AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -inagC_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 MJ1100 205 phosphomannomutase (pmmB) #7 MJ1101 27 glucose-1-phosphate thymidylyltransferase (strD) #8 MJ1420 100 glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (glmS) Motif number 1 TTTAACTATTTTATAATTTTATATCAAAAAAT 1 31 0 TTTAATTTAT 0.783574 -270 TAAAAAAGTAAATTATTTTTAACTATTTTATA 1 48 0 AATATTTTAA 0.941582 -253 AATAAAACAATTATAACTTTAAAAAAGTAAAT 1 67 0 TTTAATTTAA 0.974128 -234 TTTAACTTATTAGAATTTTTAATAATAAAACA 1 90 0 TAAATTTTAA 0.935454 -211 TCTAATAAGTTAAAAATTTTAACATATATAAT 1 108 1 TAAAATTTAA 0.778862 -193 ATAATTTACTATTTAACTTTAAATCATAATAT 1 135 1 ATTAATTTAA 0.941577 -166 TGTTTTTCTTTTTTAATTTTAATAATTTTTTG 2 14 1 TTTAATTTAA 0.977179 -55 ATAAAATAAATAATAACTTTAACAATTGTGAA 3 36 1 TATAATTTAA 0.991286 -25 CCTCATTTTATAGTAACTTTAATACACTGTAT 5 51 0 TATAATTTAA 0.991479 -29 ACTTAATGTTTTAAAATTTTAATGTCTTTCAA 6 65 1 TTAAATTTAA 0.498294 -141 AAGTGTTCCTTATTAATTTTAATACTTTTGAA 6 92 0 TATAATTTAA 0.99135 -114 ATGTTTTGATTATTATCTTTAATGATTATAGC 6 172 1 TATATTTTAA 0.983591 -34 AACTATTTTTAAATTTTGGTGA 7 1 1 AATATTTTAA 0.941582 -27 TATATAATATATTTAAAAGAGAATTA 8 5 1 TATATTTTAA 0.980269 -96 ATAATATTAATACTAATTTTAAATAATTCTCT 8 28 0 TATAATTTAA 0.99135 -73 ** *** ***** Masking position 5 Map Score: 36.6485 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 213 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 2 AGTAAATTATTTTTAACTATTTTATAATTTT 1 43 0 TTTTAACATT 0.975266 -258 TAATTTACTTTTTTAAAGTTATAATTGTTTT 1 65 1 TTTTAAATTA 0.715231 -236 TTATTAGAATTTTTAATAATAAAACAATTAT 1 85 0 TTTTAATATA 0.936833 -216 ATGTTAAAATTTTTAACTTATTAGAATTTTT 1 102 0 TTTTAACTAT 0.698797 -199 AAGTTAAAAATTTTAACATATATAATTTACT 1 114 1 TTTTAACTAT 0.698797 -187 ACTATTTAACTTTAAATCATAATATATATAG 1 142 1 TTTAAATATA 0.724759 -159 GCCAACTATTCTTTAATTTTTTGTATGGTGC 1 219 0 CTTTAATTTT 0.930062 -82 TCTTTTTTAATTTTAATAATTTTTTGATATT 2 20 1 TTTTAATATT 0.982381 -49 TTTAATAATTTTTTGATATTTTTTAGGTGAT 2 31 1 TTTTGATTTT 0.82926 -38 TAAATAATAACTTTAACAATTGTGAAACC 3 42 1 CTTTAACATT 0.945329 -19 GTATTTGTTACTTCAACTATTTAAATC 4 7 0 CTTCAACATT 0.761884 -42 CTATTAGATTTTTCAATGATTGTATTTGTTA 4 28 0 TTTCAATATT 0.911797 -21 TATATATTGTCATTAATCATTTTTGAAATCA 6 29 0 CATTAATATT 0.717257 -177 ACATTAAAATTTTAAAACATTAAGTTTTTAT 6 59 0 TTTAAAAATT 0.742563 -147 TGTTTTAAAATTTTAATGTCTTTCAAAAGTA 6 71 1 TTTTAATTCT 0.734252 -135 TCCTTATTAATTTTAATACTTTTGAAAGACA 6 87 0 TTTTAATCTT 