AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_hinf_reg_100.orf -o00480_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0111 300 glutathione transferase (bphH) #2 HI0161 215 glutathione reductase (gor) #3 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #4 HI0559 194 sulfite synthesis pathway protein (cysQ) Motif number 1 TGTTTTAAATTTTTTGGTATTCAAGCCAATTAG 1 49 1 TTTTTGTTTA 0.889953 -252 AATTAGGAACTTTATTCTATTATAAAATTATAT 1 76 1 TTTATCTTTT 0.948033 -225 TAGAAAATTTATCTTTCAATTGACATCAATATC 1 117 1 ATCTTCATTA 0.634319 -184 TTTGATATGTTTTTTAGAGTAATGTTCTGGATA 1 146 0 TTTTTGATAT 0.702228 -155 TTAAAATTGCTTCTTACTATTGTTTAATCGTAA 1 209 0 TTCTTCTTTT 0.953761 -92 TATTGATGGAATTATACTGTTTTATACGTGGAA 1 253 0 ATTATCTTTT 0.932918 -48 AGATTGAACAATCTTCCTCTTTTTCTATCACGC 2 31 1 ATCTTCTTTT 0.926602 -185 TTATGAATATTTTTTACTCTTTTGAACAGATGA 2 111 0 TTTTTCTTTT 0.973782 -105 ATTACATCAATTTATAGCATTCTTTATAAAAAT 2 149 1 TTTATGCTTT 0.76798 -67 AAACTAAAATTTTTTTGTATTCTGCCTAATTTT 2 177 0 TTTTTGTTTT 0.945129 -39 ATACAAAAAAATTTTAGTTTAAAAAAGGTTCAA 2 190 1 ATTTTGTTAA 0.696492 -26 TTCGATTGGTTTTTTTCTCTAGAATACGGCATT 3 15 1 TTTTTCTTAA 0.891149 -61 AATTATTCCTTATTCGGCTTCCGA 3 62 0 ATTATCCTAT 0.673377 -14 GGAATGGTATTTTATGCTCTATTTGTAATGCCG 4 19 1 TTTATCTTAT 0.914182 -176 TCAGCATAAAATTATTCTCTTGTTTTTGGCAGC 4 57 0 ATTATCTTTT 0.932936 -138 GCGTGTTGTCTTCTTTCAATTCAACATGAACCT 4 170 0 TTCTTCATTA 0.739191 -25 ***** ** ** * Masking position 5 Map Score: 14.8493 Number of sites scoring better than the average of aligned sites = 1256 Number in coding regions = 925 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 2 CTTTGATAATAAAAAAGCGTGGAAAT 1 1 0 AAAAAATAAT 0.975237 -300 AAAGCCTTACAATAACTGTTTTAAATTTTTTGGTAT 1 33 1 AATAACTAAT 0.928476 -268 CATTACTCTAAAAAACATATCAAAGTATCTAAATTG 1 155 1 AAAAACTAAT 0.98928 -146 TATTCCACGTATAAAACAGTATAATTCCATCAATAG 1 251 1 ATAAAATAAT 0.847132 -50 GGCTTCACATAAAATCATTTCAAACTAATCATCTGT 2 83 1 AAAATCTAAT 0.928497 -133 TAATTTTTATAAAGAATGCTATAAATTGATGTAATT 2 148 0 AAAGAATAAT 0.891462 -68 ATTTTAGTTTAAAAAAGGTTCAAACT 2 200 1 AAAAAATAAT 0.975238 -16 TTCTAGAGAAAAAAACCAATCGAACCAA 3 3 0 AAAAACTAAC 0.950608 -73 CTGTTTTTGATAAAACTGTTGCAAATGCTTACCTGA 4 136 0 TAAAACTAAT 0.928498 -59 CAGTTTTATCAAAAACAGGTTCATGTTGAATTGAAA 4 154 1 AAAAACTATT 0.928492 -41 ****** * ** * Masking position 10 Map Score: 9.96747 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 88 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TATTATAAAATTATATCTATAACATAGAAA 1 93 1 TTATATCTAT 0.883659 -208 ATCTTTCAATTGACATCAATATCCAGAACA 1 127 1 TGACATCAAT 0.916996 -174 TGAACTAATATTATAACAATTTAGATACTT 1 177 0 TTATAACAAT 0.96357 -124 AATATCTAACTTATTAAAATTGCTTCTTAC 1 225 0 TTATTAAAAT 0.68893 -76 AACAGTATAATTCCATCAATAGCTCATAAA 1 265 1 TTCCATCAAT 0.959272 -36 ATAAAACCAATTACATCAATTTATAGCATT 2 140 1 TTACATCAAT 0.976522 -76 ATAGCATTCTTTATAAAAATTAGGCAGAAT 2 162 1 TTATAAAAAT 0.858124 -54 GCGTGTTGTCTTCTTTCAATTCAACATGAA 4 173 0 TTCTTTCAAT 0.897926 -22 ********** Masking position 9 Map Score: 4.83532 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 215 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GTTATAGATATAATTTTATAATAGAATAAA 1 86 0 TAATTTTATA 0.958797 -215 TAAAGTGAACTAATATTATAACAATTTAGA 1 182 0 TAATATTATA 0.876055 -119 TAGTTTGAAATGATTTTATGTGAAGCCTAG 2 80 0 TGATTTTATG 0.982641 -136 TTGATGTAATTGGTTTTATGAATATTTTTT 2 129 0 TGGTTTTATG 0.962265 -87 AACAAGAGAATAATTTTATGCTGACGCTAA 4 66 1 TAATTTTATG 0.981287 -129 ********** Masking position 6 Map Score: 3.07396 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 51 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TCAATATCCAGAACATTACTCTAAAAAACA 1 142 1 GAACATTACT 0.900716 -159 CTCTAGAATACGGCATTATTTTCGACATTA 3 31 1 CGGCATTATT 0.968821 -45 GCATTATTTTCGACATTACTCGGAAGCCGA 3 43 1 CGACATTACT 0.986292 -33 GCAGCAACCACGGCATTACAAATAGAGCAT 4 32 0 CGGCATTACA 0.980111 -163 GGTAAGCAATCAGCAATACTTGGTTAAGTA 4 104 0 CAGCAATACT 0.956285 -91 ********** Masking position 5 Map Score: 2.55413 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 93 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ATTTCCACGCTTTTTTATTATCAAAGCCTT 1 10 1 CTTTTTATTA 0.891236 -291 CTTACAATAACTGTTTTAAATTTTTTGGTAT 1 38 1 CTTTTTAAAT 0.883948 -263 GAACTTTATTCTATTATAAAATTATATCTAT 1 82 1 CTTTATAAAA 0.75208 -219 TAGTAAGAAGCAATTTTAATAAGTTAGATAT 1 223 1 CATTTTAATA 0.711194 -78 TGGAATTATACTGTTTTATACGTGGAATATC 1 249 0 CTTTTTATAC 0.962724 -52 CAATCTTCCTCTTTTTCTATCACGCTATTTC 2 39 1 CTTTTCTATC 0.77781 -177 TTCTATCACGCTATTTCATTCTACATACTAG 2 53 1 CTTTTCATTC 0.911086 -163 ATATTTTTTACTCTTTTGAACAGATGATTAG 2 107 0 CTTTTTGAAC 0.928963 -109 AGTTTGAACCTTTTTTAAACTAAAATTTTT 2 196 0 CTTTTTAAAC 0.980086 -20 ** ******** Masking position 5 Map Score: 3.8533 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 205 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 TAGAATAAAGTTCCTAATTGGCTTGAATACCAAA 1 61 0 TCTATGGCTT 0.996842 -240 TATTTCATTCTACATACTAGGCTTCACATAAAAT 2 64 1 TCTATGGCTT 0.996847 -152 AATTATTCCTTATTCGGCTTCCGAGTAATG 3 56 0 TCTATGGCTT 0.996847 -20 * * ** * ***** Masking position 6 Map Score: 0.252052 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: -1.53234e-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 9 ********** No masking Map Score: -1.53234e-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 10 ********** No masking Map Score: -1.53234e-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