AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ioxyR_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0161 215 glutathione reductase (gor) #2 HI0571 122 hydrogen peroxide-inducible genes activator (oxyR) #3 HI1349 273 conserved hypothetical protein Motif number 1 TTAGTTTGAAATGATTTTATGTGAAGCCTAGTAT 1 77 0 ATATTTATGA 0.915466 -139 CAAAAGAGTAAAAAATATTCATAAAACCAATTAC 1 120 1 AAAATATTAA 0.817469 -96 AAAGAATGCTATAAATTGATGTAATTGGTTTTAT 1 140 0 ATAATTATAA 0.950907 -76 AGAATACAAAAAAATTTTAGTTTAAAAAAGGTTC 1 187 1 AAATTTATTA 0.91211 -29 TACAGCACGTAAAATTTAAATTAACAACCAATAG 2 22 0 AAATTTATAA 0.974467 -101 ATTCAATTAAAAGAATAGAATTAATTGATTATGA 2 79 0 AAAATAATAA 0.887032 -44 TTCCCTATAGAAAAATTCAATTAAAAGAATAGAA 2 93 0 AAAATTATAA 0.976604 -30 TATAATTTTTAATATTTTTCCTAAGGATATGTT 3 10 0 AAATTTTTAA 0.959784 -264 TTATTAAATCAAAATTTATTGTTAGCCGCGATAG 3 51 1 AAATTTTTTA 0.855524 -223 AGTTTTAATGAATATTTAATCAAACTATCGCGGC 3 75 0 AAATTTAAAA 0.804622 -199 TTGTTTGTTAAGAAATTGTAATAAATAGAAGCTA 3 131 0 AGAATTTTAA 0.832698 -143 GGCTAAGACTATCAATTATATTGAATAGAACAAT 3 165 1 ATAATTTTGA 0.86066 -109 ATACGTTTCTATAATTTGAAGTGAAATTGTTCTA 3 190 0 ATATTTATGA 0.915466 -84 TTTCTAGTTGAATAATTGAGCTAATGCCCTCCCT 3 238 0 AAAATTATAA 0.97666 -36 ** **** * *** Masking position 4 Map Score: 17.7042 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 354 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 AGCCTAGTATGTAGAATGAAATAGCGTGAT 1 57 0 GTAGAATGAA 0.705804 -159 TTGAAATGATTTTATGTGAAGCCTAGTATG 1 76 0 TTTATGTGAA 0.805388 -140 GAACAGATGATTAGTTTGAAATGATTTTAT 1 91 0 TTAGTTTGAA 0.924395 -125 GATGTAATTGGTTTTATGAATATTTTTTAC 1 127 0 GTTTTATGAA 0.711057 -89 TTCTGCCTAATTTTTATAAAGAATGCTATA 1 161 0 TTTTTATAAA 0.733416 -55 TAAACTAAAATTTTTTTGTATTCTGCCTAA 1 181 0 TTTTTTTGTA 0.567719 -35 CAAAAAAATTTTAGTTTAAAAAAGGTTCAA 1 193 1 TTAGTTTAAA 0.803365 -23 CTATTGGTTGTTAATTTAAATTTTACGTGC 2 22 1 TTAATTTAAA 0.519405 -101 ATTCTATTCTTTTAATTGAATTTTTCTATA 2 92 1 TTTAATTGAA 0.814345 -31 AACAATAAATTTTGATTTAATAAGTACAGT 3 44 0 TTTGATTTAA 0.626933 -230 GCCGCGATAGTTTGATTAAATATTCATTAA 3 75 1 TTTGATTAAA 0.82526 -199 AAGATCACAGTTTTAATGAATATTTAATCA 3 87 0 TTTTAATGAA 0.910071 -187 TGTTAAGAAATTGTAATAAATAGAAGCTAT 3 130 0 TTGTAATAAA 0.610961 -144 AGACTATCAATTATATTGAATAGAACAATT 3 170 1 TTATATTGAA 0.91178 -104 TTTCTATAATTTGAAGTGAAATTGTTCTAT 3 189 0 TTGAAGTGAA 0.672957 -85 ********** Masking position 10 Map Score: 9.7406 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 1187 Number in noncoding regions = 323 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 3 AGATTGTTCAATCTTCCTCACTGTAGATAT 1 15 0 ATCTTCCTCA 0.929835 -201 AGATTGAACAATCTTCCTCTTTTTCTATCA 1 31 1 ATCTTCCTCT 0.955075 -185 TTATGAATATTTTTTACTCTTTTGAACAGA 1 114 0 TTTTTACTCT 0.868699 -102 TTTTTTTGTATTCTGCCTAATTTTTATAAA 1 171 0 TTCTGCCTAA 0.931026 -45 TGTTTTTTCTCCTATTGGTTGTTAA 2 6 1 TTTCTCCTAT 0.941364 -117 TATATCATAATTTTCCCTATAATACAGCAC 2 48 0 TTTTCCCTAT 0.976004 -75 GAGATTTTCCCTATAGAAAAATTC 2 109 0 TTTTCCCTAT 0.976004 -14 