AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ifis_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 tgt 126 Queuine tRNA Ribosyl Transferase #2 mgtE 300 Mg++ Transporter (CBS Domain) #3 secD/secF 300 Protein Export #4 CT741 104 hypothetical protein #5 ygcA 85 rRNA Methyltransferse #6 hctA 300 Histone-Like Developmental Protein #7 nrdA 300 Ribonucleoside Reductase, Large Chain #8 nrdB 37 Ribonucleoside Reductase, Small Chain Motif number 1 TCCGAAGACAAAGGTTTTCTTCGGGCTTTT 1 19 1 AAGGTTTTCT 0.886754 -108 AGGTTTTCTTCGGGCTTTTTTCACTATGTC 1 30 1 CGGGCTTTTT 0.925529 -97 CGACCAGGAAAGCGTTCCCTGGACCACACC 3 12 0 AGCGTTCCCT 0.920538 -289 GGGGAGACTCCGGGCTCCTTCTCTTGTCAT 3 160 1 CGGGCTCCTT 0.902664 -141 TGTCATTGAGAGGGCTTTCTTTTGTCAACA 3 184 1 AGGGCTTTCT 0.992729 -117 CATTAGGAATAAGGCTTTCTTGTT 4 5 0 AAGGCTTTCT 0.964592 -100 TATTTTAGCGCTTTCTCTTTTTTATA 5 7 1 AGCGCTTTCT 0.984226 -79 TTTTTTATAGAGGGCACTTTTATCAACAGG 5 28 1 AGGGCACTTT 0.820077 -58 TTTTATCAACAGGGCCCTCTTTCCTCTTCT 5 45 1 AGGGCCCTCT 0.958755 -41 AACAAGGTTCAGCGCTTTCTATTAAAAGAA 6 53 1 AGCGCTTTCT 0.984226 -248 GGGTCTGAATAGGGTTTCTTTTAATAGAAA 6 68 0 AGGGTTTCTT 0.891883 -233 AGAAGCTAGCAACGTTTCCTGCAATTGAAA 7 103 0 AACGTTTCCT 0.723876 -198 GTATAAGATAAGGGCTCTCTCTACCGTTTT 7 221 1 AGGGCTCTCT 0.991692 -80 ********** Masking position 10 Map Score: 20.144 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 298 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 2 GGGTGAGTCCGAAGACAAAGGTTTTCTTCGG 1 12 1 GAAGAAAAGG 0.927427 -115 GAATCATTCTAAAGAGAGAGGGAGAAAAGAC 1 57 0 AAAGAAGAGG 0.965271 -70 TATATAAAGAACGGAGAAGGGCGTGAAAGAG 2 229 1 ACGGAAAGGG 0.957463 -72 AAGCCCTCTCAATGACAAGAGAAGGAGCCCG 3 170 0 AATGAAAGAG 0.90377 -131 GTTAACACAGGAAGATAGGGGGATCAATCCT 4 51 0 GAAGAAGGGG 0.979694 -54 CCTCTATAAAAAAGAGAAAGCGCTAAAATA 5 10 0 AAAGAAAAGC 0.776326 -76 AGAAGGGATCAATGAGAAGAGGAAAGAGGGC 5 58 0 AATGAAAGAG 0.90377 -28 AAAAAAGAGAAGGGATCAATGAGA 5 72 0 AAAGAAAGGG 0.991734 -14 TTTAGAAAAGAAAGAAAGGAGCTTGTTCTCT 6 24 0 AAAGAAGGAG 0.965271 -277 TTTTTAAGTATAAGATAAGGGCTCTCTCTAC 7 214 1 TAAGAAAGGG 0.949785 -87 CGTTTTTTTGACGGATAGGGGGACTAGAGGC 7 245 1 ACGGAAGGGG 0.954649 -56 ***** ***** Masking position 5 Map Score: 11.5813 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 217 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 3 AAAAGTCTTCCGAGACTCTTAAACAAGAGTCCTT 2 93 0 CAGCTCTAAC 0.970244 -208 TTTTCGTAAAAAAGTCTCTTAATAGATAGTCTGA 2 132 1 AAGCTCTATA 0.973864 -169 CATTCGGTCTAAAGTCTCGCCAAATCTAATACCT 2 165 0 AAGCTCGAAA 0.94317 -136 TTCTTTATATAAAGACTCTTAAAAGTCGTCTATT 2 206 0 AAGCTCTAAA 0.986117 -95 GAAGGAAGATCTAGGCTCTTCAAAACATATATGT 3 211 0 CAGCTCTAAA 0.992886 -90 TATGTGCTGCATAGGGTCTGAATAGGGTTTCTTT 6 77 0 AAGGTCTATA 0.8775 -224 GGATCCTTACCTAGATTCTAGAAAATGGTTGCAT 6 200 1 CAGTTCTAAA 0.969624 -101 GGAAACGTTGCTAGCTTCTATATATGGTATACAA 7 114 1 CAGTTCTATA 0.943644 -187 TTTGAGTATGCGAGCCCCTAAAAACCCAAGATAT 7 165 0 CAGCCCTAAA 0.970244 -136 * ** **** *** Masking