AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00471_mtub_reg_300.orf -o00471_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 Rv1335 21 hypothetical protein Rv1335 #2 murE 22 murE #3 hypothetical 267 hypothetical protein Rv2160c #4 Rv2161c 102 hypothetical protein Rv2161c #5 PE_PGRS 209 PE_PGRS #6 Rv2166c 300 hypothetical protein Rv2166c Motif number 1 GTGTGCGCGCCCTGTCGGTAGG 2 5 1 GCGCGCCCTG 0.925294 -18 CGCCGACGTCGGCCGCCAAAC 3 2 1 GCCGACGTCG 0.956155 -266 AGGATCTGCGCCCGGGTTTGGCGGCCGACG 3 17 0 CCCGGGTTTG 0.928336 -251 CGCAGATCCTGCGCGCCGCGATGGATATCG 3 37 1 GCGCGCCGCG 0.543505 -231 CGATGGATATCGCCTCGGTGAAGGGGCTCT 3 55 1 CGCCTCGGTG 0.683982 -213 AAGGGGCTCTCGGGGCTGTCCATCGGCGAG 3 75 1 CGGGGCTGTC 0.88841 -193 GCTGTCCATCGGCGAGCTTGCCGGGCGGCT 3 89 1 GGCGAGCTTG 0.744379 -179 GAGCTTGCCGGGCGGCTGGGCATGAGCAAG 3 102 1 GGCGGCTGGG 0.700742 -166 CCGGAACAGGCCCGACTTGCTCATGCCCAG 3 117 0 CCCGACTTGC 0.861724 -151 AGCTGCAGCTGGCGACCGTCGAGGCCGCCG 3 166 1 GGCGACCGTC 0.899022 -102 CGACCGTCGAGGCCGCCGTGAGCGTGTTCG 3 178 1 GGCCGCCGTG 0.787514 -90 CGTGTTCGAAGCCGAGGTCGTGGCTCCCGC 3 200 1 GCCGAGGTCG 0.85461 -68 CCGGTCCACCCCGGGCGGCGCTGCCATCGC 3 228 0 CCGGGCGGCG 0.511511 -40 TGGACCGGGTGCGCGCCCTCATGCATGC 3 250 1 GCGCGCCCTC 0.883139 -18 CCCGGGCCCCGAGCGAGCGGT 4 2 1 CCGGGCCCCG 0.523856 -101 TGACAGCACGCCCCAGGCGGACCATCGTTA 4 47 1 CCCCAGGCGG 0.692351 -56 CGGCGGCGGCTTTCATTAAGCACG 4 89 0 GGCGGCTTTC 0.922581 -14 GGCGGCGGCGCCGGTAACGG 5 1 1 GGCGGCGGCG 0.504083 -209 AAACGAACCGGCGCGCGCCGTTACCGGCGC 5 18 0 GCGCGCGCCG 0.572307 -192 CGCAACATGTGCGCGCTGACGATCGGGTTG 5 66 1 GCGCGCTGAC 0.876386 -144 CGAAAGCCCTGCCGACGGTGTCGCAGGTCT 5 150 1 GCCGACGGTG 0.968993 -60 CCCGCACCTCCGACCAGCTCA 5 199 0 CCGCACCTCC 0.854626 -11 GGGTGAACCGCCCCGGTGAGTCCGGAGACT 6 26 0 CCCCGGTGAG 0.871539 -275 CCGGTGACGACCCGGCTGGGTGAACCGCCC 6 43 0 CCCGGCTGGG 0.683584 -258 CCGGGTCGTCACCGGCTGTCGGCGATATTG 6 58 1 ACCGGCTGTC 0.684837 -243 CCCAGTTGTGCCCCACTTGGCCCCACTTGC 6 102 1 CCCCACTTGG 0.92813 -199 CCCCACTTGGCCCCACTTGCCACCCATTTG 6 112 1 CCCCACTTGC 0.861736 -189 CCACCCATTTGCCCGGCGACATGCGGTTTT 6 131 1 GCCCGGCGAC 0.821999 -170 GCGCGGCTAGCCCGGCTACGACCTCAGAAA 6 158 0 CCCGGCTACG 0.846218 -143 CCACTGAAGCGCGCGGCTAGCCCGGCTACG 6 168 0 GCGCGGCTAG 0.728884 -133 GCGGCGTTTTGCCGTCTCTGTACCACTGAA 6 190 0 GCCGTCTCTG 0.757358 -111 GACGGCAAAACGCCGCTTTGATACCCCAGT 6 204 1 CGCCGCTTTG 0.953722 -97 CCCCACAATCCCCCACTTTGCCCCATAACT 6 231 0 CCCCACTTTG 0.948203 -70 GGGGCACCTCCCTGCCAAATC 6 290 0 GGGCACCTCC 0.748292 -11 ********** Masking position 6 Map Score: 49.4619 Number of sites scoring better than the average of aligned sites = 124036 Number in coding regions = 116189 Number in noncoding regions = 7847 Number of orfs with sites within 600 bp upstream = 1738 Fraction of orfs with sites within 600 bp upstream = 0.279152 Motif number 2 GTGTGCGCGCCCTGTCGGTAGG 2 6 1 CGCGCCTTCT 0.860193 -17 TCCATCGCGGCGCGCAGGATCTGCGCCCGGGTTT 3 28 0 CGCGCAGTCC 0.99487 -240 AAGGGGCTCTCGGGGCTGTCCATCGGCGAGCTTG 3 75 1 CGGGGCGCCC 0.991446 -193 GCCCAGCCGCCCGGCAAGCTCGCCGATGGACAGC 3 89 0 CCGGCAGTCC 0.992395 -179 ATGAGCAAGTCGGGCCTGTTCCGGCATTTCGGCG 3 123 1 CGGGCCGTCG 0.993528 -145 ACCTCGGCTTCGAACACGCTCACGGCGGCCTCGA 3 184 0 CGAACAGTCG 0.852281 -84 CCGGTCCACCCCGGGCGGCGCTGCCATCGCGGGA 3 224 0 CCGGGCGGCC 0.972616 -44 CATGAGGGCGCGCACCCGGTCCACCCCGGGCGGC 3 239 0 CGCACCGTCC 0.996237 -29 ACAGCACGCCCCAGGCGGACCATCGTTAAACACG 4 49 1 CCAGGCGCCC 0.955464 -54 GGTAACGGCGCGCGCCGGTTCGTTTCGGCTCCAA 5 23 1 CGCGCCGTCT 0.990471 -187 ATCGTCAGCGCGCACATGTTGCGCAAAAGTTGTT 5 55 0 CGCACAGTGC 0.861042 -155 AGAGCTTCCGCCAACCCGATCGTCAGCGCGCACA 5 73 0 CCAACCGTCC 0.983189 -137 CCCGCACCTCCGACCAGCTCAGCACAACTTCAC 5 187 0 CCGACCGTCC 0.994427 -23 CCGGACTCACCGGGGCGGTTCACCCAGCCGGGTC 6 31 1 CGGGGCGTCC 0.99728 -270 ****** * ** * Masking position 1 Map Score: 29.5917 Number of sites scoring better than the average of aligned sites = 8972 Number in coding regions = 8380 Number in noncoding regions = 592 Number of orfs with sites within 600 bp upstream = 440 Fraction of orfs with sites within 600 bp upstream = 0.0706714 Motif number 3 CGCCGACGTCGGCCGCCAAACCCGGGC 3 8 1 GTCGGCCGCC 0.550782 -260 CGGCGCGCAGGATCTGCGCCCGGGTTTGGC 3 25 0 GATCTGCGCC 0.976354 -243 CGGGGCTGTCCATCGGCGAGCTTGCCGGGC 3 85 1 CATCGGCGAG 0.738256 -183 CGGCGAGCTTGCCGGGCGGCTGGGCATGAG 3 98 1 GCCGGGCGGC 0.812517 -170 TGTTCCGGCATTTCGGCGCCAAGGAGCAGC 3 139 1 TTTCGGCGCC 0.96939 -129 CGGCGGCCTCGACGGTCGCCAGCTGCAGCT 3 166 0 GACGGTCGCC 0.838701 -102 CCGTGAGCGTGTTCGAAGCCGAGGTCGTGG 3 193 1 GTTCGAAGCC 0.493553 -75 CCCGCGATGGCAGCGCCGCCCGGGGTGGAC 3 225 1 CAGCGCCGCC 0.869514 -43 GTGACCGCTCGCTCGGGGCCCGGG 4 5 0 GCTCGGGGCC 0.878809 -98 GCTTAATGAAAGCCGCCGCCG 4 92 1 AGCCGCCGCC 0.80703 -11 CGCGCGCCGTTACCGGCGCCGCCGCC 5 7 0 TACCGGCGCC 0.991248 -203 AGCCGAAACGAACCGGCGCGCGCCGTTACC 5 23 0 AACCGGCGCG 0.835863 -187 CGCCGGTTCGTTTCGGCTCCAACAACTTTT 5 35 1 TTTCGGCTCC 0.700291 -175 TTAAAAGAGCTTCCGCCAACCCGATCGTCA 5 82 0 TTCCGCCAAC 0.400378 -128 ACGAATCCCAGACCTGCGACACCGTCGGCA 5 159 0 