AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_bsub_reg_300.orf -o00750_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 yclB 89 similar to phenylacrylic acid decarboxylase #2 serC 146 phosphoserine aminotransferase #3 hit 300 Hit-like protein #4 yjlC 300 yjlC #5 yjlD 39 similar to NADH dehydrogenase #6 yjmA 197 similar to glucuronate isomerase #7 yjmB 67 similar to Na+:galactoside symporter #8 yjmC 104 similar to malate dehydrogenase #9 yugK 103 similar to NADH-dependent butanol dehydrogenase #10 yugJ 229 similar to NADH-dependent butanol dehydrogenase #11 hom 200 homoserine dehydrogenase #12 yutH 152 yutH Motif number 1 GAGGTTATTTTATTTTGTGAACATTTCGCAAACATC 2 14 1 TTTTTGAATT 0.964266 -133 TCCGTCAATTTCTTTTGATAATTCTAATTTTTTATC 2 48 1 TTTTTGAATA 0.969012 -99 AAAAATTCAGTTTTTTGATAAAAAATTAGAATTATC 2 64 0 TTTTTGAAAT 0.973356 -83 GGTAAGCACCTCATTTGTCAATAAAATGAAGACTTG 3 132 0 TATTTGAAAA 0.909036 -169 CAATTGTTTATTTTTAGATAAAAATAATACTGAATA 4 117 1 TTTTAGAATA 0.768613 -184 GTAAACATTTATTTTTGTAAATGATTGTGCATGAAT 4 175 1 ATTTTGAATT 0.846461 -126 GTTTGCTGATTTTTTTGGAAAGGGTAGTGCCTCTCC 4 250 0 TTTTTGAATA 0.969011 -51 GATCAATCTCTTTTTTGAAAATGAAATGTTAACGCT 6 90 0 TTTTTGAAAA 0.979965 -108 ATATTTAAAATAATTTGTAAATAAAATGTGTTTGTA 8 27 1 TATTTGAAAA 0.90881 -78 TCCCTTTTTCTTTTTTGTCAACTTATGTTACAATGG 9 39 1 TTTTTGAAAT 0.976874 -65 AATCTATAACTGTTTTAATAATTCATGGAGGAGGTT 10 18 0 TTTTTAAAAT 0.735613 -212 CATTAGGCTGAATTTTGCGAATGTAAACGCTTAACG 11 64 0 ATTTTGAAAA 0.909049 -137 AGCCCGCTCCTGTTTTGACAAGACATCATTAGGCTG 11 90 0 TTTTTGAAAT 0.976875 -111 * ***** ** ** Masking position 10 Map Score: 15.3394 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 156 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 AAGAAAGCGCCTCCTTATCATACCTTTTAGGTATTAAT 1 11 1 CCCTTACTTT 0.965256 -79 TTCAATCATACTCCTGATATATCCATATGAAAAATATC 1 62 0 CCCGTTCTAT 0.852808 -28 TATGATCTCTCCCTGTTTTCCACGTTAATGTATAAA 2 121 0 CCCTTTCGTT 0.955402 -26 CTGCGATAAACACCTCATTTGACAATTTGCTTCATACA 3 76 0 CCCCTTCTTT 0.990835 -225 CTTTGGTAAGCACCTCATTTGTCAATAAAATGAAGACT 3 134 0 CCCCTTCTAA 0.737648 -167 GGTGAACGCTCGCCGTTCATCCTGTTTTCTATTTTCTG 3 215 1 CCCTCTTTTT 0.932065 -86 GAGGGTTCCTCCTTATGAAATTGTTTAGTATGTATA 3 275 0 CCCTTATTTT 0.924329 -26 GGTAGTGCCTCTCCCTGTCTCACGCTTTTAAGGCATAA 4 226 0 CCCTTTCTTT 0.988479 -75 GTATATCCTCCGTCCTTTATATCAATTTGAATCTGAGA 5 11 0 CTCTTTCTTT 0.945002 -29 GTCCTCACCGTCTTTCATTCTATTTCAAAATGT 6 175 0 CCCTTTTTAT 0.924329 -23 GCAAGTGCCTCCTTCCTTTTCAGTTTTTTGGGCACT 8 79 0 CCCTCTCTTT 0.968949 -26 CGTTTGGCTGCTTCCCTTTTTCTTTTTTGTCAACTTAT 9 27 1 CTCCTTTTTT 0.904937 -77 TCCAATATGTCACAATCTATAACTGTTTTAATAATTCA 10 29 0 CCATTTCTTT 0.809697 -201 GCTGGCCTGCCCTCGCTTATATCAGCTTCTTTCCCAGC 10 99 1 CTCCTTCCTT 0.746036 -131 GACATCTCCTCCTTAGATTTTTTATTATGCAGA 10 207 0 CCCCTATTTT 0.938993 -23 AAAAACTCCACCTTTCTTTTGATTGTCCTCTTG 11 178 0 CCCCTTTGAT 