AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -intrC_mjan_opreg_300.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 TTTTATATCAAAAAATGAAATATAACATAA 1 17 0 AAAAATGAAA 0.893941 -284 TTTTGATATAAAATTATAAAATAGTTAAAA 1 34 1 AAATTATAAA 0.901478 -267 TTATAACTTTAAAAAAGTAAATTATTTTTA 1 59 0 AAAAAAGTAA 0.943843 -242 TTAGAATTTTTAATAATAAAACAATTATAA 1 83 0 TAATAATAAA 0.792422 -218 TAATAAGTTAAAAATTTTAACATATATAAT 1 110 1 AAAATTTTAA 0.856505 -191 GATTTAAAGTTAAATAGTAAATTATATATG 1 130 0 TAAATAGTAA 0.859429 -171 GGCACCATACAAAAAATTAAAGAATAGTTG 1 218 1 AAAAAATTAA 0.951203 -83 TATTAAAATTAAAAAAGAAAAACATTT 2 8 0 AAAAAAGAAA 0.962581 -61 AAATATCAAAAAATTATTAAAATTAAAAAA 2 22 0 AAATTATTAA 0.856699 -47 TATCACCTAAAAAATATCAAAAAATTATTA 2 33 0 AAAATATCAA 0.758003 -36 AATAATGATGATAAAATAAATAATAACTTT 3 26 1 ATAAAATAAA 0.889899 -35 TTAAAAAAGTAAAAAATTAAAGAA 6 5 0 AAAAAATTAA 0.951203 -36 TTTAAATTTTAAAATTTAAAAAAGTAAAAA 6 20 0 AAAATTTAAA 0.901476 -21 TTTAAATTTTAAAATTTAAAG 6 30 1 AAAATTTAAA 0.901476 -11 TAAGTATTACTAAAAATAAAGATATATAAA 7 22 0 TAAAAATAAA 0.920889 -260 ATAAACTATTTAAATAGTAAGGCAACTTAG 7 59 0 TAAATAGTAA 0.859429 -223 GTTTATTACTAAAAAAGAAAAATTAATCAT 7 83 1 AAAAAAGAAA 0.962581 -199 TCTTTAATTTAAATAAGTAATAAAAAATAT 7 124 1 AAATAAGTAA 0.846322 -158 AAGTAATAAAAAATATGAAAAAAACAAAAT 7 138 1 AAATATGAAA 0.734163 -144 AAATAACTCATTAATAGTAACAAAATTAAA 7 164 1 TTAATAGTAA 0.608219 -118 TTTATTATTAATAAAATAAACTTTAATTTT 7 185 0 ATAAAATAAA 0.889899 -97 TTTATTTTATTAATAATAAAATACCGTTAA 7 195 1 TAATAATAAA 0.792422 -87 TTTATCTTATATAAATTTAACGGTATTTTA 7 211 0 ATAAATTTAA 0.62945 -71 TATAAAAATTTAATTATAAAAGTCCATAAA 8 50 0 TAATTATAAA 0.78109 -251 AATATAATTATAAATATAAAAATTTAATTA 8 64 0 TAAATATAAA 0.915698 -237 TAATATGGAAATAAAAGAAAATATCCAGTA 8 162 1 ATAAAAGAAA 0.874427 -139 ATTTTAGTGTAAAATATAAATTTTTCTATC 8 198 0 AAAATATAAA 0.965427 -103 TTACACTAAAATAATTTTAATAAATAATAT 8 216 1 ATAATTTTAA 0.605338 -85 AATTTAAATTAAAATATAAAAAT 9 4 0 AAAATATAAA 0.965427 -84 ********** Masking position 3 Map Score: 44.272 Number of sites scoring better than the average of aligned sites = 3224 Number in coding regions = 2300 Number in noncoding regions = 924 Number of orfs with sites within 600 bp upstream = 576 Fraction of orfs with sites within 600 bp upstream = 0.0925153 Motif number 2 ATATAAAATTATAAAATAGTTAAAAATAATTTA 1 39 1 ATAAATTTAA 0.811189 -262 TAATAAAACAATTATAACTTTAAAAAAGTAAAT 1 67 0 ATTTAATTAA 0.732896 -234 TTTTAACTTATTAGAATTTTTAATAATAAAACA 1 90 0 