AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0851 300 molybdopterin-guanine dinucleotide biosynthesis protein B (mobB) #2 HI0853 140 heme-binding lipoprotein (dppA) #3 HI1123 80 oligopeptide ABC transporter, permease protein (oppB) #4 HI1124 295 oligopeptide ABC transporter, periplasmic-binding protein (oppA) #5 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #6 HI1188 300 DNA helicase II (uvrD) Motif number 1 ATGAAATATTATTTTTTTGCTCATTATTGCTTATGCT 1 94 1 ATTTTCCTTT 0.908341 -207 GCCACATATTATTTTCCCTCCACTAATTGACGAAATT 1 150 0 ATTTTCATAT 0.974162 -151 ATTGGCGGACTTATTTTTGCCAATTATGCAGCAAAAC 1 222 1 TTATTCATTT 0.792589 -79 AATACGACGATTTTTAACCGCACTTAAATACGAGTAA 3 15 0 TTTTTGATTA 0.767671 -66 ATCGTCGTATTTTTTGACCGCACTTTTCGCCCATTTT 3 41 1 TTTTTGATTT 0.950097 -40 CTTTTCGCCCATTTTGGTTGGAGTTGTT 3 63 1 ATTTTGATTT 0.970914 -18 ATAAATTACCCTTTTAATGCTAATTGTGCTATCGTAA 4 50 0 CTTTTCATTT 0.938532 -246 CTTTTAGCAATTTTTTTAGCGATTTATTAGACACAAC 4 151 1 TTTTTCATTT 0.976612 -145 ACAAAACTCAATTTTTCTTCAAATAATTTCCTGACAA 4 190 1 ATTTTCATAT 0.971856 -106 CAAAAATTCATTTTTGTAAAGATTTGTCAGGAAATTA 4 213 0 TTTTTAATTT 0.865469 -83 ACAAAAATGAATTTTTGAGCTAATAAATAGAAGACTT 4 233 1 ATTTTCATAA 0.867292 -63 AGAGTATTATATTTTTTACCGATTAATTTCTTTGAAG 5 17 1 ATTTTCATAT 0.974159 -73 AGTGCGGTGAATTTTTACCGCACTTTTATTATCTACG 5 54 1 ATTTTGATTT 0.970914 -36 TTTGAAAGCTATTTTTATACTATTTATAAACAAACTT 6 114 0 ATTTTCATTT 0.986521 -187 AGGGTAGAACATTTTAAGAATAATATTAAGCGGGATT 6 188 0 ATTTTAATAT 0.853135 -113 ***** * * ** * Masking position 5 Map Score: 19.3862 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 341 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 2 ACGATTTTTAACCGCACTTAAATACGAGTA 3 16 0 ACCGCACTTA 0.990946 -65 GTATTTTTTGACCGCACTTTTCGCCCATTT 3 47 1 ACCGCACTTT 0.997208 -34 GTAAAAATTCACCGCACTCTTCAAAGAAAT 5 42 0 ACCGCACTCT 0.993851 -48 GTGAATTTTTACCGCACTTTTATTATCTAC 5 60 1 ACCGCACTTT 0.997208 -30 AAAATGTTCTACCCTACTTTTGATATACTC 6 210 1 ACCCTACTTT 0.951441 -91 ********** Masking position 6 Map Score: 9.32921 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 808 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 3 CTTAGTGATGATGTGGCAAAAGTTGCTATTC 1 14 1 ATGGGCAAAA 0.974194 -287 CATAAGCAATAATGAGCAAAAAAATAATATT 1 98 0 AATAGCAAAA 0.925041 -203 TTGCCTTGTGATGGGGCGTAAATTTCGTCAA 1 130 1 ATGGGCGTAA 0.84738 -171 TCCCTCCACTAATTGACGAAATTTACGCCCC 1 142 0 AATGACGAAA 0.882388 -159 CGCCAATAGCAAGAAGCGAAACAATGCCAAG 1 198 0 AAGAGCGAAA 0.945575 -103 TTTGCTGCATAATTGGCAAAAATAAGTCCGC 1 226 0 AATGGCAAAA 0.977202 -75 TTTGCCAATTATGCAGCAAAACATTCTTAAT 1 237 1 ATGAGCAAAA 0.915646 -64 CTCCAACCAAAATGGGCGAAAAGTGCGGTCA 3 55 0 AATGGCGAAA 0.983419 -26 AGGGTAATTTATGTAGGAAAATATTTACAAT 4 75 1 ATGAGGAAAA 0.584301 -221 AAATATTTACAATAGGAAAAATCAATACATC 4 93 1 AATGGAAAAA 0.868666 -203 TCAGGAAATTATTTGAAGAAAAATTGAGTTT 4 193 0 ATTGAAGAAA 0.499503 -103 CCTCCTTGTCATTAGGCGATATTTTTATAAA 4 270 0 ATTGGCGATA 0.844916 -26 CAAAGAAATTAATCGGTAAAAAATATAATAC 5 20 0 AATGGTAAAA 0.789502 -70 *** ******* Masking position 1 Map Score: 12.798 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 847 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 ATAACAGGCATTGCTAGAATAGCAACTTTT 1 31 0 TTGCTAGAAT 0.910969 -270 GCAACCGCTTTTCCTAAAAGGATGAAATAT 1 73 1 TTCCTAAAAG 0.915377 -228 ATTAATTTGTTATAATCCATAGAATT 2 7 1 TTGTTATAAT 0.616145 -134 AAATTTCCCTTTTTTTAAATAAAAAAATTC 2 32 0 TTTTTTAAAT 0.585763 -109 AAAGGGAAATTTGCTTATATCTTATTGATA 2 50 1 TTGCTTATAT 0.632675 -91 TGTATTCTCCTTGAATGGACTTGTTT 4 7 1 CTCCTTGAAT 0.748628 -289 TTGAATGGACTTGTTTAAATCTAATCAGGT 4 21 1 TTGTTTAAAT 0.915998 -275 GCTAAAAAAATTGCTAAAAGTGATGATATG 4 141 0 TTGCTAAAAG 0.903052 -155 AACTCAATTTTTCTTCAAATAATTTCCTGA 4 194 1 TTCTTCAAAT 0.795812 -102 ACCGATTAATTTCTTTGAAGAGTGCGGTGA 5 34 1 TTCTTTGAAG 0.746325 -56 TTTCTCATTTTTCCAAAAATACCCATGATG 6 49 0 TTCCAAAAAT 0.698578 -252 TTACCTCTCATTCCTAAAATGCAAGGTTTC 6 75 0 TTCCTAAAAT 0.959252 -226 CTTAATATTATTCTTAAAATGTTCTACCCT 6 195 1 TTCTTAAAAT 0.936175 -106 TATCTTTAATCTGTTTAAATTTACAGTTAT 6 277 0 CTGTTTAAAT 0.759887 -24 ********** Masking position 9 Map Score: 8.81131 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 380 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 GATCCCCCGCCTCTCATATCATCACTTTTA 4 127 1 CTCTCATATC 0.951365 -169 TGAGTTGTGTCTAATAAATCGCTAAAAAAA 4 161 0 CTAATAAATC 0.886041 -135 TTAGACACAACTCACAAAACTCAATTTTTC 4 177 1 CTCACAAAAC 0.967346 -119 AAATAATTTCCTGACAAATCTTTACAAAAA 4 210 1 CTGACAAATC 0.971513 -86 AAGCGGGATTCTCCTATATCCTTAAACTCA 6 168 0 CTCCTATATC 0.907377 -133 TTTTGATATACTCACAAATCTTATTGTTTC 6 227 1 CTCACAAATC 0.991741 -74 ********** Masking position 6 Map Score: 2.84542 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ATTTTTTTATTTAAAAAAAGGGAAATTTGC 2 34 1 TTAAAAAAAG 0.911934 -107 TTAAGTGCGGTTAAAAATCGTCGTATTTTT 3 25 1 TTAAAAATCG 0.941237 -56 GAGTTGTGTCTAATAAATCGCTAAAAAAAT 4 160 0 TAATAAATCG 0.872121 -136 ATTTTTGAGCTAATAAATAGAAGACTTTTT 4 243 1 TAATAAATAG 0.933119 -53 GGCGATATTTTTATAAAAAGTCTTCTATTT 4 257 0 TTATAAAAAG 0.893673 -39 AATTAATCGGTAAAAAATATAATACTCTTG 5 15 0 TAAAAAATAT 0.627581 -75 AAAAGTTTGTTTATAAATAGTATAAAAATA 6 112 1 TTATAAATAG 0.963737 -189 TATAAATAGTATAAAAATAGCTTTCAAAGC 6 123 1 ATAAAAATAG 0.83781 -178 TTTAAACAGATTAAAGATAGTTT 6 288 1 TTAAAGATAG 0.884475 -13 ********** Masking position 5 Map Score: 6.87989 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 127 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 GAATAGCAACTTTTGCCACATCATCACTAA 1 15 0 TTTTGCCACA 0.969773 -286 GAGCAACCGCTTTTCCTAAAAGGATGAAAT 1 71 1 TTTTCCTAAA 0.932062 -230 GCGGACTTATTTTTGCCAATTATGCAGCAA 1 226 1 TTTTGCCAAT 0.823549 -75 ATTAAGAATGTTTTGCTGCATAATTGGCAA 1 238 0 TTTTGCTGCA 0.954389 -63 ATTGTAAATATTTTCCTACATAAATTACCC 4 76 0 TTTTCCTACA 0.968869 -220 TGCGGTGAATTTTTACCGCACTTTTATTAT 5 56 1 TTTTACCGCA 0.893213 -34 GGTTTCTCATTTTTCCAAAAATACCCATGA 6 51 0 TTTTCCAAAA 0.756086 -250 ********** Masking position 4 Map Score: 3.13741 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 253 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 CAAAACATTCTTAATTTATTAACCCCGATC 1 253 1 TTAATTTATT 0.939092 -48 ATTAATTTGTTATAATCCATA 2 2 1 TTAATTTGTT 0.97202 -139 TTTTTACCGATTAATTTCTTTGAAGAGTGC 5 29 1 TTAATTTCTT 0.928362 -61 GATTAAGTCATTAAACAACATT 6 3 1 TTAAGTCATT 0.823751 -298 AAACAAACTTTTAATTCGTTTACCTCTCAT 6 94 0 TTAATTCGTT 0.966443 -207 AAACTATCTTTAATCTGTTTAAATTTACA 6 282 0 TTAATCTGTT 0.927019 -19 ********** Masking position 4 Map Score: 2.82027 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 47 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: -2.49157e-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 10 ********** No masking Map Score: -2.49157e-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: -2.49157e-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