AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_mjan_pyro_300.orf -o047_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ01128 21 M_jannaschii_chromosome RMJ02772 29 M_jannaschii_chromosome Input sequences: #1 RMJ15817 120 M_jannaschii_chromosome #2 RMJ08873 166 M_jannaschii_chromosome #3 RMJ09513 108 M_jannaschii_chromosome #4 RMJ07037 64 M_jannaschii_chromosome #5 RMJ03862 33 M_jannaschii_chromosome #6 RMJ14786 89 M_jannaschii_chromosome #7 RMJ06121 273 M_jannaschii_chromosome #8 RMJ14683 177 M_jannaschii_chromosome #9 RMJ10436 145 M_jannaschii_chromosome #10 RMJ15659 136 M_jannaschii_chromosome #11 RPH00713 51 Pyrococcus_OT3 #12 RPH00710 47 Pyrococcus_OT3 Motif number 1 AATTAAGAAAATTTAAAATAATGTTAAAGA 1 12 1 ATTTAAAATA 0.753599 -109 ATTAAAAAATCCAATAAGGA 3 1 1 ATTAAAAAAT 0.973517 -108 GATAATCATAATTAAAAAACTAATTGAAGC 3 34 1 ATTAAAAAAC 0.944914 -75 ATTTTTAATATTTTAAAATCTTCATCCTGT 3 76 0 TTTTAAAATC 0.684214 -33 ATTTTAAAATATTAAAAATTATAGAGCTGT 3 87 1 ATTAAAAATT 0.973722 -22 TAGCAAAAAAATTAAATAATATGATTTAAA 4 31 1 ATTAAATAAT 0.764901 -34 AAATAATATGATTTAAAGATTTGGTGAAAT 4 44 1 ATTTAAAGAT 0.871779 -21 TCACCAAAAGGTTAAAAAATTAAAGAAAT 5 10 0 GTTAAAAAAT 0.855906 -24 CTAAAAACACAATAAAAAACATAAATACCT 6 25 1 AATAAAAAAC 0.752655 -65 TTGTTCTTTTATTTAAAATCTGTCCCTCTA 7 19 0 ATTTAAAATC 0.918064 -255 TATACATATTATCAAAAATTGATTTAGATA 7 82 1 ATCAAAAATT 0.834453 -192 ATGTTTGTTTTTTTAAAATTAACACTAATT 7 112 0 TTTTAAAATT 0.824051 -162 TGCAAAAAATAATAAAAAATGTTTGTTTTT 7 130 0 AATAAAAAAT 0.867866 -144 CTCAATCCTAATTAAAAGTTATCGTTGGAA 7 177 1 ATTAAAAGTT 0.912567 -97 TGGAAAATCTTTTTAAAAATACCAACATTG 7 202 1 TTTTAAAAAT 0.823802 -72 TTGATTTAGAATTAAAAGATGCATTTTTAA 7 229 1 ATTAAAAGAT 0.912541 -45 TTAAAAATATATTAAAAATGCATCTTTTAA 7 240 0 ATTAAAAATG 0.913427 -34 AAGATAATATATTAAAAATATATTAAAAAT 7 251 0 ATTAAAAATA 0.824024 -23 GTAAAGAACTAATAAAAAAGGAATATCATA 8 82 1 AATAAAAAAG 0.651642 -96 TAATAATAAAGTTTAAAGTTAGTGACAGTG 8 116 0 GTTTAAAGTT 0.522039 -62 GTTTTTTAAAATTAAAAATGAATGTAATAA 8 140 0 ATTAAAAATG 0.913427 -38 CATTTTTAATTTTAAAAAACTTAAAACAGA 8 150 1 TTTAAAAAAC 0.768314 -28 TCAAAAACATATCAAAAATTTAATTGGGTA 9 42 0 ATCAAAAATT 0.834453 -104 CAAGTTTAATATTTAAAATTTAATTAAGGT 9 86 0 ATTTAAAATT 0.959905 -60 TATAGTTATAATTTAATAATTTAGAAC 9 129 1 ATTTAATAAT 0.677446 -17 AATAAGGTATATTTAAAAAT 10 1 0 ATTTAAAAAT 0.957623 -136 GTTAGCTAATATTAAAAAATAAGGTATATT 10 18 0 ATTAAAAAAT 0.973517 -119 