TTAAATTTAA 0.490501 -211 TTCTAATAAGTTAAAAATTTTAACATATATAAT 1 107 1 TTAAAATTAA 0.559843 -194 TTAAAGTTAAATAGTAAATTATATATGTTAAAA 1 124 0 ATATAATATA 0.524742 -177 ACCTCTATATATATTATGATTTAAAGTTAAATA 1 144 0 ATATATTTTA 0.833231 -157 TAGGGGCACCATACAAAAAATTAAAGAATAGTT 1 214 1 ATAAAAATTA 0.656925 -87 TATCAAAAAATTATTAAAATTAAAAAAGAAAAA 2 16 0 TTATAATTAA 0.875193 -53 GATAAAATAAATAATAACTTTAACAATTGTGAA 3 35 1 ATATAATTAA 0.966367 -26 CCCTCATTTTATAGTAACTTTAATACACTGTAT 5 51 0 ATATAATTAA 0.966527 -29 CTTTAAATTTTAAAATTTAAAAAAGTAAA 6 22 0 ATTTAATTTA 0.669645 -19 AATAACTACTTTTTATATATCTTTA 7 3 1 TAATACTTTA 0.381327 -279 AACTTAGGTAATATTAAGTATTACTAAAAATAA 7 33 0 ATATAAATTA 0.751716 -249 TTTTTTAGTAATAAACTATTTAAATAGTAAGGC 7 66 0 ATAACTTTAA 0.489291 -216 TATTACTAAAAAAGAAAAATTAATCATTATTAA 7 86 1 AAAAAATTAA 0.850099 -196 TATTTAAATTAAAGACATTTTTAATAATGATTA 7 106 0 AAAACATTTA 0.483304 -176 TATTATTAATAAAATAAACTTTAATTTTGTTAC 7 180 0 AAATAATTTA 0.868896 -102 TATTAATAATAAAATACCGTTAAATTTATATAA 7 202 1 AAATACTTAA 0.770098 -80 TAACACATTTATAGTACTCTTTATCTTATATAA 7 227 0 ATATACTTTA 0.888452 -55 ATAATTATAAATATAAAAATTTAATTATAAAAG 8 58 0 ATAAAATTTA 0.930951 -243 GTATAATGTCATAAAACAATTAATACCCCAATC 8 99 1 ATAAACTTAA 0.87203 -202 TACCCCAATCTTATTAACTTTAAATAAACTAAT 8 122 1 TTATAATTAA 0.876214 -179 GTATTCACAGATAGAAAAATTTATATTTTACAC 8 189 1 ATAAAATTTA 0.930961 -112 ATTTTACACTAAAATAATTTTAATAAATAATAT 8 213 1 AAATAATTAA 0.891492 -88 AAATAATATCATAGTAATAATAATTTAACGAAA 8 237 1 ATATAAATAA 0.803727 -64 AATTTACGGTATATTCAATTTAAATTAAAATAT 9 17 0 ATATCATTAA 0.86571 -71 *** *** **** Masking position 13 Map Score: 29.1461 Number of sites scoring better than the average of aligned sites = 1751 Number in coding regions = 1169 Number in noncoding regions = 582 Number of orfs with sites within 600 bp upstream = 427 Fraction of orfs with sites within 600 bp upstream = 0.0685834 Motif number 3 AAAATGAAATATAACATAATCAATA 1 6 0 ATAACATAAT 0.797646 -295 ATAATTTTATATCAAAAAATGAAATATAAC 1 21 0 ATCAAAAAAT 0.83322 -280 ATATAAAATTATAAAATAGTTAAAAATAAT 1 39 1 ATAAAATAGT 0.845863 -262 ATTTTTAATAATAAAACAATTATAACTTTA 1 78 0 ATAAAACAAT 0.881346 -223 ACAAAAAATTAAAGAATAGTTGGCGATGAC 1 226 1 AAAGAATAGT 0.467306 -75 CCTAAAAAATATCAAAAAATTATTAAAATT 2 28 0 ATCAAAAAAT 0.83322 -41 ACACTATACTATACAATAATGATGATAAAA 3 12 1 ATACAATAAT 0.725159 -49 ATGATGATAAAATAAATAATAACTTTAACA 3 30 1 AATAAATAAT 0.690229 -31 AAATACAATCATTGAAAAATCTAATAG 4 32 1 ATTGAAAAAT 0.783784 -17 TATTACTAAAAAAGAAAAATTAATCATTAT 