGAAGC 0.861604 -24 ATTCCCCAACTGCAAAAGGAAATAAAAGCTGCTAATGAC 9 32 1 TGAAAAAAGC 0.942514 -269 ACCTTTCGGGTTCAATACCGGGAAAAAGCCACTGCCCAA 9 131 0 TTAATGAAGC 0.958598 -170 TGGTTTTGAAGTCAAACTGATTAAAACGCATGACATTGT 9 235 1 GTAAATAAGC 0.784483 -66 ** *** * ** ** Masking position 15 Map Score: 18.0279 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 190 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 AATGCAGTTGTTTGTAAATTTATCAGCCAAG 3 53 0 TTTGAAATTT 0.944493 -248 ATTTAGCACTTTTGTAAAATGGGCAAATGCA 3 78 0 TTTGAAAATG 0.871389 -223 AAGGGCTTTATTTGAAAATTGACCCGTTAAA 3 110 1 TTTGAAATTG 0.964673 -191 TAAACGCTATTTTGCGCTTTTTAAAGCTTGC 3 163 0 TTTGGCTTTT 0.798158 -138 TCAGTTTTATTTTGAAAAATTCTAAATAAGA 3 211 1 TTTGAAAATT 0.808501 -90 TGCAGTACATTTTAGGCATTGATTTTGGTTT 4 280 0 TTTAGCATTG 0.673048 -21 CAGGTCAAGATTTGGAAATTTTTCGCAAAAC 6 146 1 TTTGAAATTT 0.944493 -128 ACATCGTAATTTGGAGAATTTTGACAATTCC 6 187 0 TTGGGAATTT 0.888632 -87 CTGTTTTGGTAAAGTTTTGTCTTTAA 7 6 1 TTGGAAAGTT 0.814044 -192 TTTGGACTTTGCTTTGCAACT 7 187 0 TTTGACTTTG 0.861642 -11 CCTTTTGCAGTTGGGGAATTGTTTCAAGTAC 9 20 0 TTGGGAATTG 0.927563 -281 GGAATTTGACTTTGTTCATTGACAGGGAAAA 9 72 0 TTTGTCATTG 0.839529 -229 TATTTGACTTTTTGGGCAGTGGCTTTTTCCC 9 120 1 TTTGGCAGTG 0.949763 -181 TGCTAGTTTGTTTGAACAGTTTCAGCTAGCA 9 190 1 TTTGACAGTT 0.920389 -111 **** ****** Masking position 2 Map Score: 13.3595 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 137 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TTCCTTAAAGCGTTCTTTAAACTGCTT 2 8 1 AAGCGTTCTT 0.969225 -39 AAGAGCTTCTAGGCTTTTTTCATTTATTAC 3 15 1 AGGCTTTTTT 0.813108 -286 TCATTTATTACAGCTTTTTCTTGGCTGATA 3 34 1 CAGCTTTTTC 0.805774 -267 GCGCTTTTTAAAGCTTGCTTATCCTCCCAT 3 151 0 AAGCTTGCTT 0.92807 -150 TGGTACATTAAAGCGGGTTTTTATTAGTTC 4 42 1 AAGCGGGTTT 0.929754 -259 AATTCATAACCAGCTTGCTTTAAATCCTTA 4 145 1 CAGCTTGCTT 0.979567 -156 CAAGTCCCTTCCGCGTGTTTGCGGTACAAA 4 206 0 CCGCGTGTTT 0.945044 -95 TTTGACAATTCCGCGGTCTTTGGTTTTGCG 6 169 0 CCGCGGTCTT 0.83325 -105 AAAAATGCTAAAGCTTTGTTTGTTGAATTA 7 34 0 AAGCTTTGTT 0.865202 -164 CTGTCTTTGCAAGCTTGTTTTAGAGTTGCA 7 164 1 AAGCTTGTTT 0.970059 -34 ATGTCATTAGCAGCTTTTATTTCCTTTTGC 9 43 0 CAGCTTTTAT 0.736781 -258 AAAGTCAAATAAGCGTGCTTCTACACGGGG 9 101 0 AAGCGTGCTT 0.930841 -200 ********** Masking position 4 Map Score: 11.4947 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 138 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 ATCAATGAGTGTTACTGGTACATTAAAGCGGG 4 27 1 GTTACGGTCA 0.914631 -274 GCATTCACAAGTTTGTGGAACTAATAAAAACC 4 57 0 GTTTGGGACT 0.893398 -244 CCTTCCGCGTGTTTGCGGTACAAAATAATTTG 4 198 0 GTTTGGGTCA 0.986561 -103 ATTGATTTTGGTTTGAAGAGAATTGGTACAGC 4 262 0 GTTTGAGAAA 0.801433 -39 ACTTGCTTCGCTTTCAGGTCAAGATTTGGAAA 6 132 1 CTTTCGGTAA 0.889718 -142 