AAGATATTTAAATTAAAATTTTGCAAATAT 10 70 0 AATTAAAATT 0.810894 -67 ********** Masking position 5 Map Score: 37.9589 Number of sites scoring better than the average of aligned sites = 2429 Number in coding regions = 1828 Number in noncoding regions = 601 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 2 GATACTCATGATTTCACCAAAACCG 2 6 0 ATTTCACCAA 0.96179 -161 TTTCCATCTTTAATCTCCAATGACCCTTCT 2 125 0 TAATCTCCAA 0.923149 -42 AATTTCACCAAATCTTTAAAT 4 54 0 ATTTCACCAA 0.96179 -11 ATTATCACCAAAAGGTTAAAA 5 23 0 TTATCACCAA 0.992537 -11 TTTATCACCAATAACACTCTT 6 79 0 TTATCACCAA 0.992537 -11 TTTTATCACCAACAAGATTTTA 9 3 1 TTATCACCAA 0.992537 -143 TTAACCACCAAGCATATAAAT 12 37 0 TAACCACCAA 0.946819 -11 ********** Masking position 9 Map Score: 11.4709 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 43 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 CTTTTTCTTTAACATTATTTTAAATTTTCTTAATTT 1 2 0 AATATTTATT 0.720866 -119 AATAATGTTAAAGAAAAAGTTGATGCATGAAATATTGTGAATTTT 1 28 1 AAAAATTAAT 0.85961 -93 TGAATAAGTTAAAGATAAAGAAAAAGCTAAAAAATACTCCAAAAT 2 62 1 AATAAGTAAT 0.82978 -105 TCATAATTAAAAAACTAATTGAAGCATTAAGACAGGCACAGGATG 3 39 1 AATAATTAAG 0.829578 -70 ATTTCACCAAATCTTTAAATCATATTATTTAATTTTTTTGCTATA 4 29 0 ATTAATTATT 0.748089 -36 ACACAATAAAAAACATAAATACCTAATTATCAATTCAATAAAAAC 6 31 1 AATAATTATT 0.966003 -59 ACGATATAACAAAAGAAACTATTGTTCTTTTATTTAAAATCTGTC 7 25 0 AAAAATTATT 0.816967 -249 TTTTAAAATTAACACTAATTTATCTAAATCAATTTTTGATAATAT 7 87 0 AATAATAATT 0.852825 -187 TGCATCTTTTAATTCTAAATCAATGTTGGTATTTTTAAAAAGATT 7 207 0 AATAATGTTT 0.691579 -67 TGAATACTTAAACTATAAATATGGATTATTCTTTTATAAAGTCGT 8 26 1 AATAATATTT 0.494721 -152 AACATATCAAAAATTTAATTGGGTATTGCGGATATAAAATCTTGT 9 22 0 AATAATGAAT 0.946504 -124 TTAATATTTAAAATTTAATTAAGGTCTTATCACATCAAATCAAAA 9 66 0 AATAATTAAT 0.972809 -80 TATAACTATAAATTATAACTATTCAAGTTTAATATTTAAAATTTA 9 94 0 AATAATTAAT 0.679051 -52 TTTAGCATAAAATGTTAAGTTGTGTTAGCTAATATTAAAAAATAA 10 26 0 AATAATGAAT 0.946505 -111 CTTTATTAAGATATTTAAATTAAAATTTTGCAAATATTTAGCATA 10 62 0 ATTAATTAAT 0.858906 -75 TATCTTAATAAAGATTAAATCAATTTATTATAAATAACCTTAGAG 10 94 1 AATAATTAAT 0.959611 -43 ** *** * * * ** Masking position 7 Map Score: 13.2139 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 295 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 AAATTAAGAAAATTTAAAATAATG 1 1 1 AAAAAAAATT 0.961824 -120 TAACTTTATAAAATTCACAATATTTCATGCATCA 1 48 0 AAACAAAATT 0.870802 -73 