AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_Nitrate_Reductase_mtub_reg_300.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 narG 300 narG #2 narH 38 narH #3 narJ 56 narJ Motif number 1 GTGTGGTTGACGGTGGCCGCCGTCAACTTGG 1 14 1 CGGTGCCGCC 0.989748 -287 CCATCGTAATCGCTACGGGCATGCAAACCCA 1 72 0 CGCTAGGGCA 0.957062 -229 CGGAAGTTGTCGCCACGCGTCCAGAAAACCA 1 100 0 CGCCAGCGTC 0.975747 -201 CCGGGCAGGACGCTGACGCCCATCCATCGAG 1 128 1 CGCTGCGCCC 0.993807 -173 CCGATGTTGACGAGAGGGGTCCCCGACCCGG 1 163 1 CGAGAGGGTC 0.988924 -138 CCCGTCAAGCCCCGGTCCGCCGGGTCGGGGA 1 182 0 CCCGGCCGCC 0.965348 -119 CCGGCCGCGCCGCATTGCGCCCGTCAAGCCC 1 201 0 CGCATGCGCC 0.952155 -100 CGCAATGCGGCGCGGCCGGCCAGCCCGTAAC 1 213 1 CGCGGCGGCC 0.951414 -88 TAACGTCCAGCGAGTGCGGTCGCGCGCCGAC 1 240 1 CGAGTCGGTC 0.97953 -61 TGCGGTCGCGCGCCGACGGCCCGGCCCCACA 1 254 1 CGCCGCGGCC 0.895893 -47 TCGTCATGAGCGGTGTGGGGCCGGGCCGTCG 1 267 0 CGGTGGGGGC 0.974825 -34 CCGCTCATGACGAGGAGGGTCATCCC 1 285 1 CGAGGGGGTC 0.9959 -16 CCGCAAGCGTCGCTCGGGCCCTTCATTGG 2 9 0 CGCTCGGCCC 0.967262 -30 GTCTCGTGTCCGAGAGCGGTCGAGCGCCACC 3 18 1 CGAGACGGTC 0.988924 -39 ***** ***** Masking position 1 Map Score: 33.3981 Number of sites scoring better than the average of aligned sites = 16608 Number in coding regions = 15457 Number in noncoding regions = 1151 Number of orfs with sites within 600 bp upstream = 729 Fraction of orfs with sites within 600 bp upstream = 0.11709 Motif number 2 TGTGGTTGACGGTGGCCGCCGTCAACTTGGTTA 1 15 1 GGCCGCCGTC 0.613348 -286 ACTTGGGTTTGCATGCCCGTAGCGATTACGATG 1 69 1 GTCCCGTAGC 0.823415 -232 CGATGGTTTTCTGGACGCGTGGCGACAACTTCC 1 97 1 CGCGCGTGGC 0.986491 -204 CGGGCAGGACGCTGACGCCCATCCATCGAGATA 1 129 1 GGCGCCCATC 0.75021 -172 CCGCCGGGTCGGGGACCCCTCTCGTCAACATCG 1 164 0 GGCCCCTCTC 0.995158 -137 CCGTCAAGCCCCGGTCCGCCGGGTCGGGGACCC 1 179 0 CGCCGCCGGG 0.719512 -122 GGCCGCGCCGCATTGCGCCCGTCAAGCCCCGGT 1 197 0 CTCGCCCGTC 0.959515 -104 GACGTTACGGGCTGGCCGGCCGCGCCGCATTGC 1 214 0 GGCCGGCCGC 0.50367 -87 GCCGTCGGCGCGCGACCGCACTCGCTGGACGTT 1 241 0 CGCCGCACTC 0.954872 -60 CGGTGTGGGGCCGGGCCGTCGGCGCGCGACCGC 1 255 0 CGCCGTCGGC 0.509458 -46 GGGATGACCCTCCTCGTCATGAGCG 1 286 0 GGCCCTCCTC 0.867514 -15 CGTCTCGCTCCGCAAGCGTCGCT 2 26 0 CCCGCTCCGC 0.905013 -13 AGTTGCTGTCTCGTGTCCGAGAGCGGT 3 5 1 GGCTCGTGTC 0.920583 -52 TGTGGTGGCGCTCGACCGCTCTCGGACACGAGA 3 19 0 CGCCGCTCTC 0.991078 -38 * * ******** Masking position 6 Map Score: 