AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -igalR_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 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #3 MJ1054 300 UDP-glucose dehydrogenase, putative #4 MJ1081 130 conserved hypothetical protein #5 MJ1083 69 iron-sulfur flavoprotein (isf) #6 MJ1084 88 shikimate 5-dehydrogenase (aroE) #7 MJ1085 25 M. jannaschii predicted coding region MJ1085 #8 MJ1662 94 methyl coenzyme M reductase system, component A2-like #9 MJ1672 34 conserved hypothetical protein #10 MJ1674 113 M. jannaschii predicted coding region MJ1674 Motif number 1 AAAAATTTGGTGATAAATTTATAGGTTTA 1 10 0 TGATAAATTT 0.94498 -77 AATTATCATATAAAAAATTTGGTGATAAAT 1 22 0 TAAAAAATTT 0.928296 -65 ATTTTTTATATGATAATTTTAAAATTTTGC 1 34 1 TGATAATTTT 0.94498 -53 TCACCTTAAATGATAAATTTCTTTTTAATG 1 63 0 TGATAAATTT 0.94498 -24 TAATATAAAATAAAAATTATTTTG 2 5 0 TAAAAATTAT 0.837943 -39 ATTAAAAAATTATGGGAAATAA 2 32 0 TAAAAAATTA 0.925666 -12 AATCTTGTGATAATAAATTC 3 1 0 TAATAAATTC 0.75206 -300 ATAGCATTACTTATAATTTTCGTTATCAAT 3 147 0 TTATAATTTT 0.914747 -154 AAGAGAAATATAATAATATTATACAATTAT 3 256 1 TAATAATATT 0.795507 -45 ATACAATTATTAATAAATAAACTCAGGGGA 3 276 1 TAATAAATAA 0.883359 -25 AGTTATAATTTAATAATTTAGAAC 4 5 0 TAATAATTTA 0.948739 -126 ACTTGAATAGTTATAATTTATAGTTATAAT 4 26 0 TTATAATTTA 0.914047 -105 AGTTTAATATTTAAAATTTAATTAAGGTCT 4 53 1 TTAAAATTTA 0.87776 -78 CAAAAACATATCAAAAATTTAATTGGGTAT 4 96 1 TCAAAAATTT 0.803616 -35 AACCTATTTCTGATAAAATACATTAGGTCA 5 24 1 TGATAAAATA 0.776474 -46 AAAGAGAAGGTAAAAAATAAATATCAAATA 6 24 0 TAAAAAATAA 0.83661 -65 AAATTAGTTTTTATAATTAAAAATTGTAAA 6 58 0 TTATAATTAA 0.810405 -31 AAATATTTAATAAATTTAATAGAGG 7 8 1 TAATAAATTT 0.950545 -18 TTAAATATGTTAATAACTTATAAACTTAGC 8 30 0 TAATAACTTA 0.752043 -65 TTAACATATTTAATAATTATTACTGCAAAT 8 47 1 TAATAATTAT 0.884767 -48 ATAACTGTGATGATAATATTTGCAGTAATA 8 64 0 TGATAATATT 0.776475 -31 AATTACCACCTTAAAATTAATTCATATTTG 10 12 1 TTAAAATTAA 0.742281 -102 TTTGTAAATTTGAAAATATACAAATATGAA 10 32 0 TGAAAATATA 0.700535 -82 TTGTGGAACCTTAAAAATAATAAAAAAGTC 10 80 0 TTAAAAATAA 0.742125 -34 TTCACCTCAAAAATTTGTGGAACCTT 10 98 0 TCAAAAATTT 0.803616 -16 ********** Masking position 1 Map Score: 32.0544 Number of sites scoring better than the average of aligned sites = 2342 Number in coding regions = 1531 Number in noncoding regions = 811 Number of orfs with sites within 600 bp upstream = 514 Fraction of orfs with sites within 600 bp upstream = 0.082557 Motif number 2 AAAATTTGGTGATAAATTTATAGGTTTA 1 9 0 GATAAATTTA 0.856881 -78 TTTTTTATATGATAATTTTAAAATTTTGCA 1 35 1 GATAATTTTA 0.91111 -52 