AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_bsub_reg_300.orf -o00410_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 ycnG 106 similar to 4-aminobutyrate aminotransferase #5 panB 245 ketopantoate hydroxymethyltransferase #6 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #7 ypjD 300 alternate gene name: jojD #8 ywhF 201 similar to spermidine synthase #9 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #10 aldX 142 aldehyde dehydrogenase Motif number 1 TACAAAATACGACAAAAACATTTTGAAAAT 1 66 1 GACAAAAACA 0.414613 -235 GGTTTATTGAAAAAGACGGATATATACTGG 1 206 1 AAAAGACGGA 0.549947 -95 ATATTTTATAAAAAAGCGGTAAATCACTGT 2 64 0 AAAAAGCGGT 0.529126 -163 CTTACAATTAAACAAAAGGATATATGGGAA 2 129 1 AACAAAAGGA 0.492959 -98 GAAAAAACACGAAAGGGGCAATGGGC 3 14 1 GAAAGGGGCA 0.959331 -16 AGAAAATACCGACAGGGGGATATTCAC 4 90 1 GACAGGGGGA 0.967473 -17 CCTTGATCCAAAAAAGGACTGGGACAGAGG 5 111 1 AAAAAGGACT 0.457106 -135 AAAGGACTGGGACAGAGGGATGAAACTCGC 5 123 1 GACAGAGGGA 0.896382 -123 GCTTGCAGAAGAAAACGGCAGATCATCTCC 5 203 1 GAAAACGGCA 0.858841 -43 GGCTGATGTGGAAAAGGGCATAAAGCAAAA 7 15 1 GAAAAGGGCA 0.968835 -286 CTAATGGAAGGAAAAGGGGTTTTGTGTGAT 7 170 0 GAAAAGGGGT 0.930765 -131 GGATGAAAAAGAAAACAGCAAACGTGCTTA 7 219 1 GAAAACAGCA 0.638929 -82 GAAACATAAAAAAAGGGGGAACCCGTT 8 8 0 AAAAGGGGGA 0.93646 -194 ACTATTATGAGAAAAAAAGATCGTTTTTAA 8 39 1 GAAAAAAAGA 0.718346 -163 TTCCTTAGGTGAAAATGAGATTTCAACCGA 8 122 1 GAAAATGAGA 0.683885 -80 ATACAGCCTCGAAAGGGAGATGACAA 8 186 1 GAAAGGGAGA 0.958121 -16 TTGCGCGATTGACAAGCAGAAGAGATTTTT 9 107 1 GACAAGCAGA 0.835697 -61 CATACCTTACAAAAAGGAGAAACGGA 9 152 1 AAAAAGGAGA 0.89838 -16 ATAGGTCCGAGAAAAGAAGAAAGCAAATGA 10 110 1 GAAAAGAAGA 0.897638 -33 ********** Masking position 4 Map Score: 16.2733 Number of sites scoring better than the average of aligned sites = 3127 Number in coding regions = 2453 Number in noncoding regions = 674 Number of orfs with sites within 600 bp upstream = 690 Fraction of orfs with sites within 600 bp upstream = 0.110826 Motif number 2 TAATTATACCTTCCGCTATTATGAAAGCGT 1 4 0 TTCGCAAAAG 0.989541 -297 TTTCTCCCGATTCCCCAAAATAAAAAGCGAGGATGTG 1 150 1 TTCCCAAAAG 0.979907 -151 CCGGCCGGGATTCTGCGCAGCAAAAAAACAGCCTGGT 2 27 0 TTCGCCAAAA 0.984083 -200 TAGTTTCTCCTTCTGATACCATCAAAAAGTTATAATT 4 15 1 TTCGAAAAAA 0.883981 -92 GCCTGCGAACTGCACCTATTATTAAAATAGATAGACA 5 61 1 TGCCCAAAAA 0.950872 -185 ACGAGAAGGATTCTTCACTTTCTAAAGTTCGGCGAGT 5 147 0 TTCTCCAAAG 0.897326 -99 TGCCGTTTTCTTCTGCAAGCCAAAAAACCTTCCGTTA 5 186 0 TTCGCAAAAA 0.988675 -60 ATGAAAAAATTGCCGCTCCGATTAAAATAAAAAATAT 7 108 1 TGCGCCAAAA 0.963952 -193 ATGCGTCCTGTTCTGCGATGTTTAAAAACGATCTTTT 8 53 0 TTCGCAAAAA 0.988589 -149 AAATCTCATTTTCACCTAAGGAAAAAGTATAGAGGAT 8 108 0 TTCCCAAAAG 0.979907 -94 *** ** * **** Masking position 14 Map Score: 11.7044 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 