AGATAAAGAAAAAGCTAAAAAATACTCCAAAATA 2 74 1 AAATAAAATA 0.877665 -93 GAAGATTTTAAAATATTAAAAATTATAGAGCTGT 3 83 1 AAATTAAATT 0.844047 -26 AAATGGTTTTATAGCAAAAAAATTAAATAATATG 4 20 1 ATAAAAAATT 0.814963 -45 TTATCACCAAAAGGTTAAAAAATTAAAGAAAT 5 9 0 AAGTAAAATT 0.783713 -25 CAATTCAATAAAAACAATAAGAGTGTTATTGGTG 6 61 1 AAAAAAAAGT 0.908454 -29 GATTTTAAATAAAAGAACAATAGTTTCTTTTGTT 7 29 1 AAAAAAAAGT 0.908455 -245 ATTTTTGATAATATGTATAAAATTATGCCCAACG 7 67 0 ATATAAAATT 0.833519 -207 GTTAATTTTAAAAAAACAAACATTTTTTATTATT 7 119 1 AAAACAAATT 0.880468 -155 ATTAGGATTGAGATATAAAACATTACTACTGCAA 7 155 0 AGATAAAATT 0.807998 -119 AATCTTTTTAAAAATACCAACATTGATTTAGAAT 7 207 1 AAAACAAATT 0.88045 -67 TGAAAGATAATATATTAAAAATATAT 7 258 0 AAATATAATT 0.711663 -16 TAATTTTAAAAAACTTAAAACAGAGTGAAACA 8 156 1 AAATAAAAGA 0.737217 -22 TTATCACATCAAATCAAAAACATATCAAAAATTT 9 51 0 AAAAAAAATA 0.863219 -95 GACCTTAATTAAATTTTAAATATTAAACTTGAAT 9 85 1 AAATTAAATT 0.84233 -61 *** ** ** *** Masking position 10 Map Score: 13.6471 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 771 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 5 AGGAGGGGATAATCATAATTAAAAAACTAA 3 27 1 AATCATAATT 0.65694 -82 TCATAATTAAAAAACTAATTGAAGCATTAA 3 39 1 AAAACTAATT 0.587676 -70 CCAAATCTTTAAATCATATTATTTAATTTT 4 38 0 AAATCATATT 0.544797 -27 ATTAAACTGTATTTCTAAAAACA 6 4 1 AAACTGTATT 0.70896 -86 AAAAACATAAATACCTAATTATCAATTCAA 6 39 1 ATACCTAATT 0.894365 -51 TTAAAAAAACAAACATTTTTTATTATTTTT 7 126 1 AAACATTTTT 0.494792 -148 TTTATATCTCAATCCTAATTAAAAGTTATC 7 170 1 AATCCTAATT 0.917691 -104 TGTACTAAACTATATTGAATACTTAA 8 7 1 AAACTATATT 0.806375 -171 ATAAAAGAATAATCCATATTTATAGTTTAA 8 33 0 AATCCATATT 0.841927 -145 TGATTATGATATTCCTTTTTTATTAGTTCT 8 86 0 ATTCCTTTTT 0.527537 -92 CACTAACTTTAAACTTTATTATTACATTCA 8 122 1 AAACTTTATT 0.928378 -56 TATATCCGCAATACCCAATTAAATTTTTGA 9 31 1 ATACCCAATT 0.614575 -115 TTAATATTTAAAATTTAATTAAGGTCTTAT 9 81 0 AAATTTAATT 0.500046 -65 ATTTTTAAATATACCTTATTTTTTAATATT 10 11 1 ATACCTTATT 0.925882 -126 AAATTGATTTAATCTTTATTAAGATATTTA 10 90 0 AATCTTTATT 0.868507 -47 ********** Masking position 1 Map Score: 5.07104 Number of sites scoring better than the average of aligned sites = 1020 Number in coding regions = 827 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 6 CATCAACTTTTTCTTTAACATTATTTTAAA 1 23 0 TTCTTTAACA 0.843788 -98 CTTTTTCTTTATCTTTAACTTATTCAAGCA 2 58 0 ATCTTTAACT 0.858187 -109 CTAACTTTCCATCTTTAATCTCCAATGACC 2 130 0 