AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00072_bsub_reg_300.orf -o00072_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mmgA 137 acetyl-CoA acetyltransferase #2 yqiK 78 similar to glycerophosphodiester phosphodiesterase #3 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #4 yxjD 78 similar to 3-oxoadipate CoA-transferase #5 yxjC 153 similar to hypothetical proteins from B. subtilis #6 yxjB 300 similar to hypothetical proteins Motif number 1 TGACGCAGCCTTCTTTTTTCATTCATTCAT 1 41 1 TTCTTTTTTC 0.681032 -97 CATTCATTCATGCCCGTTTCAAAGCATACA 1 60 1 TGCCCGTTTC 0.980618 -78 GGTTTCACCTCATTCAGAAGATAGA 1 123 0 CACCTCATTC 0.917445 -15 ACGATTTGCTCACCCTATTCTCAAATTTTT 3 53 1 CACCCTATTC 0.925226 -248 AATAAAAAGTTGCTTCTTTCCGCTAATTTT 3 90 1 TGCTTCTTTC 0.923184 -211 TCTTTACAAATTCTCCATTCTGGTCAAAGA 3 250 1 TTCTCCATTC 0.782375 -51 ATGACCACCTCTTCCTGATGTTTGG 3 286 0 CACCTCTTCC 0.885274 -15 ATTGATGCCCCTTTCGTTTTCTTCT 4 64 0 TGCCCCTTTC 0.989917 -15 AAAGGAAAGCTCCTTTTTTCGGAGCTTTCC 5 19 0 TCCTTTTTTC 0.863364 -135 GCTGTTTCCGTCCCCTTTCCATATGTACGA 5 77 0 TCCCCTTTCC 0.937433 -77 ACACACATCCCCCGTTTCCGCGAACTAG 5 136 0 CCCCCGTTTC 0.978732 -18 TGTATGGGTTTCCCCGTTTCCATCATACAA 6 119 0 TCCCCGTTTC 0.980618 -182 TATTTGTCTATGCCTTTTTCATTTATCTAA 6 254 1 TGCCTTTTTC 0.96059 -47 GATAAAAAACACCCCATTCATTCATTTTT 6 282 0 CACCCCATTC 0.959241 -19 ********** Masking position 8 Map Score: 18.6185 Number of sites scoring better than the average of aligned sites = 1602 Number in coding regions = 1258 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 2 TGCGTCAAACAGCCTCCTTCTAACAACTAT 1 18 0 AGCCTCCTTC 0.869527 -120 TGTTTGACGCAGCCTTCTTTTTTCATTCAT 1 37 1 AGCCTTCTTT 0.926043 -101 TACAATTTCTAGTTGTCTTCTATGAATGTA 1 86 0 AGTTGTCTTC 0.962653 -52 CAAACCCTAAAGTTTTCTCCATTATACTTA 2 49 0 AGTTTTCTCC 0.911433 -30 CCTCAATTAGAGCCATCCTCATAGACAAAT 3 132 1 AGCCATCCTC 0.857812 -169 CAAATCTGCTCGTTATCTTTCTAACAACAG 3 157 1 CGTTATCTTT 0.750296 -144 CCTGCATTCGCGTTGTCTTTACAAATTCTC 3 235 1 CGTTGTCTTT 0.82294 -66 ATGCCCCTTTCGTTTTCTTCTACACTAGAC 4 55 0 CGTTTTCTTC 0.971025 -24 CTTTTTTCGGAGCTTTCCTCTACCAT 5 7 0 AGCTTTCCTC 0.974888 -147 CGAAAAAAGGAGCTTTCCTTTTTTAATCGG 5 28 1 AGCTTTCCTT 0.926043 -126 GTCAGTACTGATTTTTCTTCACTATAAGGT 6 70 1 ATTTTTCTTC 0.811365 -231 GCAGAAAGGGAGTTTTTTTCATGATTATCC 6 149 1 AGTTTTTTTC 0.811365 -152 ********** Masking position 6 Map Score: 10.4841 Number of sites scoring better than the average of aligned sites = 1307 Number in coding regions = 1177 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 AAGGCTGCGTCAAACAGCCTCCTTCTAACA 1 23 0 CAAACAGCCT 0.978957 -115 ATTGATACAGCCTTAATCCTAGA 2 4 1 GATACAGCCT 0.911187 -75 CGTTATCTTTCTAACAACAGGAAATGATCG 3 167 1 CTAACAACAG 0.80928 -134 AGATAAAAGCCAAACATCAGGAAGAGGTGG 3 277 1 CAAACATCAG 0.930689 -24 AAAGGGGACGGAAACAGCCGATGCGGACAG 5 89 1 GAAACAGCCG 0.979883 -65 CCGTTTCCATCATACAACAAATATCCAGGA 6 106 0 CATACAACAA 0.832982 -195 CGGGGAAACCCATACAGCAGAAAGGGAGTT 6 133 1 CATACAGCAG 0.981853 -168 CAGGTGTAGACAAACTGCCAGACCTGGCCA 6 202 1 CAAACTGCCA 0.892897 -99 ********** Masking position 4 Map Score: 5.20247 Number of sites scoring better than the average of aligned sites = 1109 Number in coding regions = 1019 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 CTTCTAACAACTATTCATTTT 1 2 0 CTATTCATTT 0.967259 -136 CCTTCTTTTTTCATTCATTCATGCCCGTTT 1 49 1 TCATTCATTC 0.969597 -89 AAGCAACTTTTTATTCATTTTAAAAAATTT 3 75 0 TTATTCATTT 0.949467 -226 CATGATTATCCAATTCATTCGTTATAGATA 6 168 1 CAATTCATTC 0.948328 -133 TGTCTATGCCTTTTTCATTTATCTAAAAAT 6 258 1 TTTTTCATTT 0.822561 -43 AAAAAACACCCCATTCATTCATTTTTAGAT 