200 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CAGTAATTATACCTTCCGCTATTATGAAAGC 1 13 0 ACCTTCCGTA 0.950494 -288 TTTGCAGGTTTTCTCCCGATTCCCCAAAATA 1 141 1 TTCTCCCGTT 0.725761 -160 TTCCCATATATCCTTTTGTTTAATTGTAAGA 2 128 0 TCCTTTTGTT 0.663548 -99 TCACATCCGCTCCTTCCCATATATCCTTTTG 2 141 0 TCCTTCCCTA 0.978392 -86 CAACATAACCTCCTGTTATTTGTGTATA 2 209 0 ACCTCCTGTA 0.950494 -18 TTGTAGTTTCTCCTTCTGATACCATCAAAAA 4 12 1 TCCTTCTGTA 0.979 -95 AAGTGAAGAATCCTTCTCGTTGTAACGGAAG 5 164 1 TCCTTCTCTT 0.958413 -82 AAGCCAAAAAACCTTCCGTTACAACGAGAAG 5 176 0 ACCTTCCGTA 0.950494 -70 GTTTTCTCCTCCTCATGTTTAGAGGAG 5 229 0 TCCTCCTCTG 0.923232 -17 AAACCCCTTTTCCTTCCATTAGATAGCGTTT 7 178 1 TCCTTCCATA 0.875072 -123 AAACCTCCTATCATCCTCTTACATGTTAGCT 7 274 0 TCATCCTCTA 0.76464 -27 TGTAAAATCCCCCTCATTTGCTTTCTTC 10 125 0 TCCCCCTCTT 0.820882 -18 ******** ** Masking position 10 Map Score: 8.2407 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 504 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 4 TTATGTTGATCACATCCTCGCTTTTTATTTTGG 1 164 0 CAATCTCCTT 0.975232 -137 ATTTTTCTTTCACATCCGCTCCTTCCCATATAT 2 148 0 CAATCGCCCT 0.99378 -79 AAGAAAACGGCAGATCATCTCCTCTAAACATGA 5 211 1 CAATCTCCCT 0.99017 -35 TGCCCTTTTCCACATCAGCCCCTC 7 2 0 CAATCGCCCT 0.99378 -299 AACGAAACCTCCTATCATCCTCTTACATGTTAG 7 276 0 CCATCTCTCT 0.935052 -25 CGGTTGAAATCTCATTTTCACCTAAGGAAAAAG 8 118 0 CTATTTCCCT 0.830318 -84 TTGTAAGCGTCTTATCAGCTTTTATTCTCGGTT 8 146 0 CTATCGCTTT 0.913941 -56 ATAACAAACTCATATCTGCGTTTTCAGCAGGAA 9 59 0 CAATCGCTTT 0.960649 -109 ** *** ** *** Masking position 4 Map Score: 7.74063 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 88 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTTAATTGTAAGACAAATAAACAATAAGTCAATA 2 107 0 AGAAAAAAAA 0.97546 -120 CGGATGTGAAAGAAAAATTAATAAAAGCGCTTAC 2 163 1 AGAAAAAAAA 0.97546 -64 CCAGAAAAAACACGAAAGGGGCAATG 3 3 1 AGAAAAACAA 0.951053 -27 GGTATCAGAAGGAGAAACTACAAA 4 1 0 GGAAAAACAA 0.941269 -106 AAATGAACCAAGCCAAATGAAAAAATTGCCGCTC 7 92 1 AGCAAAAAAA 0.892356 -209 TCATAATAGTAGAAACATAAAAAAAGGGGGAACC 8 15 0 AGAACAAAAA 0.892356 -187 AGGATGGCGGGGAAAAAGTAAAGATGCGTCCTGT 8 79 0 GGAAAAAAGA 0.933767 -123 TTTCACCTAAGGAAAAAGTATAGAGGATGGCGGG 8 102 0 GGAAAAATGA 0.716432 -100 AAGGTTTGTCAGAAAAAATAACAAACTCATATCT 9 75 0 AGAAAAAAAA 0.97546 -93 ATAATAGGTCCGAGAAAAGAAGAAAGCAAATGAG 10 107 1 CGAAAAAAAA 0.924421 -36 *** *** ** ** Masking position 7 Map Score: 8.1598 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 244 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 CAACATAACCTCCTGTTATTTGTG 2 213 0 AACACCTCCT 0.938185 -14 TTTAGAAAGTGAAGAATCCTTCTCGTTGTAACG 5 158 1 GAAGCCTTCT 0.938185 -88 TAATACCTGTAAAACCGCCCTCAGCCAGATTGT 7 48 1 AAAACCCTCA 0.823859 -253 TGAACGAAACCTCCTATCATCCTCT 7 286 0 AACGCCTCCT 0.978863 -15 GGGAAAAAGTAAAGATGCGTCCTGTTCTGCGAT 