AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -inagC_mtub_opreg_300.orf -g0.656 -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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glmU 254 glmU #2 lprJ 300 lprJ #3 Rv1691 38 hypothetical protein Rv1691 #4 Rv3329 59 hypothetical protein Rv3329 #5 Rv3330 68 hypothetical protein Rv3330 #6 sugI 95 sugI #7 glmS 21 glmS Motif number 1 ACCCGACGCGGGTGACGCGCGCCAGG 1 6 0 GGTGCGCGCG 0.990505 -249 CCCGCGTCGGGTTTTCCGGCGCCTTATCCGG 1 25 1 GTTTCCGGCG 0.977221 -230 TTTCCGGCGCCTTATCCGGCCCTTTATCCGG 1 37 1 CTTACCGGCC 0.928749 -218 GGCCCTTTATCCGGTCCGGCCACATCAACAA 1 54 1 CCGGCCGGCC 0.920033 -201 AAGGGTATCGGTTTGCGTGGGGCCGGTGGGT 1 83 1 GTTTCGTGGG 0.740592 -172 GGGGCCGGTGGGTAGACGGCGACAGCGTTGA 1 101 1 GGTAACGGCG 0.919863 -154 AGTTCAGGTTCGAGTCCTGGCGACGGAGCTT 1 222 1 CGAGCCTGGC 0.656997 -33 CCAGCGGAGTCCAAACCCGCCAAAGATAAGT 2 36 0 CCAACCCGCC 0.726519 -265 ACTAGTCGTGGGATACCAGCGGAGTCCAAAC 2 51 0 GGATCCAGCG 0.900255 -250 ACGACTAGTCGGTGGCCGGGGGAAATGCCGA 2 73 1 GGTGCCGGGG 0.99483 -228 GTGAAGTCCACCAATCGGGGGACGATCGGCC 2 123 1 CCAACGGGGG 0.911282 -178 ACCGGGTAGGGGGGCACCGCGGGCCGATCGT 2 144 0 GGGGACCGCG 0.78607 -157 ATGTGTGCGCGTTAACCGGGTAGGGGGGCAC 2 158 0 GTTACCGGGT 0.886781 -143 GTTGGCCACTGTTGTCGAGGTGCCTTAAATG 2 249 1 GTTGCGAGGT 0.810417 -52 GCGACAACAACGAGAAGCGGGAG 2 288 1 CGAGAGCGGG 0.603893 -13 TAGTTACGGGGCGCAGCAACCCC 3 3 1 GTTAGGGGCG 0.777011 -36 TCGGTAGAGGTTACGGGGGTTGCTGCGCC 3 20 0 GGTTCGGGGG 0.97938 -19 GTGTCGTCGTGTTGGCGAGCGCAGCGCTAGG 4 28 0 GTTGCGAGCG 0.973433 -32 CCGACCGCGAGGAGCCGCGCTGTGACTGGCG 5 20 0 GGAGCGCGCT 0.896526 -49 GCGGCTCCTCGCGGTCGGGCCGCCGATCACC 5 33 1 GCGGCGGGCC 0.957114 -36 CGACGCCGAAGGTATCGGGGTAAGCAG 6 7 0 GGTACGGGGT 0.928196 -89 CTTCGGCGTCGTTTGCGGGCGGGCATCCTAG 6 27 1 GTTTCGGGCG 0.975399 -69 GGGCGGGCATCCTAGCCGGCCTTGGTCGGCA 6 43 1 CCTACCGGCC 0.933949 -53 GAAATCGGGGCTTGACCAGCGGTTGACCGC 6 76 1 CTTGCCAGCG 0.949723 -20 AGCAGACCAGGGTAGTGCAGC 7 10 0 GCAGCCAGGG 0.932323 -12 **** ****** Masking position 9 Map Score: 32.7562 Number of sites scoring better than the average of aligned sites = 44942 Number in coding regions = 41659 Number in noncoding regions = 3283 Number of orfs with sites within 600 bp upstream = 1427 Fraction of orfs with sites within 600 bp upstream = 0.2292 Motif number 2 CCGGAAAACCCGACGCGGGTGACGCGCGCCAGG 