AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0079 300 hypothetical protein Rv0079 #2 Rv0081 94 hypothetical protein Rv0081 #3 nuoA 300 nuoA #4 nuoH 115 nuoH Motif number 1 TTGGGCCGTTCACGACCCAGCCT 1 3 1 GGGCGTTCAC 0.867955 -298 AGCAGATGCAGCGCATGAGGCTGGGTCGTGA 1 20 0 GCGCTGAGGC 0.955807 -281 TTTGAGTGTGGCAGTTTCCGTCGCTGCGCAG 1 88 0 GCAGTTCCGT 0.728364 -213 CCACACGTGCGCCCAGTAGGCTTTGAGTGTG 1 109 0 GCCCGTAGGC 0.961816 -192 CCTACTGGGCGCACGTGTGGCAACGAGTCGA 1 120 1 GCACTGTGGC 0.906823 -181 GGCCCAACGGCGGCATTTCGTGTGGATCGAC 1 146 0 CGGCTTTCGT 0.753683 -155 CGGAAAATTCGGCTAGTCCGCGGCCCAACGG 1 167 0 GGCTGTCCGC 0.935821 -134 CCGAATTTTCCGGGTGGTGACACAGCCCACA 1 186 1 CGGGGGTGAC 0.808509 -115 GTGACACAGCCCACATTTGGCATGGGACTTT 1 202 1 CCACTTTGGC 0.848371 -99 GGGACTTTCGGCCCTGTCCGCGTCCGTGTCG 1 225 1 GCCCGTCCGC 0.992549 -76 CCTGTCCGCGTCCGTGTCGGCCAGACAAGCT 1 237 1 TCCGGTCGGC 0.769167 -64 CAAGCTTTGGGCATTGGCCACAATCGGGCCA 1 262 1 GCATGGCCAC 0.65649 -39 CTGCTCGGCTTTCGATTGTGGCCCGA 1 285 0 CGGCTTCGAT 0.522943 -16 CCGATTGGCCGCGGGCGGCCCGCACGCAT 2 9 1 CCGCGGCGGC 0.995166 -86 GCGCTTATCAGGGGGTTAGACCAACATTCAT 3 40 1 GGGGTTAGAC 0.494408 -261 TCATACAATTCGCCGGGACGCGCAATCCCCA 3 67 1 CGCCGGACGC 0.978636 -234 GCTGGGTCCGGCGTCGGTCGCTGCGAAGCAA 3 101 0 GCGTGGTCGC 0.907398 -200 CCCACATTCCCGGGGTCAGGCTGGTGCATAC 3 158 0 CGGGTCAGGC 0.63487 -143 CCGGGAATGTGGGGTGGCCGTTGCGCGACTA 3 176 1 GGGGGGCCGT 0.962119 -125 CGGCCCGAAGCCCCGGTTCGTCACGGCAGCC 3 225 1 CCCCGTTCGT 0.868209 -76 GGGCGGTGACCGGGCTGCCGTGACGAACCGG 3 237 0 CGGGTGCCGT 0.904951 -64 GCCCGGTCACCGCCCGGCCGCCGCGCTGGCG 3 253 1 CGCCGGCCGC 0.994472 -48 CCCGGCCGCCGCGCTGGCGGCCCCGTACGAC 3 265 1 GCGCGGCGGC 0.995278 -36 GCGTCTCCCCTTGCCGCGAGCGCGCGT 4 7 1 CCCCTGCCGC 0.988171 -109 CGTACTGGGGGCACCTCCCGCTTGCGGGGGA 4 40 0 GCACTCCCGC 0.878933 -76 CGGGAGGTGCCCCCAGTACGCCGACACACCG 4 51 1 CCCCGTACGC 0.970243 -65 ACTCCTTGCGCGAGGGTCCGCACTGGTACAT 4 88 0 CGAGGTCCGC 0.968548 -28 CCTCGCGCAAGGAGTGGCGGCC 4 104 1 GGAGGGCGGC 0.975803 -12 **** ****** Masking position 10 Map Score: 43.7235 Number of sites scoring better than the average of aligned sites = 101923 Number in coding regions = 95557 Number in noncoding regions = 6366 Number of orfs with sites within 600 bp upstream = 1671 Fraction of orfs with sites within 600 bp upstream = 0.268391 Motif number 2 ACGACCCAGCCTCATGCGCTGCATCTGCTCGCCAACC 1 22 1 CCACCGTCTG 0.983022 -279 CATGTCCAGAGCGAGCCTCAGCTTCTGCGCAGCGACG 1 64 1 GGACCGTCTG 0.912538 -237 