0.793526 -23 CAGCTTCACCCAATCTTTTTTACTAGTTTAT 12 4 1 CTCCCATTTT 0.528559 -149 * ** * * * * *** Masking position 1 Map Score: 16.5982 Number of sites scoring better than the average of aligned sites = 1014 Number in coding regions = 811 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 GATGAGGTTATTTTATTTTGTGAACATTTCG 2 10 1 ATTTTTTTTT 0.915264 -137 TCTTTTGATAATTCTAATTTTTTATCAAAAAA 2 58 1 ATTCTATTTT 0.824111 -89 TATCACAAAAATTCAGTTTTTTGATAAAAAAT 2 74 0 ATTCATTTTT 0.927958 -73 TGATAGGATAATTGTATTATTTTATACATTAA 2 101 1 ATTGTTTATT 0.485434 -46 TTCATCCTGTTTTCTATTTTCTGCATTTCTGT 3 230 1 TTTCTTTTTT 0.876567 -71 GACTTATTCAATTGTTTATTTTTAGATAAAAA 4 109 1 ATTGTTATTT 0.82827 -192 ATCTTGCCATATTCAGTATTATTTTTATCTAA 4 130 0 ATTCATATTT 0.8171 -171 GGTAGTAAACATTTATTTTTGTAAATGATTGT 4 171 1 ATTTATTTTT 0.789308 -130 GCTTTCTGGCAATGTCTTTTTTTATGTTTATG 6 56 1 AATGTTTTTT 0.82827 -142 CTTTGGGATCAATCTCTTTTTTGAAAATGAAA 6 100 0 AATCTTTTTT 0.927958 -98 TAACGTTAACATTTTGATTTGTTTTTATTTTA 6 143 0 ATTTTATTTT 0.576757 -55 TATTTTAAATATTCTTTATATTATATTG 8 7 0 ATTCTTATAT 0.466331 -98 CCTCCTTCCTTTTCAGTTTTTTGGGCACTCTC 8 76 0 TTTCATTTTT 0.711237 -29 TGCTTCCCTTTTTCTTTTTTGTCAACTTATGT 9 35 1 TTTCTTTTTT 0.876567 -69 TACAATGGAAAATCTGTTTTTTACCAGCATCA 9 67 1 AATCTTTTTT 0.927958 -37 TCCTCCTTAGATTTTTTATTATGCAGAATGTC 10 202 0 ATTTTTATTT 0.789307 -28 TTTATTTTCTAATTATTTTTGTCAGATTTTCT 11 13 0 AATTATTTTT 0.56509 -188 ATATGACAAGATTCTTTATTTTCTAATTATTT 11 27 0 ATTCTTATTT 0.927958 -174 TGAGTTAACAATTGTCTTTTCCAAGAGGACAA 11 157 1 ATTGTTTTTC 0.730731 -44 AGCTTCACCCAATCTTTTTTACTAGTTTATAC 12 12 1 AATCTTTTTC 0.715396 -141 ***** **** * Masking position 3 Map Score: 15.1125 Number of sites scoring better than the average of aligned sites = 1515 Number in coding regions = 1184 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 358 Fraction of orfs with sites within 600 bp upstream = 0.0575008 Motif number 4 AGACTTGTTTAATGCCTAACGATTCCTGCGAT 3 107 0 AAGCTAACGA 0.935003 -194 GTGCTTACCAAAGGCATAACACATTTTCTTCA 3 159 1 AAGCTAACAC 0.975783 -142 TCACGCTTTTAAGGCATAAGAATAAGGATTGT 4 213 0 AAGCTAAGAA 0.976376 -88 TTATGCCTTAAAAGCGTGAGACAGGGAGAGGC 4 226 1 AAGCTGAGAC 0.973769 -75 ACTATCCGAAAATTCTTAAGACACAGAGGTGG 7 43 1 AATCTAAGAC 0.879817 -25 TGCGAATGTAAACGCTTAACGCATTGATATGA 11 53 0 AAGCTAACGC 0.958013 -148 GTTTATACAAAATGCTTGAGAAGTTTACGACT 12 36 1 AAGCTGAGAA 0.959023 -117 TAATCCGAAGAAGGCGCAAGAAAAAGTCGTAA 12 60 0 AAGCCAAGAA 0.916511 -93 ** ** ****** Masking position 9 Map Score: 5.4862 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 76 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTAGAATTATCAAAAGAAATTGACGGATGT 2 45 0 CAAAAGAAAT 0.806659 -102 TAATTTTTTATCAAAAAACTGAATTTTTGT 2 72 1 TCAAAAAACT 0.673771 -75 AATTATCCTATCACAAAAATTCAGTTTTTT 2 84 0 TCACAAAAAT 0.673771 -63 GAGGTGCTTACCAAAGGCATAACACATTTT 3 156 1 CCAAAGGCAT 0.93248 -145 