8 71 0 AAAGCGTCCT 0.932275 -131 GAAGCACCCTCCAAAAAAATAAA 9 1 1 GAAGCCTCCA 0.974085 -167 AAAAGACACCTCCAATCATTAGAC 10 2 1 AAAGCCTCCA 0.987163 -141 TTCTTACAGAAAAGGTACCACCTTATAATAGGT 10 83 1 AAAGCCACCT 0.951617 -60 TGTAAAATCCCCCTCATTTGCTTTCT 10 127 0 AAAACCCTCA 0.823861 -16 **** ****** Masking position 2 Map Score: 3.63857 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 233 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 TATACTGGCCCTCATGCTGATTACGGTGCC 1 228 1 CTCATGCTGA 0.873239 -73 TTCACATCCGCTCCTTCCCATATATCCTTT 2 143 0 CTCCTTCCCA 0.866219 -84 TTTGTAGTTTCTCCTTCTGATACCATCAAA 4 11 1 CTCCTTCTGA 0.974172 -96 GTATTTTCTTATCATTCTGACTTCTCTTTG 4 69 0 ATCATTCTGA 0.900648 -38 GTGAATATCCCCCTGTCGGTATTTTC 4 91 0 ATCCCCCTGT 0.871474 -16 GGCGAGTTTCATCCCTCTGTCCCAGTCCTT 5 124 0 ATCCCTCTGT 0.86223 -122 AAAGTGAAGAATCCTTCTCGTTGTAACGGA 5 163 1 ATCCTTCTCG 0.867842 -83 GTTTTCTCCTCCTCATGTTTAGAGG 5 231 0 CTCCTCCTCA 0.976113 -15 GAAACCTCCTATCATCCTCTTACATGTTAG 7 276 0 ATCATCCTCT 0.796417 -25 CGGTTGAAATCTCATTTTCACCTAAGGAAA 8 121 0 CTCATTTTCA 0.466065 -81 TTTTATCAAATTCCTGCTGAAAACGCAGAT 9 49 1 TTCCTGCTGA 0.767666 -119 TGTAAAATCCCCCTCATTTGCTTTCT 10 127 0 ATCCCCCTCA 0.944515 -16 ********** Masking position 2 Map Score: 6.27782 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 812 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 8 TTCTGTAGTCTCCATTATACAGTAATTATACC 1 31 0 TCATTAACAG 0.961437 -270 CTGGGTCAAAAGCAATTTGCAGGTTTTCTCCC 1 126 1 ACAATTGCAG 0.829229 -175 ATCCGTCTTTTTCAATAAACCGTTCCAGTTTT 1 195 0 TCAATAACCG 0.903468 -106 GGGATAAAATTTCAGTTCACCGGCCAGCGGCA 1 254 0 TCAGTTACCG 0.862975 -47 TTGGTATACTTCCATTGGGCAGTATCGCCTGC 5 35 1 TCATTGGCAG 0.921486 -211 TAATAATAGGTGCAGTTCGCAGGCGATACTGC 5 53 0 TCAGTTGCAG 0.943143 -193 CTTGGTTCATTTCAATATGCAGAACAATCTGG 7 72 0 TCAATAGCAG 0.961015 -229 CCCTTTTCCTTCCATTAGATAGCGTTTATATT 7 182 1 TCATTAATAG 0.709656 -119 GACACCTCCAATCATTAGACAGATCTTAGATA 10 15 1 ACATTAACAG 0.88737 -128 * ***** **** Masking position 6 Map Score: 2.49934 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 246 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 TTTATAAAAACCTCATGTTCTGGGTCAAAAGCA 1 107 1 CTCTGTCTGG 0.977106 -194 CGGCCAGCGGCACCGTAATCAGCATGAGGGCCA 1 233 0 CCCTATCAGC 0.922808 -68 AGCAAAAAAACAGCCTGGTCAGCCGGCTGTTTG 2 13 0 CGCTGTCAGC 0.995196 -214 CCCCCAAGCACATCATGATCAAGCA 6 3 0 CTCTGTCAAG 0.878161 -29 CGCCCTCAGCCAGATTGTTCTGCATATTGAAAT 7 63 1 CGATGTCTGC 0.953779 -238 AGTAAAGATGCGTCCTGTTCTGCGATGTTTAAA 8 64 0 CTCTGTCTGC 0.990213 -138 AAACTCATATCTGCGTTTTCAGCAGGAATTTGA 9 54 0 CGCTTTCAGC 0.96974 -114 * ** ** ***** Masking position 6 Map Score: 1.77093 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 456 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TACAGTAATTATACCTTCCGCTATTATGAA 1 16 0 