AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -inagC_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 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 TAAAATTATAAAATAGTTAAAAATAATTTACT 1 42 1 AAAAGTAAAA 0.963543 -259 AAAACAATTATAACTTTAAAAAAGTAAATTAT 1 64 0 TAATTTAAAA 0.920657 -237 ATAATTGTTTTATTATTAAAAATTCTAATAAG 1 85 1 TATATTAAAA 0.957114 -216 TAAAAATTCTAATAAGTTAAAAATTTTAACAT 1 101 1 AATAGTAAAA 0.973463 -200 TAGTAAATTATATATGTTAAAATTTTTAACTT 1 114 0 TATTGTAAAA 0.93883 -187 CTATATATATTATGATTTAAAGTTAAATAGTA 1 141 0 TATATTAAAG 0.882685 -160 TCACAAATGTAATAATACAAAACCTCTATATA 1 166 0 AATATAAAAA 0.693278 -135 TGTATTATTACATTTGTGAAAAATGTGGAAAA 1 179 1 CATTGTAAAA 0.86841 -122 GGCACCATACAAAAAATTAAAGAATAGTTGGC 1 218 1 AAAAATAAAG 0.801066 -83 AAAAAATTATTAAAATTAAAAAAGAAAAACAT 2 13 0 TAAATTAAAA 0.941539 -56 TATCACCTAAAAAATATCAAAAAATTATTAAA 2 31 0 AAATATAAAA 0.896041 -38 GGTTTCACAATTGTTAAAGTTATTATTTA 3 42 0 CAATGTAAAG 0.615446 -19 TAACAAATACAATCATTGAAAAATCTAATAG 4 28 1 AATATTAAAA 0.97468 -21 GTTACTATAAAATGAGGGAAAAAG 5 66 1 AATAGGAAAA 0.761476 -14 TTAATGACAATATATATAAAAACTTAATGTTT 6 44 1 TATTATAAAA 0.874155 -162 ATAAAAACTTAATGTTTTAAAATTTTAATGTC 6 59 1 AATTTTAAAA 0.965198 -147 ATGTCTTTCAAAAGTATTAAAATTAATAAGGA 6 86 1 AAATATAAAA 0.896041 -120 TTAATACCTCAATTATTACAAAATGTTTTGAT 6 150 1 AATATTCAAA 0.76226 -56 TCATTAAAGATAATAATCAAAACATTTTGTAA 6 165 0 TAAAATAAAA 0.874169 -41 CCTTTGCTATAATCATTAAAGATAATAATCAA 6 177 0 AATATTAAGA 0.762261 -29 TTATATCACCAAAATTTAAAAATAGTT 7 6 0 AAATTTAAAA 0.952339 -22 TATATAATATATTTAAAAGAGAATTATTT 8 8 1 TATTTTAAAG 0.844262 -93 TTTAAAAGAGAATTATTTAAAATTAGTATTAA 8 22 1 AATATTAAAA 0.974678 -79 CTAAAGTAATAAATAGTTAAAACCCATAAACA 8 60 0 AAAAGTAAAA 0.963543 -41 *** *** **** Masking position 10 Map Score: 35.0693 Number of sites scoring better than the average of aligned sites = 2541 Number in coding regions = 1853 Number in noncoding regions = 688 Number of orfs with sites within 600 bp upstream = 452 Fraction of orfs with sites within 600 bp upstream = 0.0725988 Motif number 2 TTTTGATATAAAATTATAAAATAGTTAAAAATAATT 1 34 1 AATTAAAATT 0.861095 -267 TTAGAATTTTTAATAATAAAACAATTATAACTTTAA 1 77 0 TATTAAAATT 0.95843 -224 AATAAGTTAAAAATTTTAACATATATAATTTACTAT 1 111 1 AATTAAAAAT 0.901365 -190 ATTTAACTTTAAATCATAATATATATAGAGGTTTTG 1 145 1 AATTAAAAAT 0.901439 -156 TTTTCTTTTTTAATTTTAATAATTTTTTGATATTTT 2 17 1 TATTAAATTT 0.95843 -52 TATACAATAATGATGATAAAATAAATAATAACTTTA 3 21 1 TATTAAAAAT 0.971443 -40 CTGCACTAATTCCAACAGTTATATTTGGTTTG 5 7 1 TATCAAATAT 0.973616 -73 TTCCCTCATTTTATAGTAACTTTAATACACTGTATA 5 50 0 TATTAATTAT 0.770013 -30 CCCATGATATTGATTTCAAAAATGATTAATGACAAT 6 19 1 TATCAAATAT 0.973616 -187 CAAAAATGATTAATGACAATATATATAAAAACTTAA 6 35 1 TATCAAAAAT 0.973616 -171 TGTTCCTTATTAATTTTAATACTTTTGAAAGACATT 6 85 0 TATTAAATTT 0.95843 -121 AATACCTCAATTATTACAAAATGTTTTGATTATTAT 6 152 1 TATCAAAGTT 0.869162 -54 TCTTTAATGATTATAGCAAAGGTGATTAA 6 187 1 TATCAAGTAT 0.843335 -19 TTATATCACCAAAATTTAAAAATAGT 7 12 0 TATCACAATT 0.77239 -16 CCATAAACAATAATATTAATACTAATTTTAAATAAT 8 33 0 TATTAAATAT 0.971443 -68 * ** *** * * ** Masking position 8 Map Score: 20.4658 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 379 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 TATTGATTATGTTATATTTCATTTTT 1 7 1 TTATGTTATA 