position 3 Map Score: 8.24556 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 4 AAAGCCCGAAGAAAACCTTTGTCTTCGGAC 1 18 0 GAAAACCTTT 0.804831 -109 ACTCGACCAGGAAAGCGTTCCCTGGACCAC 3 15 0 GAAAGCGTTC 0.796966 -286 AAAACCAACCGAAAACTCTCGCCCGGCGAC 3 43 0 GAAAACTCTC 0.763095 -258 GTTGACAAAAGAAAGCCCTCTCAATGACAA 3 183 0 GAAAGCCCTC 0.682965 -118 AACAAGAAAGCCTTATTCCTAATGC 4 6 1 GAAAGCCTTA 0.923085 -99 ATAAAAAAGAGAAAGCGCTAAAATA 5 6 0 GAAAGCGCTA 0.972582 -80 GAAGAGGAAAGAGGGCCCTGTTGATAAAAG 5 44 0 GAGGGCCCTG 0.735813 -42 TCTTTTAATAGAAAGCGCTGAACCTTGTTT 6 52 0 GAAAGCGCTG 0.981163 -249 AAACGGTAGAGAGAGCCCTTATCTTATACT 7 220 0 GAGAGCCCTT 0.922889 -81 ********** Masking position 2 Map Score: 8.61395 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 90 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 5 CGAAGCTTACAGTGCAAAATAATTTAGGGT 2 20 1 AGTGCAAAAT 0.944154 -281 GTCGTCTATTAGCGACACATTCGGTCTAAA 2 186 0 AGCGACACAT 0.859779 -115 AGGGCGTGAAAGAGCAAAATAGAAACGAAG 2 246 1 AGAGCAAAAT 0.981652 -55 TCCGGAAGTTAGCGCAACATCCAATTTTTC 2 275 0 AGCGCAACAT 0.949032 -26 TTTGATGTCCAGAGACAAATTTGGATTGGA 3 125 0 AGAGACAAAT 0.946288 -176 CGAATAACGAAGAGCCTCATA 3 290 1 AGAGCCTCAT 0.904791 -11 TCCTCTGTTAATAGAAAAATTTTTTATAAA 6 113 0 ATAGAAAAAT 0.812508 -188 TTTCTTTTCGAGAGCAAACTTTTAAGCATG 7 49 0 AGAGCAAACT 0.909709 -252 GTTTCCTGCAATTGAAAAATAGCATAAACT 7 90 0 ATTGAAAAAT 0.577957 -211 TTAAAAAATCAGAGCATTATCCTTTGAGTA 7 191 0 AGAGCATTAT 0.792486 -110 GCTTCAAAATAGAGAATAATGCGTATTCA 7 282 1 AGAGAATAAT 0.918062 -19 ********** Masking position 1 Map Score: 7.20193 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 195 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 6 CATGAATTTTATTATTTTTTTAGAATTCGC 1 87 1 ATTATTTTTT 0.719785 -40 AGCGCAACATCCAATTTTTCTTCGTTTCTA 2 265 0 CCAATTTTTC 0.876694 -36 AATCTTTTCTGCAATTTTTTGGACAACACG 3 96 0 GCAATTTTTT 0.940221 -205 AGTTTTATAAAAAATTTTTCTATTAACAGA 6 110 1 AAAATTTTTC 0.847323 -191 TTATCAATAGGTTATTTTTCCTCTGTTAAT 6 131 0 GTTATTTTTC 0.928098 -170 GTTGTTTTAAACTATTTTTTTCAGTTTTAA 6 262 0 ACTATTTTTT 0.883745 -39 ACAACTAGAGGATATTTTTTC 6 290 1 GATATTTTTT 0.903801 -11 CTCTCGAAAAGAAATTTTTCATCGCAGTTT 7 65 1 GAAATTTTTC 0.922473 -236 CGCAGTTTATGCTATTTTTCAATTGCAGGA 7 87 1 GCTATTTTTC 0.974478 -214 ********** Masking position 5 Map Score: 6.327 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 135 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 TTTTTCACTATGTCTTTTCTCCCTCTCTCT 1 46 1 TGTCTTTTCT 0.963833 -81 GCACTGTAAGCTTCGTTTCTTCTG 2 5 0 CTTCGTTTCT 0.969863 -296 TCCAATTTTTCTTCGTTTCTATTTTGCTCT 2 256 0 CTTCGTTTCT 0.969863 -45 TTGAGAGGGCTTTCTTTTGTCAACATATAT 3 189 1 TTTCTTTTGT 0.883905 -112 AGCTCCTTTCTTTCTTTTCTAAACAAGGTT 6 32 1 TTTCTTTTCT 0.975372 -269 CGATGAAAAATTTCTTTTCGAGAGCAAACT 7 59 0 TTTCTTTTCG 0.924162 -242 GGACTAGAGGCGTCTTTGCTTCAAAATAGA 7 265 1 CGTCTTTGCT 0.908277 -36 ********** Masking position 6 Map Score: 5.39144 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 94 