AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i148_Rubredoxin_mjan_reg_100.orf -o148_mjan_100.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 Input sequences: #1 RMJ07936 89 M_jannaschii_chromosome #2 RMJ13354 75 M_jannaschii_chromosome #3 RMJ01522 39 M_jannaschii_chromosome #4 RMJ14619 28 M_jannaschii_chromosome #5 RMJ10200 71 M_jannaschii_chromosome #6 RMJ08904 180 M_jannaschii_chromosome Motif number 1 GTGTTAAATATATAGTAATTTCATTGAAAGTT 1 9 0 TATATATTTT 0.848654 -81 ATTTAACACATATTATAAATTTCTAAATCTTTTT 1 34 1 TATTTAATTT 0.910595 -56 TCTTTTTAATTAATTGTAATTGTTTTTTGAGGTG 1 61 1 TAATGTATTT 0.971279 -29 TTTTATTTTATATTTGCTTTTCTT 2 1 0 TATTGCTTTT 0.976127 -75 ATTTAAGTTTTATTGGTTTTTATTTTATATTTGC 2 18 0 TATTGTTTTT 0.990701 -58 CTCCTTTTTATTTTATCTTTTGTTTATTTAAGTT 2 43 0 TTTTTCTTTT 0.809076 -33 AAAGTTTAATTAAAATAATTTTATTATT 3 5 0 TAAATATTTT 0.700938 -35 GTCAGTTTATTAAAGGTGATTATTG 4 14 1 TAAAGTATTT 0.933934 -15 GTTTTTAGTTTATTATTTTTTACTTTATAAAAAT 6 17 0 TATTTTTTTT 0.974179 -164 ATATGCAAGTTATTAGTTTTTAGTTTATTATTTT 6 32 0 TATTGTTTTT 0.990701 -149 ACGATTATCGTATTTGTGATTTTTTATATGCAAG 6 57 0 TATTGTATTT 0.987789 -124 ACAAATACGATAATCGTCTTTAATTTCATTATAT 6 74 1 TAATGTTTTT 0.978039 -107 TTATGCGAAATTTAAGTGATTAATGATATATACC 6 107 1 TTTAGTATTT 0.908203 -74 CTTTGTGCTATTTTTGTCATTATTTATCTTAGTC 6 148 0 TTTTGTATTT 0.959473 -33 **** ** *** * Masking position 10 Map Score: 22.8345 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 619 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 AACTTTCAATGAAATTACTATATA 1 5 1 TTCAATGAAA 0.790453 -85 GAAATTACTATATATTTAACACATATTATA 1 21 1 TATATTTAAC 0.513457 -69 ACAATTACAATTAATTAAAAAGATTTAGAA 1 54 0 TTAATTAAAA 0.914471 -36 AAAGCAAATATAAAATAAAAACCAATAAAA 2 15 1 TAAAATAAAA 0.970829 -61 CCAATAAAACTTAAATAAACAAAAGATAAA 2 36 1 TTAAATAAAC 0.975864 -40 AAACAAAAGATAAAATAAAAAGGAGGGGAG 2 52 1 TAAAATAAAA 0.970829 -24 AATAATAAAATTATTTTAAT 3 1 1 AATAATAAAA 0.799748 -39 TAAAATTATTTTAATTAAACTTTTTGGTGA 3 16 1 TTAATTAAAC 0.928565 -24 AATAATCACCTTTAATAAACTGACTTT 4 8 0 TTTAATAAAC 0.961264 -21 TTAAATAAAACGCGATGTGA 5 1 1 TTAAATAAAA 0.969537 -71 AATCACACCTTTACATGAACTATTTACATA 5 51 0 TTACATGAAC 0.748207 -21 CCCATTTTTATAAAGTAAAAAATAATAAAC 6 14 1 TAAAGTAAAA 0.862521 -167 TAAAGTAAAAAATAATAAACTAAAAACTAA 6 24 1 AATAATAAAC 0.829203 -157 TTTCGCATAATATAATGAAATTAAAGACGA 6 87 0 TATAATGAAA 0.907187 -94 ********** Masking position 8 Map Score: 19.998 Number of sites scoring better than the average of aligned sites = 1146 Number in coding regions = 826 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 3 AAAACCAATAAAACTTAAATAAACAAAAGAT 2 32 1 AACTTAAATA 0.966155 -44 CCAAAAAGTTTAATTAAAATAATTTTATTAT 3 12 0 TATTAAAATA 0.857848 -28 AACTATTTACATACTTACATATAGACATATA 5 33 0 AACTTACATA 0.960754 -39 TAAAAACTAATAACTTGCATATAAAAAATCA 6 44 1 TACTTGCATA 0.945355 -137 ATATCATTAATCACTTAAATTTCGCATAATA 6 105 0 TACTTAAATT 0.933662 -76 TACCTCTAACTGACTAAGATAAATAATGACA 6 137 1 TACTAAGATA 0.95694 -44 AGATAAATAATGACAAAAATAGCACAAAGGT 6 153 1 TACAAAAATA 0.915422 -28 * ********* Masking position 3 Map Score: 2.53429 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 174 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 CAATGAAATTACTATATATTTAACACATAT 1 17 1 ACTATATATT 0.835867 -73 TATTTAACACATATTATAAATTTCTAAATC 1 33 1 ATATTATAAA 0.851993 -57 ATTGGTTTTTATTTTATATTTGCTTTTCTT 2 11 0 ATTTTATATT 0.946749 -65 CCTCCTTTTTATTTTATCTTTTGTTTATTT 2 48 0 ATTTTATCTT 0.861534 -28 AATTAAAATAATTTTATTATT 3 2 0 ATTTTATTAT 0.702759 -38 ATTATTTTTTACTTTATAAAAATGGGATT 6 10 0 ACTTTATAAA 0.885552 -171 CGTATTTGTGATTTTTTATATGCAAGTTAT 6 53 0 ATTTTTTATA 0.755881 -128 TAAATTTCGCATAATATAATGAAATTAAAG 6 91 0 ATAATATAAT 0.508816 -90 TAAGTGATTAATGATATATACCTCTAACTG 6 119 1 ATGATATATA 0.757311 -62 ********** Masking position 5 Map Score: 3.37186 Number of sites scoring better than the average of aligned sites = 1592 Number in coding regions = 1150 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 366 Fraction of orfs with sites within 600 bp upstream = 0.0587857 Motif number 5 TATATATTTAACACATATTATAAATTTCTA 1 29 1 ACACATATTA 0.65968 -61 CAAAAAACAATTACAATTAATTAAAAAGAT 1 60 0 TTACAATTAA 0.636534 -30 ATTTCCACCTCAAAAAACAATTAC 1 76 0 CCACCTCAAA 0.815767 -14 TATAAAATAAAAACCAATAAAACTTAAATA 2 23 1 AAACCAATAA 0.797983 -53 TGTCTCACCAAAAAGTTTAATTAA 3 26 0 TCACCAAAAA 0.905868 -14 CAATAATCACCTTTAATAAACTGACT 4 13 0 TCACCTTTAA 0.96645 -16 TAATCACACCTTTACATGAACTATT 5 57 0 ACACCTTTAC 0.933706 -15 ATATAAAAAATCACAAATACGATAATCGTC 6 62 1 TCACAAATAC 0.829891 -119 TTAATGATATATACCTCTAACTGACTAAGA 6 126 1 ATACCTCTAA 0.876753 -55 ********** Masking position 3 Map Score: 0.579239 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 770 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 6 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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: 5.92755e-14 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