AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_bsub_reg_300.orf -o00510_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 yisP 300 alternate gene name: yucD; similar to phytoene synthase #2 ykcA 300 similar to ABC transporter (binding protein) #3 ykcB 250 similar to hypothetical proteins from B. subtilis #4 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #5 yllA 70 yllA #6 yllB 125 similar to hypothetical proteins #7 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #8 ftsL 39 cell-division protein #9 spoVD 116 penicillin-binding protein #10 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #11 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #12 spoVE 60 spoVE #13 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #14 tagE 160 UDP-glucose:polyglycerol phosphate glucosyltransferase #15 tagD 300 glycerol-3-phosphate cytidylyltransferase #16 ywaB 300 alternate gene name: ipa-6d; similar to quinone biosynthesis Motif number 1 TCCTAATTGTATATGAAGAAAATGCCGATTC 1 254 0 ATATAAGAAA 0.690235 -47 GCAAATTTCGAAAATCAGAAAATTTA 2 6 0 AAAACAGAAA 0.836217 -295 CCTAATACATAAAACACGAACTTTGTAAATA 2 109 0 AAAAACGAAC 0.828667 -192 CATAGCAGAAGTAAGAAGAAATTACTTCTCA 4 106 0 GTAAAAGAAA 0.866712 -54 TTCTGCTATGATAATACGTAAATGCTAAATT 4 127 1 ATAAACGTAA 0.794353 -33 CTGTTTACCCATAAAAAGAAACCCTGAACTA 6 35 0 ATAAAAGAAA 0.96302 -91 CTGAAGGCATAAAAAAAGAAAGCCTGCATAA 9 25 0 AAAAAAGAAA 0.953374 -92 AAATTCAGGCATAAAATGAAACAAGCCTAAA 9 78 1 ATAAATGAAA 0.88401 -39 TATTTACGCTAAAATATGAACTGTATGCTTA 10 81 1 AAAAATGAAC 0.817531 -95 GACTTCAATGATAAAAAGAACGAATTAGAAT 10 137 1 ATAAAAGAAC 0.951214 -39 TCTTATTTCAATAAGAAGTACTTTAATTAGA 14 40 0 ATAAAAGTAC 0.901517 -121 TCTTATTGAAATAAGAAGTACTTTTTGATGC 14 55 1 ATAAAAGTAC 0.901517 -106 AAAACATTCCAAAATATGTAATTACACTCAG 15 109 0 AAAAATGTAA 0.737501 -192 TCGTTCAAGTGAAAGCAGAAACCTAATGAAA 16 123 1 GAAACAGAAA 0.560412 -178 CGAGAAGCGTATAATAAGAAAGAAAACGCCT 16 160 1 ATAAAAGAAA 0.96302 -141 CTGCCGGCTGAAAAAAAGTAAGCCTTTTAAT 16 264 1 AAAAAAGTAA 0.90566 -37 **** ****** Masking position 3 Map Score: 13.758 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 543 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 2 TGCTGTGCGTCTTGTTACTTTTACAAAGTAA 1 223 1 CTGTTACTTT 0.801405 -78 GAAAATGCCGATTCTTACTTTGTAAAAGTAA 1 237 0 ATCTTACTTT 0.687469 -64 TTTTAAGCACATGGGATCTTTGAGAAGTAAT 4 86 1 AGGGATCTTT 0.775958 -74 CTGAACTAGTCAGGGTTCTTTAAAACTTTAT 6 12 0 CGGGTTCTTT 0.948771 -114 TGACTAGTTCAGGGTTTCTTTTTATGGGTAA 6 31 1 AGGTTTCTTT 0.960113 -95 TGCATAACGACGGCTTTCTTT 