26.6627 Number of sites scoring better than the average of aligned sites = 21466 Number in coding regions = 19896 Number in noncoding regions = 1570 Number of orfs with sites within 600 bp upstream = 857 Fraction of orfs with sites within 600 bp upstream = 0.137649 Motif number 3 ATCGTAATCGCTACGGGCATGCAAACCCAAG 1 70 0 CTCGGGCATG 0.820819 -231 TGGCGACAACTTCCGGGCAGGACGCTGACGC 1 116 1 TTCGGGCAGG 0.993431 -185 GTCCCCGACCCGGCGGACCGGGGCTTGACGG 1 181 1 CGCGGACCGG 0.991127 -120 GACCGGGGCTTGACGGGCGCAATGCGGCGCG 1 196 1 TGCGGGCGCA 0.960732 -105 GGCGCAATGCGGCGCGGCCGGCCAGCCCGTA 1 211 1 GGGCGGCCGG 0.946651 -90 TCGCTGGACGTTACGGGCTGGCCGGCCGCGC 1 222 0 TTCGGGCTGG 0.987814 -79 GCGAGTGCGGTCGCGCGCCGACGGCCCGGCC 1 249 1 TCCGCGCCGA 0.93417 -52 TCATGAGCGGTGTGGGGCCGGGCCGTCGGCG 1 264 0 TGGGGGCCGG 0.997516 -37 ACACCGCTCATGACGAGGAGGGTCATCCC 1 282 1 TGCGAGGAGG 0.858074 -19 CCAATGAAGGGCCCGAGCGACGCTT 2 5 1 TGAGGGCCCG 0.980692 -34 CGAGCGACGCTTGCGGAGCGAGACG 2 24 1 TTCGGAGCGA 0.83253 -15 GCTCGACCGCTCTCGGACACGAGACAGCAAC 3 12 0 TCCGGACACG 0.936638 -45 CCCTCATTGTGGTGGCGCTCGACCGCTCTCG 3 28 0 GGGGCGCTCG 0.779135 -29 GCCACCACAATGAGGGACCGACTG 3 43 1 TGGGGACCGA 0.974888 -14 ** ******** Masking position 5 Map Score: 19.0372 Number of sites scoring better than the average of aligned sites = 23693 Number in coding regions = 22021 Number in noncoding regions = 1672 Number of orfs with sites within 600 bp upstream = 943 Fraction of orfs with sites within 600 bp upstream = 0.151462 Motif number 4 GTTGTTCTAACCAAGTTGACGGCGGCCACC 1 25 0 CCAAGTTGAC 0.990141 -276 CTTGGTTAGAACAACGTGACAAAACGTTAA 1 40 1 ACAACGTGAC 0.960668 -261 GCATGCAAACCCAAGTTAACGTTTTGTCAC 1 55 0 CCAAGTTAAC 0.971375 -246 GTCCAGAAAACCATCGTAATCGCTACGGGC 1 83 0 CCATCGTAAT 0.947451 -218 TGACGCCCATCCATCGAGATACCCGATGTT 1 141 1 CCATCGAGAT 0.929398 -160 TCGAGATACCCGATGTTGACGAGAGGGGTC 1 154 1 CGATGTTGAC 0.95838 -147 ********** Masking position 3 Map Score: 3.44248 Number of sites scoring better than the average of aligned sites = 2100 Number in coding regions = 1957 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 ********** No masking Map Score: 8.19556e-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 6 ********** No masking Map Score: 8.19556e-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 7 ********** No masking Map Score: 8.19556e-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