AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iarcA_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 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #2 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #3 MJ0792 300 M. jannaschii predicted coding region MJ0792 #4 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #5 MJ0793 60 M. jannaschii predicted coding region MJ0793 #6 MJ0794 48 M. jannaschii predicted coding region MJ0794 #7 MJ0795 79 M. jannaschii predicted coding region MJ0795 #8 MJ1411 300 glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent (gapN) #9 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 TTATTAAAAATATTACTATTTTCTTGTTCTTTTT 1 120 1 TATTATTTTT 0.70009 -135 TTTCTTGTTCTTTTTTTATTTATACTATGCCAAT 1 139 1 TTTTTTTTAA 0.919616 -116 CTATGCCAATTTTTTCATTTAGGATTATTTTTTT 1 163 1 TTTTTATTGA 0.718911 -92 TCATCAGATATTTAAAACTTATAAATCAAAATAG 1 205 0 TTTAAATTTA 0.863986 -50 AAAGTTTTATTTTTAATTTTAAAATCATTTTGGT 2 17 0 TTTTATTTAA 0.508418 -178 AGTAATGCATTATAAGTATTTATATTTTGTGTTG 2 58 1 TATAATTTAA 0.833068 -137 TATGTGAAAGTATTTTTATTAATATTGCTATAAT 2 151 1 TATTTTTTAA 0.909385 -44 TTTTAACTATTTTATAATTTTATATCAAAAAATG 3 30 0 TTTATATTAA 0.801816 -271 TAATTTACTTTTTTAAAGTTATAATTGTTTTATT 3 65 1 TTTTAATTTA 0.899086 -236 GTTATAATTGTTTTATTATTAAAAATTCTAATAA 3 82 1 TTTTATTTAA 0.828069 -219 TATGTTAAAATTTTTAACTTATTAGAATTTTTAA 3 100 0 TTTTTATTTA 0.87526 -201 AATAGTAAATTATATATGTTAAAATTTTTAACTT 3 114 0 TATATTTTAA 0.897072 -187 TATAATTTACTATTTAACTTTAAATCATAATATA 3 134 1 TATTTATTAA 0.830296 -167 ACAAAACCTCTATATATATTATGATTTAAAGTTA 3 148 0 TATATTTTTA 0.905752 -153 GGTTTTGTATTATTACATTTGTGAAAAATGTGGA 3 174 1 TATTAATTTA 0.889181 -127 CCAACTATTCTTTAATTTTTTGTATGGTGCCCCT 3 215 0 TTTAATTTGA 0.837688 -86 TGTTTTTCTTTTTTAATTTTAATAATTTTTTGAT 4 14 1 TTTTATTTAA 0.511626 -55 TTAAAGTTATTATTTATTTTATCATCATTATTGT 5 24 0 TATTTTTTTA 0.916351 -37 AAATAATAACTTTAACAATTGTGAAACC 5 43 1 TTTAAATTTA 0.889181 -18 CTATTAGATTTTTCAATGATTGTAT 6 34 0 TATTAATTTA 0.889168 -15 ACAAACCAAATATAACTGTTGGAATTAGTGCAG 7 10 0 TATAATTTGA 0.819731 -70 TTAATTTGATTATTTAGATTAAAATCAGACCGAT 8 30 0 TATTTGTTAA 0.591277 -271 AAAGGATTTTTATTTAATTTCTAAGGGTTTGTTA 8 61 0 TATTTATTTA 0.860508 -240 TTATTAAGATTTTTAGGATTTTTAATTTTGTTGT 8 169 0 TTTTAGTTTA 0.759238 -132 TATGTGTGCTTATAATTATTAAGATTTTTAGGAT 8 184 0 TATAATTTAA 0.918128 -117 ACATTTAATGTTTATATATTATGTGTGCTTATAA 8 203 0 TTTATTTTTT 0.642207 -98 CCTCTTTCATTTTAAATGTTTTTAACAAACATTT 8 231 0 TTTAATTTTA 0.932551 -70 ATTAATACGGTATATTTATTGTTTCTATTTCTAT 9 35 0 TATATTTTTT 0.611623 -192 TAAAGATATTTTTAAGTATTAATACGGTATATTT 9 52 0 TTTAATTTAA 0.831473 -175 AAGGAAGGCATTTAAATATTTATTGTCAAATATT 9 125 0 TTTAATTTAT 0.621668 -102 ***** * ** * * Masking position 9 Map Score: 34.7929 Number of sites scoring better than the average of aligned sites = 2714 Number in coding regions = 1759 Number in noncoding regions = 955 Number of orfs with sites