ATTCATCGTACCACAGAAATGCAGAAAATA 3 244 0 CCACAGAAAT 0.943781 -57 AATAGCAAACACAAAAAACTCCAATTCGAT 4 57 0 ACAAAAAACT 0.747438 -244 ACTACCCTTTCCAAAAAAATCAGCAAACTG 4 258 1 CCAAAAAAAT 0.949396 -43 TCTGGCATTGCCAAAAGCATTCCTTTCCGA 6 24 1 CCAAAAGCAT 0.896142 -174 ATAAACATAAAAAAAGACATTGCCAGAAAG 6 57 0 AAAAAGACAT 0.491986 -141 GAGATTGATCCCAAAGGAATATAAAGGTAA 6 116 1 CCAAAGGAAT 0.943781 -82 TGGAGAGTGCCCAAAAAACTGAAAAGGAAG 8 74 1 CCAAAAAACT 0.912957 -31 TGTTAACTCAACACAGACATATAAGTTACA 11 137 0 ACACAGACAT 0.795781 -64 ********** Masking position 5 Map Score: 6.38803 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 545 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 GATCTCTCCCTGTTTTCCACGTTAATGTATA 2 123 0 TGTTTTCCCG 0.875058 -24 TAAGTCAAAATCCTTTACTCTCTCTGAAAAT 4 84 0 TCCTTTACCT 0.80106 -217 ATCCAATTCTCCTTTACTATAAGCAGTTTG 4 281 0 TCCTTTACAT 0.876708 -20 CCAAAAGCATTCCTTTCCGAGTGCTTTCTGG 6 34 1 TCCTTTCCAG 0.978944 -164 GGAAAATCTGTTTTTTACCAGCATCATTTGG 9 73 1 TTTTTTACAG 0.898982 -31 TTATATCAGCTTCTTTCCCAGCACCTTGCAA 10 115 1 TTCTTTCCAG 0.957465 -115 GAGAGCTGATTGCTTTACATGTGGTGAGGAC 10 174 1 TGCTTTACTG 0.796685 -56 TTAACAATTGTCTTTTCCAAGAGGACAATCA 11 161 1 TCTTTTCCAG 0.959454 -40 TCACCCAATCTTTTTTACTAGTTTATACAAA 12 16 1 TTTTTTACAG 0.898982 -137 ******** ** Masking position 6 Map Score: 4.7876 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 270 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 GCGATAAACACCTCATTTGACAATTTGCTT 3 82 0 CCTCATTTGA 0.970332 -219 TTGGTAAGCACCTCATTTGTCAATAAAATG 3 140 0 CCTCATTTGT 0.948918 -161 GAGGGTTCCTCCTTATGAAATTGTTTA 3 284 0 CCTCCTTATG 0.865911 -17 TTTTTACCAGCATCATTTGGAGGTTTTACT 9 84 1 CATCATTTGG 0.963125 -20 GGCCAGCTTCCCTCATATGGAGAATGCATG 10 76 0 CCTCATATGG 0.948879 -154 GACATCTCCTCCTTAGATTTTTTATTA 10 213 0 CCTCCTTAGA 0.944231 -17 TTTGACAAGACATCATTAGGCTGAATTTTG 11 83 0 CATCATTAGG 0.941493 -118 ********** Masking position 6 Map Score: 4.39551 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 115 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 ATGAGGTTATTTTATTTTGTGAACATTTCG 2 12 1 TTTATTTTGT 0.925303 -135 GGATAATTGTATTATTTTATACATTAACGT 2 106 1 ATTATTTTAT 0.677663 -41 ATTGGACATGTTTATTTTCTATCCA 3 6 0 TTTATTTTCT 0.959514 -295 TAAACAAGTCTTCATTTTATTGACAAATGA 3 128 1 TTCATTTTAT 0.757051 -173 CATCCTGTTTTCTATTTTCTGCATTTCTGT 3 232 1 TCTATTTTCT 0.831724 -69 TTATTTTACCTTTATATTCCTTTGGGATCA 6 121 0 TTTATATTCC 0.824277 -77 TTGATTTGTTTTTATTTTACCTTTATATTC 6 132 0 TTTATTTTAC 0.914079 -66 TTAAATATTCTTTATATTATATTG 8 5 0 TTTATATTAT 0.805938 -100 ACCAGATGGTTTTATTTTGCAAGGTGCTGG 10 132 0 TTTATTTTGC 0.898166 -98 GACAAGATTCTTTATTTTCTAATTATTTTT 11 25 0 TTTATTTTCT 0.959514 -176 ********** Masking position 5 Map Score: 6.91266 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 270 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 9 TTATTTTATTTTGTGAACATTTCGCAAACAT 2 18 