9 1 0 CGCTTTCTTT 0.971456 -116 GTCGTTATGCAGGCTTTCTTTTTTTATGCCT 9 21 1 AGCTTTCTTT 0.954816 -96 CTTATTTAGGCTTGTTTCATTTTATGCCTGA 9 82 0 CTGTTTCATT 0.842401 -35 AGAAAAAATGCTGATATCTTTCAAGATTAGC 10 36 1 CGATATCTTT 0.74308 -140 CAACATTCTAATTCGTTCTTTTTATCATTGA 10 141 0 ATCGTTCTTT 0.777236 -35 CTTTTCTCCTCCTGTTTCTTTCAAACGACAT 11 88 0 CTGTTTCTTT 0.930548 -25 TTTAGGATCCTGATATCATTGGTTCAATAT 14 10 1 CGATATCATT 0.535717 -151 GTACTTTTTGATGCTTACATTGATTTTTGTG 14 72 1 AGCTTACATT 0.717444 -89 TCTGTTGTTCATTCGTTCATTCAATTGTAAA 15 60 0 ATCGTTCATT 0.581931 -241 ATTAGGAAGGAGCGTTTCTTTAA 15 288 1 ACGTTTCTTT 0.719085 -13 CTTTTGACTCCAGGTATCTTTTCCTTTATTA 16 37 0 CGGTATCTTT 0.921111 -264 GCTTCTCGCCCTGATTTCATTAGGTTTCTGC 16 137 0 CGATTTCATT 0.793005 -164 TTCTATTAAAAGGCTTACTTTTTTTCAGCCG 16 268 0 AGCTTACTTT 0.864215 -33 * ********* Masking position 10 Map Score: 13.0351 Number of sites scoring better than the average of aligned sites = 1653 Number in coding regions = 1421 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 3 CAATTAGCCCTTTTTTCCGTGATTCCTCTATTA 1 112 1 TTTTTCCTAT 0.864168 -189 GCATCTGATATTTCCTCCCTAATAAGGCATGCT 3 78 0 TTTCTCCTAT 0.952198 -173 TTATTTTTCACTCCTTTTTGTCTAACTTT 3 232 0 TTCCTCCTTT 0.935031 -19 TATTCACCACTTCGCTCCACAACTTCATTTTAC 6 67 0 TTCCTCCCAC 0.875639 -59 TTGCCCCACTTTCTCTCCTTAACTCACCACTAT 6 97 0 TTCCTCCTAC 0.920942 -29 GCTTTCTTTTTTTATGCCTTCAGAGGAGCATCG 9 33 1 TTTTGCCTAG 0.664257 -84 GAGACCGTTCACTCCTTATTTAGGCTTGTT 9 97 0 TTCCTCCTTT 0.935031 -20 TATTCATGATTTTTTTCCATATGAAAAATCTTT 11 43 0 TTTTTCCTTG 0.866363 -70 TGTCCTTTTCTCCTCCTGTTTCTTTCAA 11 95 0 TTTCTCCCTG 0.924638 -18 TTCTTTTTTCCCCCAGTCTAAGTTTC 13 107 0 TTTTTCCCAG 0.816671 -16 TTTTTTACTCCCTTTCGGCATCTAGA 14 145 0 TTTCTCCTTC 0.925795 -16 TTTGGAATGTTTTTCTCCTCATGAGTACTTAAC 15 127 1 TTTCTCCCTG 0.924638 -174 TATTATACGCTTCTCGCCCTGATTTCATTAGGT 16 143 0 TTCCGCCTAT 0.814545 -158 AAGAAGGCGTTTTCTTTCTTATTATACGCTTCT 16 162 0 TTTTTTCTTT 0.375282 -139 AAAAACTCCTTTTGCTTCCTTATCTATCATAAT 16 224 0 TTTCTTCTAT 0.681344 -77 *** **** * ** Masking position 2 Map Score: 11.5085 Number of sites scoring better than the average of aligned sites = 803 Number in coding regions = 623 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 4 TATAACTGGCAGGTTAGAGATCAATGGTTTACTT 1 28 0 AGTTAGGAAA 0.981569 -273 TATTGGAGTGAGTTTAGTGATGAAATTTTTTGAA 1 62 0 ATTTAGGAAA 0.937604 -239 CACTATTTCAAAGTTAGACAAAAAGGAGTGAAAA 3 223 1 AGTTAGCAAA 0.973009 -28 TGAGTATAGCATGTTACCGAAAAAGC 5 3 0 AGTTACGAAA 0.94192 -68 TACCTGTCCAAATTCAGGCATAAAATGAAACAAG 