within 600 bp upstream = 540 Fraction of orfs with sites within 600 bp upstream = 0.0867331 Motif number 2 AACTTATAAATCAAAATAGCTTTGATGAAAAA 1 192 0 TCAAAATCTT 0.934329 -63 TTAATCACCAAAATGATTTTAAAATTAAA 2 8 1 CCAAAATTTT 0.885317 -187 TTAAACCATATCAAAAATGATTAAAATACTCA 2 100 0 TCAAAAAATT 0.794437 -95 TACTTTCACATAAAAATGTTTTGTTGGTGACT 2 131 0 TAAAAATTTT 0.97604 -64 GCAATATTAATAAAAATACTTTCACATAAAAA 2 147 0 TAAAAATTTT 0.976347 -48 ATAAAATAGTTAAAAATAATTTACTTTTTTAA 3 49 1 TAAAAATTTT 0.976263 -252 TTTTTAATTTTAATAATTTTTTGATATTTTTT 4 23 1 TAATAATTTT 0.908411 -46 ATAATCAAATTAACAAACCCTTAGAAATTAAA 8 51 1 TAACAAACTT 0.786065 -250 AGAAATTAAATAAAAATCCTTTGAACTAATTA 8 73 1 TAAAAATTTT 0.976347 -228 TAAATGTTTTTAACAAACATTTAATGTTTATA 8 221 0 TAACAAATTT 0.888694 -80 TATTAATACTTAAAAATATCTTTAAACTATAC 9 62 1 TAAAAATCTT 0.950001 -165 TATACTGTCTTCAAAATTAATTAAAGTTTATT 9 89 1 TCAAAATATT 0.863285 -138 TAAAGTTTATTAATAAATATTTGACAATAAAT 9 110 1 TAATAAATTT 0.880817 -117 AAATATTTGACAATAAATATTTAAATGCCTTC 9 124 1 CAATAAATTT 0.648672 -103 ACTGGTTACTTCAAAATGTTTTTGAAAGACAC 9 178 1 TCAAAATTTT 0.968663 -49 AGACACTATATAAAAAAGTTTTTGGTGCTGTC 9 204 1 TAAAAAATTT 0.961932 -23 ******* *** Masking position 6 Map Score: 21.5852 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 437 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 3 GAGGGTATCCTATTTTTGGTGATAAAAA 1 237 1 TTTTTTGGTG 0.989681 -18 AATTTTAAAATCATTTTGGTGATTAA 2 6 0 TATTTTGGTG 0.904208 -189 TATAAGTATTTATATTTTGTGTTGTTTTTTG 2 68 1 TTATTTTGTG 0.962672 -127 TATTTTGTGTTGTTTTTTGTTGAGTATTTTA 2 80 1 TTTTTTTGTT 0.797765 -115 CATAAAAATGTTTTGTTGGTGACTTAAACCA 2 124 0 TTTGTTGGTG 0.94274 -71 CCAACAAAACATTTTTATGTGAAAGTATTTT 2 136 1 ATTTTATGTG 0.671719 -59 CTATAATTAATCTTTTTGGTGATAAGT 2 178 1 TTTTTTGGTG 0.989681 -17 TTTTTTGATATTTTTTAGGTGATATAATGGG 4 39 1 TTTTTAGGTG 0.968544 -30 TTTTAGGTGATATAATGGGTGATAATAC 4 51 1 TTAATGGGTG 0.736915 -18 TTCCAACAGTTATATTTGGTTTGTATCAACT 7 20 1 TTATTTGGTT 0.894271 -60 TTAATGTTTATATATTATGTGTGCTTATAAT 8 202 0 TTATTATGTG 0.892238 -99 GTAACTAATTTATAATTTGTGCCTCTTTCAT 8 255 0 TTAATTTGTG 0.840444 -46 CAACATTCTTTTTATTTGGTGGAATC 8 285 1 TTATTTGGTG 0.986454 -16 TATATAAAAAAGTTTTTGGTGCTGTCT 9 210 1 ATTTTTGGTG 0.94736 -17 * ********* Masking position 6 Map Score: 21.1501 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 272 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 CCAGTGCCTTATTAAAAATATTACTATTTTCTT 1 112 1 ATAAAAAATA 0.477676 -143 AATAGCTTTGATGAAAAAAATAATCCTAAATGA 1 177 0 ATAAAAAAAA 0.898296 -78 GGATACCCTCATCAGATATTTAAAACTTATAAA 1 214 0 ATAGATATAA 0.553572 -41 TGATTTTAAAATTAAAAATAAAACTTTTAAGGG 2 24 1 ATAAAAAAAA 0.898296 -171 TCAAAAATGATTAAAATACTCAACAAAAAACAA 2 89 0 TTAAATATAA 0.887156 -106 TATGGTTTAAGTCACCAACAAAACATTTTTATG 2 122 1 GTACCAAAAA 0.597026 -73 AAAATGAAATATAACATAATCAATA 3 3 0 ATACATATAA 0.882249 -298 ATAATTTTATATCAAAAAATGAAATATAACATA 3 18 0 ATAAAAATAA 0.92458 -283 