AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_mgen_reg_300.orf -o00450_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/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 MG014 239 ABC transporter, ATP-binding protein #2 MG015 46 ABC transporter, ATP-binding protein #3 MG017 65 ATP-dependent RNA helicase, putative #4 MG018 188 ATP-dependent RNA helicase, putative #5 MG019 41 heat shock protein (dnaJ) #6 MG040 158 lipoprotein, putative #7 MG042 197 spermidine/putrescine ABC transporter, ATP-binding protein (potA) Motif number 1 ATTTTGGTTAAATTAAAATTGTTATAATAATTA 1 172 0 AATTAATGTT 0.985263 -68 ACCCCTCGAATTTTAACAGTTTTTATAATCAAA 1 205 1 TTTTAATTTT 0.78792 -35 AAAATTAGCTGTTTTGATTATAAAA 1 225 0 AATTAGTTTT 0.926408 -15 TGAAGTAATTAATCTCTTTAAAATCTTTC 2 28 0 AATTAACTTT 0.872449 -19 ATAAATTTAATAGTGTTGAAAGACAAA 3 5 1 ATTTAATGTT 0.952724 -61 GCTGATCAAAAATTAATAATGTTTGTCTTTCAA 3 26 0 AATTAATGTT 0.985274 -40 AAATTGCGCTTTTTAAAACTGTTTTTGATGATT 4 143 1 TTTTAATGTT 0.793964 -46 TTCTGCTAAATCAATGGTTTTGTAATCATCA 4 168 0 AATCAATTTT 0.950971 -21 CAAGAATTATAATTAACACTCTAAGGATGCAAG 5 13 1 AATTAATCTA 0.795795 -29 TAATTAATCTTCTAGTATTTAGTT 6 2 1 AATTAATCTA 0.795794 -157 TCTAGTATTTAGTTAGTTATTTTGCAAAAAAGG 6 21 1 AGTTAGTTTT 0.758649 -138 ACAACTATAAAACTAATCCTTTTTTGCAAAATA 6 38 0 AACTAATTTT 0.950967 -121 TAAAAAGTAGTATCAAACATTTTTTTATCTTTT 6 93 1 TATCAATTTT 0.787637 -66 ACGGTATTTTAGCTAATTATTTTTAGTAAAAAG 6 131 0 AGCTAATTTT 0.828859 -28 TATTTTAATCAATTAAATCTGTTTATTTTTTAA 7 18 1 AATTAATGTT 0.985264 -180 TAAAAACACAATTTAACCTTGTTTCTATTTAAC 7 54 1 ATTTAATGTT 0.952722 -144 GCCTTTTTCAAACCAATTTTGTTAAATAGAAAC 7 74 0 AACCAATGTT 0.852972 -124 TGCTGTAAAAAATTAAGATATTTTTTATCAAAA 7 116 1 AATTAAATTT 0.821883 -82 TTGTTATACTAATTAACGTTTTTTATTGAAAAT 7 163 1 AATTAATTTT 0.984734 -35 TTTTATTGAAAATTAAGTATTTAAA 7 183 1 AATTAATTTA 0.92501 -15 ****** **** Masking position 12 Map Score: 28.3587 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 415 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 ATTTAGCTGATCAAAAATTAATAATGTTTGT 3 33 0 TCAAAAATAA 0.981857 -33 CTCAAAAAACTAATACATCAAAC 4 3 1 CAAAAAATAA 0.928724 -186 TGCTTGTTCATAAAAAAGTAAACGGTTGAAG 4 33 0 TAAAAAATAA 0.971388 -156 AACTAAATACTAGAAGATTAATTA 6 4 0 TAGAAGATAA 0.672682 -155 AAATCACAACTATAAAACTAATCCTTTTTTG 6 45 0 TATAAAATAA 0.893885 -114 TATAGAGATACCAAAAAGTAAATCACAACTA 6 64 0 CCAAAAATAA 0.954084 -95 TGGTATCTCTATAAAAAGTAGTATCAAACAT 6 82 1 ATAAAAATAG 0.623908 -77 TAAAAAGAAATCAAAAGATAAAAAAATGTTT 6 107 0 TCAAAAGTAA 0.89517 -52 ATTTCTTTTTACTAAAAATAATTAGCTAAAA 6 127 1 ACTAAAATAA 0.769218 -32 GTTTTTACTATTAAAAAATAAACAGATTTAA 7 30 0 TTAAAAATAA 0.954873 -168 AATTTTGCTGTAAAAAATTAAGATATTTTTT 7 111 1 TAAAAAATAA 0.971381 -87 ATATTTTTTATCAAAAATTAGCATAAAAAAT 7 133 1 TCAAAAATAG 0.944763 -65 ACGTTTTTTATTGAAAATTAAGTATTTAAA 7 178 1 TTGAAAATAA 0.890372 -20 ******* *** Masking position 5 Map Score: 15.2399 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 308 