AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_tpal_reg_100.orf -o00290_tpal_100.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 TP0452 278 isoleucyl-tRNA synthetase (ileS) #2 TP0586 88 leucyl-tRNA synthetase (leuS) #3 TP1035 152 valyl-tRNA synthetase (valS) Motif number 1 ATTTTCAAGATGTGGGGAAGGGTTTCCTGCCTTCGTC 1 16 1 TGGGAGGTCC 0.923586 -263 TTCGATTGCAGAAGGTGTAATGTGGGGCATTATTGCA 1 79 1 GGGGAAGTGG 0.996248 -200 GATACCCCACGTGTGCGTAATCGCACGTGCTCTGCCA 1 139 0 GTGGAACGCG 0.902802 -140 ATCTGGTGCAGGTGGGGAAAGGTGTGGCGCCGGTCAT 1 173 1 GGGGAAGTGG 0.996248 -106 TCATAAGACGTATGGGGAAAAGGAAGGACGAAAATGA 1 206 1 TGGGAAGGGG 0.996248 -73 GCTCAGAATCGCATAAGGAGCGTAAGGCATTATATCA 1 240 0 GTAGAGGTGG 0.961443 -39 CCTTATGCGATTCTGAGCAACGGAGGTTGT 1 259 1 TTGGAAGGGT 0.942076 -20 AGGTACACCTGGGTGTGCACGGGTTGCAGCCCCT 2 8 0 GTGGACGGGC 0.987781 -81 ACCTTGCAACGTAGATGTACCGGCGTGTACAATGCCC 2 41 1 GGAGACGGTG 0.801286 -48 CCAAAAGCTCTGGGGAGGAGCGGCTGGCAGTGACGGC 3 50 1 TGGGAGGGGG 0.996536 -103 ACAGCAGATAGGATGAAAAGTGTACGGTTTTTTATCC 3 105 0 GTGAAGGTGG 0.92804 -48 TCATCCTATCTGCTGTGAAATGGGAGCTCAACGAATT 3 126 1 TTGGAAGGGC 0.98476 -27 * ** * ** ** ** Masking position 9 Map Score: 16.6735 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 880 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 GGATTTTCAAGATGTGGGGAAGGGTTTCCT 1 14 1 GATGTGGGGA 0.89973 -265 GAACTGCGACGAAGGCAGGAAACCCTTCCC 1 30 0 GAAGGCAGGA 0.811788 -249 AATTGGCAGAGCACGTGCGATTACGCACAC 1 136 1 GCACGTGCGA 0.958812 -143 GCGATTACGCACACGTGGGGTATCTGGTGC 1 152 1 ACACGTGGGG 0.914657 -127 GGTATCTGGTGCAGGTGGGGAAAGGTGTGG 1 170 1 GCAGGTGGGG 0.992895 -109 CTCTGTGTATGCAGAGGGCATTGTACACGC 2 63 0 GCAGAGGGCA 0.960285 -26 CTCTGCATACACAGAGGGGATT 2 77 1 ACAGAGGGGA 0.969952 -12 GTATCCAAAAGCTCTGGGGAGGAGCGGCTG 3 46 1 GCTCTGGGGA 0.958384 -107 GGAGCGGCTGGCAGTGACGGCAAGAAACTT 3 66 1 GCAGTGACGG 0.909346 -87 CCATTTCACAGCAGATAGGATGAAAAGTGT 3 119 0 GCAGATAGGA 0.96405 -34 ********** Masking position 9 Map Score: 9.16886 Number of sites scoring better than the average of aligned sites = 1385 Number in coding regions = 1245 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 TCGTATTCGATTGCAGAAGGTGTAATGTGG 1 74 1 TTGCAGAAGG 0.911245 -205 TGGGGCATTATTGCATACGTAATACTCAAT 1 101 1 TTGCATACGT 0.73143 -178 GTGTGCGTAATCGCACGTGCTCTGCCAATT 1 136 0 TCGCACGTGC 0.828707 -143 ACGTGCGATTACGCACACGTGGGGTATCTG 1 148 1 ACGCACACGT 0.901812 -131 GGGGTATCTGGTGCAGGTGGGGAAAGGTGT 1 168 1 GTGCAGGTGG 0.94844 -111 CGGTCATAAGACGTATGGGGAAAAGGAAGG 1 203 1 ACGTATGGGG 0.799988 -76 TTGCTCAGAATCGCATAAGGAGCGTAAGGC 1 249 0 TCGCATAAGG 0.881364 -30 ACACCTGGGTGTGCACGGGTTGCAGCCCCT 2 11 0 GTGCACGGGT 0.88757 -78 ACCCGTGCACACCCAGGTGTACCTTGCAAC 2 21 1 ACCCAGGTGT 0.785856 -68 GTACCTTGCAACGTAGATGTACCGGCGTGT 2 39 1 ACGTAGATGT 0.817055 -50 CCCTCTGTGTATGCAGAGGGCATTGTACAC 2 65 0 ATGCAGAGGG 0.978011 -24 CCCTCTGCATACACAGAGGGGATT 2 75 1 ACACAGAGGG 0.88541 -14 ********** Masking position 5 Map Score: 6.25148 Number of sites scoring better than the average of aligned sites = 2694 Number in coding regions = 2516 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 CGCAGTTCTGATGATGCCTTTTTCGTATTC 1 52 1 ATGATGCCTT 0.98604 -227 TACGTATGCAATAATGCCCCACATTACACC 1 92 0 ATAATGCCCC 0.990936 -187 CGAAAATGATATAATGCCTTACGCTCCTTA 1 234 1 ATAATGCCTT 0.991769 -45 ACCGGCGTGTACAATGCCCTCTGCATACAC 2 59 1 ACAATGCCCT 0.990936 -30 ********** Masking position 5 Map Score: 4.34545 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TTTTGGATACATAAAAAACCCGTCCTGAAT 3 26 0 ATAAAAAACC 0.989232 -127 CATGTACCGGATAAAAAACCGTACACTTTT 3 97 1 ATAAAAAACC 0.989232 -56 ********** Masking position 5 Map Score: 0.0923632 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: -3.81261e-13 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: -3.81261e-13 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: -3.81261e-13 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