AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mgen_reg_100.orf -o294_mgen_100.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMG02253 110 Mycoplasma #2 RMG00273 137 Mycoplasma #3 RMG02389 24 Mycoplasma #4 RMG03341 101 Mycoplasma #5 RMG04342 161 Mycoplasma #6 RMG01004 115 Mycoplasma Motif number 1 TCAATAAAACTCGATAATAACT 1 3 1 AATAAAACTC 0.818607 -108 GTAAAACTGCAATAATATTGTTATAAACAA 1 68 0 AATAATATTG 0.94283 -43 TACATTATGCAGTAAAACTGCAATAATATT 1 79 0 AGTAAAACTG 0.934164 -32 TTTCTATAAAAATAAATCAGGTTT 2 5 0 AATAAATCAG 0.900739 -133 ATTCACTACTAATAATTTAAATTAAGCACT 2 49 1 AATAATTTAA 0.839886 -89 CAGCTTGAAGTAAAATTAATCCTA 3 9 1 AGTAAAATTA 0.927725 -16 TTATAACCACAATAATTTTAAATTTTAA 4 9 0 AATAATTTTA 0.885573 -93 AGATGTCATCAGTAAATTTATCTTCTTTTA 4 77 1 AGTAAATTTA 0.879824 -25 ATTAGTTAAAAATAAAGTTACTTA 5 5 0 AATAAAGTTA 0.815795 -157 ATTTTTAACTAATAAAACAGTTTGTAGTGT 5 22 1 AATAAAACAG 0.940864 -140 CATTGCTATTAATAAGACAAAACAAAGGCG 5 88 1 AATAAGACAA 0.849147 -74 CAATTATTTTAATAATTTTGGTAATTAATA 6 20 1 AATAATTTTG 0.903899 -96 TAATATTACTAATAAGATAGTAAATAAGAA 6 52 0 AATAAGATAG 0.882649 -64 CTATCTTATTAGTAATATTAAGCTTAGTGC 6 62 1 AGTAATATTA 0.89133 -54 AAATAGAGCTAATAAAAGAA 6 106 1 AATAAAAGAA 0.750103 -10 ********** Masking position 5 Map Score: 14.7823 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 316 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 CGATAATAACTAAAAGCCATAAAACCTTGGTTTT 1 22 1 TAAAGCAAAA 0.995245 -89 ATAAACAAGCTAAAAACCACAAAACCAAGGTTTT 1 42 0 TAAAACAAAA 0.953534 -69 CCCTAGCTTATAAGGGATAAAAAAGAAGTTTATA 4 34 0 TAAGGAAAAA 0.971428 -68 ATCGATAAAAGAAGATAAATTTACTGATG 4 83 0 TAAAGAGAAA 0.916304 -19 GTAGTGTTTGTAACAGCTTACAAATTTGTCATTT 5 45 1 TAAAGCTAAA 0.974034 -117 TTTGTCTTATTAATAGCAATGAAAAGTGAAAAAT 5 75 0 TAAAGCAAAA 0.995245 -87 TAAGACAAAACAAAGGCGATGAAAATCATTTATC 5 100 1 CAAGGCAAAA 0.97866 -62 CTTAGTGCAATAATGGCAACGAAAATAGAGCTAA 6 84 1 TAAGGCAAAA 0.994242 -32 GGCAACGAAAATAGAGCTAATAAAAGAA 6 98 1 ATAAGCAAAA 0.855356 -18 *** *** * *** Masking position 3 Map Score: 12.0654 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 131 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 ATAAAACTCGATAATAACTAAAAGCCATAA 1 14 1 ATAATAACTA 0.825012 -97 TTTTAGCTTGTTTATAACAATATTATTGCA 1 61 1 TTTATAACAA 0.959978 -50 AAAACTTCCCTTTATAATCAAATATCGCC 2 119 1 TTTATAATCA 0.78891 -19 AAAAAAGAAGTTTATAACCACAATAATTTT 4 20 0 TTTATAACCA 0.974456 -82 AGTAACTTTATTTTTAACTAATAAAACAGT 5 13 1 TTTTTAACTA 0.884299 -149 TTTTGTCTTATTAATAGCAATGAAAAGTGA 5 80 0 TTAATAGCAA 0.874573 -82 AGTTAAGAACAATTATTTTAAT 6 3 1 TTAAGAACAA 0.874734 -113 TAAGAAATTATTAATTACCAAAATTATTAA 6 28 0 TTAATTACCA 0.936951 -88 TAATAATTTCTTATTTACTATCTTATTAGT 6 45 1 TTATTTACTA 0.749109 -71 ********** Masking position 2 Map Score: 5.6485 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 280 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TATTAATCCCTTTAGATTGCTTAACTCTTT 2 89 1 TTTAGATTGC 0.95789 -49 CATTTTTCACTTTTCATTGCTATTAATAAG 5 74 1 TTTTCATTGC 0.993551 -88 TGATAAATGATTTTCATCGCCTTTGTTTTG 5 105 0 TTTTCATCGC 0.989056 -57 ATTAGCTCTATTTTCGTTGCCATTATTGCA 6 89 0 TTTTCGTTGC 0.989056 -27 ********** Masking position 7 Map Score: 3.29263 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 10 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ACAAGCTAAAAACCACAAAACCAAGGTTTT 1 42 0 AACCACAAAA 0.943185 -69 TATGCAGTAAAACTGCAATAATATTGTTAT 1 74 0 AACTGCAATA 0.979377 -37 ATTGCAGTTTTACTGCATAATGTAAAATTA 1 85 1 TACTGCATAA 0.883193 -26 AGAAGTTTATAACCACAATAATTTTAAATT 4 15 0 AACCACAATA 0.943178 -87 TAGCAATGAAAAGTGAAAAATGACAAATTT 5 66 0 AAGTGAAAAA 0.827334 -96 ATATTAAGCTTAGTGCAATAATGGCAACGA 6 76 1 TAGTGCAATA 0.875589 -40 ********** Masking position 7 Map Score: 0.612437 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 161 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: -1.16996e-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: -1.16996e-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: -1.16996e-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