AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_tpal_reg_300.orf -o00950_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0218 300 sigma factor SigB regulation protein, putative #2 TP0220 28 anti-sigma F factor antagonist (spoIIAA-1) #3 TP0223 267 aspartate aminotransferase (tpaaT) Motif number 1 GTAGTTGGAATACGCACCAATACCTTT 1 4 0 TACGCACCAC 0.939546 -297 GCTAAGAGCGCACGCGACCGTGCAGAAAGCGTAG 1 34 0 CACGCGACCA 0.991327 -267 CTTGAAAGTTCAAGCAACGGCGGATGGGCGTTTT 1 91 0 CAAGCAACGA 0.705825 -210 CCTTTTACCCCACGCGCCCCTTTCTGTAGCCTAC 1 131 0 CACGCGCCCC 0.999505 -170 AAAGAAACACCACGCACGCGAGAATAATCCTTTT 1 159 0 CACGCACGCA 0.996048 -142 TCAGATAGCACACGCACCCATCACGATGAAGCCA 1 214 0 CACGCACCCC 0.999029 -87 TCAGAGCACACAAGCCCGCGCAGCCACACGGATG 3 44 0 CAAGCCCGCC 0.988772 -224 ACAGTGTAGACACGCCCCCTGACCCTGTCAATTT 3 107 0 CACGCCCCCC 0.998829 -161 GCGTTTAACGCACGCGCGCCTTCAGAGAGGTCCA 3 147 0 CACGCGCGCA 0.998008 -121 AACGGTGGTGCACGCGCTGTTATCTCCTCTTGGT 3 193 1 CACGCGCTGC 0.985939 -75 GTGGGGAAAATACGCGCGCAAACCAAGAGGAGAT 3 214 0 TACGCGCGCC 0.995278 -54 ********* * Masking position 2 Map Score: 26.8855 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 721 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 AGTTGGAATACGCACCAATACCTTT 1 4 0 CGCACCATCC 0.97502 -297 TAAGAGCGCACGCGACCGTGCAGAAAGCGTAG 1 34 0 CGCGACCTCA 0.985124 -267 TTTTACCCCACGCGCCCCTTTCTGTAGCCTAC 1 131 0 CGCGCCCTTC 0.990745 -170 AGAAACACCACGCACGCGAGAATAATCCTTTT 1 159 0 CGCACGCAAA 0.86966 -142 AGATAGCACACGCACCCATCACGATGAAGCCA 1 214 0 CGCACCCTAC 0.977416 -87 AGCACACAAGCCCGCGCAGCCACACGGATGAG 3 42 0 CCCGCGCGCA 0.965766 -226 GTGAATCGACAGCCCGACTTCAGAGCACACAA 3 65 0 AGCCCGATCA 0.753191 -203 TCAATTTATGCACCCCAGTGAATCGACAGCCC 3 82 0 CACCCCATAA 0.744586 -186 AGTGTAGACACGCCCCCTGACCCTGTCAATTT 3 107 0 CGCCCCCGCC 0.9956 -161 GTTTAACGCACGCGCGCCTTCAGAGAGGTCCA 3 147 0 CGCGCGCTCA 0.997691 -121 ACAGCGCGTGCACCACCGTTCCTTCAAGAGCA 3 181 0 CACCACCTCC 0.903502 -87 AACGGTGGTGCACGCGCTGTTATCTCCTCTTG 3 193 1 CACGCGCGTA 0.881084 -75 GGGGAAAATACGCGCGCAAACCAAGAGGAGAT 3 214 0 CGCGCGCACC 0.992384 -54 CCGCGCCTCTGCATTCTGTGCAA 3 255 0 CGCGCCTTCA 0.978284 -13 ******* * ** Masking position 3 Map Score: 21.7907 Number of sites scoring better than the average of aligned sites = 2220 Number in coding regions = 2054 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 ACGCGACCGTGCAGAAAGCGTAGTTGGAAT 1 27 0 GCAGAAAGCG 0.99115 -274 AGATTTCTCAAGAGGAAGGGGAAAACGCCC 1 70 1 AGAGGAAGGG 0.979278 -231 TTCAAGCAACGGCGGATGGGCGTTTTCCCC 1 87 0 GGCGGATGGG 0.958444 -214 CAAGTAGGCTACAGAAAGGGGCGCGTGGGG 1 128 1 ACAGAAAGGG 0.981892 -173 CTCGTGTGTCGCAGGATGAGTTGGCTTCAT 1 193 1 GCAGGATGAG 0.978123 -108 ACCATTTGCCGCAGGAAGCTCATCCGTGTG 3 24 1 GCAGGAAGCT 0.972814 -244 GGATTGTTGCACAGAATGCAGAGGCGCGG 3 249 1 ACAGAATGCA 0.865634 -19 ********** Masking position 6 Map Score: 6.22866 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 565 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 AGCGGAGATTTCTCAAGAGGAAGGGGAAAA 1 65 1 TCTCAAGAGG 0.968189 -236 AACTTTCAAGTCTCAAGTAGGCTACAGAAA 1 115 1 TCTCAAGTAG 0.984684 -186 ACAACGTGTTTTTGAAGCAGCCATACAAAG 1 271 1 TTTGAAGCAG 0.937834 -30 GCTTGTGTGCTCTGAAGTCGGGCTGTCGAT 3 63 1 TCTGAAGTCG 0.993145 -205 CATGGACCTCTCTGAAGGCGCGCGTGCGTT 3 145 1 TCTGAAGGCG 0.991855 -123 ********** Masking position 5 Map Score: 3.24683 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 GCGGATGGGCGTTTTCCCCTTCCTCTTGAG 1 76 0 GTTTTCCCCT 0.991196 -225 GAGAATAATCCTTTTACCCCACGCGCCCCT 1 144 0 CTTTTACCCC 0.948704 -157 TGCTATCTGAGTTTTCTTCCCACAGTTTAA 1 238 1 GTTTTCTTCC 0.952113 -63 CGCTCCCGAACTTTTCCTCATTTC 2 5 0 CTTTTCCTCA 0.963121 -24 TGCACGCGCTGTTATCTCCTCTTGGTTTGC 3 201 1 GTTATCTCCT 0.903705 -67 TTGCGCGCGTATTTTCCCCACGGGATTGTT 3 227 1 ATTTTCCCCA 0.965911 -41 ********** Masking position 5 Map Score: 3.01295 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 214 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTCTTTCTCGTGTGTCGCAGGATGAGTTGG 1 187 1 TGTGTCGCAG 0.989047 -114 TCTGAGTTTTCTTCCCACAGTTTAAAAGAC 1 243 1 CTTCCCACAG 0.962366 -58 TGTGTAACCATTTGCCGCAGGAAGCTCATC 3 18 1 TTTGCCGCAG 0.984122 -250 GAGAGGTCCATGTCTCACAGTGTAGACACG 3 127 0 TGTCTCACAG 0.988186 -141 CCCACGGGATTGTTGCACAGAATGCAGAGG 3 243 1 TGTTGCACAG 0.962632 -25 ********** Masking position 3 Map Score: 2.37726 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 88 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TGAAAGTTCAAGCAACGGCGGATGGGCGTT 1 93 0 AGCAACGGCG 0.984794 -208 GCCATACAAAGGGAACGGTAG 1 290 1 GGGAACGGTA 0.949389 -11 GGAAAAGTTCGGGAGCGCCGT 2 18 1 GGGAGCGCCG 0.985226 -11 CCGTTCCTTCAAGAGCAGCGTTTAACGCAC 3 168 0 AAGAGCAGCG 0.955727 -100 CTGCTCTTGAAGGAACGGTGGTGCACGCGC 3 180 1 AGGAACGGTG 0.987198 -88 ACCAAGAGGAGATAACAGCGCGTGCACCAC 3 197 0 GATAACAGCG 0.887025 -71 ********** Masking position 4 Map Score: 2.36688 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 435 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GCGTTTTCCCCTTCCTCTTGAGAAATCTCC 1 68 0 CTTCCTCTTG 0.94364 -233 CGTGGTGTTTCTTTCTCGTGTGTCGCAGGA 1 179 1 CTTTCTCGTG 0.972331 -122 GATGAGTTGGCTTCATCGTGATGGGTGCGT 1 207 1 CTTCATCGTG 0.972369 -94 GCAGGAAGCTCATCCGTGTGGCTGCGCGGG 3 34 1 CATCCGTGTG 0.950319 -234 TCAATTTATGCACCCCAGTGAATCGACAGC 3 84 0 CACCCCAGTG 0.920065 -184 GGGGGCGTGTCTACACTGTGAGACATGGAC 3 122 1 CTACACTGTG 0.909332 -146 TTCTGTGCAACAATCCCGTGGGGAAAATAC 3 235 0 CAATCCCGTG 0.957145 -33 ********** Masking position 9 Map Score: 3.35786 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 377 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 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