ATCTTTAATC 0.849907 -37 CTAATCAGCTTTAATTACTAACTTTC 2 151 0 AGCTTTAATT 0.742605 -16 CTTCAATTAGTTTTTTAATTATGATTATCC 3 33 0 TTTTTTAATT 0.89142 -76 CAGCTCTATAATTTTTAATATTTTAAAATC 3 86 0 ATTTTTAATA 0.901939 -23 TTAAATCATATTATTTAATTTTTTTGCTAT 4 30 0 TTATTTAATT 0.630245 -35 ATTTCACCAAATCTTTAAATCATATTATTT 4 44 0 ATCTTTAAAT 0.689307 -21 ATTTCTTTAATTTTTTAACCTT 5 3 1 TTCTTTAATT 0.955816 -31 GAAACTATTGTTCTTTTATTTAAAATCTGT 7 26 0 TTCTTTTATT 0.765476 -248 TAAAAGATGCATTTTTAATATATTTTTAAT 7 241 1 ATTTTTAATA 0.901939 -33 TTTTTAATATATTTTTAATATATTATCTTT 7 252 1 ATTTTTAATA 0.901939 -22 ATATGGATTATTCTTTTATAAAGTCGTTAA 8 44 1 TTCTTTTATA 0.765476 -134 TTTTTATTAGTTCTTTACTACACTCTTTAA 8 70 0 TTCTTTACTA 0.732862 -108 TATTACATTCATTTTTAATTTTAAAAAACT 8 141 1 ATTTTTAATT 0.901939 -37 ATATACCTTATTTTTTAATATTAGCTAACA 10 19 1 TTTTTTAATA 0.891421 -118 AATTGATTTAATCTTTATTAAGATATTTAA 10 89 0 ATCTTTATTA 0.674663 -48 ********** Masking position 5 Map Score: 18.8717 Number of sites scoring better than the average of aligned sites = 1470 Number in coding regions = 1215 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 7 TGAAATATTGTGAATTTTATAAAGTTATGAAA 1 55 1 TGAATTATAA 0.974823 -66 GTATCTATAATGAATTATATAAATTAATGCTT 2 31 1 TGAATTATAA 0.974623 -136 AATTAATGCTTGAATAAGTTAAAGATAAAGAA 2 52 1 TGAATATTAA 0.734449 -115 CCCTCCTTATTGGATTTTTTAAT 3 2 0 TGGATTTTAA 0.662748 -107 TTATAGCAAAAAAATTAAATAATATGATTTAA 4 28 1 AAAATTATAA 0.492522 -37 ATTTCTTTAATTTTTTAACCTTTTGGTG 5 7 1 TTAATTTTAA 0.802099 -27 TACCTAATTATCAATTCAATAAAAACAATAAG 6 50 1 TCAATTATAA 0.863451 -40 TATCAAAAATTGATTTAGATAAATTAGTGTTA 7 91 1 TGATTTATAA 0.804411 -183 TAAATTAGTGTTAATTTTAAAAAAACAAACAT 7 110 1 TTAATTAAAA 0.744349 -164 TAATAAAAAAGGAATATCATAATCACACTGTC 8 91 1 GGAATAATAA 0.620861 -87 AAATTAAAAATGAATGTAATAATAAAGTTTAA 8 130 0 TGAATGATAA 0.877421 -48 ACATTCATTTTTAATTTTAAAAAACTTAAAAC 8 145 1 TTAATTAAAA 0.744349 -33 ATTTATAGTTATAATTTAATAATTTAGAAC 9 126 1 ATAATTATAA 0.759684 -20 ****** **** Masking position 11 Map Score: 4.62318 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 635 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 ********** No masking Map Score: -5.58897e-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 9 ********** No masking Map Score: -5.58897e-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 10 ********** No masking Map Score: -5.58897e-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