AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifur_hpyl_opreg_300.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP1024 167 co-chaperone-curved DNA binding protein A (CbpA) #2 HP1027 159 ferric uptake regulation protein (fur) #3 HP1339 262 biopolymer transport protein (exbB) Motif number 1 CTCATCGTGGATTTAAACTCAATATTTTAGTTA 1 17 1 ATTTAACAAT 0.98258 -151 ATTAAAAGGAATTTTAACTAAAATATTGAGTTT 1 31 0 ATTTAAAAAA 0.782596 -137 AAATAGTTTTATTAGAATACTATCATAAATCTT 1 133 0 ATTAAACTAT 0.965599 -35 TATAAGTTACATTAAAATGCGACAATGGTAATA 2 14 1 ATTAAACGAC 0.910203 -146 GACAATGGTAATAAAAAATCAATATTTTTGGAT 2 34 1 ATAAAACAAT 0.975652 -126 ACTCATTATTATTTTAATTCAATCCAAAAATAT 2 55 0 ATTTAACAAT 0.958669 -105 TTATTATACAATAATAATGCGATGAAACATAGA 2 92 0 ATAAAACGAT 0.94521 -68 ATAATTGTTCATTTTAAATTAATTCAATCATAC 3 61 0 ATTTAATAAT 0.837243 -202 AAAATGAACAATTATAATACAAACTGGATTTAA 3 79 1 ATTAAACAAA 0.965323 -184 TAAGCTAATAATTACAATCAAATCCAAACGCTC 3 126 0 ATTAAAAAAT 0.85757 -137 TGTTTTAATAATAACAAGTCAATAATGATTAAG 3 155 0 ATAAAACAAT 0.975652 -108 ACTTGTTATTATTAAAACAATATAATCAACAAA 3 169 1 ATTAAAATAT 0.885012 -94 **** ** **** Masking position 7 Map Score: 16.6974 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 217 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 AGCGCAATTAAAAGGAATTTTAACTAAAATA 1 39 0 AAAGGATTTT 0.971745 -129 TGCATTATCTAAAAGCATTATCAATAAACTT 1 87 1 AAAAGCTTAT 0.883929 -81 TGACTAACACTAAAGATTTATGATAGTATTC 1 121 1 TAAAGATTAT 0.923537 -47 GATCACCTTTAAAATAGTTTTATTAGAATAC 1 146 0 AAAATATTTT 0.876392 -22 ATTCAATCCAAAAATATTGATTTTTTATTAC 2 41 0 AAAATATGAT 0.786387 -119 ATTAAAATAATAATGAGTTTTATCTATGTTT 2 70 1 TAATGATTTT 0.92504 -90 CTTATCCGTAAAATGATTTTTATAACTAGAA 2 127 0 AAATGATTTT 0.972735 -33 TCATGCCAAAAAAGGATTTTTCTCAA 3 6 0 AAAGGATTTT 0.986418 -257 CCAAAATGATAAAGGAATGTTGGTTTGTTGA 3 194 0 AAAGGATGTT 0.976721 -69 ****** **** Masking position 8 Map Score: 9.63379 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 548 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 AAAACTCATCGTGGATTTAAACTCAATATT 1 13 1 GTGGATTTAA 0.969818 -155 TATCAATAAACTTGATTGACTAACACTAAA 1 105 1 CTTGATTGAC 0.920228 -63 ATCAATATTTTTGGATTGAATTAAAATAAT 2 51 1 TTGGATTGAA 0.988224 -109 CTCATGCTAGTATGATTGAATTAATTTAAA 3 52 1 TATGATTGAA 0.878197 -211 ATAATACAAACTGGATTTAAATGGTTGGTC 3 92 1 CTGGATTTAA 0.98342 -171 ATAAGAGCGTTTGGATTTGATTGTAATTAT 3 122 1 TTGGATTTGA 0.952622 -141 ********** Masking position 5 Map Score: 3.4357 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 157 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 AATCAAGTTTATTGATAATGCTTTTAGATA 1 92 0 ATTGATAATG 0.853803 -76 AAAATGCGACAATGGTAATAAAAAATCAAT 2 27 1 AATGGTAATA 0.844447 -133 ATTGAATTAAAATAATAATGAGTTTTATCT 2 65 1 AATAATAATG 0.973556 -95 ATTATTATACAATAATAATGCGATGAAACA 2 96 0 AATAATAATG 0.973556 -64 ATTATTATTGTATAATAATATTCTAGTTAT 2 107 1 TATAATAATA 0.722246 -53 ATTTAAAATGAACAATTATAATACAAACTG 3 75 1 AACAATTATA 0.692249 -188 TGATTAAGCTAATAATTACAATCAAATCCA 3 133 0 AATAATTACA 0.857814 -130 ACAAGTCAATAATGATTAAGCTAATAATTA 3 145 0 AATGATTAAG 0.872881 -118 ATATTGTTTTAATAATAACAAGTCAATAAT 3 162 0 AATAATAACA 0.931402 -101 AATGCTCCAAAATGATAAAGGAATGTTGGT 3 201 0 AATGATAAAG 0.938251 -62 ********** Masking position 6 Map Score: 8.33901 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 227 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TCATCGTGGATTTAAACTCAATATTTTAGT 1 18 1 TTTAAACTCA 0.819945 -150 TTAAAAGGAATTTTAACTAAAATATTGAGT 1 33 0 TTTTAACTAA 0.66022 -135 TTTAAACCCGTTTCAGCGCAATTAAAAGGA 1 54 0 TTTCAGCGCA 0.962417 -114 ATCTGCATTATCTAAAAGCATTATCAATAA 1 84 1 TCTAAAAGCA 0.906837 -84 TTAAAATAGTTTTATTAGAATACTATCATA 1 139 0 TTTATTAGAA 0.61666 -29 TTTATCTATGTTTCATCGCATTATTATTGT 2 88 1 TTTCATCGCA 0.896405 -72 CATGAGCGGCTTTTAACGAACTCATGCCAA 3 28 0 TTTTAACGAA 0.9265 -235 TCCTTTATCATTTTGGAGCATTTATGCGAA 3 209 1 TTTTGGAGCA 0.811802 -54 TTTTGGAGCATTTATGCGAACGAATGCTTC 3 219 1 TTTATGCGAA 0.900595 -44 GAGCATGCACTCTTTAAGAAGCATTCGTTC 3 236 0 TCTTTAAGAA 0.652826 -27 ACTCTAAGAGCATGCACTCTTT 3 251 0 TCTAAGAGCA 0.9261 -12 ********** Masking position 10 Map Score: 4.96845 Number of sites scoring better than the average of aligned sites = 1844 Number in coding regions = 1672 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 ********** No masking Map Score: 1.65089e-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: 1.65089e-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: 1.65089e-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