AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -iarcA_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 HI0181 300 formate transporter #2 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #3 HI1088 248 superoxide dismutase (sodA) #4 HI1218 279 L-lactate permease (lctP) #5 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) Motif number 1 ATTCCCCCAGATAATCATCCACTTTTC 1 2 0 ATAATCATTT 0.948879 -299 TCCCATATTAATATTCGCTCAATTTCATACATTCAG 1 89 0 ATATTTATTC 0.844318 -212 GGTTTGTTTAATTAAAGACAAAATTCCCATATTAAT 1 113 0 ATTAACATTC 0.686752 -188 ACAAACTTTGATATTTTGCAAGGTTTGTTTAATTAA 1 134 0 ATATTCATTT 0.968996 -167 GTTTGTTGAAATAATTTTTGCTTTTCTTTGCAATGA 1 164 1 ATAATTCTTC 0.791884 -137 AAATACTTCTATAATTGGTGCTATTTTACTCTCCTC 1 205 0 ATAATTCTTT 0.86346 -96 AAAGTATTAAATTTTCATCAACTTTTTCAATGTCAA 1 259 1 ATTTTCATTT 0.956826 -42 AAAAAATGCTATATAGATCACATTTTTGATATAAAT 2 66 0 ATATACCTTT 0.912179 -235 TCTATATAGCATTTTTTACTATTTTTTATCCTTATG 2 85 1 ATTTTCATTT 0.95682 -216 CAGTATTCTAATATTTGATGAAATTTTCGCAACTCA 3 37 1 ATATTTATTT 0.899504 -212 AGGTTTATTGATTTAAAACAAAATTTAATAAATTCA 3 102 1 ATTTACATTT 0.861859 -147 ACATTTAATGATCTAAATCAATTTTTTTGCTATTAT 3 156 1 ATCTACATTT 0.753065 -93 TTTTTTTGCTATTATTTGCTCAATTTTGGTTATAGA 3 177 1 ATTATCCTTT 0.939452 -72 AATTCTCACTATAATGCGCAAAATTTGGAGAATGAA 4 29 0 ATAATCATTT 0.940021 -251 ASSAATCTTTATCATATTCTATATTCTTCTATTAAT 4 97 1 ATCATCATTC 0.791955 -183 CATTTCTTACATTTTTATTACTATTTGTGTTTAGTT 4 138 0 ATTTTTCTTT 0.884759 -142 AAAATTTAACATTTTGTTCCATTTCTTACATTTTT 4 158 0 ATTTTTCTTC 0.819597 -122 ATTTTATGAGATATTGATCACATTTTCTTAAAATAG 4 189 1 ATATTCCTTT 0.973557 -91 AACGTTAAAAATATTGACCGCACTTTTACGGTCTTT 5 74 0 ATATTCCTTT 0.973633 -40 ***** * * *** Masking position 14 Map Score: 24.9701 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 547 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 ATTCACGGTATTACGCGAATAAAACAAGTTTCAAATT 1 36 1 TTCATAAAAA 0.689454 -265 ATGTATGAAATTGAGCGAATATTAATATGGGAATTTT 1 93 1 TTAATATTAA 0.770022 -208 GAGAGTAAAATAGCACCAATTATAGAAGTATTTGTAG 1 208 1 TACATTATAA 0.49797 -93 TTTGTAGTCGTAAACTTGTTAAAAGTATTAAATTTTC 1 238 1 TAATTAAAAA 0.770015 -63 CTAAGTCAATTAAATAAAATATAACAAATAAGCCCTA 2 22 1 TAAATATAAA 0.542803 -279 ATAAGCCCTATTTTTGTATTTATATCAAAAATGTGAT 2 49 1 TTTTTTATAA 0.751304 -252 ATGTGATCTATATAGCATTTTTTACTATTTTTTATCC 2 79 1 TAATTTTTAA 0.64775 -222 CATAATTATTTTTAAAGGTTAAAAAAACACCAGTTAT 2 161 0 TTATTAAAAA 0.859075 -140 TTGTTGGAACTAATGTTGTTTATACAAAGGAGTTGAG 2 273 1 TATTTTATAA 