9 69 1 ATTCAGCAAA 0.679617 -48 GAAAGAGATGTTACTGAATAATGGAGCTTGA 11 8 1 AGTTACGAAA 0.941933 -105 TCCAAGCTTCATGTTAGACAGGAGGCTTGGAAAT 13 18 0 AGTTAGCAAG 0.882602 -105 GGTTATCGTTATGTTATAGAGAAACTTAGACTGG 13 87 1 AGTTATGAAA 0.856056 -36 CTACCCGGATACTTTAGTCACAAAAATCAATGTA 14 87 0 ATTTAGCAAA 0.910487 -74 AACACTACTGACGTTAGCGATTAAATTCTAAAAA 15 238 0 AGTTAGGAAA 0.981569 -63 * ***** ** ** Masking position 6 Map Score: 8.73117 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 AATGCCATACAACAGGTAGAATGTAAACAT 1 164 0 AACAGGTAGA 0.83336 -137 GTAGAAACAACAAAGGGGGAGATTTGT 4 8 0 CAAAGGGGGA 0.868585 -152 ATTTATTGGAGAAAGGAAGTTCTAGAAG 5 53 1 GAAAGGAAGT 0.920242 -18 ACGCAAAATTAAAAGGAGGTCATCAGCCT 8 21 1 AAAAGGAGGT 0.857758 -19 CCTGAATTTGGACAGGTAGAACGATGCTCC 9 57 0 GACAGGTAGA 0.938496 -60 GTTTGAAAGAAACAGGAGGAGAAAAGGACA 11 93 1 AACAGGAGGA 0.948273 -20 CTTCATGTTAGACAGGAGGCTTGGAAATAC 13 16 0 GACAGGAGGC 0.945089 -107 GAGAAACTTAGACTGGGGGAAAAAAGAA 13 105 1 GACTGGGGGA 0.88525 -18 TCTAGATGCCGAAAGGGAGTAAAAAA 14 145 1 GAAAGGGAGT 0.91876 -16 CCTTTTAATAGAAAGGAAGAGGAAG 16 286 1 GAAAGGAAGA 0.956513 -15 ********** Masking position 2 Map Score: 5.37758 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 303 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 6 CGAGATATGCATTATTATTTTTAATGCCATACAAC 1 181 0 ATATTTTAAT 0.917664 -120 AAACTGTAGAAATACCTGTTTTAATGGTCTATAAA 2 54 1 ATATTTTAAT 0.921527 -247 GTAAATAAAAATTATGAATTTTATTCGTTTATAGA 2 81 0 ATATTTTATT 0.651946 -220 TGTTCTAATAACAAAGTATTTTATTCGCATGAGAA 2 213 0 AAATTTTATT 0.537121 -88 ACCCATATTTGCAAAGGGTTTTAAGCCATTTCTCC 3 117 0 GAATTTTAAG 0.766289 -134 AATAAAGTTTTAAAGAACCCTGACT 6 1 1 ATATTTAAAG 0.68363 -125 ATAACACTCTAAAAACAATTTCAATTCATCCTGAT 7 24 1 AAATTTCAAT 0.826572 -46 CAAATGATGTGGTAATGATTTTAAGCATACAGTTC 10 98 0 GTATTTTAAG 0.8427 -78 TTCCATATGAAAAATCTTTTTCAAGCTCCATTATT 11 27 0 AAATTTCAAG 0.796534 -86 ATCAAAAAGTACTTCTTATTTCAATAAGAAGTACT 14 49 0 ATTTTTCAAT 0.399897 -112 TATCCGGGTAGATATAAATTTCAATGATCATATAT 14 110 1 GTATTTCAAT 0.81219 -51 TGTAAAATTGGAAACATATTTAAATTTAATGTAAA 15 31 0 GAATTTAAAT 0.472139 -270 CGCTAACGTCAGTAGTGTTTTTAATAGTGTTTAAC 15 253 1 ATATTTTAAT 0.921538 -48 TTTTAAGTACATTACACTTTTTAAAAGTTAAAAAG 16 70 0 ATATTTTAAA 0.598711 -231 ACAGGTACAGAAAAATTTTTTTAAGTACATTACAC 16 88 0 AAATTTTAAG 0.855157 -213 GCTGAAAAAAAGTAAGCCTTTTAATAGAAAGGAAG 16 270 1 ATATTTTAAT 0.921455 -31 * ** ******* Masking position 9 Map Score: 6.61524 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 254 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 