AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_bsub_mtub_300.orf -o164_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yrvO 101 similar to NifS protein homolog #2 yrzC 199 similar to hypothetical proteins #3 yurY 300 similar to ABC transporter (ATP-binding protein) #4 Rv1284 206 hypothetical protein Rv1284 #5 cysD 93 cysD #6 Rv1287 53 hypothetical protein Rv1287 #7 Rv3025c 96 hypothetical protein Rv3025c #8 Rv3027c 260 hypothetical protein Rv3027c #9 fixB 38 fixB #10 fixA 230 fixA Motif number 1 TACGGTTTTCCGTTACCCTGTAATTAAGTA 2 25 0 CGTTACCCTG 0.811612 -175 TGTCCCAATGCGACGCGGTGGTTGGGC 4 8 0 CGACGCGGTG 0.902718 -199 TCGCCGGGCTCGCTACCCTGTCCCAATGCG 4 26 0 CGCTACCCTG 0.895692 -181 GGCGGCACGCCATCGCCGGGCTCGCTACCC 4 38 0 CATCGCCGGG 0.826584 -169 CCCCATCAACCGGCGCGCTGGCGGCACGCC 4 57 0 CGGCGCGCTG 0.903526 -150 TGGGGTCACCCGTGATCCGGATGGTTCCGC 4 82 1 CGTGATCCGG 0.934071 -125 CTCAGATCGACGCCGCGGTGAATTTTAACA 4 150 0 CGCCGCGGTG 0.842999 -57 CCTCGGGTATCGCGGTGTGGACTTTGCTAC 4 179 0 CGCGGTGTGG 0.963154 -28 CCTAGGCTGACGGCTCGGGCTG 5 3 0 CGGCTCGGGC 0.769664 -91 GGCAGCCCGCCGAGATGGGGCTGCGTTGAC 5 48 1 CGAGATGGGG 0.894396 -46 CTGCTGCGGCCGTGGCCTGCGCGCACGTTC 7 42 1 CGTGGCCTGC 0.874928 -55 CGTTCTGCGTCGCCGCCCGGGCCAGTATTC 7 67 1 CGCCGCCCGG 0.98149 -30 CACGCCTCGGCGTGTCGGGGTCTTTTGCGA 8 28 0 CGTGTCGGGG 0.968452 -233 CCCGACACGCCGAGGCGTGGGGGGCCTTGG 8 39 1 CGAGGCGTGG 0.943906 -222 AACGTTGTGACGTGTCGGTGCACGTCAGAT 8 98 0 CGTGTCGGTG 0.894669 -163 ATAGCACCAACGTGGCGCAGCCGATCAGCT 8 138 0 CGTGGCGCAG 0.921137 -123 CCTGTCGCGACGCCATGCGGTTTGTCACTG 8 192 0 CGCCATGCGG 0.967024 -69 CAGGGAATAGCGCGGTCCGGTTGACGATCC 8 220 0 CGCGGTCCGG 0.986446 -41 CGGATACTCCCGGTGCCCGGTTCGCGAATC 10 39 0 CGGTGCCCGG 0.968456 -192 GTGCCTCGCCCACGACCGGCGGATACTCCC 10 58 0 CACGACCGGC 0.585237 -173 CTCTACCACCCGCTATGGTGTGAGGGCGCA 10 103 1 CGCTATGGTG 0.803004 -128 GGTAAGTTCGCGTGGTGCGCCCTCACACCA 10 118 0 CGTGGTGCGC 0.952525 -113 ATAGTAATATCGCTGTGCGGTTGCAAAACG 10 150 1 CGCTGTGCGG 0.980845 -81 CGCAGTCGAGCGCTGCGGGCCGCCTTCGAG 10 194 1 CGCTGCGGGC 0.975701 -37 ********** Masking position 1 Map Score: 35.162 Number of sites scoring better than the average of