AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -intrC_mjan_opreg_100.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0792 300 M. jannaschii predicted coding region MJ0792 #2 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #3 MJ0793 60 M. jannaschii predicted coding region MJ0793 #4 MJ0794 48 M. jannaschii predicted coding region MJ0794 #5 MJ0795 79 M. jannaschii predicted coding region MJ0795 #6 MJ1089 40 cobalt transport protein (cbiQ) #7 MJ1091 281 cobalamin biosynthesis protein (cbiM) #8 MJ1345 300 O-linked GlnNAc transferase #9 MJ1346 87 glutamine synthetase (glnA) Motif number 1 GATTATGTTATATTTCATTTTTTGATATAAA 1 15 1 TTTTCATTTT 0.891962 -286 TTTTAACTATTTTATAATTTTATATCAAAAA 1 33 0 TTATAATTTT 0.954646 -268 ATAATTTACTTTTTTAAAGTTATAATTGTTT 1 64 1 TTTTAAAGTT 0.893974 -237 TATGTTAAAATTTTTAACTTATTAGAATTTT 1 103 0 TTTTAACTTA 0.880108 -198 AATTTTAACATATATAATTTACTATTTAACT 1 122 1 TTATAATTTA 0.918815 -179 TATAATTTACTATTTAACTTTAAATCATAAT 1 134 1 TTTTAACTTT 0.931735 -167 ACAAAACCTCTATATATATTATGATTTAAAG 1 151 0 TTATATATTA 0.794927 -150 CGCCAACTATTCTTTAATTTTTTGTATGGTG 1 220 0 TTTTAATTTT 0.983188 -81 ATGTTTTTCTTTTTTAATTTTAATAATTTTT 2 13 1 TTTTAATTTT 0.983188 -56 TAATAATTTTTTGATATTTTTTAGGTGATAT 2 33 1 TGATATTTTT 0.696176 -36 TTAAAGTTATTATTTATTTTATCATCATTAT 3 27 0 TTTTATTTTA 0.941152 -34 GGTTTCACAATTGTTAAAGTTATTATTTATT 3 40 0 TGTTAAAGTT 0.643519 -21 TTCTTTAATTTTTTACTTTTTT 6 2 1 TTTTAATTTT 0.983188 -39 ATTTTTTACTTTTTTAAATTTTAAAATTTAA 6 18 1 TTTTAAATTT 0.975236 -23 TTTTTATATATCTTTATTTTTAGTAATACTT 7 20 1 TTTTATTTTT 0.967464 -262 TAATGATTAATTTTTCTTTTTTAGTAATAAA 7 84 0 TTTTCTTTTT 0.807616 -198 ATTAAAAATGTCTTTAATTTAAATAAGTAAT 7 114 1 TTTTAATTTA 0.969186 -168 AATAAAATAAACTTTAATTTTGTTACTATTA 7 175 0 ATTTAATTTT 0.842208 -107 CTCTTTATCTTATATAAATTTAACGGTATTT 7 213 0 TTATAAATTT 0.934094 -69 TCCCAATATTTGTTTATTTTGCATTTCC 8 8 0 TTTTATTTTG 0.769335 -293 TATAATTAAATTTTTATATTTATAATTATAT 8 62 1 TTTTATATTT 0.952436 -239 CACATTAGTTTATTTAAAGTTAATAAGATTG 8 127 0 TTTTAAAGTT 0.89397 -174 GATAGAAAAATTTATATTTTACACTAAAATA 8 198 1 TTATATTTTA 0.851988 -103 TTTACGAATTTCGTTAAATTATTATTACTAT 8 247 0 TGTTAAATTA 0.819327 -54 ATTTTTATATTTTAATTTAAAT 9 2 1 TTTTATATTT 0.952436 -86 CGGTATATTCAATTTAAATTAAAATATAAAA 9 13 0 ATTTAAATTA 0.659021 -75 CTTCCATATATATATAATTTACGGTATATTC 9 34 0 TTATAATTTA 0.918815 -54 * ********* Masking position 5 Map Score: 41.6447 Number of sites scoring better than the average of