AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00100_mjan_reg_300.orf -o00100_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e 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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0703 24 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA2) Input sequences: #1 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #2 MJ0704 95 M. jannaschii predicted coding region MJ0704 #3 MJ0861 131 conserved hypothetical protein #4 MJ0862 176 carotenoid biosynthetic gene ERWCRTS isolog #5 MJ0863 70 heterodisulfide reductase, subunit B2 (hdrB2) #6 MJ0864 160 heterodisulfide reductase, subunit C2 (hdrC2) #7 MJ1081 130 conserved hypothetical protein #8 MJ1083 69 iron-sulfur flavoprotein (isf) #9 MJ1084 88 shikimate 5-dehydrogenase (aroE) #10 MJ1085 25 M. jannaschii predicted coding region MJ1085 Motif number 1 AGTAGTGTTTATTTTTTCATTAGATTGAATT 1 31 0 ATTTTTCATT 0.743599 -95 TTTTACAGAAACATATTTAAAAGATGGTGTT 1 62 1 AATATTTAAA 0.776707 -64 GAGGTATAGAACTATTTTATTATTTTT 1 109 1 ATATTTTATT 0.84957 -17 TATTTGTAGGAGATTTTAATAAATGGATATC 2 44 1 AATTTTAATA 0.91823 -52 ATCCCATTTATGATTTTTATTTTTATCTTAG 3 32 1 TATTTTTATT 0.928076 -100 TAGGCTGTAAATTTATTTAAAATAATTAAAT 3 67 1 ATTATTTAAA 0.784912 -65 TAAAATAATTAAATATTTATAAACATTAAAA 3 84 1 AATATTTATA 0.913789 -48 CACATCCTTTAATTTTTTATAATTTTAATGT 3 106 0 ATTTTTTATA 0.948292 -26 CATTAGCATTTTATATTTAAATATTTTTTAT 4 13 1 TATATTTAAA 0.649989 -164 TATATTTAAATATTTTTTATTATTCATAATT 4 24 1 TTTTTTTATT 0.932288 -153 TTATTATTCATAATTTTTATTTTATTTCTTT 4 40 1 TATTTTTATT 0.928074 -137 ATTTTATTTCTTTTTTTAATATTTTTGATAA 4 58 1 TTTTTTAATA 0.865006 -119 GTCAATACTAACTTTTTTATAATGTGTCTAT 4 90 1 ATTTTTTATA 0.948419 -87 ATAATGTGTCTATTTTTAATTTGTTATTAAA 4 108 1 TTTTTTAATT 0.899455 -69 TAACTTTGTGAAATTTTAATAACAAATTAAA 4 122 0 AATTTTAATA 0.918224 -55 GTTATATAGCAAATATTTATATAGTATTTGG 4 149 1 AATATTTATA 0.913789 -28 TTTTATTGTTTAATTTTAATTCTAATTTTAT 5 16 0 TATTTTAATT 0.893958 -55 TATTTCCTTTAATTTTTTATTGTTTAATTTT 5 30 0 ATTTTTTATT 0.96252 -41 AACCCCCTCATGTTTTTAATTTCTCTTTAAA 6 28 1 TTTTTTAATT 0.90019 -133 AATAAATTTTAAAATTTAATTTAAAGAGAAA 6 47 0 AAATTTAATT 0.775222 -114 AAATTTTAAAATTTATTTATAATGAGGTATT 6 61 1 ATTATTTATA 0.915239 -100 GTTCTAAATTATTAAATTATAACTATA 7 7 1 ATTATTAAAT 0.705564 -124 CTTGAATAGTTATAATTTATAGTTATAATTT 7 24 0 TTAATTTATA 0.562135 -107 GACCTTAATTAAATTTTAAATATTAAACTTG 7 51 0 AATTTTAAAT 0.838017 -80 AAACATATCAAAAATTTAATTGGGTATTGCG 7 99 1 AAATTTAATT 0.775222 -32 TTGTGTTATTTGATATTTATTTTTTACCTTC 9 18 1 TATATTTATT 0.888521 -71 TGTAATTTACAATTTTTAATTATAAAAACTA 9 53 1 ATTTTTAATT 0.943016 -36 AATTATAAAAACTAATTTAATGTGATAAT 9 70 1 ATAATTTAAT 0.533105 -19 AAATATTTAATAAATTTAATA 10 1 1 AATATTTAAT 0.830047 -25 * ********* Masking position 6 Map Score: 39.3805 Number of sites scoring better than the average of aligned sites = 3683 Number in coding