AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_mjan_reg_100.orf -o00561_mjan_100.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 MJ0818 162 M. jannaschii predicted coding region MJ0818 #2 MJ1113 300 N-acetylglucosamine-1-phosphate transferase #3 MJ1214 49 type I restriction-modification enzyme 1, R subunit #4 MJ1217 41 conserved hypothetical protein #5 MJ1219 69 M. jannaschii predicted coding region MJ1219 #6 MJ1220 69 type I restriction-modification enzyme 1, M subunit #7 MJ1530 178 ribosomal protein S18 alanine acetyltransferase Motif number 1 GTTTTAAAAGAAACTTTTAGAAAAAGTTTCATC 1 31 0 AAACTTAAAA 0.842061 -132 TTAAAACCTCAAAGCTTTTTAATTTGGAACGCT 1 57 1 AAAGTTTAAT 0.736839 -106 GAACGCTATAAAAAGATTACTATAATTTATTAG 1 83 1 AAAATTATAT 0.799939 -80 GCAAGTTACTAAAGAATTTCTAAAGTGATATA 1 141 1 AAAGTTTTAA 0.804146 -22 TATGAAATATAAAAATATCCTAATTAATATCTT 2 14 1 AAAAATCTAA 0.907888 -287 AAAAATCAGTAAAAAGATATTAATTAGGATATT 2 27 0 AAAAATATAA 0.946325 -274 AAGATAAGCCAAAAATATCCAAAAAATCAGTAA 2 48 0 AAAAATCAAA 0.953796 -253 AATACTTTTCAAAATATTTAAAAACAAATAGAT 2 91 0 AAAATTTAAA 0.966219 -210 AAATATTTTGAAAAGTATTTTATGATGGACTTT 2 105 1 AAAAATTTAT 0.864041 -196 AAGGATAACTAAAACTATTAAAAAAATTGCACC 2 147 0 AAAAATTAAA 0.976129 -154 CCTAAGCAATAAAAGTAGATTAATAATGGCAAG 2 177 0 AAAAAGATAA 0.756204 -124 GGAAGTAAGGAAAATAATAAAAGAATTTCTATA 2 209 1 AAAAATAAAG 0.814668 -92 TTTTTGCTAAAAAATTATAGAAATTCTTTTATT 2 224 0 AAAAATAAAA 0.973633 -77 TTTTTTAGCAAAAAACATATATATCCTAAACTT 2 243 1 AAAAATAATA 0.694178 -58 TAATGAAGATAAAAGAAGTTAAAGTTTAGGATA 2 264 0 AAAAAGTAAA 0.877961 -37 TTTCACCAGCAAAATTTTATTAACAATAAAAAT 4 17 0 AAAATTATAA 0.924993 -25 CTAATCAATCAAACAAATTAAATTAACTTCCAG 5 36 0 AAACATTAAT 0.733198 -34 TTACATAGTGAAAACATTAAAATAACTATCTAA 6 35 1 AAAATTAAAT 0.893718 -35 CCCCTTTATGAAAGCGTTCAAAATTCA 7 5 0 AAAGTTCAAA 0.812791 -174 TTAGTATTTCAAAATGTTTTAAAAGACTCTATA 7 52 1 AAAATTTAAA 0.966219 -127 AGACTCTATAAAAAGAATTTAAAATAATACTAA 7 75 1 AAAAATTAAA 0.976129 -104 TTCATTGATTAAAATTATTCAAAGGCTTTACTA 7 140 1 AAAAATTAAA 0.976129 -39 **** *** *** Masking position 3 Map Score: 32.0371 Number of sites scoring better than the average of aligned sites = 2578 Number in coding regions = 1859 Number in noncoding regions = 719 Number of orfs with sites within 600 bp upstream = 489 Fraction of orfs with sites within 600 bp upstream = 0.0785416 Motif number 2 TCTAAAAGTTTCTTTTAAAACCTCAAAGCT 1 43 1 TCTTTTAAAA 0.936516 -120 ATTATAGTAATCTTTTTATAGCGTTCCAAA 1 79 0 TCTTTTTATA 0.875956 -84 AAGATTACTATAATTTATTAGGATAATCCT 1 95 1 TAATTTATTA 0.569049 -68 TAACTTGCTATTTTTTAATAAGGCAGGATT 1 119 0 TTTTTTAATA 0.933607 -44 TTAATTAGGATATTTTTATATTTCATAATT 2 11 0 TATTTTTATA 0.866758 -290 CTATCTATTTGTTTTTAAATATTTTGAAAA 2 89 1 GTTTTTAAAT 0.50043 -212 TTTTGAAAAGTATTTTATGATGGACTTTAA 2 110 1 TATTTTATGA 0.652806 -191 TTGCACCAATGCTTTTAAAGTCCATCATAA 2 124 0 GCTTTTAAAG 0.739215 -177 TTGGTGCAATTTTTTTAATAGTTTTAGTTA 2 145 1 TTTTTTAATA 0.933607 -156 TTATAGAAATTCTTTTATTATTTTCCTTAC 2 213 0 TCTTTTATTA 0.875563 -88 CCTCAATGGATTTTTTAATGTATGGATT 3 9 0 TTTTTTAATG 0.862582 -41 TTTTTTGAGGGATTTTAAGAGCTGGAAGTT 5 15 1 GATTTTAAGA 0.805971 -55 AGCTGGAAGTTAATTTAATTTGTTTGATTG 5 34 1 TAATTTAATT 0.695086 -36 CTTAGATAGTTATTTTAATGTTTTCACTAT 6 39 0 TATTTTAATG 0.931192 -31 TTTTATAGAGTCTTTTAAAACATTTTGAAA 7 58 0 TCTTTTAAAA 0.936516 -121 TATTTTAAATTCTTTTTATAGAGTCTTTTA 7 71 0 TCTTTTTATA 0.875956 -108 ATTTTAGTATTATTTTAAATTCTTTTTATA 7 81 0 TATTTTAAAT 0.828875 -98 