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 TTCTCCCTCTCTCTTTAGAATGATTCATGA 1 62 1 CTCTTTAGAA 0.747439 -65 ATTTTATTATTTTTTTAGAATTCGCTTAGA 1 92 1 TTTTTTAGAA 0.904333 -35 TGTAAAGTATCTTTTTATAGTGAAGGACTC 2 71 1 CTTTTTATAG 0.938572 -230 TAATAGACGACTTTTAAGAGTCTTTATATA 2 205 1 CTTTTAAGAG 0.853071 -96 CTTCTCCGTTCTTTATATAAAGACTCTTAA 2 218 0 CTTTATATAA 0.629782 -83 GCGCTTTCTCTTTTTTATAGAGGGCACTTT 5 18 1 TTTTTTATAG 0.874874 -68 AGCTTGTTCTCTTGTTAGAAGATTC 6 6 0 CTTGTTAGAA 0.786859 -295 GCGCTGAACCTTGTTTAGAAAAGAAAGAAA 6 38 0 TTGTTTAGAA 0.786704 -263 AATAGGGTTTCTTTTAATAGAAAGCGCTGA 6 61 0 CTTTTAATAG 0.839472 -240 AATAGAAAAATTTTTTATAAAACTATGTGC 6 104 0 TTTTTTATAA 0.858452 -197 TATTTTTCCTCTGTTAATAGAAAAATTTTT 6 119 0 CTGTTAATAG 0.673935 -182 CATGCAACCATTTTCTAGAATCTAGGTAAG 6 205 0 TTTTCTAGAA 0.64695 -96 ********** Masking position 7 Map Score: 6.16903 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 319 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TTTGTCTTCGGACTCACCCA 1 1 0 GACTCACCCA 0.951478 -126 TCGGTCTAAAGTCTCGCCAAATCTAATACC 2 166 0 GTCTCGCCAA 0.957424 -135 CTCGCCCGGCGACTCGACCAGGAAAGCGTT 3 26 0 GACTCGACCA 0.963404 -275 CAACCGAAAACTCTCGCCCGGCGACTCGAC 3 38 0 CTCTCGCCCG 0.984361 -263 GGAGCCCGGAGTCTCCCCCATTTTTTGATG 3 148 0 GTCTCCCCCA 0.981893 -153 GATAAGGGCTCTCTCTACCGTTTTTTTGAC 7 227 1 CTCTCTACCG 0.842688 -74 ********** Masking position 4 Map Score: 1.93348 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 AACAGATACACTTAGGCAGCGACCCTAAAT 2 41 0 CTTAGGCAGC 0.9803 -260 TAGCCCAACGCTCAAGCAGCGGGAAGGAAG 3 237 0 CTCAAGCAGC 0.9803 -64 GTGAATTCTGCGAATGCAGCTACTTAGCCC 3 261 0 CGAATGCAGC 0.97201 -40 CTATTCAGACCCTATGCAGCACATAGTTTT 6 86 1 CCTATGCAGC 0.97201 -215 GGTAAGGATCCTAAAGCAGCTTTATTTGAC 6 181 0 CTAAAGCAGC 0.98339 -120 ********** Masking position 4 Map Score: 3.37533 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 39 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 CCTTCACTATAAAAAGATACTTTACAAACA 2 67 0 AAAAAGATAC 0.846976 -234 TTTTTTGGACAACACGGTAGCTTTCAATGC 3 82 0 AACACGGTAG 0.927367 -219 AACAAGAAAGCCTTATTCCT 4 1 1 AACAAGAAAG 0.674664 -104 TTCCTTCTGGAAAAGGATTGATCCCCCTAT 4 38 1 AAAAGGATTG 0.863144 -67 ATTAGGGTTAAAAAGGATAGGTTAACACAG 4 72 0 AAAAGGATAG 0.933015 -33 TTCTTTTCTAAACAAGGTTCAGCGCTTTCT 6 43 1 AACAAGGTTC 0.696729 -258 TAGATTCTAGAAAATGGTTGCATGAATTTG 6 211 1 AAAATGGTTG 0.748549 -90 ATTAAAACTGAAAAAAATAGTTTAAAACAA 6 261 1 AAAAAAATAG 0.643929 -40 AAAAAGCACAAAAAAGCTAGATGTTTTATG 7 11 1 AAAAAGCTAG 0.883294 -290 ATCCGTCAAAAAAACGGTAGAGAGAGCCCT 7 231 0 AAAACGGTAG 0.94718 -70 ********** Masking position 4 Map Score: 1.91881 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 184 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: -2.3992e-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 13 ********** No masking Map Score: -2.3992e-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: -2.3992e-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