regions = 2479 Number in noncoding regions = 1204 Number of orfs with sites within 600 bp upstream = 664 Fraction of orfs with sites within 600 bp upstream = 0.10665 Motif number 2 AAAGTAGTGTTTATTTTTTCATTAGATTGA 1 34 0 TTATTTTTTC 0.690251 -92 TAGAACTATTTTATTATTTTT 1 115 1 TTATTATTTT 0.818976 -11 GTAGTTATAATAATTTTTTTAA 2 3 0 TAATTTTTTT 0.954904 -93 TTTATGATTTTTATTTTTATCTTAGATGTT 3 38 1 TTATTTTTAT 0.812695 -94 TGTTAGGCTGTAAATTTATTTAAAATAATT 3 64 1 TAAATTTATT 0.58473 -68 TATAAATATTTAATTATTTTAAATAAATTT 3 75 0 TAATTATTTT 0.828562 -57 TAATTTTTTATAATTTTAATGTTTATAAAT 3 98 0 TAATTTTAAT 0.603378 -34 TCACATCCTTTAATTTTTTATAATTTTAAT 3 108 0 TAATTTTTTA 0.929371 -24 CATTAGCATTTTATATTTAAATATTTTTTA 4 13 1 TTATATTTAA 0.600214 -164 TTATATTTAAATATTTTTTATTATTCATAA 4 23 1 ATATTTTTTA 0.374801 -154 TTCATAATTTTTATTTTATTTCTTTTTTTA 4 46 1 TTATTTTATT 0.866841 -131 TTTCTTTTTTTAATATTTTTGATAAAGTCA 4 64 1 TAATATTTTT 0.918326 -113 AAGTCAATACTAACTTTTTTATAATGTGTC 4 88 1 TAACTTTTTT 0.780057 -89 TGTCTATTTTTAATTTGTTATTAAAATTTC 4 114 1 TAATTTGTTA 0.486339 -63 ATTTTAATTCTAATTTTATTGGAT 5 5 0 TAATTTTATT 0.874445 -66 TTTTATTGTTTAATTTTAATTCTAATTTTA 5 17 0 TAATTTTAAT 0.603378 -54 TTATTTCCTTTAATTTTTTATTGTTTAATT 5 32 0 TAATTTTTTA 0.929371 -39 AAGGAAATAATAAGATTTTTGGTGATAAG 5 52 1 TAAGATTTTT 0.655028 -19 CATGAGGGGGTTATTTTATTTAACTTCTT 6 10 0 TTATTTTATT 0.866841 -151 TCTCTTTAAATTAAATTTTAAAATTTATTT 6 49 1 TTAAATTTTA 0.482423 -112 TAATTTATAGTTATAATTTAATAATTTAGA 7 13 0 TTATAATTTA 0.608191 -118 ACTTGAATAGTTATAATTTATAGTTATAAT 7 26 0 TTATAATTTA 0.608191 -105 TATTCAAGTTTAATATTTAAAATTTAATTA 7 47 1 TAATATTTAA 0.609155 -84 CAATACCCAATTAAATTTTTGATATGTTTT 7 98 0 TTAAATTTTT 0.672115 -33 AAATAGGTTTTAATAGTTTTTC 8 3 0 TAATAGTTTT 0.485933 -67 TATTTGATATTTATTTTTTACCTTCTCTTT 9 24 1 TTATTTTTTA 0.927718 -65 TCTTTGTAATTTACAATTTTTAATTATAAA 9 49 1 TTACAATTTT 0.287791 -40 TCACATTAAATTAGTTTTTATAATTAAAAA 9 65 0 TTAGTTTTTA 0.684643 -24 CCTCTATTAAATTTATTAAATATTT 10 9 0 TAAATTTATT 0.58473 -17 ********** Masking position 3 Map Score: 28.5832 Number of sites scoring better than the average of aligned sites = 4055 Number in coding regions = 2907 Number in noncoding regions = 1148 Number of orfs with sites within 600 bp upstream = 669 Fraction of orfs with sites within 600 bp upstream = 0.107453 Motif number 3 AACACTACTTTTTACAGAAACATATTTAAA 1 53 1 TTTACAGAAA 0.632958 -73 TCATCCAACTATAACACCATCTTTTAAATA 1 75 0 ATAACACCAT 0.45174 -51 AACATTAAAATTATAAAAAATTAAAGGATG 3 105 1 TTATAAAAAA 0.664926 -27 AGTATTGACTTTATCAAAAATATTAAAAAA 4 69 0 TTATCAAAAA 0.944661 -108 AATAGACACATTATAAAAAAGTTAGTATTG 4 92 0 TTATAAAAAA 0.664926 -85 TGTTATTAAAATTTCACAAAGTTATATAGC 4 129 1 ATTTCACAAA 0.898356 -48 AATTTCACCAAATACTATATA 4 166 0 ATTTCACCAA 0.854243 -11 CTTATCACCAAAAATCTTATT 5 60 0 TTATCACCAA 0.938295 -11 AACTATATATATAACCAAAACCCTACCTTA 6 126 1 ATAACCAAAA 0.731962 -35 TTATCACATCAAATCAAAAACATATCAAAA 