AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ytsC 101 similar to ABC transporter (ATP-binding protein) #2 ytsA 96 similar to two-component response regulator [YtsB] #3 ytrD 29 similar to cytochrome c oxidase subunit #4 ytrA 300 similar to transcriptional regulator (GntR family) #5 yusC 300 similar to ABC transporter (ATP-binding protein) Motif number 1 TCACATGCTTTTCTTTTTTGTTCGCCGTAT 1 19 1 TTCTTTTTTG 0.915728 -83 AGCCCGGCATTCCTTTTTATAATGAGATTA 1 58 1 TCCTTTTTAT 0.983411 -44 TTACGCAGTCTCCTTTATATTGGATAATCT 1 82 0 TCCTTTATAT 0.954703 -20 CCGCACTTTTTCCTTTTTTATCAAGTGTAT 2 69 0 TCCTTTTTTA 0.941462 -28 ACAAAGTCAATCCTTTTTTTACAAAAAAAC 4 12 0 TCCTTTTTTT 0.991327 -289 TAATATAAAATCATTTATATATTGACATTA 4 98 1 TCATTTATAT 0.823092 -203 TTACGTTTGTTTCGTTTTTTATGTTTCATA 4 139 0 TTCGTTTTTT 0.907513 -162 TGATCGCTTGTTCTTTTTTTCTTGTTCTTG 4 195 1 TTCTTTTTTT 0.965885 -106 TGATCAATTATACTTTTTTGCCATTCAAAA 4 235 0 TACTTTTTTG 0.811341 -66 GTATAATTGATCATTTTTATCTATAAAAGG 4 252 1 TCATTTTTAT 0.92901 -49 AAGTTGACATCATTTATTTTATTGACATT 5 10 1 TCATTTATTT 0.899706 -291 TAAGAAATCTTCCGGTTTTTTCTGCAAAAG 5 255 0 TCCGGTTTTT 0.8718 -46 ********** Masking position 6 Map Score: 16.2001 Number of sites scoring better than the average of aligned sites = 2045 Number in coding regions = 1479 Number in noncoding regions = 566 Number of orfs with sites within 600 bp upstream = 568 Fraction of orfs with sites within 600 bp upstream = 0.0912303 Motif number 2 ACGGCGAACAAAAAAGAAAAGCATGTGACATT 1 15 0 AAAAGAAAGC 0.540033 -87 CGTATCGAAGGAAAAGCCCGGCATTCCTTTTT 1 44 1 GAAAGCCGGC 0.99402 -58 TGCGAACGAGCCGGCTGAGACAGCC 2 4 1 GACGACCGGC 0.760393 -93 ATGCGCTATAGAAAAAGCCGGCTGTCTCAGCC 2 23 0 GAAAACCGGC 0.977321 -74 ATAAAAAAGGAAAAAGTGCGGTGAGTCGA 2 78 1 AAAAGGCGGT 0.870085 -19 CGTTTTTTTGTAAAAAAAGGATTGACTTTGT 4 10 1 GTAAAAAGGA 0.622875 -291 ATATATTGACATTAAGGGAGGCAGTTATGAAA 4 114 1 ATAAGGAGGC 0.934875 -187 TCTTAATGTAGAATAGCACGGCGAATGATTAA 5 39 0 GATAGACGGC 0.917393 -262 TATTTCTCTTATCAAGAGAGGTGGAGGGAAGT 5 94 1 ATAAGGAGGT 0.76013 -207 GAAGTGCCCTATGAAGCCCGGCAACCATCAAC 5 121 1 ATAAGCCGGC 0.978119 -180 CTGCACACTTGAGCAGAAAGGCTTATATAAAA 5 213 0 GACAGAAGGC 0.964905 -88 CTGCTCAAGTGTGCAGAAAGGCTTTTCTTTTG 5 229 1 GTCAGAAGGC 0.95429 -72 TTCTTTTGCAGAAAAAACCGGAAGATTTCTTA 5 253 1 GAAAACCGGA 0.869095 -48 TTAGAATAGTGTTAAGGCAGGTGATTGCT 5 282 1 GTAAGCAGGT 0.945545 -19 ** *** ***** Masking position 11 Map Score: 13.5831 Number of sites scoring better than the average of aligned sites = 2399 Number in coding regions = 2167 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 3 CGAAAATGTCACATGCTTTT 1 1 1 CGAAAATGTC 0.841346 -101 GCCGTATCGAAGGAAAAGCCCGGCATTCCT 1 42 1 AGGAAAAGCC 