0.624346 -28 TTGCGAAAATTTCATCAAATATTAGAATACTGTCACT 3 32 0 TTAATATTAA 0.769417 -217 ATCGATAGGTTTATTGATTTAAAACAAAATTTAATAA 3 96 1 TTTTTAAAAA 0.788296 -153 TCATTAAATGTTTTTCCTTTTTTAAAAAGTGAATTTA 3 130 0 TTTTTTTTAA 0.672035 -119 ATAACCAAAATTGAGCAAATAATAGCAAAAAAATTGA 3 173 0 TTAATAATAA 0.832212 -76 AATGTATTCCTTCTATTGTTAAAAACAGATTTCGTTG 3 222 0 TTTTTAAAAA 0.787788 -27 AAAGATTTTTAATGCCATATTAACATTAGCAGGAT 4 70 0 TTAATATTAA 0.770022 -210 TTGTGTTTAGTTATAGCATTAATAGAAGAATATAGAA 4 113 0 TTTTTAATAA 0.845293 -167 TTCCATTTCTTACATTTTTATTACTATTTGTGTTTA 4 141 0 TTCTTATTAA 0.801372 -139 ATGCAAAGCATATACCTATTTTAAGAAAATGTGATCA 4 203 0 TAATTTTAAA 0.553827 -77 GACCGCACTTTTACGGTCTTTATAGGATGGGTTTCTG 5 58 0 TTCTTTATAA 0.766835 -56 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGCAC 5 87 0 TAATTAAAAA 0.770018 -27 ** * ****** * Masking position 10 Map Score: 10.8551 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 608 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 GTCAATTTGATCTAAGTCAATTAAATAA 2 8 1 TGATCTAATC 0.987434 -293 ATCACATTTTTGATATAAATACAAAAATAGG 2 55 0 TGATATAATA 0.774262 -246 ATCAAAAATGTGATCTATATAGCATTTTTTA 2 72 1 TGATCTATTA 0.942733 -229 TTAAATTGACTTATCTACATAATTATTTTTA 2 184 0 TTATCTACTA 0.7676 -117 ATAAACCTATCGATCTACTTCTAAAGAGTTA 3 79 0 CGATCTACTC 0.945363 -170 AAACATTTAATGATCTAAATCAATTTTTTTG 3 154 1 TGATCTAATC 0.987434 -95 TAAGAAAATGTGATCAATATCTCATAAAATT 4 188 0 TGATCAATTC 0.883003 -92 TCACATCTTTTAATCTAACTCTGAGGATATT 4 257 1 TAATCTAATC 0.910652 -23 ******** ** Masking position 7 Map Score: 4.14662 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 65 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AAACTTGTTAAAAGTATTAAATTTTCATCAACTTT 1 249 1 AAAGTTATTT 0.955468 -52 TTAACAAGGCGATGCCTTAAATAATCCCTAATTAC 2 235 0 GATGTTATAT 0.803938 -66 ATCTACTTCTAAAGAGTTATGTGTTTGAGTTGCGA 3 63 0 AAAGTTTTTT 0.848487 -186 GAAGTAGATCGATAGGTTTATTGATTTAAAACAAA 3 89 1 GATATTATAT 0.683132 -160 AACAAAATTTAATAAATTCACTTTTTAAAAAAGGA 3 118 1 AATATTATTT 0.813252 -131 TAAAAAAGGAAAAACATTTAATGATCTAAATCAAT 3 143 1 AAAATTATAT 0.933784 -106 AATAATAGCAAAAAAATTGATTTAGATCATTAAAT 3 158 0 AAAATTATAG 0.726459 -91 AGAATATGATAAAGATTTTTAATGCCATATTAA 4 82 0 AAAGTTTAT 0.154273 -198 AAATGGAANCAAAATGTTAAATTTTATGAGATATT 4 169 1 AAAATTATTT 0.912516 -111 AGTTAGATTAAAAGATGTGATTATTTTATGGATTT 4 242 0 AAAGGTATTT 0.809463 -38 TCTGCCCACCAAAGATTTCATTAATCGGTGGGCTT 5 27 0 AAAGTTATAT 0.96404 -87 **** ** * * ** Masking position 2 Map Score: 3.01054 