6 278 0 CCATTCATTC 0.980447 -23 ********** Masking position 5 Map Score: 4.84399 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 110 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 AGGAGGCTGTTTGACGCAGCCTTCTTTTTTCA 1 30 1 TTGACGACCT 0.874578 -108 TATACTTATTTTGTCGGCTCCACTCTAGGATT 2 25 0 TTGTCGCCCA 0.974942 -54 AAGGTTACGCTTGGCTGACCCACCCGTCAAAC 3 23 1 TTGGCTACCA 0.958011 -278 CGTCAAACGATTTGCTCACCCTATTCTCAAAT 3 47 1 TTTGCTACCT 0.910171 -254 TTTTTTCTAATTGGCGCCTCAATTAGAGCCAT 3 116 1 TTGGCGCCAA 0.921142 -185 TGCATTCGCGTTGTCTTTACAAATTCTCCATT 3 237 1 TTGTCTTCAA 0.720327 -64 AAAGCTCCTTTTTTCGGAGCTTTCCTCTACCA 5 12 0 TTTTCGACTT 0.680846 -142 GCATCGGCTGTTTCCGTCCCCTTTCCATATGT 5 81 0 TTTCCGCCCT 0.841671 -73 CAGTACTGATTTTTCTTCACTATAAGGTTCCA 6 72 1 TTTTCTCCTA 0.680846 -229 AACGAATGAATTGGATAATCATGAAAAAAACT 6 159 0 TTGGATACAT 0.388659 -142 GTCTGGCAGTTTGTCTACACCTGTCATTATCT 6 193 0 TTGTCTCCCT 0.978828 -108 CTAGGTTTATTTGTCTATGCCTTTTTCATTTA 6 247 1 TTGTCTTCCT 0.926541 -54 ****** * *** Masking position 2 Map Score: 5.36169 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 1058 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 TCTTCTGAATGAGGTGAAACC 1 127 1 GAGGTGAAAC 0.995 -11 TTTAGGGTTTGAGGTGAAACG 2 68 1 GAGGTGAAAC 0.995 -11 AAATATCCAGGAGCTGGAACCTTATAGTGA 6 88 0 GAGCTGGAAC 0.989093 -213 ********** Masking position 8 Map Score: 1.91228 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 12 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ACCCTATTCTCAAATTTTTTAAAATGAATAAAAAGT 3 64 1 CATTTTAAAG 0.978951 -237 AGATAACGAGCAGATTTGTCTATGAGGATGGCTCTA 3 139 0 CATTTTATGG 0.938284 -162 GAGCAAGTTCCATGATTTTCAAAAGGGCTATACGAC 3 198 0 CAATTTAAAG 0.950316 -103 CCGATGCGGACAGGTTTTTGTAAACGCTTTCTAGTT 5 106 1 CATTTTAAAG 0.987275 -48 CAGACCTGGCCAATTTTTGAGATAGGCCTAGGTTTA 6 220 1 CATTTGATAG 0.971054 -81 CCCATTCATTCATTTTTAGATAAATGAAAAAGGCAT 6 263 0 CATTTGAAAG 0.5524 -38 ** *** * *** * Masking position 7 Map Score: 1.8898 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 69 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 GATACAGCCTTAATCCTAGAGTGGAGCCGACAAAATAA 2 14 1 TATCCATGCC 0.978828 -65 AGCAAATCGTTTGACGGGTGGGTCAGCCAAGCGTAACC 3 25 0 TGACGGGGCC 0.945817 -276 CAACAGGAAATGATCGGGTCGTATAGCCCTTTTGAAAA 3 181 1 TATCGGTGCC 0.9956 -120 CTTTTGAAAATCATGGAACTTGCTCGCCTGCATTCGCG 3 209 1 TATGGAGGCC 0.982403 -92 GTATTTGCTGTGATCGCGATTTACAGCCTGACTGGTCT 4 21 1 TATCGGTGCC 0.995597 -58 TTTCCTTTTTTAATCGGAATAGTTGGCCCACGCTTCTC 5 41 1 TATCGAGGCC 0.992499 -113 ATCAGTACTGACATGCTGGTATCCCGCCAACATCATAT 6 44 0 AATGCGTGCC 0.893216 -257 * **** * * *** Masking position 16 Map Score: 1.98423 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 144 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TTCTTCTACACTAGACCAGTCAGGCTGTAAA 4 40 0 CTAGACCATC 0.959882 -39 AATAGTTGGCCCACGCTTCTCGTACATATGG 5 58 1 CCACGCTTTC 0.930688 -96 GGCAGTTTGTCTACACCTGTCATTATCTATA 6 190 0 CTACACCTTC 0.985203 -111 AGACAAACTGCCAGACCTGGCCAATTTTTGA 6 209 1 CCAGACCTGC 0.967104 -92 ACAAATAAACCTAGGCCTATCTCAAAAATTG 6 230 0 CTAGGCCTTC 0.993485 -71 GTTTATTTGTCTATGCCTTTTTCATTTATCT 6 251 1 CTATGCCTTT 0.855865 -50 ******** ** Masking position 3 Map Score: 0.611852 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 114 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 ********** No masking Map Score: -2.03683e-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: -2.03683e-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 12 ********** No masking Map Score: -2.03683e-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