1 10 0 CGACGGGACG 0.659452 -245 GATAAAGGGCCGGATAAGGCGCCGGAAAACCCGA 1 31 0 CGGATGGCCG 0.553393 -224 CCGGCCACATCAACAAGGGTATCGGTTTGCGTGG 1 69 1 CAACAGGTCG 0.856582 -186 TCAGCACAGTCAACGCTGTCGCCGTCTACCCACC 1 107 0 CAACGGTCCG 0.85168 -148 ACTGTGCTGACGGCGTTGACACCGTCTAAAGTCA 1 131 1 CGGCGGACCG 0.659508 -124 AAAGTCACATCGATGTGCAATCCGTCGTGGTGTA 1 158 1 CGATGCACCG 0.621445 -97 AGATAAGTCAGGAAGTGGAAATCGACTACAACG 2 10 0 GGAAGGATCG 0.881631 -291 TATCTTTGGCGGGTTTGGACTCCGCTGGTATCCC 2 39 1 GGGTTGACCG 0.793643 -262 ACGATCCACCGGATGCGGGATTCGGCATTTCCCC 2 91 0 GGATGGGTCG 0.955142 -210 ACCAATCGGGGGACGATCGGCCCGCGGTGCCCCC 2 132 1 GGACGCGCCG 0.985989 -169 GACTCTTGTTGGCCACTGTTGTCGAGGTGCCTTA 2 242 1 GGCCAGTTCG 0.87514 -59 TCGGTAGAGGTTACGGGGGTTGCTG 3 24 0 CGGTAGGACG 0.906391 -15 CGCTAGGCTCGGGCAATGACCTCG 4 1 0 GGGCAGATCG 0.98022 -59 AGTAGGTGATCGGCGGCCCGACCGCGAGGAGCCG 5 34 0 CGGCGCCCCG 0.736886 -35 CCGCAAACGACGCCGAAGGTATCGGGGTAAGCAG 6 11 0 CGCCGGGTCG 0.985343 -85 GTTTGCGGGCGGGCATCCTAGCCGGCCTTGGTCG 6 37 1 GGGCACTCCG 0.701984 -59 CGGCCTTGGTCGGCACCGAAATCGGGGCTTGACC 6 59 1 CGGCAGATCG 0.516904 -37 ***** ** *** Masking position 14 Map Score: 25.4052 Number of sites scoring better than the average of aligned sites = 45594 Number in coding regions = 43820 Number in noncoding regions = 1774 Number of orfs with sites within 600 bp upstream = 852 Fraction of orfs with sites within 600 bp upstream = 0.136845 Motif number 3 GGAAAACCCGACGCGGGTGACGCGCGCCAGG 1 11 0 ACGCGGTGAC 0.965379 -244 CGCCGTCTACCCACCGGCCCCACGCAAACCG 1 91 0 CCACCGCCCC 0.706023 -164 GTAGACGGCGACAGCGTTGACTGTGCTGACG 1 112 1 ACAGCGTGAC 0.8414 -143 GACTGTGCTGACGGCGTTGACACCGTCTAAA 1 130 1 ACGGCGTGAC 0.978576 -125 ATCAGAGGTGCTGCCGATTACACCACGACGG 1 179 0 CTGCCGTTAC 0.718658 -76 GAGTCCAAACCCGCCAAAGATAAGTCAGGAA 2 30 0 CCGCCAAGAT 0.663086 -271 GCATTTCCCCCGGCCACCGACTAGTCGTGGG 2 70 0 CGGCCACGAC 0.977591 -231 GTCCACCAATCGGGGGACGATCGGCCCGCGG 2 128 1 CGGGGGCGAT 0.785509 -173 GGACGATCGGCCCGCGGTGCCCCCCTACCCG 2 142 1 CCCGCGTGCC 0.877942 -159 GCGCTAGGCTCGGGCAATGACCTCG 4 5 0 CGGGCATGAC 0.977932 -55 CTTTCGTCCCGCCAGTCACAGCGCGGCTC 5 9 1 CCGCCATCAC 0.976268 -60 CGCGGTCGGGCCGCCGATCACCTACTCTGCA 5 42 1 CCGCCGTCAC 0.991465 -27 GGATGCCCGCCCGCAAACGACGCCGAAGGTA 6 24 0 CCGCAACGAC 0.882894 -72 GCACCGAAATCGGGGCTTGACCAGCGGTTGA 6 71 1 CGGGGCTGAC 