AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #2 ywlB 66 alternate gene name: ipc-28d #3 spoIIR 140 alternate gene name: ipc-27d, csfX #4 prfA 125 peptide chain release factor 1 Motif number 1 GTGGATAAGTATGTGTATAAACTGCAC 1 8 0 ATGTGTATAA 0.941761 -149 GCTAATAAAGAAGTGGATAAGTATGTGTAT 1 20 0 AAGTGGATAA 0.973833 -137 TATCCACAAATTGTGGACAACGCTAATAAA 1 41 0 TTGTGGACAA 0.873003 -116 TGTCCACAATTTGTGGATAACGCTTGTTTT 1 52 1 TTGTGGATAA 0.975267 -105 CGTTTTATTGTTGTGAATAAGGAGTTTGGT 1 132 1 TTGTGAATAA 0.965711 -25 TCTAGCCCTATTATGGACAAGGAGAGCCTG 3 90 0 TTATGGACAA 0.794917 -51 CATTATAGTATAGTGATTAACCCCAGTCAA 4 71 0 TAGTGATTAA 0.857312 -55 ********** Masking position 9 Map Score: 10.4571 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 155 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 ACACATACTTATCCACTTCTTTATTAGCGTT 1 22 1 ATCCACTCTT 0.755539 -135 GATTTTTTTCACCCTGCACGTTTATCCCAGG 3 63 1 ACCCTGCCGT 0.979216 -78 TCCCAGGCTCTCCTTGTCCATAATAGGGCTA 3 87 1 TCCTTGTCAT 0.779529 -54 CGTGCTTTGTTTCTAGCCCTATTATGGACAA 3 100 0 TTCTAGCCTA 0.713705 -41 GTCCCCACCGTTCCTCTCCGTGCTTTGTTTC 3 118 0 TTCCTCTCGT 0.979455 -23 CATCCCTCCTCGAATTCCAGTAT 4 3 1 TCCCTCCCGA 0.989871 -123 CTGGAAAAGCTCCCTCTGCTATACTGGAATT 4 23 0 TCCCTCTCTA 0.967156 -103 AGCATTTCAATCCCAGCTGGAAAAGCTCCCT 4 39 0 TCCCAGCGGA 0.88983 -87 CACCTCTGTTTTCCTGTGCGTAACATTCTCA 4 99 0 TTCCTGTCGT 0.983021 -27 ******* *** Masking position 3 Map Score: 5.27847 Number of sites scoring better than the average of aligned sites = 1421 Number in coding regions = 1222 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 3 GGACAACGCTAATAAAGAAGTGGATAAGTAT 1 26 0 AATAAAGAGT 0.940818 -131 GTCCTGTAATAAAACAAGCGTTATCCACAAA 1 61 0 AAAACAAGGT 0.97567 -96 TTTTGAAAGTATAAAAGATGTCCTGTAATAA 1 80 0 ATAAAAGAGT 0.940816 -77 TTTCAAAAGGATTACACGCGTAAAACAATCG 1 103 1 ATTACACGGT 0.864478 -54 TTACACGCGTAAAACAATCGTTTTATTGTTG 1 114 1 AAAACAATGT 0.909851 -43 GAAAGAACGCAAAAACGGGGTGAACGG 2 50 1 AAAAACGGGT 0.94647 -17 TACGCACAGGAAAACAGAGGTGAAGACC 4 108 1 AAAACAGAGT 0.986918 -18 ******** ** Masking position 4 Map Score: 2.8166 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 669 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 4 TTACGCGTGTAATCCTTTTGAAAGTATAAA 1 96 0 AATCCTTTTG 0.9895 -61 CGCGTAAAACAATCGTTTTATTGTTGTGAA 1 119 1 AATCGTTTTA 0.959545 -38 CTGGTCTAAAAATAGATTTGCCTCATAGAT 2 15 1 AATAGATTTG 0.931846 -52 CTGGGATTGAAATGCTTTTGACTGGGGTTA 4 54 1 AATGCTTTTG 0.980845 -72 ********** Masking position 7 Map Score: 0.452912 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 222 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TAACGCTTGTTTTATTACAGGACATCTTTT 1 69 1 TTTATTACAG 0.885617 -88 CAAATCTATTTTTAGACCAGATGA 2 5 0 TTTAGACCAG 0.940879 -62 TTTTGCGTTCTTTCTTCCAATCTATGAGGC 2 34 0 TTTCTTCCAA 0.787467 -33 GCTAGATTTTTTTCACCCTGCACGTTTATC 3 59 1 TTTCACCCTG 0.868852 -82 ACCCTGCACGTTTATCCCAGGCTCTCCTTG 3 73 1 TTTATCCCAG 0.992006 -68 CAAAAGCATTTCAATCCCAGCTGGAAAAGC 4 44 0 TCAATCCCAG 0.953585 -82 AGTATAGTGATTAACCCCAGTCAAAAGCAT 4 65 0 TTAACCCCAG 0.972102 -61 AATGAGAATGTTACGCACAGGAAAACAGAG 4 97 1 TTACGCACAG 0.934966 -29 ********** Masking position 1 Map Score: 5.05031 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 654 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 ********** No masking Map Score: -1.32571e-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: -1.32571e-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: -1.32571e-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