0.876316 -119 TCAAAACATTTTGTAATAATTGAGGTATTAA 6 150 0 TTGTAATATT 0.823119 -56 TTACAAAATGTTTTGATTATTATCTTTAATG 6 165 1 TTTTGATATT 0.899474 -41 TGATTATTATCTTTAATGATTATAGCAAAGG 6 178 1 CTTTAATATT 0.960784 -28 AACTATTTTTAAATTTTGGTGATATAA 7 7 1 TTTTAAATTT 0.901318 -21 AATAATTCTCTTTTAAATATATTATATA 8 8 0 TTTTAAAATA 0.822291 -93 TAATACTAATTTTAAATAATTCTCTTTTAAA 8 22 0 TTTAAATATT 0.905422 -79 TTAAAATTAGTATTAATATTATTGTTTATGG 8 38 1 TATTAATTTA 0.463231 -63 TGTTTATGGGTTTTAACTATTTATTACTTTA 8 60 1 TTTTAACATT 0.975266 -41 ******* *** Masking position 6 Map Score: 31.3507 Number of sites scoring better than the average of aligned sites = 2425 Number in coding regions = 1858 Number in noncoding regions = 567 Number of orfs with sites within 600 bp upstream = 412 Fraction of orfs with sites within 600 bp upstream = 0.0661741 Motif number 3 AAATGAAATATAACATAATCAATA 1 1 0 TAATAAAATA 0.944676 -300 AATTTTATATCAAAAAATGAAATATAACATAATC 1 15 0 CAAAATAATA 0.731657 -286 GAATTTTTAATAATAAAACAATTATAACTTTAAA 1 76 0 TAAAAAATTA 0.90446 -225 GTTTTATTATTAAAAATTCTAATAAGTTAAAAAT 1 91 1 TAAATTAATA 0.646653 -210 TCCACATTTTTCACAAATGTAATAATACAAAACC 1 174 0 TAAAATAATA 0.958148 -127 TTGTGAAAAATGTGGAAAATAATAGGGGCACCAT 1 192 1 TTGAAAAATA 0.914453 -109 ATTATTAAAATTAAAAAAGAAAAACATTT 2 6 0 TAAAAAAAAA 0.7673 -63 CTAAAAAATATCAAAAAATTATTAAAATTAAAAA 2 23 0 TAAAAAATTA 0.904594 -46 ACCCATTATATCACCTAAAAAATATCAAAAAATT 2 37 0 TACTAAAATA 0.848363 -32 AACACTATACTATACAATAATGATGATAA 3 6 1 TTCTATAATA 0.55032 -55 ACAATAATGATGATAAAATAAATAATAACTTTAA 3 24 1 TAAAAAAATA 0.976127 -37 TTTAAATAGTTGAAGTAACAAATACAATCATTGA 4 13 1 TAGTAAAATA 0.914559 -36 ATACAATCATTGAAAAATCTAATAG 4 34 1 TAAAATAATA 0.958148 -15 CATTAATCATTTTTGAAATCAATATCATGGGTGT 6 16 0 TTGAAAAATA 0.881955 -190 CTTTCAAAAGTATTAAAATTAATAAGGAACACTT 6 90 1 TTAAAAAATA 0.661155 -116 AATAATTCTCTTTTAAATATATTATATA 8 5 0 TTAAATATTA 0.507495 -96 AAATATCTCCTAAAGTAATAAATAGTTAAAACCC 8 67 0 TAGTAAAATA 0.914477 -34 * * **** **** Masking position 11 Map Score: 21.2251 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 848 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 4 TTTTATAATTTTATATCAAAAAATGAAATA 1 25 0 TTATATCAAA 0.934771 -276 TTATCACCCATTATATCACCTAAAAAATAT 2 46 0 TTATATCACC 0.987001 -23 GTATTATCACCCATTATATCA 2 58 0 TATTATCACC 0.855477 -11 TTATTATTTATTTTATCATCATTATTGTAT 3 22 0 TTTTATCATC 0.892595 -39 TATATTTGGTTTGTATCAACTATACAGTGT 5 30 1 TTGTATCAAC 0.958309 -50 TTCCCTCATTTTATAGTAACTTTAATACAC 5 56 