CGATGTTTATTTTAGTAGTGCTTTTTCTTATT 6 212 1 TTTAGAGTCT 0.48215 -62 GTTTAAGCAGCTTTGCAGTTCTTTACATTGTA 7 133 0 CTTTGAGTCT 0.914023 -65 TTGCTGCCTTTGCGGCTCAATGAA 8 6 0 CTTTGGGCCA 0.927738 -19 TTGGGGAATTGTTTCAAGTACACCAGTCAA 9 9 0 GTTTCAGTCA 0.947382 -292 AACCCTAAACCTTTCGGGTTCAATACCGGGAA 9 146 0 CTTTCGGTCA 0.965598 -155 AAGGTTTAGGGTTAGCGGACAACGTTGCTAGT 9 165 1 GTTAGGGAAA 0.706643 -136 ACTTAAGTGGTTTTGAAGTCAAACTGATTAAA 9 228 1 TTTTGAGTAA 0.721953 -73 TACGTTACAGCTTTGAAGTGCAA 9 288 1 CTTTGAGTCA 0.970686 -13 ***** *** ** Masking position 3 Map Score: 10.3642 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 197 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TCCTTAAAGCGTTCTTTAAACTGCTTGGTC 2 12 1 GTTCTTTAAA 0.973525 -35 GCTATTTTGCGCTTTTTAAAGCTTGCTTAT 3 159 0 GCTTTTTAAA 0.856584 -142 AACAGTAGGTGTTTTTTAAACGCTATTTTG 3 180 0 GTTTTTTAAA 0.878654 -121 ACTGATAGCTTTTCTTAAAAAATAACTTTT 3 253 1 TTTCTTAAAA 0.770202 -48 CATAACCAGCTTGCTTTAAATCCTTAAAAA 4 149 1 TTGCTTTAAA 0.901466 -152 CTGTACCAATTCTCTTCAAACCAAAATCAA 4 263 1 TCTCTTCAAA 0.80394 -38 TTTTCATTTTGCGCTTTAAAATCTAACAG 6 255 1 GCGCTTTAAA 0.936814 -19 CGAGCAGTCTTTTCTTTACAATGTAAAGAA 7 117 1 TTTCTTTACA 0.901466 -81 CAGCTTTGCAGTTCTTTACATTGTAAAGAA 7 128 0 GTTCTTTACA 0.947298 -70 ********** Masking position 5 Map Score: 5.96085 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 127 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CAGCTTTTTCTTGGCTGATAAATTTACAAA 3 44 1 TTGGCTGATA 0.890947 -257 GAGATATAATTTTACTGATAGCTTTTCTTA 3 240 1 TTTACTGATA 0.878687 -61 ATCAATGAGTGTTACTGGTACATTAAAGCG 4 27 1 GTTACTGGTA 0.890947 -274 ACTTGGATACTTGACTGGTAGTGGAAGTGG 4 91 1 TTGACTGGTA 0.98983 -210 GTCAATGGTATTGACTAGTGCTGTACCAAT 4 243 1 TTGACTAGTG 0.894686 -58 TTGACTGGTGTACTTGAAAC 9 1 1 TTGACTGGTG 0.984961 -300 ACTTTGTTCATTGACAGGGAAAATGTCATT 9 65 0 TTGACAGGGA 0.861449 -236 ********** Masking position 2 Map Score: 2.61381 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CTTTGTTTAATTATAATTGGG 1 16 0 TTTGTTTAAT 0.925015 -11 CGAAAATTCTTTTTACTAAT 3 291 1 TTTTACTAAT 0.795846 -10 TAAAGCGGGTTTTTATTAGTTCCACAAACT 4 50 1 TTTTATTAGT 0.795847 -251 AAATCCTTTTTTTAGTTGATT 5 6 0 TTTTTTTAGT 0.925016 -16 ATGGCAATCCTTTGTTTAATCATCGGTTTA 6 73 1 TTTGTTTAAT 0.925015 -201 ATTACGATGTTTATTTTAGTAGTGCTTTTT 6 208 1 TTATTTTAGT 0.660406 -66 TTAGTAGTGCTTTTTCTTATTTTAGGGTTA 6 223 1 TTTTTCTTAT 0.795847 -51 TAAAGCTTTGTTTGTTGAATTAAAGACAAA 7 26 0 TTTGTTGAAT 0.742418 -172 TTTTTCATTATTTTTCTTATGATTTTTATT 7 59 1 TTTTTCTTAT 0.795847 -139 ********** Masking position 2 Map Score: 1.74854 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 48 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AATAAAGCCCTTGATTTAGCACTTTTGTAA 3 92 0 TTGATTTAGC 0.963506 -209 