TCAGCTTCTGCGCAGCGACGGAAACTGCCACACTCAA 1 81 1 CCAGCGACTG 0.969659 -220 TAGTCCGCGGCCCAACGGCGGCATTTCGTGTGGATCG 1 148 0 CCAGCGTTTC 0.944935 -153 TCCGGGTGGTGACACAGCCCACATTTGGCATGGGACT 1 194 1 GCAGCATTTG 0.911003 -107 GCGGCCCGCACGCATCCGCACTATCTGATAAATTCTT 2 25 1 CCACCCTCTG 0.989949 -70 AGCATTTGTTGTTAATCTCGGCATTTGCC 3 3 0 GTACCGTTTG 0.975908 -298 CTAACCCCCTGATAAGCGCAGCATTTGTTGTTAATCT 3 22 0 GTACCGTTTG 0.975132 -279 CGCCGGGACGCGCAATCCCCAGTTTTGCTTCGCAGCG 3 77 1 CCACCATTTG 0.986244 -224 CGACGCCGGACCCAGCCACGGGTTCTGCTTCGACTCG 3 116 1 CCACCGTCTG 0.975696 -185 ACGGCCACCCCACATTCCCGGGGTCAGGCTGGTGCAT 3 160 0 CCACCGTCAG 0.881417 -141 CTGTGACGGCCCGAAGCCCCGGTTCGTCACGGCAGCC 3 219 1 CGACCGTCGT 0.806498 -82 CCCCAGTACGCCGACACACCGATTTTGATGTACCAGT 4 61 1 CGACCGTTTG 0.945715 -55 * ** * * * **** Masking position 4 Map Score: 23.6203 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 721 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 GGTTGGCGAGCAGATGCAGCGCATGAGGCTGG 1 27 0 CGATGCAGGC 0.958181 -274 CATCTGCTCGCCAACCTCGTACATGTCCAGAG 1 43 1 CAACCTCGAC 0.735921 -258 CGTCGCTGCGCAGAAGCTGAGGCTCGCTCTGG 1 69 0 CGAAGCTGGG 0.962489 -232 ACACGAAATGCCGCCGTTGGGCCGCGGACTAG 1 154 1 CGCCGTTGGC 0.820617 -147 CCGATTGTGGCCAATGCCCAAAGCTTGTCTGG 1 257 0 CAATGCCCAA 0.722851 -44 GGGCCACAATCGAAAGCCGAGCAG 1 287 1 CAAAGCCGGC 0.992772 -14 GGCAAATGCCGAGATTAACAACAA 3 3 1 CAATGCCGGA 0.980569 -298 AGATTAACAACAAATGCTGCGCTTATCAGGGG 3 22 1 CAATGCTGGC 0.96471 -279 GAATGTTGGTCTAACCCCCTGATAAGCGCAGC 3 37 0 CAACCCCCGA 0.932712 -264 TTCGCAGCGACCGACGCCGGACCCAGCCACGG 3 105 1 CGACGCCGAC 0.991972 -196 CGAGTCGAAGCAGAACCCGTGGCTGGGTCCGG 3 121 0 CGAACCCGGG 0.981503 -180 ATGCACCAGCCTGACCCCGGGAATGTGGGGTG 3 160 1 CGACCCCGGA 0.990382 -141 CTGTGACGGCCCGAAGCCCCGGTTCGTCACGG 3 219 1 CGAAGCCCGG 0.97277 -82 GGTCACCGCCCGGCCGCCGCGCTGGCGGCCCC 3 257 1 CGCCGCCGGC 0.99496 -44 * ******* ** Masking position 1 Map Score: 21.6479 Number of sites scoring better than the average of aligned sites = 13277 Number in coding regions = 12384 Number in noncoding regions = 893 Number of orfs with sites within 600 bp upstream = 628 Fraction of orfs with sites within 600 bp upstream = 0.100867 Motif number 4 TTGGGCCGTTCACGACCCAGCCT 1 4 1 GGCCGTTCAC 0.876133 -297 CTTTGAGTGTGGCAGTTTCCGTCGCTGCGC 1 90 0 GGCAGTTTCC 0.839695 -211 GCCGCCGTTGGGCCGCGGACTAGCCGAATT 1 163 1 GGCCGCGGAC 0.62781 -138 TGCCAAATGTGGGCTGTGTCACCACCCGGA 1 194 0 GGGCTGTGTC 0.839489 -107 GCCCACATTTGGCATGGGACTTTCGGCCCT 1 210 1 GGCATGGGAC 