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 356 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GAATTCCCCCAGATAATCATCCACTTTTC 1 10 0 AGATAATCAT 0.805545 -291 CAAACCTTGCAAAATATCAAAGTTTGTTGA 1 143 1 AAAATATCAA 0.57087 -158 GGAGGAGAGTAAAATAGCACCAATTATAGA 1 204 1 AAAATAGCAC 0.606399 -97 TTACGACTACAAATACTTCTATAATTGGTG 1 221 0 AAATACTTCT 0.442707 -80 TAAAAGTATTAAATTTTCATCAACTTTTTC 1 257 1 AAATTTTCAT 0.589856 -44 AAAATATAACAAATAAGCCCTATTTTTGTA 2 37 1 AAATAAGCCC 0.884802 -264 GTTATTATAGAGATAATCCAAATTGGCGGC 2 136 0 AGATAATCCA 0.676926 -165 TAACCTTTAAAAATAATTATGTAGATAAGT 2 177 1 AAATAATTAT 0.623924 -124 GCGATGCCTTAAATAATCCCTAATTACTCA 2 232 0 AAATAATCCC 0.960492 -69 TCCCATACAAATTATCCTTTCATTCTCC 4 9 1 AAATTATCCT 0.939893 -271 CAGGATTACCAAATTCTCACTATAATGCGC 4 46 0 AAATTCTCAC 0.840364 -234 TAAATCCATAAAATAATCACATCTTTTAAT 4 241 1 AAATAATCAC 0.946227 -39 AAAATATCCTCAGAGTTAGA 4 270 0 AAAATATCCT 0.833782 -10 ********** Masking position 3 Map Score: 3.73935 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 942 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 AATCAAACTCCAACTATTGACATTGA 1 285 0 AACTCCAACA 0.977976 -16 CTAATTACTCAACTCCAATCAGCTAAGTTTA 2 212 0 AACTCCAATA 0.85207 -89 AAATTTTCGCAACTCAAACACATAACTCTTT 3 57 1 AACTCAAACC 0.788468 -192 TATAGACCAAAACCTCAACGAAATCTGTTTT 3 207 1 AACCTCAACA 0.922458 -42 GGTGGGCTTAAAGCCCACCTACAGA 5 5 0 AAGCCCACCA 0.979051 -109 GGTGGGCTTTAAGCCCACCGATTAATGAAAT 5 17 1 AAGCCCACCA 0.979051 -97 GGTGGGCAGAAACCCATCCTATAAAGACCGT 5 52 1 AACCCATCCA 0.862495 -62 ********* * Masking position 2 Map Score: 0.586845 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 141 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 GCAAAAATTATTTCAACAAACTTTGATATT 1 155 0 TTTCAACAAA 0.957218 -146 AGTATTAAATTTTCATCAACTTTTTCAATG 1 261 1 TTTCATCAAC 0.949771 -40 ACAACATTAGTTCCAACAATGATTAACAAG 2 262 0 TTCCAACAAT 0.923982 -39 GTTGCGAAAATTTCATCAAATATTAGAATA 3 40 0 TTTCATCAAA 0.93065 -209 CGAAATCTGTTTTTAACAATAGAAGGAATA 3 225 1 TTTTAACAAT 0.837146 -24 CCACCAAAGATTTCATTAATCGGTGGGCTT 5 27 0 TTTCATTAAT 0.835934 -87 ********** Masking position 5 Map Score: 1.65183 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 307 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 ********** No masking Map Score: 1.21035e-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: 1.21035e-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: 1.21035e-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