aligned sites = 2035 Number in coding regions = 1906 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 CGAGGAATATGGACGCCGGCTGGAAACAAGAAT 3 18 1 GGACGCGGCG 0.867983 -283 TATGAAAAAAGCAAGCGGATTTCTGCGGGAGCT 3 79 1 GCAAGCGATC 0.830693 -222 GCGTCGCATTGGGACAGGGTAGCGAGCCCGGCG 4 22 1 GGGACAGGTC 0.454397 -185 CCATCAACCGGCGCGCTGGCGGCACGCCATCGC 4 52 0 GCGCGCGGCC 0.940781 -155 CGCATCAGAATCGGCCCGAGCGGAACCATCCGG 4 98 0 TCGGCCGAGG 0.463805 -109 TTGTTAAAATTCACCGCGGCGTCGATCTGAGTA 4 149 1 TCACCGGGCC 0.834676 -58 GTGCGCCAGTGCGCCCTAGGCTGACGGCTCGGG 5 14 0 GCGCCCAGGG 0.723238 -80 GGGCGCACTGGCGCACCGGCAGCCCGCCGAGAT 5 31 1 GCGCACGGCC 0.969571 -63 CGCTGTCAACGCAGCCCCATCTCGGCGGGCTGC 5 49 0 GCAGCCCATC 0.724107 -45 CTATGCAACCAGGCTTCCCTATCGCTG 5 77 0 GCAACCGGCC 0.839681 -17 GGACAGCAGAGCAACCAGGCCGGC 6 2 0 GCAACCGGCG 0.753079 -52 GCTGTCCCTGGCAAGCGGGTGGCACAATCCTGA 6 28 1 GCAAGCGGTC 0.888531 -26 CAATCTGGCTGGGGCCAGACCAC 7 1 0 GGGGCCGACC 0.919447 -96 CGCAGAACGTGCGCGCAGGCCACGGCCGCAGCA 7 43 0 GCGCGCGGCC 0.960234 -54 CCTAGAATACTGGCCCGGGCGGCGACGCAGAAC 7 68 0 TGGCCCGGCC 0.934501 -29 TTGCGACTGCTCGCGCAGGGAAC 8 1 0 TCGCGCGGGC 0.919054 -260 AGGTGAGCAGGCGCCAAGGCCCCCCACGCCTCG 8 49 0 GCGCCAGGCC 0.889216 -212 CATCTGACGTGCACCGACACGTCACAACGTTGA 8 97 1 GCACCGCACC 0.770502 -164 GATGCTCATAGCACCAACGTGGCGCAGCCGATC 8 142 0 GCACCACGTC 0.624112 -119 GACAGGATCGTCAACCGGACCGCGCTATTCCCT 8 216 1 TCAACCGACC 0.875184 -45 TGTTAAGGCAGGCTAACCCGTGGCATCGGA 10 8 1 GCAGGCAACG 0.332555 -223 CATCGGATTCGCGAACCGGGCACCGGGAGTATC 10 34 1 GCGAACGGGC 0.826469 -197 TTCGCGTGGTGCGCCCTCACACCATAGCGGGTG 10 109 0 GCGCCCCACC 0.981644 -122 CACACGTTTTGCAACCGCACAGCGATATTACTA 10 151 0 GCAACCCACC 0.927443 -80 GTCGAGCGCTGCGGGCCGCCTTCGAGGAGGACG 10 198 1 GCGGGCGCCC 0.862592 -33 ****** *** * Masking position 2 Map Score: 32.6703 Number of sites scoring better than the average of aligned sites = 2905 Number in coding regions = 2679 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 GAATATGGACGCCGGCTGGAAACAAGAATG 3 22 1 GCCGGCTGGA 0.890337 -279 CAACCACCGCGTCGCATTGGGACAGGGTAG 4 14 1 GTCGCATTGG 0.715613 -193 GCACGCCATCGCCGGGCTCGCTACCCTGTC 4 34 0 GCCGGGCTCG 0.806275 -173 