GACCTGCGAC 0.97632 -51 CCCGCACCTCCGACCAGCTCAGCA 5 196 0 CACCTCCGAC 0.877631 -14 GAGACTCTCTGATCTGAGACC 6 2 0 GATCTGAGAC 0.721768 -299 GCCCCGGTGAGTCCGGAGACTCTCTGATCT 6 17 0 GTCCGGAGAC 0.944729 -284 CCGGACTCAATATCGCCGACAGCCGGTGAC 6 65 0 TATCGCCGAC 0.914817 -236 TTGAGCCCCAGTTGTGCCCCACTTGGCCCC 6 96 1 GTTGTGCCCC 0.265428 -205 CCACCCATTTGCCCGGCGACATGCGGTTTT 6 131 1 GCCCGGCGAC 0.989113 -170 CGCGCGGCTAGCCCGGCTACGACCTCAGAA 6 159 0 GCCCGGCTAC 0.891097 -142 CTCACCCAAACACCTCAGCCACCATACCCC 6 257 0 CACCTCAGCC 0.707093 -44 ********** Masking position 10 Map Score: 26.145 Number of sites scoring better than the average of aligned sites = 54624 Number in coding regions = 51333 Number in noncoding regions = 3291 Number of orfs with sites within 600 bp upstream = 1332 Fraction of orfs with sites within 600 bp upstream = 0.213942 Motif number 4 GTCGGCCGCCAAACCCGGGCGCAGATCCTG 3 18 1 AAACCCGGGC 0.48817 -250 CCCGGGCGCAGATCCTGCGCGCCGCGATGG 3 31 1 GATCCTGCGC 0.935743 -237 TCGCCTCGGTGAAGGGGCTCTCGGGGCTGT 3 64 1 GAAGGGGCTC 0.825366 -204 GCTCGCCGATGGACAGCCCCGAGAGCCCCT 3 76 0 GGACAGCCCC 0.705398 -192 GGCCCGACTTGCTCATGCCCAGCCGCCCGG 3 109 0 GCTCATGCCC 0.854346 -159 CGAAATGCCGGAACAGGCCCGACTTGCTCA 3 124 0 GAACAGGCCC 0.94889 -144 GTCGCCAGCTGCAGCTGCTCCTTGGCGCCG 3 152 0 GCAGCTGCTC 0.914362 -116 CCTCGGCTTCGAACACGCTCACGGCGGCCT 3 187 0 GAACACGCTC 0.830516 -81 CGAGGTCGTGGCTCCCGCGATGGCAGCGCC 3 212 1 GCTCCCGCGA 0.888561 -56 TCCCGCGATGGCAGCGCCGCCCGGGGTGGA 3 224 1 GCAGCGCCGC 0.909323 -44 ATGAGGGCGCGCACCCGGTCCACCCCGGGC 3 242 0 GCACCCGGTC 0.91621 -26 GTGACCGCTCGCTCGGGGCCCGGG 4 5 0 GCTCGGGGCC 0.842804 -98 GGCATTGACAGCACGCCCCAGGCGGACCAT 4 42 1 GCACGCCCCA 0.725238 -61 CGTGTTTAACGATGGTCCGCCTGGGGCGTG 4 53 0 GATGGTCCGC 0.597771 -50 GGCGGCGGCGCCGGTAACGGC 5 2 1 GCGGCGGCGC 0.496503 -208 GGCGGCGCCGGTAACGGCGCGCGCCGGTTC 5 14 1 GTAACGGCGC 0.696793 -196 GAGCCGAAACGAACCGGCGCGCGCCGTTAC 5 24 0 GAACCGGCGC 0.906219 -186 CCCGCACCTCCGACCAGCTCAGC 5 197 0 GCACCTCCGA 0.880067 -13 CCGGCTGGGTGAACCGCCCCGGTGAGTCCG 6 32 0 GAACCGCCCC 0.975968 -269 TTCTGAGGTCGTAGCCGGGCTAGCCGCGCG 6 159 1 GTAGCCGGGC 0.744081 -142 GGGGCACCTCCCTGCCAAATCCA 6 288 0 GCACCTCCCT 0.672547 -13 ********** Masking position 1 Map Score: 22.0957 Number of sites scoring better than the average of aligned sites = 37353 Number in coding regions = 34656 Number in noncoding regions = 2697 Number of orfs with sites within 600 bp upstream = 1199 Fraction of orfs with sites within 600 bp upstream = 0.19258 Motif number 5 