AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_aquae_reg_100.orf -o00910_aquae_100.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 0.99514 -196 TTAAGCTGATTTAGTACCTTTGTTCAATTGTAA 1 70 1 TTACCTTTGT 0.963915 -127 ACGAAAAATTTCCATACCTTTGTAAAAGCGTAT 1 125 1 TCACCTTTGT 0.847813 -72 CTTCCTTCCTCCTTGTAAGTTATT 1 183 0 TTTCCTCCTT 0.982735 -14 AACTTTCATTTTACAACCTCTGTAAGGACTTAC 2 33 1 TTACCTCTGT 0.989548 -88 GTAGTTATGTTTTGTAAGTCCTTACAGAGGTTG 2 46 0 TTAAGTCCTT 0.8271 -75 CCGGAACTTTTTGGCACGTTTTTTGCAAGAGTT 2 79 1 TTACGTTTTT 0.8683 -42 CTTTCACTCCTCCTGAGGAAACTCT 2 106 0 TTTCCTCCTG 0.930065 -15 CTTTTCACCTCCTTCACTCAAACT 3 120 0 TTACCTCCTT 0.99514 -14 TTTCTACCTCCGAGACCTTTAAA 5 1 1 TTACCTCCGA 0.9722 -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 TTTTTCGTGTTTACAATTTTGTTAACATGTT 1 102 0 TTACATTTTG 0.743881 -95 ACAAAGGTATGGAAATTTTTCGTGTTTACAA 1 117 0 GGAAATTTTC 0.925281 -80 ATAACTACCCGGAACTTTTTGGCACGTTTTT 2 71 1 GGAACTTTTG 0.93634 -50 CTCCTCCTGAGGAAACTCTTGCAAAAAACGT 2 94 0 GGAAATCTTG 0.930951 -27 AATTTTGTAGCTACATTTTTGTT 3 3 0 CTACATTTTG 0.811135 -131 GACGCTTTGCGTACAATTTTGTAGCTACATT 3 17 0 GTACATTTTG 0.967058 -117 AACAGTTCTTGGAAACTTTTCTCTGATTGTG 3 50 0 GGAAATTTTC 0.925281 -84 AACAGAACGGGGAGAATTTGGCACGCTTTTT 3 83 1 GGAGATTTGG 0.969546 -51 ACATAGTAAAGGGGAGTTTGCATAAAGTAGA 4 19 0 GGGGATTTGC 0.90771 -126 TGCGAAGTTCGTGAACTTTGCCTTCAGGTGT 4 56 0 GTGAATTTGC 0.860725 -89 ***** ***** Masking position 7 Map Score: 7.23346 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 367 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 ATTCCAACAATAAAAAGGAGGTAAAAA 1 8 0 TAAAAAGGAG 0.874799 -189 AAGTTATACGTATACGGGAGGTAACCT 2 8 0 TATACGGGAG 0.942902 -113 TGTTAAAACAGAACGGGGAGAATTTGGCAC 3 77 1 GAACGGGGAG 0.986196 -57 ATGGACATAGTAAAGGGGAGTTTGCATAAA 4 24 0 TAAAGGGGAG 0.995775 -121 AGTAAGGGCTGTAAGGGAAGAGCCGGA 4 128 1 GTAAGGGAAG 0.941866 -17 CTCAAAACTCTTAAGGGGTGGCAGA 7 16 1 TTAAGGGGTG 0.96891 -15 ********** Masking position 7 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 4 CTTTGTTCAATTGTAAACATGTTAACAAAA 1 87 1 TTGTAAACAT 0.903997 -110 GTTAACAAAATTGTAAACACGAAAAATTTC 1 107 1 TTGTAAACAC 0.960393 -90 TTCCATACCTTTGTAAAAGCGTATTCTGAA 1 134 1 TTGTAAAAGC 0.935496 -63 CTTACAGAGGTTGTAAAATGAAAGTTATAC 2 29 0 TTGTAAAATG 0.934441 -92 GAGGAAACTCTTGCAAAAAACGTGCCAAAA 2 87 0 TTGCAAAAAA 0.946034 -34 CTCAAACTAATTGCAAAAAGCGTGCCAAAT 3 98 0 TTGCAAAAAG 0.985866 -36 AAAGGGGAGTTTGCATAAAGTAGAATAATA 4 13 0 TTGCATAAAG 0.935333 -132 ********** Masking position 5 Map Score: 5.24094 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 132 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 CTTCCTCCTTGTAAGTTATTATGCAATTTCCG 1 171 0 GTAGTTATAT 0.977388 -26 TTTGCATAAAGTAGAATAATATC 4 2 0 GTAAATATAT 0.963589 -143 AGGGCGGTATGATACTATTTTAAAGGTC 5 24 0 GTAGATATAT 0.989456 -18 AATGTAGGATATTCTAATAAAAACT 6 13 0 GTAGATATCT 0.984596 -15 *** **** *** Masking position 7 Map Score: 0.43745 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** 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 7 ********** 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 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