7 86 1 AAAGAAAAAT 0.803644 -196 TTAAATAAGTAATAAAAAATATGAAAAAAA 7 132 1 AATAAAAAAT 0.708128 -150 AAATATGAAAAAAACAAAATAACTCATTAA 7 148 1 AAAACAAAAT 0.583827 -134 TTTATTATTAATAAAATAAACTTTAATTTT 7 185 0 ATAAAATAAA 0.559006 -97 TATTTTATTAATAATAAAATACCGTTAAAT 7 197 1 ATAATAAAAT 0.73424 -85 GAAATGCAAAATAAACAAATATTGGGATAA 8 12 1 ATAAACAAAT 0.856588 -289 AAATATTGGGATAAACAAGTAATTTATGGA 8 28 1 ATAAACAAGT 0.582194 -273 ATAATTATAAATATAAAAATTTAATTATAA 8 61 0 ATATAAAAAT 0.773574 -240 ATTATACGCTATAATATAATTATAAATATA 8 76 0 ATAATATAAT 0.711936 -225 GTATAATGTCATAAAACAATTAATACCCCA 8 99 1 ATAAAACAAT 0.881346 -202 TTAACTTTAAATAAACTAATGTGGAAATAA 8 135 1 ATAAACTAAT 0.84585 -166 GTATTCACAGATAGAAAAATTTATATTTTA 8 189 1 ATAGAAAAAT 0.926057 -112 ATATTTTACACTAAAATAATTTTAATAAAT 8 211 1 CTAAAATAAT 0.652626 -90 AAATAATTTTAATAAATAATATCATAGTAA 8 224 1 AATAAATAAT 0.690229 -77 TTAAATTAAAATATAAAAAT 9 1 0 ATATAAAAAT 0.773574 -87 TTTGATTGAATAATTCTGGAAGTA 9 74 0 ATTGAATAAT 0.766958 -14 ********** Masking position 8 Map Score: 22.8616 Number of sites scoring better than the average of aligned sites = 1897 Number in coding regions = 1419 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 4 AATTATAAAATAGTTAAAAATAATTTACTT 1 45 1 TAGTTAAAAA 0.736875 -256 TACTTTTTTAAAGTTATAATTGTTTTATTA 1 70 1 AAGTTATAAT 0.745192 -231 TTAGAATTTTTAATAATAAAACAATTATAA 1 83 0 TAATAATAAA 0.662555 -218 AAATTCTAATAAGTTAAAAATTTTAACATA 1 104 1 AAGTTAAAAA 0.711292 -197 TTTTTCACAAATGTAATAATACAAAACCTC 1 172 0 ATGTAATAAT 0.728773 -129 TAAATAGTTGAAGTAACAAATACAATCATT 4 15 1 AAGTAACAAA 0.900873 -34 AAATTTAAAAAAGTAAAAAATTAAAGAA 6 9 0 AAGTAAAAAA 0.893828 -32 TCTTTATTTTTAGTAATACTTAATATTACC 7 30 1 TAGTAATACT 0.606502 -252 TTTTCTTTTTTAGTAATAAACTATTTAAAT 7 74 0 TAGTAATAAA 0.967543 -208 TAATTTAAATAAGTAATAAAAAATATGAAA 7 128 1 AAGTAATAAA 0.963266 -154 AACTCATTAATAGTAACAAAATTAAAGTTT 7 168 1 TAGTAACAAA 0.911748 -114 GGTATTTTATTATTAATAAAATAAACTTTA 7 190 0 TATTAATAAA 0.775898 -92 ATAGCGTATAATGTCATAAAACAATTAATA 8 94 1 ATGTCATAAA 0.547598 -207 ACTAAAATAATTTTAATAAATAATATCATA 8 220 1 TTTTAATAAA 0.482105 -81 AATAATATCATAGTAATAATAATTTAACGA 8 238 1 TAGTAATAAT 0.919093 -63 ********** Masking position 6 Map Score: 13.1 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 378 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 5 CCCCTATTATTTTCCACATTTTTCACAAATGT 1 188 0 TTCCAATTTT 0.971549 -113 TTTTGTATGGTGCCCCTATTATTTTCCACATT 1 200 0 TCCCCATTAT 0.966322 -101 