7 82 1 AAATCAAAAA 0.688958 -49 AATCAAAAACATATCAAAAATTTAATTGGG 7 93 1 ATATCAAAAA 0.95745 -38 GATTTTATATCCGCAATACCCAATTA 7 115 0 ATATCCGCAA 0.781315 -16 CTAATGTATTTTATCAGAAATAGGTTTTAA 8 20 0 TTATCAGAAA 0.933753 -50 TAAATATCAAATAACACAAAAGTGTT 9 7 0 ATAACACAAA 0.926608 -82 ********** Masking position 9 Map Score: 9.26122 Number of sites scoring better than the average of aligned sites = 1428 Number in coding regions = 1165 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 4 TTAAAAAAATTATTATAACTAC 2 2 1 TAAAAAATTA 0.74609 -94 ATAACTACAATATTCACATTATTTGTAGGAG 2 25 1 TATCACATTA 0.979147 -71 GGGATAACAGTATTAACAATACTGTT 3 6 0 TATAACAATA 0.853204 -126 ATTAAATATTTATAAACATTAAAATTATAAA 3 91 1 TAAAACATTA 0.967712 -41 AAATTAAAAATAGACACATTATAAAAAAGTT 4 99 0 TAACACATTA 0.974744 -78 AAAGAGAAATTAAAAACATGAGGGGGTTATT 6 25 0 TAAAACATGA 0.888425 -136 AAGTGTCTAATACTAACATTCGAAGTTTCTA 6 96 1 TATAACATTC 0.896153 -65 AATTAAGGTCTTATCACATCAAATCAAAAAC 7 72 1 TTTCACATCA 0.799645 -59 ATTATCACATTAAATTAGTTTT 9 77 0 TTTCACATTA 0.937538 -12 ** ******** Masking position 6 Map Score: 5.21218 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 88 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GTAGTGTTTATTTTTTCATTAGATTGAATTC 1 30 0 TTTTTTCTTA 0.419584 -96 ATAGAACTATTTTATTATTTTT 1 114 1 TTTATTATTT 0.725575 -12 TATGATTTTTATTTTTATCTTAGATGTTAGG 3 40 1 ATTTTTACTT 0.675518 -92 TTATAAATATTTAATTATTTTAAATAAATTT 3 75 0 TTAATTATTT 0.770889 -57 TCCTTTAATTTTTTATAATTTTAATGTTTAT 3 102 0 TTTTATATTT 0.599908 -30 TATTTAAATATTTTTTATTATTCATAATTTT 4 26 1 TTTTTTATAT 0.599902 -151 AATTTTTATTTTATTTCTTTTTTTAATATTT 4 51 1 TTATTTCTTT 0.919742 -126 TAATGTGTCTATTTTTAATTTGTTATTAAAA 4 109 1 ATTTTTATTT 0.801827 -68 TAATTTTTTATTGTTTAATTTTAATTCTAAT 5 21 0 TTGTTTATTT 0.822629 -50 AAAAATCTTATTATTTCCTTTAATTTTTTAT 5 41 0 TTATTTCTTT 0.919761 -30 GGGGGTTATTTTATTTAACTTCTT 6 4 0 TTATTTACTT 0.919528 -157 CTCATGTTTTTAATTTCTCTTTAAATTAAAT 6 34 1 TAATTTCCTT 0.717451 -127 ATAAATTTTAAAATTTAATTTAAAGAGAAAT 6 46 0 AAATTTATTT 0.604267 -115 GATAAGACCTTAATTAAATTTTAAATATTAA 7 56 0 TAATTAATTT 0.386979 -75 AATTCTGACCTAATGTATTTTATCAGAAATA 8 28 0 TAATGTATTT 0.549121 -42 TTGATATTTATTTTTTACCTTCTCTTTGTAA 9 27 1 TTTTTTACTT 0.900006 -62 TTATAAAAACTAATTTAATGTGATAAT 9 72 1 TAATTTATGT 0.549271 -17 ******* *** Masking position 6 Map Score: 7.26636 Number of sites scoring better than the average of aligned sites = 2753 Number in coding regions = 1979 Number in noncoding regions = 774 Number of orfs with sites within 600 bp upstream = 487 Fraction of orfs with sites within 600 bp upstream = 0.0782204 Motif number 6 ********** No masking Map Score: 1.63668e-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 7 ********** No masking Map Score: 1.63668e-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: 1.63668e-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