AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_mjan_reg_300.orf -o110_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ10374 225 M_jannaschii_chromosome #2 RMJ06726 108 M_jannaschii_chromosome #3 RMJ10646 245 M_jannaschii_chromosome #4 RMJ07954 32 M_jannaschii_chromosome Motif number 1 CTATTATTATTACTAATACTTTAAAGCTTTTTGA 1 41 1 TTAATATTAA 0.895309 -185 CGGAAGTTATTAAAAATAATGATAATATTGTTGG 1 77 1 TAAATATATA 0.857777 -149 TAAATCTATCTCGAAAAATTTAAATATTGCTCAT 1 112 1 TAAAAATAAA 0.983782 -114 ATTGCTCATATATAAAAAATGAAATTGCCATAAC 1 137 1 TAAAAATAAA 0.984128 -89 AAAATTCCTAAAACTTTAAATAACTCTTT 2 6 1 TTAAAATTAA 0.970185 -103 AACTTGCATATCTTAAAAATTTAAAAAAGAGTTA 2 31 0 TTAAAATTAA 0.969841 -78 GATATGCAAGTTCTAAGATTATAAATTTTATTCT 2 53 1 TTAAGATTAA 0.918528 -56 TGATAAAAAGTTTAAAGAATAAAATTTATAATCT 2 68 0 TAAAGATAAA 0.953837 -41 TGTATCCCTCAAAAAAATGATAAAAAGTTTAA 2 87 0 TAAAAATATA 0.957102 -22 GTGATTAATATGATAAAAGTAAAAAATCTAAACG 3 23 1 TTAAAATAAA 0.98413 -223 TTGATGTGAATGCAAAAATAGAAAAGGGAAAATT 3 84 1 TAAAAAAAAA 0.879084 -162 TCATTAGGTTTTATAAAAATTATACC 4 3 0 TTAAAATATA 0.951682 -30 * ***** * *** Masking position 8 Map Score: 19.4459 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 548 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 2 GTAATTATATAATATCAAAAGCGGGATAGT 1 12 0 AATATCAAAA 0.964587 -214 TAATAACTTCCGTATCAAAAAGCTTTAAAG 1 59 0 CGTATCAAAA 0.951024 -167 ATATATGAGCAATATTTAAATTTTTCGAGA 1 120 0 AATATTTAAA 0.71172 -106 AAATATTGCTCATATATAAAAAATGAAATT 1 133 1 CATATATAAA 0.882798 -93 TTAATGGTATCACCTCAAAATGTTATGGCA 1 162 0 CACCTCAAAA 0.950082 -64 TTAGAACTTGCATATCTTAAAAATTTAAAA 2 39 0 CATATCTTAA 0.914046 -70 ATAAAAGTAAAAAATCTAAACGCTGGTTAT 3 35 1 AAAATCTAAA 0.845064 -211 TTTTTGCATTCACATCAAATAGTATCTGCA 3 72 0 CACATCAAAT 0.927755 -174 AAAGTCCCTCCACATCAAAAAGCAAGG 3 229 1 CACATCAAAA 0.987873 -17 ********** Masking position 5 Map Score: 6.80339 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 501 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 TTATCATTATTTTTAATAACTTCCGTATCA 1 72 0 TTTTAATAAC 0.928561 -154 TCGAGATAGATTTAACCAACAATATTATCA 1 96 0 TTTAACCAAC 0.947579 -130 TTCCTAAAACTTTAAATAACTCTTTTTTAA 2 15 1 TTTAAATAAC 0.967227 -94 ATCTTAAAAATTTAAAAAAGAGTTATTTAA 2 26 0 TTTAAAAAAG 0.930861 -83 AAATCCACATTTTTAAAAACGTTGTTTGGT 3 148 1 TTTTAAAAAC 0.960927 -98 CGTTGTTTGGTTTAACAAAAATATATTCTG 3 167 1 TTTAACAAAA 0.856092 -79 GGTATAATTTTTATAAAACCTAATGAACA 4 10 1 TTTATAAAAC 0.908439 -23 ********** Masking position 8 Map Score: 5.88164 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 250 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TAAAAAATGAAATTGCCATAACATTTTGAG 1 149 1 AATTGCCATA 0.965373 -77 TTAAAAGAATAATTGCCCTATTATTGGGGG 1 188 1 AATTGCCCTA 0.970046 -38 AGTATCTGCAATTTTCCATAACCAGCGTTT 3 52 0 ATTTTCCATA 0.975618 -194 AACTGTGGTAATTTTCCCTTTTCTATTTTT 3 97 0 ATTTTCCCTT 0.967895 -149 AAAAATGTGGATTTTCCACTACCATTAGGT 3 132 0 ATTTTCCACT 0.926366 -114 ********** Masking position 4 Map Score: 2.98054 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 181 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 TTAAAAATAATGATAATATTGTTGGTTAAA 1 86 1 TGATAATATT 0.960893 -140 CATTTTGAGGTGATACCATTAAAAGAATAA 1 170 1 TGATACCATT 0.922773 -56 GGAAAATTGCAGATACTATTTGATGTGAAT 3 65 1 AGATACTATT 0.974364 -181 TAATCTCTCCAGAATATATTTTTGTTAAAC 3 176 0 AGAATATATT 0.881864 -70 TATTCTGGAGAGATTATATTTAAGGATAAA 3 190 1 AGATTATATT 0.96089 -56 ********** Masking position 3 Map Score: 1.77038 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 124 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ********** No masking Map Score: 7.91135e-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: 7.91135e-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: 7.91135e-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