1 TTGTAACATT 0.765778 -129 ATTGTTTAGTATGTATACATTCATCGTACCA 3 261 0 ATGTTACATT 0.91582 -40 TACCTTCTATATGATAACACTTTTTGAACAA 4 26 0 ATGAAACACT 0.914264 -275 TGAAAATGAAATGTTAACGCTGTCATAAACA 6 80 0 ATGTAACGCT 0.963197 -118 CTATTTCAAAATGTTAACGTTAACATTTTGA 6 158 0 ATGTAACGTT 0.9639 -40 TGGAGAATGCATGTATAGATTCTCCAATATG 10 58 0 ATGTTAGATT 0.768182 -172 ACGCATTGATATGACAAGATTCTTTATTTTC 11 36 0 ATGAAAGATT 0.768182 -165 AATTTTGCGAATGTAAACGCTTAACGCATTG 11 59 0 ATGTAACGCT 0.963197 -142 CCGGCTGTGTATGACTACGATGTGATGAGCC 12 110 1 ATGATACGAT 0.644459 -43 **** ****** Masking position 7 Map Score: 2.58124 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 153 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 GAGCTTATATGAAGAAAATGTGTTATGCCTTT 3 168 0 GAAAAAATTG 0.983971 -133 AACACTTTTTGAACAAAATTTGAACGTGAAT 4 10 0 GAAAAAATTG 0.983971 -291 AATATGGCAAGATGAAAAACTGGGTAGTAAAC 4 149 1 GATAAAAATG 0.890313 -152 AATAATTTGTAAATAAAATGTGTTTGTAGGGG 8 35 1 AAAAAAATTG 0.904732 -70 GGAGAAAATCTGACAAAAATAA 11 1 1 GGAAAAATTG 0.957349 -200 GCCTTCTTCGGATTAAAATATGTATTCATAAT 12 77 1 GATAAAATTG 0.970502 -76 *** ***** ** Masking position 6 Map Score: 2.61889 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 57 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TGAATTGATGAATTCTTCATGTATGAAGCA 3 57 1 AATTCTTCAT 0.585701 -244 GAACGGCGAGCGTTCACCCTGAATGCAGAG 3 203 0 CGTTCACCCT 0.958281 -98 GAACGCTCGCCGTTCATCCTGTTTTCTATT 3 218 1 CGTTCATCCT 0.955113 -83 AGTATGTATACATTCATCGTACCACAGAAA 3 255 0 CATTCATCGT 0.919006 -46 TCTATACATGCATTCTCCATATGAGGGAAG 10 70 1 CATTCTCCAT 0.885717 -160 CAGCTCTCACCGATCAGCATACCAGATGGT 10 152 0 CGATCAGCAT 0.851565 -78 GTGGTGAGGACATTCTGCATAATAAAAAAT 10 194 1 CATTCTGCAT 0.936821 -36 CATATCAATGCGTTAAGCGTTTACATTCGC 11 54 1 CGTTAAGCGT 0.747333 -147 ACATTCGCAAAATTCAGCCTAATGATGTCT 11 76 1 AATTCAGCCT 0.870495 -125 ********** Masking position 4 Map Score: 1.03674 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 900 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 12 CCTCATTTGACAATTTGCTTCATACATGAA 3 72 0 CAATTTGCTT 0.731836 -229 TTGAATAAGTCAAAATCCTTTACTCTCTCT 4 90 0 CAAAATCCTT 0.97093 -211 TGAATTCATGCACAATCATTTACAAAAATA 4 184 0 CACAATCATT 0.839528 -117 TGCATGAATTCACAATCCTTATTCTTATGC 4 202 1 CACAATCCTT 0.975806 -99 CAGGGAGAGGCACTACCCTTTCCAAAAAAA 4 247 1 CACTACCCTT 0.843724 -54 AAAAAATCAGCAAACTGCTTATAGTAAAGG 4 271 1 CAAACTGCTT 0.902892 -30 CTAGTTTATACAAAATGCTTGAGAAGTTTA 12 33 1 CAAAATGCTT 0.962162 -120 ********** Masking position 2 Map Score: 1.80435 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 216 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 13 ********** No masking Map Score: -4.13293e-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: -4.13293e-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: -4.13293e-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