ATATAAAATTATAAAATAGTTAAAAATAATTTA 3 39 1 ATAAATATAA 0.912395 -262 AATTATAACTTTAAAAAAGTAAATTATTTTTAA 3 58 0 TTAAAAATAA 0.901543 -243 TTGTTTTATTATTAAAAATTCTAATAAGTTAAA 3 89 1 ATAAAAATTA 0.559341 -212 GTTAAAAATTTTAACATATATAATTTACTATTT 3 116 1 TTACATAAAA 0.803231 -185 ATGATTTAAAGTTAAATAGTAAATTATATATGT 3 129 0 GTAAATATAA 0.814951 -172 GGGGCACCATACAAAAAATTAAAGAATAGTTGG 3 216 1 ACAAAAATAA 0.804932 -85 ATTATTAAAATTAAAAAAGAAAAACATTT 4 7 0 TTAAAAAAAA 0.869777 -62 CACCCATTATATCACCTAAAAAATATCAAAAAA 4 39 0 ATACCTAAAA 0.748589 -30 AATAATGATGATAAAATAAATAATAACTTTAAC 5 26 1 ATAAATAAAA 0.882426 -35 TATTTGTTACTTCAACTATTTAAATC 6 4 0 TTAACTATAA 0.81131 -45 AATAGTTGAAGTAACAAATACAATCATTGAAAA 6 17 1 GTACAAAAAA 0.728703 -32 CTGATTTTAATCTAAATAATCAAATTAACAAAC 8 36 1 TCAAATATAA 0.726167 -265 TAAAAATCCTTTGAACTAATTAATAAATTCTAA 8 83 1 TTAACTATAA 0.812899 -218 TTCAAACATATTCAACAAGACAATCCATCAACC 8 134 1 TTAACAAAAA 0.78652 -167 CATCAACCAAACAACAAAATTAAAAATCCTAAA 8 159 1 ACACAAATAA 0.747981 -142 GATTCCACCAAATAAAAAGAATGTTG 8 285 0 TCACCAATAA 0.553195 -16 ** ***** * ** Masking position 8 Map Score: 22.9352 Number of sites scoring better than the average of aligned sites = 2018 Number in coding regions = 1398 Number in noncoding regions = 620 Number of orfs with sites within 600 bp upstream = 407 Fraction of orfs with sites within 600 bp upstream = 0.065371 Motif number 5 AACCTTTTAGTAAAAGGTTCATCAAAACGG 1 43 0 TAAAAGGTTC 0.813991 -212 AACCTTTTACTAAAAGGTTCATGTGAAGGA 1 54 1 TAAAAGGTTC 0.813991 -201 TATTTTGATTTATAAGTTTTAAATATCTGA 1 206 1 TATAAGTTTT 0.614728 -49 TTACTTCCCTTAAAAGTTTTATTTTTAATT 2 33 0 TAAAAGTTTT 0.943873 -162 ATTTACTTTTTTAAAGTTATAATTGTTTTA 3 67 1 TTAAAGTTAT 0.882301 -234 ATTATATATGTTAAAATTTTTAACTTATTA 3 110 0 TTAAAATTTT 0.5281 -191 ATATTATGATTTAAAGTTAAATAGTAAATT 3 137 0 TTAAAGTTAA 0.809071 -164 TTCACAATTGTTAAAGTTATTATTTATTTT 5 38 0 TTAAAGTTAT 0.882301 -23 ATACAGTGTATTAAAGTTACTATAAAATGA 7 51 1 TTAAAGTTAC 0.875784 -29 ATAAAAGTTTCCATTCCGAAT 8 2 1 TAAAAGTTTC 0.94176 -299 TAACAAACATTTAATGTTTATATATTATGT 8 213 0 TTAATGTTTA 0.664653 -88 TCTTTCATTTTAAATGTTTTTAACAAACAT 8 233 0 TAAATGTTTT 0.759555 -68 ATCCCTCTTATTAACGTTTAATAGAAATAG 9 15 1 TTAACGTTTA 0.492461 -212 TCAAAATTAATTAAAGTTTATTAATAAATA 9 99 1 TTAAAGTTTA 0.913667 -128 ACACTATATAAAAAAGTTTTTGGTGCTGTC 9 206 1 AAAAAGTTTT 0.612699 -21 ********** Masking position 4 Map Score: 14.5983 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 405 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 6 CGCTACGCTCGGCAGTGCCTC 1 2 0 GGCAGTGCCT 0.996902 -253 AGCGTAGCGAGGCAGTGCATCCGTTTTGAT 1 23 1 GGCAGTGCAT 0.987804 -232 AATTAGGATTACCAGTGCCTTATTAAAAAT 1 101 1 ACCAGTGCCT 0.987804 -154 ATGGAGCTGAGCCAGTGCCTACACAACCAC 3 265 1 GCCAGTGCCT 0.996902 -36 ********** Masking position 6 Map Score: 5.67642 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 1 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TATGCTCTATTTCCTTCACATGAACCTTTT 