AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_mgen_reg_300.orf -o119_mgen_300.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 RMG00079 158 Mycoplasma #2 RMG02201 20 Mycoplasma #3 RMG01155 197 Mycoplasma #4 RMG02204 52 Mycoplasma Motif number 1 AATTAATCTTCTAGTATTTAGTTAGTTATT 1 12 1 CTAGTATTTA 0.88688 -147 TAGTTGTGATTTACTTTTTGGTATCTCTAT 1 64 1 TTACTTTTTG 0.824843 -95 ATGTTTGATACTACTTTTTATAGAGATACC 1 83 0 CTACTTTTTA 0.96734 -76 TAGTATCAAACATTTTTTTATCTTTTGATT 1 100 1 CATTTTTTTA 0.922428 -59 TATCTTTTGATTTCTTTTTACTAAAAATAA 1 118 1 TTTCTTTTTA 0.965575 -41 AATTTTGATTACTTAAAGAT 2 6 1 TGATTACTTA 0.601454 -15 TTAAATCTGTTTATTTTTTAATAGTAAAAA 3 30 1 TTATTTTTTA 0.977522 -168 AAGGTTAAATTGTGTTTTTACTATTAAAAA 3 44 0 TGTGTTTTTA 0.856626 -154 TTTAACCTTGTTTCTATTTAACAAAATTGG 3 65 1 TTTCTATTTA 0.923655 -133 AAAAATATCTTAATTTTTTACAGCAAAATT 3 111 0 TAATTTTTTA 0.957154 -87 AAAAATTAAGATATTTTTTATCAAAAATTA 3 123 1 ATATTTTTTA 0.834374 -75 TTTTTTATGCTAATTTTTGATAAAAAATAT 3 133 0 TAATTTTTGA 0.839429 -65 ATTAGTATAACAATTTTTTATGCTAATTTT 3 146 0 CAATTTTTTA 0.943717 -52 TAATTAACGTTTTTTATTGAAAATTAAGTA 3 172 1 TTTTTATTGA 0.756366 -26 TATTGAAAATTAAGTATTTAAA 3 186 1 TAAGTATTTA 0.789366 -12 GAAGTCAGTATTTTtTCTTAATGTGCATCT 4 13 0 TTTTtTCTTA 0.878005 -40 TTCTGCTCCCCTTCTTTTTATTA 4 40 1 CTTCTTTTTA 0.954546 -13 ********** Masking position 5 Map Score: 23.902 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 771 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 TAGTTAGTTATTTTGCAAAAAAGGATTAGT 1 30 1 TTTTGCAAAA 0.495303 -129 TTTGATTTCTTTTTACTAAAAATAATTAGC 1 123 1 TTTTACTAAA 0.683306 -36 ATGACGGTATTTTAGCTAATTATTTTTAGT 1 137 0 TTTAGCTAAT 0.724958 -22 AATAAACAGATTTAATTGATTAAAATATGC 3 15 0 TTTAATTGAT 0.658884 -183 TAAATTGTGTTTTTACTATTAAAAAATAAA 3 39 0 TTTTACTATT 0.904112 -159 TTCAAACCAATTTTGTTAAATAGAAACAAG 3 71 0 TTTTGTTAAA 0.638811 -127 AGGCTATCAATTTTGCTGTAAAAAATTAAG 3 103 1 TTTTGCTGTA 0.908287 -95 TTATGCTAATTTTTGATAAAAAATATCTTA 3 129 0 TTTTGATAAA 0.849044 -69 TAACAATTTTTTATGCTAATTTTTGATAAA 3 139 0 TTATGCTAAT 0.945784 -59 TAAAAAATTGTTATACTAATTAACGTTTTT 3 156 1 TTATACTAAT 0.903971 -42 AATTAACGTTTTTTATTGAAAATTAAGTAT 3 173 1 TTTTATTGAA 0.886173 -25 AGTCAGTATTTTtTCTTAATGTGCATCTTG 4 11 0 TTtTCTTAAT 0.849727 -42 ********** Masking position 2 Map Score: 14.586 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 639 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TTGCAAAATAACTAACTAAATACTAGAAGA 1 18 0 ACTAACTAAA 0.890686 -141 GTAAATCACAACTATAAAACTAATCCTTTT 1 48 0 ACTATAAAAC 0.975041 -111 TTTTGGTATCTCTATAAAAAGTAGTATCAA 1 79 1 TCTATAAAAA 0.822429 -80 TATAAAAAGTAGTATCAAACATTTTTTTAT 1 91 1 AGTATCAAAC 0.927774 -68 TTGTGTTTTTACTATTAAAAAATAAACAGA 3 35 0 ACTATTAAAA 0.963955 -163 TAGTAAAAACACAATTTAACCTTGTTTCTA 3 51 1 ACAATTTAAC 0.898151 -147 TAACCTTGTTTCTATTTAACAAAATTGGTT 3 67 1 TCTATTTAAC 0.945504 -131 AAATTGTTATACTAATTAACGTTTTTTATT 3 160 1 ACTAATTAAC 0.965936 -38 CTTAATTTTCAATAAAAAACGTTAATTAGT 3 170 0 AATAAAAAAC 0.663908 -28 TTGAAAATTAAGTATTTAAA 3 188 1 AGTATTTAAA 0.890561 -10 ********** Masking position 4 Map Score: 9.99425 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 228 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 ********** No masking Map Score: 3.15071e-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 5 ********** No masking Map Score: 3.15071e-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 6 ********** No masking Map Score: 3.15071e-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