0.979574 -60 TGCGAACGAGCCGGCTGAGACA 2 3 1 CGAACGAGCC 0.95225 -94 CATGCGCTATAGAAAAAGCCGGCTGTCTCA 2 26 0 AGAAAAAGCC 0.984919 -71 TGATAAAAAAGGAAAAAGTGCGGTGAGTCG 2 76 1 GGAAAAAGTG 0.773371 -21 TAGGTTTGGAGGGAAGTGAG 3 20 1 GGGAAGTGAG 0.540363 -10 CGAAACAAACGTAACGTGCCAATGCTGATT 4 155 1 GTAACGTGCC 0.698643 -146 CAAGAAAAAAAGAACAAGCGATCACAGATG 4 189 0 AGAACAAGCG 0.91167 -112 AATTTCCGGACGAAAAAGACTATATATTTC 5 70 1 CGAAAAAGAC 0.892463 -231 GAGAGGTGGAGGGAAGTGCCCTATGAAGCC 5 109 1 GGGAAGTGCC 0.960218 -192 AAAGGCTTATATAAAATGCCTTTCTCTCAT 5 199 0 ATAAAATGCC 0.852903 -102 TTTTCTGCAAAAGAAAAGCCTTTCTGCACA 5 238 0 AAGAAAAGCC 0.790735 -63 TTTCTTTTGCAGAAAAAACCGGAAGATTTC 5 252 1 AGAAAAAACC 0.811379 -49 ********** Masking position 4 Map Score: 10.3422 Number of sites scoring better than the average of aligned sites = 3419 Number in coding regions = 3040 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 322 Fraction of orfs with sites within 600 bp upstream = 0.0517186 Motif number 4 TTTTCCTTTTTTATCAAGTGTATAGCAAAACGCCAGCA 2 54 0 TAGTGTAGCA 0.972762 -43 TAAATGATTTTATATTAGTGTCTATAGTGTATTACTTC 4 77 0 TAGTGTATAT 0.966168 -224 CATAACTGCCTCCCTTAATGTCAATATATAAATGATTT 4 105 0 TAATGTATAA 0.946309 -196 GCACGGCGAATGATTAAATGTCAATAAAATAAATGATG 5 18 0 TAATGTATAA 0.94711 -283 TTGGCACCATTTCAACAGTGTTGATGGTTGCCGGGCTT 5 134 0 TAGTGTATGT 0.959475 -167 TAAGCCTTTCTGCTCAAGTGTGCAGAAAGGCTTTTCTT 5 220 1 TAGTGTAGAA 0.987543 -81 GAAGATTTCTTAGAATAGTGTTAAGGCAGGTGATTGCT 5 273 1 TAGTGTAGGA 0.984997 -28 * ***** *** * Masking position 7 Map Score: 1.94803 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 29 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ACAGATGCCGCAATCAGCATTGGCACGTTA 4 166 0 CAATCAGCAT 0.909962 -135 CATTCAAAACCGATCATCACAAGAACAAGA 4 214 0 CGATCATCAC 0.939031 -87 ACTTTTTTGCCATTCAAAACCGATCATCAC 4 224 0 CATTCAAAAC 0.733829 -77 ACTTTCTATACGATCTGAACCTTTTATAGA 4 271 0 CGATCTGAAC 0.934187 -30 AGCCCGGCAACCATCAACACTGTTGAAATG 5 135 1 CCATCAACAC 0.910163 -166 TCACACGAAGCGTTCAGCTTTGAAAGATGA 5 173 1 CGTTCAGCTT 0.89289 -128 TTATATAAGCCTTTCTGCTCAAGTGTGCAG 5 215 1 CTTTCTGCTC 0.909774 -86 AAAGAAAAGCCTTTCTGCACACTTGAGCAG 5 229 0 CTTTCTGCAC 0.964966 -72 ********** Masking position 4 Map Score: 1.7048 Number of sites scoring better than the average of aligned sites = 1702 Number in coding regions = 1590 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 ********** No masking Map Score: -1.62471e-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 7 ********** No masking Map Score: -1.62471e-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 8 ********** No masking Map Score: -1.62471e-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