TAACAATTAGCCCTTTTTTCCGTGATTCCT 1 109 1 CCCTTTTTTC 0.815932 -192 TAAAAAGAAACCCTGAACTAGTCAGGGTTC 6 25 0 CCCTGAACTA 0.508938 -101 CCACTTTCTCTCCTTAACTCACCACTATTC 6 95 0 TCCTTAACTC 0.87401 -31 GACCGTTCACTCCTTATTTAGGCTTGTTTC 9 95 0 TCCTTATTTA 0.841494 -22 GCAGAAAAAATGCTGATATCTTTCAAGATT 10 34 1 TGCTGATATC 0.590201 -142 TGTCCTTTTCTCCTCCTGTTTC 11 101 0 TCCTTTTCTC 0.87401 -12 TTTAGGATCCTGATATCATTGGTTCAA 14 8 1 TCCTGATATC 0.924996 -153 CAAAAAGTACTTCTTATTTCAATAAGAAGT 14 52 0 TTCTTATTTC 0.654567 -109 CTGTTTGTATTCCTTATATCGACATATTTC 15 207 0 TCCTTATATC 0.937465 -94 ACGCTTCTCGCCCTGATTTCATTAGGTTTC 16 140 0 CCCTGATTTC 0.942116 -161 AATGACTTCTCCCTTATTTCACAAGATACC 16 197 0 CCCTTATTTC 0.951887 -104 TCCTTTTGCTTCCTTATCTATCATAATGAC 16 221 0 TCCTTATCTA 0.872366 -80 ********** Masking position 4 Map Score: 6.93109 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 351 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 8 TTCTAATAACAAAGTATTTTATTCGCATGA 2 216 0 AAAGTATTTT 0.558159 -85 AAGTAAGAAGAAATTACTTCTCAAAGATCC 4 99 0 AAATTACTTC 0.846498 -61 TAGGGCTGCCGATTTACTTCAAGACAAGCC 12 12 0 GATTTACTTC 0.651066 -49 CGAATGTATTTCCAAGCCTCCT 13 3 1 AATGTATTTC 0.924236 -120 ATATCTAATTAAAGTACTTCTTATTGAAAT 14 37 1 AAAGTACTTC 0.640406 -124 TAAGCATCAAAAAGTACTTCTTATTTCAAT 14 59 0 AAAGTACTTC 0.640406 -102 CATATTTTGGAATGTTTTTCTCCTCATGAG 15 122 1 AATGTTTTTC 0.689672 -179 TAAAAAGTGTAATGTACTTAAAAAAATTTT 16 82 1 AATGTACTTA 0.799364 -219 ********** Masking position 2 Map Score: 0.831403 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 173 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 AGGTATTTCTACAGTTTTATCTGCTGTACA 2 41 0 ACAGTTTTAT 0.854492 -260 GACCATTAAAACAGGTATTTCTACAGTTTT 2 53 0 ACAGGTATTT 0.77438 -248 CCATATTTGCAAAGGGTTTTAAGCCATTTC 3 120 0 AAAGGGTTTT 0.840814 -131 AATTGTTTTTAGAGTGTTATACACGAAGAA 7 14 0 AGAGTGTTAT 0.735517 -56 GTTTTGTTGGACAGGGTTATCGCATCAATT 13 55 0 ACAGGGTTAT 0.978003 -68 GTCCAACAAAACAGGGTTATCGTTATGTTA 13 73 1 ACAGGGTTAT 0.978003 -50 AGGAATACAAACAGGTTTTTAGAATTTAAT 15 223 1 ACAGGTTTTT 0.942962 -78 ********** Masking position 3 Map Score: 2.15964 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 90 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 ********** No masking Map Score: -6.0585e-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 11 ********** No masking Map Score: -6.0585e-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 12 ********** No masking Map Score: -6.0585e-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