1 65 0 TTCCTTCACA 0.763248 -190 GGATTATTTTTTTCATCAAAGCTATTTTGA 1 184 1 TTTCATCAAA 0.828064 -71 TTTTTATCACCAAAAATAGGA 1 244 0 TTTTATCACC 0.9277 -11 TTAATAAAAATACTTTCACATAAAAATGTT 2 143 0 TACTTTCACA 0.582159 -52 TTTTATAATTTTATATCAAAAAATGAAATA 3 25 0 TTATATCAAA 0.828959 -276 TTATCACCCATTATATCACCTAAAAAATAT 4 46 0 TTATATCACC 0.912398 -23 GTATTATCACCCATTATATCA 4 58 0 TATTATCACC 0.820211 -11 TTATTATTTATTTTATCATCATTATTGTAT 5 22 0 TTTTATCATC 0.664982 -39 ATTGTATTTGTTACTTCAACTATTTAAATC 6 11 0 TTACTTCAAC 0.822629 -38 TATATTTGGTTTGTATCAACTATACAGTGT 7 30 1 TTGTATCAAC 0.77759 -50 TAAATGCTCTTATTTTCAAATTTCAAACAT 8 113 1 TATTTTCAAA 0.606731 -188 AAGCTACTGGTTACTTCAAAATGTTTTTGA 9 173 1 TTACTTCAAA 0.743436 -54 ********** Masking position 8 Map Score: 3.32162 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 702 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 TTCTTTCCTATGCTCTATTTCCTTCACATG 1 73 0 TGCTCTATTT 0.909862 -182 ACTATTTTCTTGTTCTTTTTTTATTTATAC 1 134 1 TGTTCTTTTT 0.916457 -121 GATGAGGGTATCCTATTTTTGGTGATAAAA 1 234 1 TCCTATTTTT 0.453497 -21 CCCTTAAAAGTTTTATTTTTAATTTTAAAA 2 27 0 TTTTATTTTT 0.632679 -168 TTATATTTTGTGTTGTTTTTTGTTGAGTAT 2 77 1 TGTTGTTTTT 0.678345 -118 TTATTAATATTGCTATAATTAATCTTTTTG 2 166 1 TGCTATAATT 0.901939 -29 TATTGATTATGTTATATTTCATTTTTTGA 3 10 1 TGTTATATTT 0.926176 -291 TTTTTAACTATTTTATAATTTTATATCAAA 3 35 0 TTTTATAATT 0.632672 -266 ACTTTTTTAAAGTTATAATTGTTTTATTAT 3 71 1 AGTTATAATT 0.720991 -230 AAATTATATATGTTAAAATTTTTAACTTAT 3 112 0 TGTTAAAATT 0.473534 -189 AAATGTTTTTCTTTTTTAATTTTAAT 4 7 1 TTTTCTTTTT 0.627872 -62 AATAATTTTTTGATATTTTTTAGGTGATAT 4 34 1 TGATATTTTT 0.715026 -35 CAATTGTTAAAGTTATTATTTATTTTATCA 5 34 0 AGTTATTATT 0.698005 -27 CTGCACTAATTCCAACAGTTA 7 2 1 TGCACTAATT 0.576169 -78 TAATTCCAACAGTTATATTTGGTTTGTATC 7 17 1 AGTTATATTT 0.743611 -63 AAAAATCCTTTGAACTAATTAATAAATTCT 8 84 1 TGAACTAATT 0.270524 -217 AAATTCTAAATGCTCTTATTTTCAAATTTC 8 107 1 TGCTCTTATT 0.889407 -194 ********** Masking position 9 Map Score: 6.84439 Number of sites scoring better than the average of aligned sites = 1306 Number in coding regions = 1137 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 9 ATTTTTAACTATTTTATAATTTTATATCAA 3 36 0 ATTTTATAAT 0.731672 -265 TATCATCATTATTGTATAGTATAGTGTT 5 9 0 ATTGTATAGT 0.948928 -52 ACTTTAATACACTGTATAGTTGATACAAAC 7 38 0 ACTGTATAGT 0.87324 -42 TTTTTCCCTCATTTTATAGTAACTTTAATA 7 59 0 ATTTTATAGT 0.916972 -21 AATTTTGAAGACAGTATAGTTTAAAGATAT 9 77 0 ACAGTATAGT 0.912831 -150 ********** Masking position 5 Map Score: 1.02555 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 23 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: -2.46258e-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 11 ********** No masking Map Score: -2.46258e-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 12 ********** No masking Map Score: -2.46258e-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