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 AATAATGGGGATGTAGCTCAACTGATAGAGC 1 40 0 ATGTAGCTAA 0.922377 -200 TTGTTATAATAATTAGTTAAATACCCTTAGG 1 156 0 AATTAGTTAA 0.936954 -84 AAAATTAGCTGTTTTGATTATAA 1 227 0 AATTAGCTTT 0.583641 -13 GCTTTGTTTTATTTAGCTGATCAAAAATTAA 3 43 0 ATTTAGCTAT 0.876618 -23 TTTTATGAAGAATTATTTCAAATAGATTATT 4 73 1 AATTATTTAA 0.729335 -116 AAAACCATTGATTTAGCAGAA 4 178 1 ATTTAGCAAA 0.965212 -11 TTAGTTAGTTATTTTGCAAAAAAGGATTAGT 6 29 1 ATTTTGCAAA 0.828043 -130 AGCTAATTATTTTTAGTAAAAAGAAATCAAA 6 123 0 TTTTAGTAAA 0.441986 -36 TACTAAAAATAATTAGCTAAAATACCGTCAT 6 136 1 AATTAGCTAA 0.978964 -23 CCTTGTTTCTATTTAACAAAATTGGTTTGAA 7 70 1 ATTTAACAAA 0.665252 -128 AAGGCTATCAATTTTGCTGTAAAAAATTAAG 7 102 1 ATTTTGCTTA 0.55219 -96 TTTTGATAAAAAATATCTTAATTTTTTACAG 7 118 0 AAATATCTAA 0.473093 -80 TTTTATCAAAAATTAGCATAAAAAATTGTTA 7 138 1 AATTAGCAAA 0.96927 -60 AAAAAACGTTAATTAGTATAACAATTTTTTA 7 156 0 AATTAGTAAA 0.909658 -42 ATTGAAAATTAAGTATTTAAA 7 187 1 AAGTATTTAA 0.438873 -11 ******** ** Masking position 4 Map Score: 10.7725 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 512 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TGCACTCAGGAGGTTGAGGGT 1 2 0 AGGTTGAGGG 0.935988 -238 TCCCCATTATTGGTGGAAGTAAATGGACTT 1 60 1 TGGTGGAAGT 0.956005 -180 GTGAGGTCGATGGTTCAAGTCCATTTACTT 1 76 0 TGGTTCAAGT 0.952509 -164 ACCCCTGATAAGGGTGAGGTCGATGGTTCA 1 89 0 AGGGTGAGGT 0.935989 -151 AGGGGTATTTTGGTTAAATTAAAATTGTTA 1 181 0 TGGTTAAATT 0.866837 -59 AAAAAGTAAACGGTTGAAGTTTGATGTATT 4 22 0 CGGTTGAAGT 0.976428 -167 AATAGAAACAAGGTTAAATTGTGTTTTTAC 7 53 0 AGGTTAAATT 0.866807 -145 ********** Masking position 7 Map Score: 1.99183 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 79 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 AATTTTAACAGTTTTTATAATCAAAACAGC 1 213 1 GTTTTTATAA 0.577409 -27 GTAAAACCAAGTTCTTGAAAGATTTTAAAG 2 12 1 GTTCTTGAAA 0.788286 -35 AGTAATTAATCTCTTTAAAATCTTTCAAGA 2 24 0 CTCTTTAAAA 0.943245 -23 TGTAGTGCTTGTTCATAAAAAAGTAAACGG 4 39 0 GTTCATAAAA 0.773416 -150 TGAAATAATTCTTCATAAAACCTTTGTAGT 4 63 0 CTTCATAAAA 0.906285 -126 CTTAAATAATCTATTTGAAATAATTCTTCA 4 78 0 CTATTTGAAA 0.855239 -111 GTTTTCAAATCTTCTTAAATAATCTATTTG 4 91 0 CTTCTTAAAT 0.763974 -98 TCAAATTGCGCTTTTTAAAACTGTTTTTGA 4 141 1 CTTTTTAAAA 0.97067 -48 TTTTTGGTATCTCTATAAAAAGTAGTATCA 6 78 1 CTCTATAAAA 0.855143 -81 TGTGTTTTTACTATTAAAAAATAAACAGAT 7 34 0 CTATTAAAAA 0.640625 -164 AACCTTGTTTCTATTTAACAAAATTGGTTT 7 68 1 CTATTTAACA 0.72557 -130 AATTGATAGCCTTTTTCAAACCAATTTTGT 7 85 0 CTTTTTCAAA 0.876417 -113 ********** Masking position 2 Map Score: 6.98479 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 503 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ********** No masking Map Score: -7.08111e-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 7 ********** No masking Map Score: -7.08111e-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 8 ********** No masking Map Score: -7.08111e-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