ATTTTTAATATTTTTCCTAAGGATATGTT 3 10 0 TTTTTCCTAA 0.974143 -264 ********** Masking position 8 Map Score: 7.63691 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 144 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 AATGCTATAAATTGATGTAATTGGTTTTATGA 1 138 0 ATTGATAATT 0.954762 -78 AAATTATGATATAGTCATAATCAATTAATTCT 2 65 1 ATAGTTAATC 0.965718 -58 AATTAAAAGAATAGAATTAATTGATTATGACT 2 77 0 ATAGATAATT 0.954889 -46 TTTAATAAGTACAGTTATAATTTTTAATATTT 3 27 0 ACAGTTAATT 0.950596 -247 GATCAAGATCACAGTTTTAATGAATATTTAAT 3 89 0 ACAGTTAATG 0.941009 -185 TTGTTAAGAAATTGTAATAAATAGAAGCTATC 3 129 0 ATTGTTAAAT 0.858837 -145 TTGAAGTGAAATTGTTCTATTCAATATAATTG 3 177 0 ATTGTTATTC 0.834663 -97 TAGTTGAATAATTGAGCTAATGCCCTCCCTTT 3 236 0 ATTGATAATG 0.946114 -38 ***** ***** Masking position 9 Map Score: 4.47122 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 147 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 ATACTAGGCTTCACATAAAATCATTTCAAA 1 77 1 TCACATAAAA 0.881387 -139 TCACATAAAATCATTTCAAACTAATCATCT 1 87 1 TCATTTCAAA 0.86213 -129 GAACCTTTTTTAAACTAAAATTTTTTTGTA 1 191 0 TAAACTAAAA 0.921714 -25 ACGTAAAATTTAAATTAACAACCAATAGGA 2 20 0 TAAATTAACA 0.822922 -103 ATAGAAAAATTCAATTAAAAGAATAGAATT 2 91 0 TCAATTAAAA 0.978147 -32 CTGTACTTATTAAATCAAAATTTATTGTTA 3 45 1 TAAATCAAAA 0.822922 -229 TAGAACAATTTCACTTCAAATTATAGAAAC 3 190 1 TCACTTCAAA 0.944618 -84 GCTCAATTATTCAACTAGAAAAAGGAAATT 3 251 1 TCAACTAGAA 0.888891 -23 ********** Masking position 3 Map Score: 3.06985 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 307 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TCTACAGTGAGGAAGATTGAACAATCTTCC 1 18 1 GGAAGATTGA 0.976868 -198 TAGAAAAAGAGGAAGATTGTTCAATCTTCC 1 28 0 GGAAGATTGT 0.990709 -188 TGTATTATAGGGAAAATTATGATATAGTCA 2 52 1 GGAAAATTAT 0.978068 -71 CATATCCTTAGGAAAAATATTAAAAATTAT 3 13 1 GGAAAAATAT 0.946405 -261 ********** Masking position 6 Map Score: 2.19133 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 25 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 TAGAATGAAATAGCGTGATAGAAAAAGAGGA 1 45 0 TAGGTGATAG 0.851543 -171 TTTTCTCCTATTGGTTGTTAATTTAAATTTT 2 15 1 TTGTTGTTAA 0.958648 -108 AAGAATAGAATTAATTGATTATGACTATATC 2 72 0 TTATTGATTA 0.868155 -51 TAAATCAAAATTTATTGTTAGCCGCGATAGT 3 55 1 TTTTTGTTAG 0.875721 -219 TTAGCCGCGATAGTTTGATTAAATATTCATT 3 72 1 TAGTTGATTA 0.832894 -202 TCTTGATCACTTATTTGATAGCTTCTATTTA 3 113 1 TTATTGATAG 0.966146 -161 AGTCTTAGCCTTGTTTGTTAAGAAATTGTAA 3 144 0 TTGTTGTTAA 0.958625 -130 TCTATTCAATATAATTGATAGTCTTAGCCTT 3 163 0 ATATTGATAG 0.836561 -111 *** ******* Masking position 6 Map Score: 3.25739 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 294 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 ********** No masking Map Score: -9.14168e-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 9 ********** No masking Map Score: -9.14168e-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 10 ********** No masking Map Score: -9.14168e-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