AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_mjan_reg_300.orf -o00280_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 MJ1008 100 branched-chain amino acid aminotransferase (ilvE) #2 MJ1009 51 phosphate transport system regulatory protein (phoU) #3 MJ1010 300 M. jannaschii predicted coding region MJ1010 #4 MJ1530 178 ribosomal protein S18 alanine acetyltransferase Motif number 1 TCTATTTGCAAAAAATAAAAATAGAGTCTA 1 20 0 AAAAATAAAA 0.934017 -81 TTGTCAAAATAAAAATAAAATGAATATTTA 1 63 0 AAAAATAAAA 0.934017 -38 TAAAAGTAAAATAAAGTATAG 2 2 0 ATAAAGTATA 0.812748 -50 TTTGGCAATATAAAAGTAAAATAAAGTATA 2 12 0 TAAAAGTAAA 0.934818 -40 TATATTGCCAAAAAATTATATGGAGGGAAA 2 30 1 AAAAATTATA 0.979061 -22 TAACTTTTGCAAAAACTATAAACACATCTT 3 52 0 AAAAACTATA 0.958371 -249 CAAAAGTTATTAAAATTAAAAATAAAAATT 3 73 1 TAAAATTAAA 0.944442 -228 AATGTTTTGCAAAAACTATAATGTTGCTAT 3 150 1 AAAAACTATA 0.958371 -151 GCCAGTAATTAAAAAGTATATCTCTTTTCT 3 244 0 AAAAAGTATA 0.977774 -57 TTACTGGCAAAAAAATGATATGAAATATAT 3 266 1 AAAAATGATA 0.917854 -35 AAGACTCTATAAAAAGAATTTAAAATAATA 4 74 1 AAAAAGAATT 0.793033 -105 AAAAAGAATTTAAAATAATACTAAAATTAA 4 84 1 TAAAATAATA 0.933733 -95 AAAATAATACTAAAATTAAAATAGAATTTA 4 95 1 TAAAATTAAA 0.944442 -84 ATTCATTGATTAAAATTATTCAAAGGCTTT 4 139 1 TAAAATTATT 0.831281 -40 ********** Masking position 5 Map Score: 23.8913 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 782 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 2 TTTTGCAAATAGACAATTTTATATATTAAATATTC 1 37 1 AGACATTTAA 0.974407 -64 ATTTTTATTTTGACAATTTAACAAAGGTGGTCTT 1 77 1 TGACATTTAA 0.828696 -24 TTATGAAGAGTTTCAAAGATACTTAGCAA 3 5 1 GAAGATTTAA 0.978452 -296 ACTTAGCAAGAAAGATTTTTGAAGATGTGTTTATA 3 31 1 AAAGATTTAA 0.992426 -270 TTTTAATTTTAATAACTTTTGCAAAAACTATAAAC 3 59 0 AATAATTTAA 0.776342 -242 AGTTTTTGCAAAACATTTTGAAATATATAGGATAT 3 132 0 AAACATTTAA 0.990979 -169 GCATCTTTCTAAATATTTTCCTATATTGGTTAGCT 3 188 0 AAATATTTAA 0.944429 -113 AAATTCTGCAAATGACTTTAGAAAAGAGATATACT 3 225 1 AATGATTTAA 0.963978 -76 TGAATTTTGAACGCTTTCATAAAGGGGGTGTTT 4 9 1 GAACGTTTAA 0.923244 -170 GAGTCTTTTAAAACATTTTGAAATACTAAGGACCA 4 46 0 AAACATTTAA 0.990979 -133 GACTCTATAAAAAGAATTTAAAATAATACTAAAAT 4 76 1 AAAGATTTAA 0.992426 -103 TAAAATTAAAATAGAATTTAATAAATTACACAACA 4 105 1 ATAGATTTAA 0.943336 -74 AAAATTATTCAAAGGCTTTACTAAAGGTTAAGTGA 4 150 1 AAAGGTTTAA 0.976412 -29 ***** *** * * Masking position 13 Map Score: 22.7383 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 361 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TTATGAAGAGTTTCAAAGATACTTAG 3 5 1 GAAGATTTAA 0.9024 -296 ACTTAGCAAGAAAGATTTTTGAAGATGTGTTT 3 31 1 AAAGATTTGA 0.980402 -270 TAACTTTTGCAAAAACTATAAACACATCTTCA 3 50 0 AAAAATATAA 0.737556 -251 AGTTTTTGCAAAAGTTATTAAAATTAAAAATA 3 65 1 AAAGTATTAA 0.656677 -236 AAATTAAAAATAAAAATTTGAACGCCCCCACT 3 85 1 TAAAATTTAA 0.855307 -216 TAGTTTTTGCAAAACATTTTGAAATATATAGG 3 136 0 AAAACTTTGA 0.973052 -165 CCAATATAGGAAAATATTTAGAAAGATGCGAA 3 194 1 AAAATTTTGA 0.907844 -107 AAATTCTGCAAATGACTTTAGAAAAGAGATAT 