ATACCTTCCG 0.987988 -285 GCAAGCCAAAAAACCTTCCGTTACAACGAG 5 179 0 AAACCTTCCG 0.987988 -67 TTTTTCTGACAAACCTTGCGCGATTGACAA 9 92 1 AAACCTTGCG 0.978114 -76 ATAAATCACCATACCTTACAAAAAGGAGAA 9 143 1 ATACCTTACA 0.883581 -25 ********** Masking position 6 Map Score: 0.620264 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 32 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TTACGGTGCCGCTGGCCGGTGAACTGAAATT 1 248 1 GCTGGCCGGG 0.958222 -53 TAATAAAAGCGCTTACAGATAGAGGCCGTAT 2 181 1 GCTTACAGAA 0.702198 -46 AATAGGTGCAGTTCGCAGGCGATACTGCCCA 5 50 0 GTTCGCAGGG 0.864131 -196 AGGTTTTTTGGCTTGCAGAAGAAAACGGCAG 5 193 1 GCTTGCAGAG 0.967339 -53 TCCTCCTCATGTTTAGAGGAGATGATCTGCC 5 219 0 GTTTAGAGGG 0.853632 -27 ATCATGATGTGCTTGGGGGCGAACA 6 17 1 GCTTGGGGGG 0.986762 -15 GAACAATCTGGCTGAGGGCGGTTTTACAGGT 7 52 0 GCTGAGGGCG 0.769324 -249 TTTGTGTGATGCTTGGAGAAATTAGATTAAA 7 149 0 GCTTGGAGAA 0.893126 -152 AAGTATAGAGGATGGCGGGGAAAAAGTAAAG 8 90 0 GATGGCGGGA 0.798709 -112 TCTGTCTAATGATTGGAGGTGTCTTTT 10 7 0 GATTGGAGGG 0.953853 -136 ********* * Masking position 3 Map Score: 0.992486 Number of sites scoring better than the average of aligned sites = 1516 Number in coding regions = 1387 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 12 ACGCTTTCATAATAGCGGAAGGTATAAT 1 7 1 TATAATGCGG 0.697258 -294 ATAGCGGAAGGTATAATTACTGTATAATGGAG 1 22 1 GATAATACTG 0.931519 -279 TGGGGAATCGGGAGAAAACCTGCAAATTGCTT 1 135 0 GAGAAACCTG 0.960934 -166 TGAAAAAGACGGATATATACTGGCCCTCATGC 1 213 1 GATATAACTG 0.603112 -88 TCCCCTCAATGAAGAATTCCGGGTCAGCT 1 282 1 GAGAATCCGG 0.974652 -19 TTTTTGCTGCGCAGAATCCCGGCCGGACAGTG 2 38 1 GAGAATCCGG 0.974792 -189 TAAAGCAAAAGTGTAATACCTGTAAAACCGCC 7 35 1 GGTAATCCTG 0.914473 -266 TTTCAACCGAGAATAAAAGCTGATAAGACGCT 8 142 1 GATAAAGCTG 0.929161 -60 * ***** **** Masking position 5 Map Score: 0.30846 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 438 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 13 TTTGTTTAATTGTAAGACAAATAAACAATA 2 115 0 TGTAAGACAA 0.921788 -112 GGAGCGGATGTGAAAGAAAAATTAATAAAA 2 159 1 TGAAAGAAAA 0.945144 -68 CGCTATCTAATGGAAGGAAAAGGGGTTTTG 7 176 0 TGGAAGGAAA 0.89289 -125 TATATTATAGTGGATGAAAAAGAAAACAGC 7 208 1 TGGATGAAAA 0.829208 -93 GATAAAATGCAGGAAGACAACATTTATTTT 9 26 0 AGGAAGACAA 0.94303 -142 GCGCAAGGTTTGTCAGAAAAAATAACAAAC 9 83 0 TGTCAGAAAA 0.761547 -85 CTTTTCTGTAAGAAAGACAACGGTGAACCA 10 67 0 AGAAAGACAA 0.913248 -76 CGAGAAAAGAAGAAAGCAAATGAGGGGGAT 10 117 1 AGAAAGCAAA 0.767696 -26 ********** Masking position 9 Map Score: 1.85289 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 431 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 14 ********** No masking Map Score: -6.62693e-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 15 ********** No masking Map Score: -6.62693e-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