0.887495 -91 TGGGACTTTCGGCCCTGTCCGCGTCCGTGT 1 224 1 GGCCCTGTCC 0.908797 -77 ACAAGCTTTGGGCATTGGCCACAATCGGGC 1 261 1 GGCATTGGCC 0.868999 -40 CGTGCGGGCCGCCCGCGGCCAATCGG 2 7 0 GCCCGCGGCC 0.518174 -88 TGTTAATCTCGGCATTTGCC 3 1 0 GGCATTTGCC 0.801577 -300 TTCATACAATTCGCCGGGACGCGCAATCCC 3 66 1 TCGCCGGGAC 0.790192 -235 GCCGGACCCAGCCACGGGTTCTGCTTCGAC 3 120 1 GCCACGGGTT 0.391013 -181 CACCCCACATTCCCGGGGTCAGGCTGGTGC 3 162 0 TCCCGGGGTC 0.899416 -139 AATGTGGGGTGGCCGTTGCGCGACTATGTT 3 181 1 GGCCGTTGCG 0.780576 -120 CCGGGGCTTCGGGCCGTCACAGTGACCTTC 3 211 0 GGGCCGTCAC 0.762336 -90 ACGGCCCGAAGCCCCGGTTCGTCACGGCAG 3 224 1 GCCCCGGTTC 0.937141 -77 CGTCACGGCAGCCCGGTCACCGCCCGGCCG 3 243 1 GCCCGGTCAC 0.916704 -58 GGGGCCGCCAGCGCGGCGGCCGGGCGGTGA 3 259 0 GCGCGGCGGC 0.580977 -42 CCGCGCTGGCGGCCCCGTACGACGGATCAT 3 273 1 GGCCCCGTAC 0.838764 -28 GCGTCTCCCCTTGCCGCGAGCGCGC 4 6 1 TCCCCTTGCC 0.775993 -110 TGCCGCGAGCGCGCGTGTTCCCCCGCAAGC 4 22 1 GCGCGTGTTC 0.843668 -94 CCCCGCAAGCGGGAGGTGCCCCCAGTACGC 4 42 1 GGGAGGTGCC 0.587123 -74 CACTCCTTGCGCGAGGGTCCGCACTGGTAC 4 90 0 GCGAGGGTCC 0.899425 -26 ********** Masking position 10 Map Score: 25.1168 Number of sites scoring better than the average of aligned sites = 49553 Number in coding regions = 46204 Number in noncoding regions = 3349 Number of orfs with sites within 600 bp upstream = 1198 Fraction of orfs with sites within 600 bp upstream = 0.192419 Motif number 5 GGCCGTTCACGACCCAGCCTCATGCGCTGC 1 14 1 GACCCAGCCT 0.478933 -287 GCTCGCTCTGGACATGTACGAGGTTGGCGA 1 50 0 GACATGTACG 0.726018 -251 GACTCGTTGCCACACGTGCGCCCAGTAGGC 1 119 0 CACACGTGCG 0.700855 -182 CCGCCGTTGGGCCGCGGACTAGCCGAATTT 1 164 1 GCCGCGGACT 0.734649 -137 CACGGACGCGGACAGGGCCGAAAGTCCCAT 1 223 0 GACAGGGCCG 0.956054 -78 TTGTCTGGCCGACACGGACGCGGACAGGGC 1 235 0 GACACGGACG 0.963558 -66 CCGATTGGCCGCGGGCGGCCCGCACGC 2 8 1 GCCGCGGGCG 0.983713 -87 AGATAGTGCGGATGCGTGCGGGCCGCCCGC 2 21 0 GATGCGTGCG 0.597714 -74 TCATACAATTCGCCGGGACGCGCAATCCCC 3 67 1 CGCCGGGACG 0.833557 -234 GCCGGACCCAGCCACGGGTTCTGCTTCGAC 3 120 1 GCCACGGGTT 0.416009 -181 GGCTGGTGCATACCTGTGCGAGTCGAAGCA 3 141 0 TACCTGTGCG 0.725024 -160 ACGGCCACCCCACATTCCCGGGGTCAGGCT 3 167 0 CACATTCCCG 0.243701 -134 AATGTGGGGTGGCCGTTGCGCGACTATGTT 3 181 1 GGCCGTTGCG 0.778378 -120 TGCCGTGACGAACCGGGGCTTCGGGCCGTC 3 223 0 AACCGGGGCT 0.622835 -78 GCCGGGCGGTGACCGGGCTGCCGTGACGAA 3 241 0 GACCGGGCTG 0.792111 -60 GCCCGGTCACCGCCCGGCCGCCGCGCTGGC 3 253 1 CGCCCGGCCG 0.747002 -48 CGCGCTGGCGGCCCCGTACGACGGATCATG 