AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 b0762 128 orf, hypothetical protein #2 modA 166 molybdate-binding periplasmic protein; permease #3 HI1692 173 molybdenum ABC transporter, permease protein (modB) #4 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 ATTGTGACGGAAAACGAACGCCACGCAAAGCTGACCGCA 1 34 1 AAACAGGAAA 0.995512 -95 GTAGATAAGAAAAAATATCGGCAGGAAAAGCAGGAAGTT 2 51 0 AAAAAGGAAA 0.988599 -116 AGGCGACAATATAACGACTAACTCGGAATTTTCCCAGCA 2 111 0 AAACAAGAAT 0.968743 -56 ATGCTCTATAATAACAAAAGGGCAGAAATATCCGCCCTT 3 32 0 AAACAGGAAT 0.9878 -142 TGAAAAATGAAAAAAATTGGGTAAGCAAAATGAATCCTT 3 134 0 AAAATGGAAA 0.969461 -40 ACCACTTAGGATTACTTAGGAACAGCAAA 4 1 0 ATACTGGAAA 0.935673 -137 ATATAGCAAAAGAAAAATTATTTAGTAAAATATATAACG 4 49 0 AAAAAAGAAA 0.971343 -89 ATTGAAATAAATAACAATCATATAGCAAAAGAAAAATTA 4 68 0 AAACAAGAAA 0.988572 -70 * *** * * * *** Masking position 4 Map Score: 8.60234 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 125 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 ACTCCCCTTTTGTGCGGTCAGCTTTGCGTGGC 1 53 0 TTGGGTCAGC 0.984971 -76 TTTTCTGTGCTTAGCGGTTAGAATAGTCTCAT 1 87 1 TAGGGTTAGA 0.985934 -42 TATCTACCTCACAAAGGTTAGCAATAACTGCT 2 83 1 AAAGGTTAGC 0.94533 -84 AACGTTACATTAAGGGGTTACCA 2 154 1 TAGGGTTACC 0.980157 -13 CCCACATTGATGAGAGGTAAGATGCTCTATAA 3 60 0 TAGGGTAAGA 0.985918 -114 AAATGAAAAAAATTGGGTAAGCAAAATGAATC 3 137 0 ATTGGTAAGC 0.882663 -37 TAAGTAATCCTAAGTGGTAAGCCTAAGCGTTA 4 22 1 TAGGGTAAGC 0.996123 -116 * ** ******* Masking position 10 Map Score: 6.39969 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 244 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CACAATAAGACTTTTGCCAGGACATTGTT 1 9 0 CTTTTGCCGG 0.989081 -120 TGTGCGGTCAGCTTTGCGTGGCGTTCGTTTT 1 44 0 GCTTTGCGGG 0.99094 -85 AAGCACTCCCCTTTTGTGCGGTCAGCTTTGC 1 58 0 CTTTTGTGGG 0.982797 -71 AAGGGGAGTGCTTTTCTGTGCTTAGCGGTTA 1 76 1 CTTTTCTGGC 0.936778 -53 CTGAATGCCCGCTTAGTCGGGCATTTTCTTT 2 15 1 GCTTAGTCGG 0.924926 -152 TCAACTTCCTGCTTTTCCTGCCGATATTTTT 2 49 1 GCTTTTCCGC 0.912323 -118 TTATTGCTAACCTTTGTGAGGTAGATAAGAA 2 79 0 CCTTTGTGGG 0.988262 -88 CTAACTCGGAATTTTCCCAGCAGTTATTGCT 2 102 0 ATTTTCCCGC 0.818305 -65 ******** ** Masking position 4 Map Score: 6.2661 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 707 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 TAGTCGTTATATTGTCGCCTACATAACGTTACATT 2 130 1 ATTTTACATA 0.898048 -37 TCAATGTGGGATATTCCCATAAACAAGGGATTTAA 3 82 1 ATATTAAACA 0.966646 -92 AGCAAAATGAATCCTTATCTAAATAGCCTCTCTTT 3 115 0 ATCTTAAATA 0.972756 -59 TAAGCGTTATATATTTTACTAAATAATTTTTCTTT 4 45 1 ATATTAAATA 0.98754 -93 ACTTGATTATATATTGAAATAAATAACAATCATAT 4 84 0 ATATTAAATA 0.98754 -54 