CACCTTAAATGATAAATTTCTTTTTAATGC 1 62 0 GATAAATTTC 0.848079 -25 CAAAATAATTTTTATTTTATATT 2 4 1 AATAATTTTT 0.893814 -40 TATTATTTCCCATAATTTTTTAAT 2 30 1 CATAATTTTT 0.811453 -14 AGAGGTTTTAAATAGATTTCCAAGTAATAG 3 33 1 AATAGATTTC 0.892203 -268 TAGCATTACTTATAATTTTCGTTATCAATA 3 146 0 TATAATTTTC 0.642947 -155 AGAGAAATATAATAATATTATACAATTATT 3 257 1 AATAATATTA 0.744992 -44 TTTATTTATTAATAATTGTATAATATTATT 3 267 0 AATAATTGTA 0.726761 -34 ATTAAACTTGAATAGTTATAATTTATAGTT 4 31 0 AATAGTTATA 0.745398 -100 TAAGACCTTAATTAAATTTTAAATATTAAA 4 55 0 ATTAAATTTT 0.824915 -76 GCAATACCCAATTAAATTTTTGATATGTTT 4 99 0 ATTAAATTTT 0.824915 -32 AATAGGTTTTAATAGTTTTTC 5 2 0 AATAGTTTTT 0.955734 -68 TTTTATCAGAAATAGGTTTTAATAGTTTTT 5 12 0 AATAGGTTTT 0.768269 -58 GAAGGTAAAAAATAAATATCAAATAACACA 6 19 0 AATAAATATC 0.669091 -70 ATCACATTAAATTAGTTTTTATAATTAAAA 6 66 0 ATTAGTTTTT 0.849822 -23 AAATATTTAATAAATTTAATAGAGG 7 9 1 AATAAATTTA 0.930491 -17 TAACATATTTAATAATTATTACTGCAAATA 8 48 1 AATAATTATT 0.491319 -47 TAACTGTGATGATAATATTTGCAGTAATAA 8 63 0 GATAATATTT 0.647379 -32 ACAAATATGAATTAATTTTAAGGTGGTAAT 10 13 0 ATTAATTTTA 0.858724 -101 AAGTCATATAAATAGTTTTTTATTTTGTAA 10 55 0 AATAGTTTTT 0.955734 -59 ********** Masking position 3 Map Score: 22.8487 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1197 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 3 TTTTAAAATTATCATATAAAAAATTTGGTGA 1 27 0 ATCATATAAA 0.730019 -60 TTTTAATGCAAAATTTTAAAATTATCATATA 1 40 0 AAATTTTAAA 0.760685 -47 ATTATGGGAAATAATATAAAATAAAAATTAT 2 15 0 ATAATATAAA 0.9552 -29 TAAATATAGCATTACTTATAATTTTCGTTAT 3 151 0 ATTACTTAAA 0.57571 -150 AAATATAATAATATTATACAATTATTAATAA 3 261 1 ATATTATAAA 0.894803 -40 TATACAATTATTAATAAATAAACTCAGGGGA 3 275 1 TTAATAAAAA 0.520616 -26 TTATAATTTAATAATTTAGAAC 4 2 0 ATAATTTAAA 0.963574 -129 TTGAATAGTTATAATTTATAGTTATAATTTA 4 23 0 ATAATTTAAG 0.747929 -108 ATTCAAGTTTAATATTTAAAATTTAATTAAG 4 48 1 AATATTTAAA 0.545896 -83 TAAAAAATAAATATCAAATAACACAAAAGTG 6 13 0 ATATCAAAAA 0.65118 -76 CCTTCTCTTTGTAATTTACAATTTTTAATTA 6 44 1 GTAATTTAAA 0.758982 -45 ATTAGTTTTTATAATTAAAAATTGTAAATTA 6 55 0 ATAATTAAAA 0.944725 -34 AAATATTTAATAAATTTAATAGA 7 3 1 ATATTTAAAA 0.865358 -23 AAATATGTTAATAACTTATAAACTTAGCAAA 8 27 0 ATAACTTAAA 0.89993 -68 AGTTATTAACATATTTAATAATTATTACTGC 8 42 1 ATATTTAAAA 0.865358 -53 TGTAAATTTGAAAATATACAAATATGAATTA 10 29 0 AAAATATAAA 0.865263 -85 TCAAATTTACAAAATAAAAAACTATTTATAT 10 49 1 AAAATAAAAA 0.805849 -65 AACCTTAAAAATAATAAAAAAGTCATATAAA 10 73 0 ATAATAAAAA 0.932322 -41 ******** ** Masking position 8 Map Score: 20.6858 Number of sites scoring better than the average of aligned sites = 1334 Number in coding regions = 982 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 4 AATTTTAAAATTATCATATAAAAAATTTGGTGA 1 27 0 TTATATTAAA 0.871068 -60 CCTATCACCTTAAATGATAAATTT 1 73 0 CTATACTAAA 0.982557 -14 ATCGAATTTACTATTACTTGGAAATCTATTTAA 3 40 0 CTATACTGAA 0.951265 -261 ATCGATAACCCTCAGACATAAAATTACAGCTAA 3 221 0 CTCAACTAAA 0.886052 -80 TATTATATTTCTCTTACATCGATAACCCTCAGA 3 238 0 CTCTACTGAT 0.439355 -63 AATTATTAAATTATAACTATAAATTATAACTAT 4 17 1 TTATACAAAA 0.860415 -114 CTATTCAAGTTTAATATTTAAAATTTAATTAAG 4 46 1 TTAAATTAAA 0.729003 -85 AATTAAGGTCTTATCACATCAAATCAAAAACAT 4 72 1 TTATACTAAA 0.979849 -59 ATTATCACATTAAATTAGTTTTTA 6 75 0 TTATACTAAA 0.979848 -14 CTAAAACCTAAAACTTTTTGCTA 8 1 1 CTAAACTAAA 0.957331 -94 TATTTAATAATTATTACTGCAAATATTATCATC 8 53 1 TTATACGAAA 0.901546 -42 AAATTACCACCTTAAAATTAATTCAT 10 4 1 TTACACTAAA 0.919101 -110 **** ** * *** Masking position 6 Map Score: 13.1834 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 155 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 ATTTGGTGATAAATTTATAGGTTTA 1 5 0 AAATTATAGG 0.937492 -82 TATCATATAAAAAATTTGGTGATAAATTTAT 1 18 0 AAATTTGGTG 0.942318 -69 ATTAAAAAATTATGGGAAATAATATA 2 28 0 AAATTATGGG 0.981534 -16 ATAATGTTCTACAATTGGGTGAAGTCGTTAA 3 100 1 ACATTGGGTG 0.894544 -201 ATTGATAACGAAAATTATAAGTAATGCTATA 3 147 1 AAATTATAAG 0.626141 -154 ATTAATAAATAAACTCAGGGGATTTAA 3 284 1 AAATCAGGGG 0.930715 -17 AACACTTTTGTGTTATTTGATA 6 2 1 ACATTTTGTG 0.884051 -87 AACTTAGCAAAAAGTTTTAGGTTTTAG 8 7 0 AAATTTTAGG 0.924089 -88 TATTATCATCACAGTTATGGGTGATAACC 8 76 1 ACATTATGGG 0.970838 -19 TTAGAAATGTAAAGTTGGGGGATTTAG 9 18 1 AAATTGGGGG 0.979592 -17 TTCACCTCAAAAATTTGTGGAACCTTAAAA 10 94 0 AAATTTGTGG 0.86605 -20 *** ******* Masking position 3 Map Score: 12.0088 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 247 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 GGAAATCTATTTAAAACCTCTTTAATCTTG 3 24 0 TTAAAACCTC 0.978634 -277 TTAAATCCCCTGAGTTTATT 3 291 0 TTAAATCCCC 0.980176 -10 GATTTTATATCCGCAATACCCAAT 4 117 0 TTATATCCGC 0.868906 -14 GAAAAACTATTAAAACCTATTTCTGATAA 5 10 1 TTAAAACCTA 0.939308 -60 CTAAAACCTAAAACTTTTTG 8 1 1 CTAAAACCTA 0.927697 -94 CTAAATCCCCCAACTTTACA 9 25 0 CTAAATCCCC 0.976185 -10 ********** Masking position 5 Map Score: 4.04221 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 237 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 ********** No masking Map Score: 3.03645e-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: 3.03645e-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: 3.03645e-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