3 225 1 AATGATTTGA 0.910859 -76 AGAAAAGAGATATACTTTTTAATTACTGGCAA 3 244 1 TATACTTTAA 0.618572 -57 CCCCTTTATGAAAGCGTTCAAAATTCA 4 6 0 AAAGCTTCAA 0.912218 -173 AGAGTCTTTTAAAACATTTTGAAATACTAAGG 4 50 0 AAAACTTTGA 0.973052 -129 GACTCTATAAAAAGAATTTAAAATAATACTAA 4 76 1 AAAGATTTAA 0.980035 -103 AACCTTTAGTAAAGCCTTTGAATAATTTTAAT 4 147 0 AAAGCTTTAA 0.985049 -32 ***** *** ** Masking position 2 Map Score: 14.0594 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 773 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 AATTTAACAAAGGTGGTCTT 1 91 1 AGGTGGTCTT 0.965461 -10 CGCCCCCAAGTGGGGGCGTTCAAATTTTTA 3 95 0 TGGGGGCGTT 0.99783 -206 CGCCCCCACTTGGGGGCGTTCATATATATC 3 107 1 TGGGGGCGTT 0.99783 -194 GCTTTCATAAAGGGGGTGTTTATTGGTCCT 4 23 1 AGGGGGTGTT 0.99665 -156 ********** Masking position 9 Map Score: 5.95278 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 = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TTAATATATAAAATTGTCTATTTGCAAAAA 1 36 0 AAATTGTCTA 0.876543 -65 CACCTTTGTTAAATTGTCAAAATAAAAATA 1 76 0 AAATTGTCAA 0.952313 -25 TTTTACTTTTATATTGCCAAAAAATTATAT 2 21 1 ATATTGCCAA 0.771711 -31 AACTATAAACACATCTTCAAAAATCTTTCT 3 39 0 ACATCTTCAA 0.743643 -262 ATTAAAAATAAAAATTTGAACGCCCCCACT 3 87 1 AAAATTTGAA 0.734485 -214 TTTTTGCAAAACATTTTGAAATATATAGGA 3 135 0 ACATTTTGAA 0.959032 -166 TATAATGTTGCTATTGTGAATGAGCTAACC 3 166 1 CTATTGTGAA 0.808753 -135 ATATAGGAAAATATTTAGAAAGATGCGAAA 3 197 1 ATATTTAGAA 0.827878 -104 CTCCTCAAATTTACTATATATTTCAT 3 285 0 AAATTTACTA 0.603296 -16 TGAATTTTGAACGCTTTCATA 4 2 1 GAATTTTGAA 0.818102 -177 GTCTTTTAAAACATTTTGAAATACTAAGGA 4 49 0 ACATTTTGAA 0.959032 -130 TAATCAATGAATGTTGTGTAATTTATTAAA 4 121 0 ATGTTGTGTA 0.578158 -58 ********** Masking position 10 Map Score: 5.17005 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 698 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 TAAGTGAATAGACTCTATTTTTATTTTTTG 1 12 1 GACTCTATTT 0.821795 -89 TTTGCAAATAGACAATTTTATATATTAAAT 1 38 1 GACAATTTTA 0.798162 -63 AAAATAAAATGAATATTTAATATATAAAAT 1 52 0 GAATATTTAA 0.81415 -49 TTTTTATTTTGACAATTTAACAAAGGTGGT 1 78 1 GACAATTTAA 0.908582 -23 ATAATTTTTTGGCAATATAAAAGTAAAATA 2 19 0 GGCAATATAA 0.905458 -33 AACTTTTGCAAAAACTATAAACACATCTTC 3 51 0 AAAACTATAA 0.679539 -250 GAAATATATAGGATATATATGAACGCCCCC 3 118 0 GGATATATAT 0.714086 -183 ATGTTTTGCAAAAACTATAATGTTGCTATT 3 151 1 AAAACTATAA 0.679539 -150 ACCAATATAGGAAAATATTTAGAAAGATGC 3 193 1 GAAAATATTT 0.745563 -108 TCCTCAAATTTACTATATATTTCATATCAT 3 280 0 TACTATATAT 0.54791 -21 TGTTTTAAAAGACTCTATAAAAAGAATTTA 4 66 1 GACTCTATAA 0.951547 -113 ********** Masking position 6 Map Score: 4.06557 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 790 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 7 ********** No masking Map Score: 2.65333e-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: 2.65333e-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 9 ********** No masking Map Score: 2.65333e-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