aligned sites = 2050 Number in coding regions = 1387 Number in noncoding regions = 663 Number of orfs with sites within 600 bp upstream = 488 Fraction of orfs with sites within 600 bp upstream = 0.078381 Motif number 2 TTTGATATAAAATTATAAAATAGTTAAAAATA 1 35 1 ATTTAAAATA 0.914107 -266 TAATTGTTTTATTATTAAAAATTCTAATAAGT 1 86 1 ATATAAAAAT 0.572568 -215 ATAAGTTAAAAATTTTAACATATATAATTTAC 1 112 1 ATTTAACATA 0.710403 -189 TTTAAAGTTAAATAGTAAATTATATATGTTAA 1 126 0 ATATAAATTA 0.595413 -175 TTTAACTTTAAATCATAATATATATAGAGGTT 1 146 1 ATCTAATATA 0.530773 -155 TCACAAATGTAATAATACAAAACCTCTATATA 1 166 0 ATATACAAAA 0.753819 -135 ATATCAAAAAATTATTAAAATTAAAAAAGAAA 2 18 0 ATATAAAATT 0.568049 -51 TAAAATTTAAAAAAGTAAAAAATTAAAGAA 6 9 0 AAATAAAAAA 0.840602 -32 TACTTTTTTAAATTTTAAAATTTAAAG 6 24 1 ATTTAAAATT 0.495812 -17 AATATTAAGTATTACTAAAAATAAAGATATAT 7 25 0 ATATAAAAAT 0.929949 -257 AAGTTGCCTTACTATTTAAATAGTTTATTACT 7 61 1 ATATTAAATA 0.595629 -221 TAAATAGTTTATTACTAAAAAAGAAAAATTAA 7 77 1 ATATAAAAAA 0.969591 -205 AAAATTAATCATTATTAAAAATGTCTTTAATT 7 101 1 ATATAAAAAT 0.572568 -181 AATTTAAATAAGTAATAAAAAATATGAAAAAA 7 129 1 ATATAAAAAA 0.969968 -153 ATAACTCATTAATAGTAACAAAATTAAAGTTT 7 166 1 ATATAACAAA 0.863304 -116 GTATTTTATTATTAATAAAATAAACTTTAATT 7 187 0 ATATAAAATA 0.95832 -95 TAAGATAAAGAGTACTATAAATGTGTTAAGTT 7 232 1 ATATATAAAT 0.739868 -50 TAATTTATGGACTTTTATAATTAAATTTTTAT 8 47 1 ATTTATAATT 0.445261 -254 ATATAATTATAAATATAAAAATTTAATTATAA 8 61 0 AATTAAAAAT 0.637714 -240 ACACTAAAATAATTTTAATAAATAATATCATA 8 218 1 ATTTAATAAA 0.62862 -83 ATAATATCATAGTAATAATAATTTAACGAAAT 8 239 1 ATATAATAAT 0.809743 -62 ATTTAACGAAATTCGTAAAATAGGGGGATTAA 8 259 1 ATCTAAAATA 0.862096 -42 ATTTAAATTAAAATATAAAAAT 9 1 0 AATTAAAAAT 0.637714 -87 * ** ******* Masking position 6 Map Score: 26.7486 Number of sites scoring better than the average of aligned sites = 1459 Number in coding regions = 974 Number in noncoding regions = 485 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 3 ATAAAATTATAAAATAGTTAAAAATAATTTACTT 1 41 1 AAAATAAAAA 0.955936 -260 TAATAAAACAATTATAACTTTAAAAAAGTAAATT 1 66 0 ATTATTTAAA 0.598946 -235 TTTATTATTAAAAATTCTAATAAGTTAAAAATTT 1 93 1 AAAATATAAG 0.796561 -208 ACTTTAAATCATAATATATATAGAGGTTTTGTAT 1 150 1 ATAATATAGA 0.564993 -151 ACATTTGTGAAAAATGTGGAAAATAATAGGGGCA 1 188 1 AAAATAAAAT 0.862842 -113 AAAAATTATTAAAATTAAAAAAGAAAAACATTT 2 10 0 AAAATAAAGA 0.768813 -59 TATCACCTAAAAAATATCAAAAAATTATTAAAAT 2 29 0 AAAATAAAAA 0.955936 -40 