ATTTTAGGCATTGATTTTGGTTTGAAGAGA 4 273 0 TTGATTTTGG 0.918664 -28 TCCGCGGTCTTTGGTTTTGCGAAAAATTTC 6 160 0 TTGGTTTTGC 0.956879 -114 GGGTTAGTTTTTCATTTTGCGCTTTAAAAT 6 247 1 TTCATTTTGC 0.980104 -27 TTCATTGAGCCGCAAAGGCA 8 1 1 TTCATTGAGC 0.906135 -24 CAGCTTTTATTTCCTTTTGCAGTTGGGGAA 9 33 0 TTCCTTTTGC 0.956879 -268 ********** Masking position 5 Map Score: 2.53167 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 58 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 CCTCCCATTAATTAACTTTTTAACGGGTCAA 3 128 0 ATTACTTTTT 0.900392 -173 TTTCTTAAAAAATAACTTTTTGAGAGGGCGA 3 263 1 AATACTTTTT 0.938572 -38 GGGGAAAGCCAATCACTATTTGCACTAATTC 4 119 1 AATACTATTT 0.900393 -182 GCTTGTTGCAAATTATTTTGTACCGCAAACA 4 190 1 AATATTTTGT 0.618504 -111 CCATTACAAACATTACTATTTGAATTGCGTC 6 46 0 CATACTATTT 0.81546 -228 AAATTCTCCAAATTACGATGTTTATTTTAGT 6 197 1 AATACGATGT 0.763163 -77 CTTTGCAGTTCTTTACATTGTAAAGAAAAGA 7 124 0 CTTACATTGT 0.728644 -74 AAAAGCTGCTAATGACATTTTCCCTGTCAAT 9 55 1 AATACATTTT 0.8741 -246 ACACGGGGAATTTGACTTTGTTCATTGACAG 9 78 0 TTTACTTTGT 0.793122 -223 AGCACGCTTATTTGACTTTTTGGGCAGTGGC 9 112 1 TTTACTTTTT 0.740717 -189 CCTTACTCTTAATGACAATGTCATGCGTTTT 9 257 0 AATACAATGT 0.845997 -44 *** ******* Masking position 5 Map Score: 3.2919 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 171 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 CTTGGTCTTAACTGTAACTGGC 2 35 1 ACTGTAACTG 0.920481 -12 AATTTTTCAAAATAAAACTGAAAACAGTAG 3 202 0 AATAAAACTG 0.847942 -99 TGCGCTTTAAAATCTAACAG 6 264 1 AATCTAACAG 0.741415 -10 ACAAAACTTTACCAAAACAG 7 1 0 ACCAAAACAG 0.771922 -197 TTCCGCTTGTACTCAAACAGAAAAGCACAG 7 87 1 ACTCAAACAG 0.966342 -111 CTGCAAAGCTGCTTAAACTGTCTTTGCAAG 7 147 1 GCTTAAACTG 0.867804 -51 ATTGATGCTAGCTGAAACTGTTCAAACAAA 9 196 0 GCTGAAACTG 0.947105 -105 GTGGTTTTGAAGTCAAACTGATTAAAACGC 9 234 1 AGTCAAACTG 0.913499 -67 ********** Masking position 6 Map Score: 0.727806 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 142 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ACCATTGACCGCTTTCCAAGTCCCTTCCGC 4 222 0 GCTTTCCAAG 0.982733 -79 TCGGTTTATTGCTATCCAACCATGGTTCTA 6 95 1 GCTATCCAAC 0.945341 -179 AGTTTAAGCAGCTTTGCAGTTCTTTACATT 7 136 0 GCTTTGCAGT 0.931923 -62 GCTTAAACTGTCTTTGCAAGCTTGTTTTAG 7 157 1 TCTTTGCAAG 0.940781 -41 TTTGGACTTTGCTTTGCAACTCTAAAACAA 7 178 0 GCTTTGCAAC 0.988069 -20 ********** Masking position 5 Map Score: 0.807225 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 19 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 ********** No masking Map Score: 1.87173e-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 13 ********** No masking Map Score: 1.87173e-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: 1.87173e-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