CTTTTTCCCTCATTTTATAGTAACTT 5 64 0 TCCCTATTTT 0.968436 -16 ACTTTTTATATATCTTTATTTTTAGTAATACT 7 18 1 TTCTTATTTT 0.700265 -264 TATTTTGTTTTTTTCATATTTTTTATTACTTA 7 137 0 TTTCAATTTT 0.769991 -145 ATTACTTGTTTATCCCAATATTTGTTTATTTT 8 19 0 TTCCCATATT 0.92668 -282 AAACAATTAATACCCCAATCTTATTAACTTTA 8 112 1 TCCCCATCTT 0.960186 -189 TTTTCTTTTATTTCCATATTATTTCCACATTA 8 151 0 TTCCAATTAT 0.915189 -150 GCGATTTTAATCCCCCTATTTTACGAATTTCG 8 265 0 TCCCCATTTT 0.989107 -36 * **** ***** Masking position 8 Map Score: 6.10398 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 225 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TCACCCATTATATCACCTAAAAAATATCAA 2 43 0 TATCACCTAA 0.968059 -26 GTATTATCACCCATTATATCACCT 2 55 0 TATCACCCAT 0.979115 -14 ATTTGGTTTGTATCAACTATACAGTGTATT 5 33 1 TATCAACTAT 0.897415 -47 TAATACTTAATATTACCTAAGTTGCCTTAC 7 43 1 TATTACCTAA 0.911039 -239 TCATATTTTTTATTACTTATTTAAATTAAA 7 126 0 TATTACTTAT 0.747218 -156 GTTATCACCCCTGAATATAATT 7 270 0 TATCACCCCT 0.944878 -12 ********** Masking position 5 Map Score: 2.08986 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 49 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 ATTTTTTGATATAAAATTATAAAATAGTTA 1 31 1 ATAAAATTAT 0.69425 -270 ACTTTAAAAAAGTAAATTATTTTTAACTAT 1 54 0 AGTAAATTAT 0.970408 -247 AAAGTTAAATAGTAAATTATATATGTTAAA 1 125 0 AGTAAATTAT 0.970408 -176 AAAAAATATCAAAAAATTATTAAAATTAAA 2 25 0 AAAAAATTAT 0.660107 -44 ATGATGATAAAATAAATAATAACTTTAACA 3 30 1 AATAAATAAT 0.748592 -31 AATTTAAAAAAGTAAAAAATTAAAGAA 6 8 0 AGTAAAAAAT 0.7571 -33 CTTTTTTAGTAATAAACTATTTAAATAGTA 7 70 0 AATAAACTAT 0.674739 -212 GGGATAAACAAGTAATTTATGGACTTTTAT 8 35 1 AGTAATTTAT 0.737069 -266 GACTTTTATAATTAAATTTTTATATTTATA 8 56 1 ATTAAATTTT 0.558256 -245 TATATTTATAATTATATTATAGCGTATAAT 8 76 1 ATTATATTAT 0.535148 -225 ATTATTTTAGTGTAAAATATAAATTTTTCT 8 201 0 TGTAAAATAT 0.571524 -100 AAATAATTTTAATAAATAATATCATAGTAA 8 224 1 AATAAATAAT 0.748592 -77 TACGAATTTCGTTAAATTATTATTACTATG 8 246 0 GTTAAATTAT 0.70127 -55 TAACGAAATTCGTAAAATAGGGGGATTAAA 8 262 1 CGTAAAATAG 0.31572 -39 TTCAATTTAAATTAAAATATAAAAAT 9 7 0 ATTAAAATAT 0.850083 -81 TTGAATATACCGTAAATTATATATATATGG 9 32 1 CGTAAATTAT 0.905178 -56 ********** Masking position 4 Map Score: 9.05545 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 498 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 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 Motif number 10 ********** 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