0 TTATAGTAAC 0.799034 -24 TCTTTAATGATTATAGCAAAGGTGATTAA 6 187 1 TTATAGCAAA 0.890628 -19 TTATATCACCAAAATTTAAA 7 18 0 TTATATCACC 0.987001 -10 ********** Masking position 5 Map Score: 6.91376 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 280 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TGTATTATTACATTTGTGAAAAATGTGGAAA 1 179 1 CATTGTGAAA 0.988249 -122 ATAACTTTAACAATTGTGAAACC 3 48 1 CATTGTGAAA 0.988249 -13 TGTCATTAATCATTTTTGAAATCAATATCAT 6 22 0 CATTTTGAAA 0.987327 -184 TTAATTTTAATACTTTTGAAAGACATTAAAA 6 81 0 TATTTTGAAA 0.93722 -125 AACTATTTTTAAATTTTGGTGAT 7 3 1 CTTTTTTAAA 0.819412 -25 ** ******** Masking position 5 Map Score: 3.15472 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 14 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TATTGATTATGTTATATTTCATTTTT 1 6 1 ATTTGTTATA 0.878338 -295 GTTAAAAATAATTTACTTTTTTAAAGTTATA 1 57 1 ATTACTTTTT 0.809988 -244 TAAAGTTATAATTGTTTTATTATTAAAAATT 1 78 1 ATTTTTTATT 0.726217 -223 AACATATATAATTTACTATTTAACTTTAAAT 1 128 1 ATTACTATTT 0.555128 -173 CTCTATATATATTATGATTTAAAGTTAAATA 1 144 0 ATTTGATTTA 0.666163 -157 CATAATATATATAGAGGTTTTGTATTATTAC 1 159 1 ATAAGGTTTT 0.490832 -142 TTTTATCATCATTATTGTATAGTATAGTGTT 3 11 0 ATTTTGTATA 0.729944 -50 TGTTAAAGTTATTATTTATTTTATCATCATT 3 29 0 ATTTTTATTT 0.576463 -32 ATTTTAAAACATTAAGTTTTTATATATATTG 6 51 0 ATTAGTTTTT 0.905663 -155 TTTTGTAATAATTGAGGTATTAATGAACGCC 6 142 0 ATTAGGTATT 0.848168 -64 TAATCAAAACATTTTGTAATAATTGAGGTAT 6 153 0 ATTTGTAATA 0.678759 -53 ATTTTAAATAATTCTCTTTTAAATATATTAT 8 14 0 ATTTCTTTTA 0.848854 -87 TAGTATTAATATTATTGTTTATGGGTTTTAA 8 45 1 ATTTTGTTTA 0.825755 -56 TTTAGGAGATATTTAGGTTTATCG 8 87 1 ATTAGGTTTA 0.907359 -14 *** ******* Masking position 1 Map Score: 6.96342 Number of sites scoring better than the average of aligned sites = 1360 Number in coding regions = 1088 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 7 AATAGTTGGCGATGACGCTCCCTATATGGA 1 240 1 GATGACGCTC 0.986737 -61 CCTTCTATAAGAAGACGTTCAAGTGTTCCT 6 114 0 GAAGACGTTC 0.966777 -92 TCTTCTTATAGAAGGCGTTCATTAATACCT 6 129 1 GAAGGCGTTC 0.748927 -77 ********** Masking position 2 Map Score: 0.935227 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 4 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ********** No masking Map Score: 1.48747e-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: 1.48747e-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: 1.48747e-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