ATTTCAATATATAATCAAGTAAATAACGTTTAATC 4 99 1 ATATTAAATA 0.987541 -39 *** * ****** Masking position 10 Map Score: 3.89356 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 13 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 AACAATGTCCTGGCAAAAGTCTTAT 1 5 1 ATGTCCTGGA 0.902099 -124 ACGGAAAACGAACGCCACGCAAAGCTGACCG 1 40 1 AACGCCACGA 0.953725 -89 GGTCAACTCCAGATATAGTCATGAG 1 114 0 AACTCCAGAA 0.961734 -15 AAGAAAAAATATCGGCAGGAAAAGCAGGAAG 2 53 0 ATCGGCAGGA 0.983938 -114 GGTTAGCAATAACTGCTGGGAAAATTCCGAG 2 98 1 AACTGCTGGA 0.973363 -69 AATAGTCATGAAGGGCGGATATTTCTGCCCT 3 22 1 AAGGGCGGAA 0.958989 -152 ATAATAACAAAAGGGCAGAAATATCCGCCCT 3 33 0 AAGGGCAGAA 0.981099 -141 ********* * Masking position 1 Map Score: 3.47246 Number of sites scoring better than the average of aligned sites = 1415 Number in coding regions = 1305 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 TTCCCTGAATGCCCGCTTAGTCGGGCA 2 8 1 AATGCCCGCT 0.97476 -159 AGAAAAAGAAAATGCCCGACTAAGCGGGCA 2 20 0 AATGCCCGAC 0.985529 -147 GATAAGAAAAAATATCGGCAGGAAAAGCAG 2 57 0 AATATCGGCA 0.903963 -110 AAAGGGCAGAAATATCCGCCCTTCATGACT 3 25 0 AATATCCGCC 0.992463 -149 TGTTTATGGGAATATCCCACATTGATGAGA 3 77 0 AATATCCCAC 0.943175 -97 ********** Masking position 3 Map Score: 1.44089 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 517 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 GTTCGTTTTCCGTCACAATAAGACTTTTGCC 1 22 0 CGTCCAATAA 0.969897 -107 GCCTACATAACGTTACATTAAGGGGTTACCA 2 146 1 CGTTCATTAA 0.961577 -21 GAGCATCTTACCTCTCATCAATGTGGGATAT 3 65 1 CCTCCATCAA 0.979488 -109 ATCTAAATAGCCTCTCTTTAAATCCCTTGTT 3 103 0 CCTCCTTTAA 0.969897 -71 TGGCGTCAGATTGAAAAATGAAAA 3 160 0 CGTCGATTGA 0.961478 -14 AAATCATCTCCTACGATTAAACGTTATTTA 4 118 0 CCTAGATTAA 0.928979 -20 **** ****** Masking position 3 Map Score: 1.40409 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 125 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 CTTTTCTGTGCTTAGCGGTTAGAATAGTCT 1 86 1 CTTAGCGGTT 0.96554 -43 AAATGCCCGACTAAGCGGGCATTCAGGGAA 2 11 0 CTAAGCGGGC 0.972149 -156 TAACGTTACATTAAGGGGTTACCA 2 153 1 TTAAGGGGTT 0.915963 -14 CTAAGTAATCCTAAGTGGTAAGCCTAAGCG 4 21 1 CTAAGTGGTA 0.96893 -117 AGTGGTAAGCCTAAGCGTTATATATTTTAC 4 34 1 CTAAGCGTTA 0.982132 -104 TCTCCTACGATTAAACGTTATTTACTTGAT 4 112 0 TTAAACGTTA 0.741896 -26 ********** Masking position 4 Map Score: 1.33199 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 396 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 ********** No masking Map Score: 1.77879e-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: 1.77879e-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: 1.77879e-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