3 274 1 GCCCCGTACG 0.95857 -27 GCGTCTCCCCTTGCCGCGAGCGCGCG 4 7 1 CCCCTTGCCG 0.68174 -109 CTTGCGGGGGAACACGCGCGCTCGCGGCAA 4 21 0 AACACGCGCG 0.703043 -95 GGGGGCACCTCCCGCTTGCGGGGGAACACG 4 35 0 CCCGCTTGCG 0.750397 -81 GATTTTGATGTACCAGTGCGGACCCTCGCG 4 81 1 TACCAGTGCG 0.444283 -35 TACCAGTGCGGACCCTCGCGCAAGGAGTGG 4 91 1 GACCCTCGCG 0.928916 -25 ********** Masking position 3 Map Score: 18.7907 Number of sites scoring better than the average of aligned sites = 48710 Number in coding regions = 45373 Number in noncoding regions = 3337 Number of orfs with sites within 600 bp upstream = 1399 Fraction of orfs with sites within 600 bp upstream = 0.224703 Motif number 6 GTTGGCGAGCAGATGCAGCGCATGAGGCTG 1 28 0 AGATGCAGCG 0.94899 -273 GTCGCTGCGCAGAAGCTGAGGCTCGCTCTG 1 70 0 AGAAGCTGAG 0.927078 -231 GATCCACACGAAATGCCGCCGTTGGGCCGC 1 149 1 AAATGCCGCC 0.879073 -152 GGCCACAATCGAAAGCCGAGCAG 1 288 1 GAAAGCCGAG 0.947215 -13 GGCAAATGCCGAGATTAACAACA 3 4 1 AAATGCCGAG 0.953289 -297 GATTAACAACAAATGCTGCGCTTATCAGGG 3 23 1 AAATGCTGCG 0.945996 -278 GTCCGGCGTCGGTCGCTGCGAAGCAAAACT 3 97 0 GGTCGCTGCG 0.845175 -204 GAGTCGAAGCAGAACCCGTGGCTGGGTCCG 3 122 0 AGAACCCGTG 0.786075 -179 TGTGACGGCCCGAAGCCCCGGTTCGTCACG 3 220 1 CGAAGCCCCG 0.831247 -81 GCGGTGACCGGGCTGCCGTGACGAACCGGG 3 236 0 GGCTGCCGTG 0.941664 -65 GTCACCGCCCGGCCGCCGCGCTGGCGGCCC 3 258 1 GGCCGCCGCG 0.977593 -43 ********** Masking position 6 Map Score: 8.54275 Number of sites scoring better than the average of aligned sites = 10762 Number in coding regions = 10044 Number in noncoding regions = 718 Number of orfs with sites within 600 bp upstream = 506 Fraction of orfs with sites within 600 bp upstream = 0.0812721 Motif number 7 TCATGCGCTGCATCTGCTCGCCAACCTCGT 1 33 1 CATCTGCTCG 0.913165 -268 ATTTCGTGTGGATCGACTCGTTGCCACACG 1 133 0 GATCGACTCG 0.986155 -168 CTGATAAATTCTTCAACTCGTCAACCGATG 2 49 1 CTTCAACTCG 0.983328 -46 AGCATTTGTTGTTAATCTCGGCATTTGCC 3 10 0 GTTAATCTCG 0.864281 -291 ACGGGTTCTGCTTCGACTCGCACAGGTATG 3 133 1 CTTCGACTCG 0.992532 -168 CGAAGCCCCGGTTCGTCACGGCAGCCCGGT 3 230 1 GTTCGTCACG 0.958126 -71 ********** Masking position 3 Map Score: 4.07523 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 813 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ********** No masking Map Score: 5.63761e-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: 5.63761e-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: 5.63761e-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