AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_aquae_reg_300.orf -o00910_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 glnB 196 nitrogen regulatory PII protein #2 nirB 120 nitrite reductase (NAD(P)H) large subunit #3 fhp 133 flavohemoprotein #4 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #5 cysM 41 cysteine synthase, O-acetylserine (thiol) lyase B #6 aq_1558 27 putative protein #7 gltB 30 glutamate synthase large subunit Motif number 1 TTTTTACCTCCTTTTTATTGTTG 1 1 1 TTACCTCCTT 0.994855 -196 TTAAGCTGATTTAGTACCTTTGTTCAATTGTAA 1 70 1 TTACCTTTGT 0.961872 -127 ACGAAAAATTTCCATACCTTTGTAAAAGCGTAT 1 125 1 TCACCTTTGT 0.840283 -72 CTTCCTTCCTCCTTGTAAGTTATT 1 183 0 TTTCCTCCTT 0.981737 -14 AACTTTCATTTTACAACCTCTGTAAGGACTTAC 2 33 1 TTACCTCTGT 0.988939 -88 GTAGTTATGTTTTGTAAGTCCTTACAGAGGTTG 2 46 0 TTAAGTCCTT 0.818764 -75 CCGGAACTTTTTGGCACGTTTTTTGCAAGAGTT 2 79 1 TTACGTTTTT 0.861618 -42 CTTTCACTCCTCCTGAGGAAACTCT 2 106 0 TTTCCTCCTG 0.926251 -15 CTTTTCACCTCCTTCACTCAAACT 3 120 0 TTACCTCCTT 0.994855 -14 TTTCTACCTCCGAGACCTTTAAA 5 1 1 TTACCTCCGA 0.970612 -41 ** ******** Masking position 9 Map Score: 12.1672 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 418 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 CGTATTCTGAAATTGGCACGGAAATTGCAT 1 153 1 AATTGGCACG 0.934678 -44 CTTGTAAGTTATTATGCAATTTCCGTGCCA 1 166 0 ATTATGCAAT 0.874133 -31 ACCCGGAACTTTTTGGCACGTTTTTTGCAA 2 77 1 TTTTGGCACG 0.98898 -44 TTTGGCACGTTTTTTGCAAGAGTTTCCTCA 2 88 1 TTTTTGCAAG 0.984008 -33 AACGGGGAGAATTTGGCACGCTTTTTGCAA 3 88 1 ATTTGGCACG 0.985698 -46 TTTGGCACGCTTTTTGCAATTAGTTTGAGT 3 99 1 TTTTTGCAAT 0.954093 -35 ATTATTCTACTTTATGCAAACTCCCCTTTA 4 14 1 TTTATGCAAA 0.836845 -131 ********** Masking position 8 Map Score: 6.56602 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 58 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 CTTGAGTTGAGCTAAAATGTTTATTTAAAT 1 36 0 GCTAAAATGT 0.963427 -161 AAACATGTTAACAAAATTGTAAACACGAAA 1 101 1 ACAAAATTGT 0.894133 -96 CAAAAAACGTGCCAAAAAGTTCCGGGTAGT 2 74 0 GCCAAAAAGT 0.946677 -47 AACAAAAATGTAGCTACAAAA 3 2 1 ACAAAAATGT 0.972096 -132 AAATGTAGCTACAAAATTGTACGCAAAGCG 3 16 1 ACAAAATTGT 0.894133 -118 CAAAAAGCGTGCCAAATTCTCCCCGTTCTG 3 85 0 GCCAAATTCT 0.942855 -49 ********** Masking position 5 Map Score: 5.69109 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 17 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TTTTTACCTCCTTTTTATTGTTGGAAT 1 8 1 CTCCTTTTTA 0.872299 -189 AGGTTACCTCCCGTATACGTATAACTT 2 8 1 CTCCCGTATA 0.941672 -113 GTGCCAAATTCTCCCCGTTCTGTTTTAACA 3 77 0 CTCCCCGTTC 0.985885 -57 TTTATGCAAACTCCCCTTTACTATGTCCAT 4 24 1 CTCCCCTTTA 0.995679 -121 TCCGGCTCTTCCCTTACAGCCCTTACT 4 128 0 CTTCCCTTAC 0.940614 -17 TCTGCCACCCCTTAAGAGTTTTGAG 7 16 0 CACCCCTTAA 0.968221 -15 ********** Masking position 4 Map Score: 3.22162 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 328 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TACAAAGGTATGGAAATTTTTCGTGTTTAC 1 119 0 TGGAAATTTT 0.86455 -78 TGCCAATTTCAGAATACGCTTTTACAAAGG 1 141 0 AGAATACGCT 0.853779 -56 ACTCCTCCTGAGGAAACTCTTGCAAAAAAC 2 96 0 AGGAAACTCT 0.984775 -25 TCTCTGATTGTGGAGACGCTTTGCGTACAA 3 32 0 TGGAGACGCT 0.962964 -102 TAACAGTTCTTGGAAACTTTTCTCTGATTG 3 52 0 TGGAAACTTT 0.959015 -82 AATGTAGGATATTCTAATAAAAACT 6 13 0 AGGATATTCT 0.800881 -15 ATACTCTCAAAACTCTTAAGGGGTGG 7 7 1 TCAAAACTCT 0.818123 -24 ********** Masking position 6 Map Score: 2.93217 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 501 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CCTTTGTTCAATTGTAAACATGTTAACAAA 1 86 1 ATTGTAAACA 0.989562 -111 TGTTTACAATTTTGTTAACATGTTTACAAT 1 96 0 TTTGTTAACA 0.899991 -101 TGTTAACAAAATTGTAAACACGAAAAATTT 1 106 1 ATTGTAAACA 0.989562 -91 TAGCTACAAAATTGTACGCAAAGCGTCTCC 3 21 1 ATTGTACGCA 0.951545 -113 ACTCAAACTAATTGCAAAAAGCGTGCCAAA 3 99 0 ATTGCAAAAA 0.89374 -35 ********** Masking position 3 Map Score: 2.35176 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 18 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ACGAAAAATTTCCATACCTTTGTAAAAGCGT 1 125 1 TCCTACCTTT 0.8904 -72 AACATAACTACCCGGAACTTTTTGGCACGTT 2 68 1 CCCGAACTTT 0.993098 -53 AGAAAAGTTTCCAAGAACTGTTAAAACAGAA 3 59 1 CCAGAACTGT 0.967703 -75 GCCAAATTCTCCCCGTTCTGTTTTAACAGTT 3 74 0 CCCGTTCTGT 0.920968 -60 CCTGCGAAGTTCGTGAACTTTGCCTTCAGGT 4 58 0 TCGGAACTTT 0.970928 -87 TTTCTACCTCCGAGACCTTTAAAATAGTAT 5 10 1 CCGGACCTTT 0.990714 -32 *** ******* Masking position 9 Map Score: 2.1612 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 274 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: -6.15168e-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 9 ********** No masking Map Score: -6.15168e-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 10 ********** No masking Map Score: -6.15168e-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