ATACTATACAATAATGATGATAAAATAAATAATA 3 17 1 ATAATATAAA 0.894239 -44 AAGTTACTATAAAATGAGGGAAAAAG 5 64 1 AAAATGAAAA 0.808927 -16 TTTAAATTTTAAAATTTAAAAAAGTAAAAAATTA 6 16 0 AAAATAAAAG 0.808927 -25 ACTAAAAATAAAGATATATAAAAAGTAGTTATT 7 10 0 AAGATAAAAA 0.73342 -272 GGTAATATTAAGTATTACTAAAAATAAAGATATA 7 26 0 AGTATAAAAA 0.596721 -256 ATCATTATTAAAAATGTCTTTAATTTAAATAAGT 7 108 1 AAAATTTAAT 0.627903 -174 TAAGTAATAAAAAATATGAAAAAAACAAAATAAC 7 137 1 AAAATAAAAA 0.955936 -145 ACGGTATTTTATTATTAATAAAATAAACTTTAAT 7 188 0 ATTATAAAAT 0.576611 -94 TATTAATAATAAAATACCGTTAAATTTATATAAG 7 202 1 AAAATTTAAA 0.853346 -80 ACCCCTGAATATAATTCAAAAAAACTTAACACAT 7 252 0 ATAATAAAAA 0.901579 -30 AAAATAAACAAATATTGGGATAAACAAGTAATTT 8 19 1 AATATATAAA 0.924024 -282 TAAATATAAAAATTTAATTATAAAAGTCCATAAA 8 50 0 AATTTATAAA 0.396573 -251 TATACGCTATAATATAATTATAAATATAAAAATT 8 70 0 AATATATAAA 0.924024 -231 ATTATAGCGTATAATGTCATAAAACAATTAATAC 8 91 1 ATAATTAAAA 0.726543 -210 ATGTGGAAATAATATGGAAATAAAAGAAAATATC 8 153 1 AATATATAAA 0.924024 -148 TTACACTAAAATAATTTTAATAAATAATATCATA 8 216 1 ATAATATAAA 0.894239 -85 TTTAATAAATAATATCATAGTAATAATAATTTAA 8 231 1 AATATGTAAT 0.408364 -70 ATTTAAATTGAATATACCGTAAATTATATATATA 9 25 1 AATATTAAAT 0.525951 -63 ***** ***** Masking position 5 Map Score: 28.5377 Number of sites scoring better than the average of aligned sites = 2893 Number in coding regions = 2160 Number in noncoding regions = 733 Number of orfs with sites within 600 bp upstream = 499 Fraction of orfs with sites within 600 bp upstream = 0.0801478 Motif number 4 TATCAAAAAATGAAATATAACATAATCAAT 1 12 0 TGAAATATAA 0.510978 -289 TAGAATTTTTAATAATAAAACAATTATAAC 1 82 0 AATAATAAAA 0.790376 -219 TTTTCACAAATGTAATAATACAAAACCTCT 1 171 0 TGTAATAATA 0.858478 -130 GAAAAATGTGGAAAATAATAGGGGCACCAT 1 196 1 GAAAATAATA 0.803955 -105 ATATTTTTTAGGTGATATAATGGGTGATAA 2 46 1 GGTGATATAA 0.852647 -23 TGATATAATGGGTGATAATAC 2 58 1 GGTGATAATA 0.939605 -11 ATACAATAATGATGATAAAATAAATAATAA 3 22 1 GATGATAAAA 0.838207 -39 AGGCAACTTAGGTAATATTAAGTATTACTA 7 40 0 GGTAATATTA 0.908208 -242 AATTTAAATAAGTAATAAAAAATATGAAAA 7 129 1 AGTAATAAAA 0.929164 -153 TTATTTTATTAATAATAAAATACCGTTAAA 7 196 1 AATAATAAAA 0.790376 -86 AAACTAATGTGGAAATAATATGGAAATAAA 8 147 1 GGAAATAATA 0.9345 -154 GAAATAATATGGAAATAAAAGAAAATATCC 8 158 1 GGAAATAAAA 0.94295 -143 ATAATATCATAGTAATAATAATTTAACGAA 8 239 1 AGTAATAATA 0.918848 -62 ********** Masking position 5 Map Score: 13.8146 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 