ACCGTTCCGAGAAAGGCCAGC 1 7 1 CGAGAAGGCC 0.945677 -15 CCGACGTCGGCCGCCAAACCCGGGCGCAGATC 3 13 1 CGCCAACCCG 0.865135 -255 CGATGGACAGCCCCGAGAGCCCCTTCACCGAG 3 68 0 CCCGAGGCCC 0.893639 -200 CCGGCAAGCTCGCCGATGGACAGCCCCGAGAG 3 81 0 CCCGATGACA 0.515996 -187 TGCTCCTTGGCGCCGAAATGCCGGAACAGGCC 3 135 0 CCCGAATGCC 0.982699 -133 TCAAACCGGACTCAATATCGCCGACAGCCGGT 6 68 0 CCAATACGCC 0.809737 -233 CGGTTTGAGCCCCAGTTGTGCCCCACTTGGCC 6 92 1 CCAGTTTGCC 0.622541 -209 CCCCACTTGCCACCCATTTGCCCGGCGACATG 6 122 1 CCCCATTGCC 0.953073 -179 GCTACGACCTCAGAAAACCGCATGTCGCCGGG 6 142 0 CGAAAACGCA 0.74457 -159 GGTACAGAGACGGCAAAACGCCGCTTTGATAC 6 196 1 CGCAAACGCC 0.970781 -105 GCCACCATACCCCACAATCCCCCACTTTGCCC 6 238 0 CCACAACCCC 0.968813 -63 AAATCCATCTCACCCAAACACCTCAGCCACCA 6 263 0 CCCCAACACC 0.963525 -38 GGGCACCTCCCTGCCAAATCCATCTCACCCAA 6 278 0 CGCCAATCCA 0.823541 -23 * ***** **** Masking position 11 Map Score: 6.79204 Number of sites scoring better than the average of aligned sites = 9392 Number in coding regions = 8506 Number in noncoding regions = 886 Number of orfs with sites within 600 bp upstream = 631 Fraction of orfs with sites within 600 bp upstream = 0.101349 Motif number 6 GCTGGCCTTTCTCGGAACGGT 1 2 0 TCTCGGAACG 0.983138 -20 GCGCGCAGGATCTGCGCCCGGGTTTGGCGGC 3 22 0 TCTGCGCCCG 0.720989 -246 GTGAAGGGGCTCTCGGGGCTGTCCATCGGCG 3 72 1 TCTCGGGGCG 0.850024 -196 GGCGCCGAAATGCCGGAACAGGCCCGACTTG 3 128 0 TGCCGGAACG 0.836085 -140 GGCGGCGGCGCCGGTAACGGCGCGCGCCGG 5 10 1 GCCGGTAACG 0.623024 -200 CCTATAACAATCTGAAAACAGGATGTCGCAC 5 117 0 TCTGAAAACG 0.912611 -93 ACTTCACGAATCCCAGACCTGCGACACCGTC 5 163 0 TCCCAGACCG 0.982321 -47 CCCGCACCTCCGACCAGCTCAGCACAA 5 193 0 CCTCCGACCG 0.926854 -17 GGTCTCAGATCAGAGAGTCTCCG 6 3 1 TCTCAGATCG 0.928279 -298 CACAACTGGGGCTCAAACCGGACTCAATATC 6 81 0 GCTCAAACCG 0.90498 -220 GGCTACGACCTCAGAAAACCGCATGTCGCCG 6 144 0 TCAGAAAACG 0.622108 -157 ATAACTGGGGTATCAAAGCGGCGTTTTGCCG 6 206 0 TATCAAAGCG 0.482039 -95 CCCCACTTTGCCCCATAACTGGGGTATCAAA 6 220 0 CCCCATAACG 0.794915 -81 ********* * Masking position 9 Map Score: 2.41333 Number of sites scoring better than the average of aligned sites = 4984 Number in coding regions = 4600 Number in noncoding regions = 384 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 7 ********** No masking Map Score: 1.68642e-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 8 ********** No masking Map Score: 1.68642e-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: 1.68642e-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