0.869498 -25 GGGGCTTGACCAGCGGTTGACCGC 6 82 1 CAGCGGTGAC 0.936055 -14 ****** **** Masking position 10 Map Score: 14.5037 Number of sites scoring better than the average of aligned sites = 37661 Number in coding regions = 35780 Number in noncoding regions = 1881 Number of orfs with sites within 600 bp upstream = 992 Fraction of orfs with sites within 600 bp upstream = 0.159332 Motif number 4 ACAGCGTTGACTGTGCTGACGGCGTTGACA 1 122 1 CTGTGCTGAC 0.979909 -133 TGACTTTAGACGGTGTCAACGCCGTCAGCA 1 135 0 CGGTGTCAAC 0.839068 -120 AGTCACATCGATGTGCAATCCGTCGTGGTG 1 160 1 ATGTGCAATC 0.7209 -95 CCAAAATCAGAGGTGCTGCCGATTACACCA 1 185 0 AGGTGCTGCC 0.965684 -70 GATCGGCCCGCGGTGCCCCCCTACCCGGTT 2 146 1 CGGTGCCCCC 0.92984 -155 AAACGCGTTAGTGTGCAAACCTTTATCCCA 2 197 1 GTGTGCAAAC 0.749731 -104 CTTTATCCCACTGTGCTGTGAACGTGACTC 2 217 1 CTGTGCTGTG 0.913659 -84 CCCGACCGCGAGGAGCCGCGCTGTGACTGG 5 22 0 AGGAGCCGCG 0.784822 -47 CGTCTGTGCAGAGTAGGTGATCG 5 56 0 CTGTGCAGAG 0.889199 -13 GCCCCGATTTCGGTGCCGACCAAGGCCGGC 6 57 0 CGGTGCCGAC 0.99399 -39 ********** Masking position 5 Map Score: 8.05839 Number of sites scoring better than the average of aligned sites = 11482 Number in coding regions = 10899 Number in noncoding regions = 583 Number of orfs with sites within 600 bp upstream = 469 Fraction of orfs with sites within 600 bp upstream = 0.0753293 Motif number 5 GCGCGCGTCACCCGCGTCGGGTTTTCCGGC 1 15 1 CCCGCGTCGG 0.981568 -240 GTTTTCCGGCGCCTTATCCGGCCCTTTATC 1 35 1 GCCTTATCCG 0.940639 -220 CTTATCCGGCCCTTTATCCGGTCCGGCCAC 1 47 1 CCTTTATCCG 0.968067 -208 CCTCCTTGAAGCTCCGTCGCCAGGACTCGA 1 231 0 GCTCCGTCGC 0.865942 -24 AATGCCGAATCCCGCATCCGGTGGATCGTG 2 96 1 CCCGCATCCG 0.985052 -205 CCGCGGTGCCCCCCTACCCGGTTAACGCGC 2 153 1 CCCCTACCCG 0.898387 -148 AGTGTGCAAACCTTTATCCCACTGTGCTGT 2 206 1 CCTTTATCCC 0.946428 -95 TACGGGGGTTGCTGCGCCCCGTAACTA 3 8 0 GCTGCGCCCC 0.890543 -31 CTTTCGTCCCGCCAGTCACA 5 1 1 CTTTCGTCCC 0.838754 -68 TCCTAGCCGGCCTTGGTCGGCACCGAAATC 6 52 1 CCTTGGTCGG 0.95497 -44 GCTGCACTACCCTGGTCTGCT 7 10 1 CCCTGGTCTG 0.877504 -12 ********** Masking position 8 Map Score: 8.13481 Number of sites scoring better than the average of aligned sites = 6874 Number in coding regions = 6258 Number in noncoding regions = 616 Number of orfs with sites within 600 bp upstream = 530 Fraction of orfs with sites within 600 bp upstream = 0.0851269 Motif number 6 GGTTTTCCGGCGCCTTATCCGGCCCTTTAT 1 34 1 CGCCTTATCC 0.839486 -221 AACCGATACCCTTGTTGATGTGGCCGGACC 1 66 0 CTTGTTGATG 0.828427 -189 ACGATCGGCCCGCGGTGCCCCCCTACCCGG 2 144 1 CGCGGTGCCC 0.9475 -157 GGAATGTGTGCGCGTTAACCGGGTAGGGGG 2 162 0 CGCGTTAACC 0.969324 -139 CCACACGAAACGCGTTAGTGTGCAAACCTT 2 190 1 CGCGTTAGTG 0.965306 -111 GAACGTGACTCTTGTTGGCCACTGTTGTCG 2 236 1 CTTGTTGGCC 0.965315 -65 CTCCCGCTTCTCGTTGTTGTCGCACTTGC 2 282 0 CTCGTTGTTG 0.925107 -19 TTCGTGTCGTCGTGTTGGCGAGCGCAGCGC 4 32 0 CGTGTTGGCG 0.985387 -28 ********** Masking position 6 Map Score: 3.45585 Number of sites scoring better than the average of aligned sites = 10049 Number in coding regions = 9464 Number in noncoding regions = 585 Number of orfs with sites within 600 bp upstream = 456 Fraction of orfs with sites within 600 bp upstream = 0.0732412 Motif number 7 GCCACATCAACAAGGGTATCGGTTTGCGTG 1 72 1 CAAGGGTATC 0.963251 -183 TCAGCACAGTCAACGCTGTCGCCGTCTACC 1 111 0 CAACGCTGTC 0.99122 -144 TAGACGGTGTCAACGCCGTCAGCACAGTCA 1 129 0 CAACGCCGTC 0.987008 -126 CGTGGGATACCAGCGGAGTCCAAACCCGCC 2 46 0 CAGCGGAGTC 0.923353 -255 GGCACCTCGACAACAGTGGCCAACAAGAGT 2 243 0 CAACAGTGGC 0.920795 -58 CCAAAGGTTTCGTGTCGTCGT 4 49 0 CAAAGGTTTC 0.905677 -11 CAAACGACGCCGAAGGTATCGGGGTAAGCA 6 12 0 CGAAGGTATC 0.818218 -84 CGGTGCCGACCAAGGCCGGCTAGGATGCCC 6 47 0 CAAGGCCGGC 0.957451 -49 ********** Masking position 1 Map Score: 4.87246 Number of sites scoring better than the average of aligned sites = 4293 Number in coding regions = 4064 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 8 CCACCGGCCCCACGCAAACCGATACCCTTG 1 82 0 CACGCAAACC 0.926501 -173 CCGTCGCCAGGACTCGAACCTGAACTATCT 1 218 0 GACTCGAACC 0.987462 -37 GATACCAGCGGAGTCCAAACCCGCCAAAGA 2 41 0 GAGTCCAAAC 0.894902 -260 GCACACATTCCACACGAAACGCGTTAGTGT 2 181 1 CACACGAAAC 0.982203 -120 CCAACACGACGACACGAAACCTTTGG 4 44 1 GACACGAAAC 0.987648 -16 ********** Masking position 7 Map Score: 0.971308 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 183 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 ********** No masking Map Score: -2.32047e-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: -2.32047e-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 11 ********** No masking Map Score: -2.32047e-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