486 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 TAATTTTATATCAAAAAATGAAATATAACA 1 20 0 TCAAAAAATG 0.660136 -281 TAAAATAGTTAAAAATAATTTACTTTTTTA 1 50 1 AAAAATAATT 0.81246 -251 TTTTTAATAATAAAACAATTATAACTTTAA 1 77 0 TAAAACAATT 0.93857 -224 GGGGCACCATACAAAAAATTAAAGAATAGT 1 216 1 ACAAAAAATT 0.887249 -85 ATTAAAAAAGAAAAACATTT 2 1 0 AAAAACATTT 0.530692 -68 CTAAAAAATATCAAAAAATTATTAAAATTA 2 27 0 TCAAAAAATT 0.924896 -42 ATTACTAAAAAAGAAAAATTAATCATTATT 7 87 1 AAGAAAAATT 0.843805 -195 TCATTAATAGTAACAAAATTAAAGTTTATT 7 171 1 TAACAAAATT 0.793712 -111 AATATAATTCAAAAAAACTTAACACATTTA 7 249 0 AAAAAAACTT 0.727959 -33 TAATTATAAATATAAAAATTTAATTATAAA 8 60 0 TATAAAAATT 0.756073 -241 TATAATGTCATAAAACAATTAATACCCCAA 8 100 1 TAAAACAATT 0.93857 -201 TATTCACAGATAGAAAAATTTATATTTTAC 8 190 1 TAGAAAAATT 0.89423 -111 TATTTTACACTAAAATAATTTTAATAAATA 8 212 1 TAAAATAATT 0.871483 -89 ********** Masking position 5 Map Score: 9.92481 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 579 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 TAACTTTAAAAAAGTAAATTATTTTTAACT 1 56 0 AAAGTAAATT 0.890504 -245 TTAAAGTTAAATAGTAAATTATATATGTTA 1 127 0 ATAGTAAATT 0.585458 -174 CACAATTGTTAAAGTTATTATTTATTTTAT 3 36 0 AAAGTTATTA 0.712703 -25 AATCATTGAAAAATCTAATAG 4 38 1 AAATCTAATA 0.56009 -11 TAGTTGATACAAACCAAATATAACTGTTGG 5 22 0 AAACCAAATA 0.759804 -58 ACAGTGTATTAAAGTTACTATAAAATGAGG 5 53 1 AAAGTTACTA 0.871245 -27 AAAATTTAAAAAAGTAAAAAATTAAAGAA 6 10 0 AAAGTAAAAA 0.608625 -31 ATTTTTAGTAATACTTAATATTACCTAAGT 7 35 1 ATACTTAATA 0.719409 -247 AATATGAAAAAAACAAAATAACTCATTAAT 7 149 1 AAACAAAATA 0.671593 -133 TAACAAAATTAAAGTTTATTTTATTAATAA 7 181 1 AAAGTTTATT 0.523613 -101 TAATTCAAAAAAACTTAACACATTTATAGT 7 245 0 AAACTTAACA 0.683041 -37 ATAAATATAAAAATTTAATTATAAAAGTCC 8 55 0 AAATTTAATT 0.674441 -246 TAGTTTATTTAAAGTTAATAAGATTGGGGT 8 123 0 AAAGTTAATA 0.958868 -178 TATGGAAATAAAAGAAAATATCCAGTATTC 8 165 1 AAAGAAAATA 0.76343 -136 TGGAAGTAGGAAACTTACTTCCAGAATTAT 9 59 1 AAACTTACTT 0.688319 -29 ********** Masking position 3 Map Score: 4.55539 Number of sites scoring better than the average of aligned sites = 1165 Number in coding regions = 925 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 7 ********** No masking Map Score: -1.0918e-12 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: -1.0918e-12 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: -1.0918e-12 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