0.814911 -294 ATGTTATATTTCATTTTTTGATATAAAATT 1 19 1 TCATTTTTTG 0.81312 -282 AACTATTTTATAATTTTATATCAAAAAATG 1 30 0 TAATTTTATA 0.899855 -271 AAAAAGTAAATTATTTTTAACTATTTTATA 1 48 0 TTATTTTTAA 0.806687 -253 AAAAATAATTTACTTTTTTAAAGTTATAAT 1 60 1 TACTTTTTTA 0.764976 -241 TATAATTGTTTTATTATTAAAAATTCTAAT 1 84 1 TTATTATTAA 0.607413 -217 GTTAAATAGTAAATTATATATGTTAAAATT 1 122 0 AAATTATATA 0.45361 -179 TCTATATATATTATGATTTAAAGTTAAATA 1 144 0 TTATGATTTA 0.761791 -157 AACTATTCTTTAATTTTTTGTATGGTGCCC 1 217 0 TAATTTTTTG 0.874165 -84 AAATGTTTTTCTTTTTTAATTTTAATAA 2 9 1 TTCTTTTTTA 0.801519 -60 TTAATTTTAATAATTTTTTGATATTTTTTA 2 26 1 TAATTTTTTG 0.874165 -43 TAATTTTTTGATATTTTTTAGGTGATATAA 2 36 1 ATATTTTTTA 0.844571 -33 TTTATCATCATTATTGTATAGTATAGTGTT 3 11 0 TTATTGTATA 0.735705 -50 ATTGTTAAAGTTATTATTTATTTTATCATC 3 32 0 TTATTATTTA 0.889851 -29 CTTTTTCCCTCATTTTATAGTAACTTTAA 5 61 0 TCATTTTATA 0.849122 -19 TTGTCATTAATCATTTTTGAAATCAATATC 6 24 0 TCATTTTTGA 0.552718 -182 TATAAAAACTTAATGTTTTAAAATTTTAAT 6 58 1 TAATGTTTTA 0.874164 -148 AATTATTACAAAATGTTTTGATTATTATCT 6 160 1 AAATGTTTTG 0.405866 -46 TCTTTTAAATATATTATATA 8 1 0 ATATTATATA 0.50739 -100 ATATTAATACTAATTTTAAATAATTCTCTT 8 27 0 TAATTTTAAA 0.632111 -74 AGTATTAATATTATTGTTTATGGGTTTTAA 8 46 1 TTATTGTTTA 0.84494 -55 ********** Masking position 4 Map Score: 20.7594 Number of sites scoring better than the average of aligned sites = 2938 Number in coding regions = 2124 Number in noncoding regions = 814 Number of orfs with sites within 600 bp upstream = 559 Fraction of orfs with sites within 600 bp upstream = 0.0897848 Motif number 4 ATCAAAAAATGAAATATAACATAATCAATA 1 11 0 GAAATATAAC 0.937345 -290 AATAATAAAACAATTATAACTTTAAAAAAG 1 72 0 CAATTATAAC 0.975293 -229 TAGAGGTTTTGTATTATTACATTTGTGAAA 1 170 1 GTATTATTAC 0.734637 -131 GTATTATCACCCATTATATC 2 59 0 GTATTATCAC 0.90849 -10 TGATACAAACCAAATATAACTGTTGGAATT 5 18 0 CAAATATAAC 0.954358 -62 ATTAATACCTCAATTATTACAAAATGTTTT 6 149 1 CAATTATTAC 0.964446 -57 ********** Masking position 5 Map Score: 4.81005 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 51 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ATAAAATTATAAAATAGTTAAAAATAATTT 1 41 1 AAAATAGTTA 0.88497 -260 GATTTAAAGTTAAATAGTAAATTATATATG 1 130 0 TAAATAGTAA 0.943402 -171 AAAAATGTGGAAAATAATAGGGGCACCATA 1 197 1 AAAATAATAG 0.637379 -104 AAAAAATTAAAGAATAGTTGGCGATGACGC 1 228 1 AGAATAGTTG 0.893467 -73 TCATCATTATTGTATAGTATAGTGTT 3 7 0 TGTATAGTAT 0.616448 -54 GATGATAAAATAAATAATAACTTTAACAAT 3 32 1 TAAATAATAA 0.74907 -29 GATTTAAATAGTTGAAGTAACAAA 4 5 1 TAAATAGTTG 0.956875 -44 TTTAATACACTGTATAGTTGATACAAACCA 5 36 0 TGTATAGTTG 0.893473 -44 TTTCCCTCATTTTATAGTAACTTTAATACA 5 57 0 TTTATAGTAA 0.621125 -23 CCTAAAGTAATAAATAGTTAAAACCCATAA 8 63 0 TAAATAGTTA 0.934552 -38 ********** Masking position 5 Map Score: 6.08344 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 332 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 6 AATAGTTGGCGATGACGCTCCCTATATGGA 1 240 1 GATGACGCTC 0.98616 -61 CCTTCTATAAGAAGACGTTCAAGTGTTCCT 6 114 0 GAAGACGTTC 0.967665 -92 TCTTCTTATAGAAGGCGTTCATTAATACCT 6 129 1 GAAGGCGTTC 0.754448 -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 7 ********** 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 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