TATTAAATTCTATTTTAATTTTAGTATTAT 7 98 0 TATTTTAATT 0.918107 -81 AATTAAAATAGAATTTAATAAATTACACAA 7 108 1 GAATTTAATA 0.744058 -71 ********** Masking position 5 Map Score: 20.6731 Number of sites scoring better than the average of aligned sites = 2575 Number in coding regions = 2025 Number in noncoding regions = 550 Number of orfs with sites within 600 bp upstream = 401 Fraction of orfs with sites within 600 bp upstream = 0.0644073 Motif number 3 ATCCTAATAAATTATAGTAATCTTTTTATA 1 89 0 ATTATAGTAA 0.899678 -74 ATAAGGCAGGATTATCCTAATAAATTATAG 1 102 0 ATTATCCTAA 0.98126 -61 GAAATATAAAAATATCCTAATTAATATCTT 2 17 1 AATATCCTAA 0.970274 -284 ATAAGCCAAAAATATCCAAAAAATCAGTAA 2 48 0 AATATCCAAA 0.953154 -253 TTGCTAAAAAATTATAGAAATTCTTTTATT 2 224 0 ATTATAGAAA 0.848183 -77 AAAAAACATATATATCCTAAACTTTAACTT 2 252 1 TATATCCTAA 0.854001 -49 AGAATTTAAAATAATACTAAAATTAAAATA 7 88 1 ATAATACTAA 0.819577 -91 ATTGATTAAAATTATTCAAAGGCTTTACTA 7 143 1 ATTATTCAAA 0.862154 -36 ********** Masking position 4 Map Score: 5.96168 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 199 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 TTAAAAGAAACTTTTAGAAAAAGTTTCATC 1 31 0 CTTTTAGAAA 0.924434 -132 CTTTAGAAATTCTTTAGTAACTTGCTATTT 1 136 0 TCTTTAGTAA 0.834749 -27 TATATCACTTTAGAAATTCTTTAGTA 1 147 0 ACTTTAGAAA 0.933201 -16 GTTATCCTTGCCATTATTAATCTACTTTTA 2 171 1 CCATTATTAA 0.818964 -130 TATAGAAATTCTTTTATTATTTTCCTTACT 2 212 0 CTTTTATTAT 0.817462 -89 AACTATCCCCTTTATAATGAAGATAAAA 2 283 0 CCTTTATAAT 0.921164 -18 CACCAGCAAAATTTTATTAACAATAAAAAT 4 17 0 ATTTTATTAA 0.822278 -25 CCTTTATATACACCCTACAT 6 1 1 CCTTTATATA 0.791963 -69 ATAAACACCCCCTTTATGAAAGCGTTCAAA 7 16 0 CCTTTATGAA 0.923181 -163 GTTTTAAAAGACTCTATAAAAAGAATTTAA 7 67 1 ACTCTATAAA 0.674333 -112 TTCTATTTTAATTTTAGTATTATTTTAAAT 7 91 0 ATTTTAGTAT 0.655136 -88 TCTCACTTAACCTTTAGTAAAGCCTTTGAA 7 157 0 CCTTTAGTAA 0.978374 -22 ********** Masking position 6 Map Score: 9.61261 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 633 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 5 AGATATATATTCAATTTTGATGAAACTTTT 1 13 1 TCAATTTTGA 0.897593 -150 TCAAAGCTTTTTAATTTGGAACGCTATAAA 1 65 1 TTAATTTGGA 0.983684 -98 ATTACTATAATTTATTAGGATAATCCTGCC 1 98 1 TTTATTAGGA 0.845123 -65 TAAAAAGATATTAATTAGGATATTTTTATA 2 21 0 TTAATTAGGA 0.963347 -280 TGAGGAAGATTTAATTTTTATTTCAG 3 34 1 TTAATTTTTA 0.888544 -16 GGAAGTTAATTTAATTTGTTTGATTGATTA 5 38 1 TTAATTTGTT 0.773846 -32 TGAATTTTGAACGCTTTCAT 7 1 1 TGAATTTTGA 0.913861 -178 ********** Masking position 4 Map Score: 3.36688 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 225 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 TTTTAGAAAAAGTTTCATCAAAATTGAATA 1 20 0 AGTTTCATCA 0.86802 -143 GATATTTTTATATTTCATAATT 2 3 0 TATTTCATAA 0.885074 -298 CTATTAAAAAAATTGCACCAATGCTTTTAA 2 136 0 AATTGCACCA 0.937997 -165 AATTTCACCAGCAAAATTTT 4 32 0 AATTTCACCA 0.971111 -10 CCCTACATCCAATTACATAGTGAAAACATT 6 23 1 AATTACATAG 0.744873 -47 TGGTCCTTAGTATTTCAAAATGTTTTAAAA 7 46 1 TATTTCAAAA 0.752873 -133 GAATTTAATAAATTACACAACATTCATTGA 7 118 1 AATTACACAA 0.937186 -61 ********** Masking position 7 Map Score: 0.498241 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 384 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 ********** No masking Map Score: 8.55083e-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: 8.55083e-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: 8.55083e-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