GCGATGGCGTGCCGCCAGCGCGCCGGTTGA 4 52 1 GCCGCCAGCG 0.971684 -155 GCGGGCCTCCTCGGGTATCG 4 197 0 GCGGGCCTCC 0.911271 -10 CAGCCCGAGCCGTCAGCCTAGGGCGCAC 5 9 1 GCCGTCAGCC 0.696154 -85 GTCAGCCTAGGGCGCACTGGCGCACCGGCA 5 22 1 GGCGCACTGG 0.749145 -72 CCCCATCTCGGCGGGCTGCCGGTGCGCCAG 5 38 0 GCGGGCTGCC 0.969641 -56 CCCGCCGAGATGGGGCTGCGTTGACAGCGA 5 53 1 TGGGGCTGCG 0.667037 -41 GCCGGCCTGGTTGCTCTGCT 6 1 1 GCCGGCCTGG 0.96989 -53 GTGGTCTGGCCCCAGCCAGA 7 1 1 GTGGTCTGGC 0.621616 -96 CGGCCGCAGCAGCGGCTGGGCAATCTGGCT 7 24 0 AGCGGCTGGG 0.908579 -73 TGCTGCGGCCGTGGCCTGCGCGCACGTTCT 7 43 1 GTGGCCTGCG 0.957122 -54 GTTCTGCGTCGCCGCCCGGGCCAGTATTCT 7 68 1 GCCGCCCGGG 0.938504 -29 CGAGGCGTGGGGGGCCTTGGCGCCTGCTCA 8 49 1 GGGGCCTTGG 0.934108 -212 CGATTAGCTGATCGGCTGCGCCACGTTGGT 8 133 1 ATCGGCTGCG 0.862725 -128 CCAGTGACAAACCGCATGGCGTCGCGACAG 8 191 1 ACCGCATGGC 0.595894 -70 AGCGCTGCGGGCCGCCTTCGAGGAGGACGA 10 202 1 GCCGCCTTCG 0.985481 -29 ********** Masking position 4 Map Score: 18.9864 Number of sites scoring better than the average of aligned sites = 3279 Number in coding regions = 3020 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 ACGGTTTTCCGTTACCCTGTAATTAAGTAA 2 24 0 GTTACCCTGT 0.990665 -176 GAAAGGGGCCTTTACCCTTTTCTAATGTAC 2 52 0 TTTACCCTTT 0.817465 -148 CGCCGGGCTCGCTACCCTGTCCCAATGCGA 4 25 0 GCTACCCTGT 0.991346 -182 TTAACAACCGGTTACCCAGTTTTCACGCAT 4 126 0 GTTACCCAGT 0.978798 -81 ATGCAACCAGGCTTCCCTATCGCTGTCAAC 5 72 0 GCTTCCCTAT 0.885183 -22 CTTCTGTGCTGATACCCAGTGACAAACCGC 8 176 1 GATACCCAGT 0.969895 -85 CGGACCGCGCTATTCCCTGTTGCTATCCAC 8 231 1 TATTCCCTGT 0.897842 -30 ********** Masking position 3 Map Score: 6.61563 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 67 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GAGGATCTTGCCAGCTATACAGACGGAGAG 1 37 1 CCAGCTATAC 0.875494 -65 ATATAAGCTTCTTGCTCTCCGTCTGTATAG 1 51 0 CTTGCTCTCC 0.983296 -51 AGCTCTCTCTGCCGCTCTACTTTCATTCTT 3 45 0 GCCGCTCTAC 0.943542 -256 CATCGCCGGGCTCGCTACCCTGTCCCAATG 4 28 0 CTCGCTACCC 0.855106 -179 GCCTGGTTGCTCTGCTGTCCCTGGCAAGCG 6 15 1 TCTGCTGTCC 0.868713 -39 GGCCTTGGCGCCTGCTCACCTAGCCCAACA 8 61 1 CCTGCTCACC 0.969007 -200 GCTATTCCCTGTTGCTATCCACCGATCCCA 8 239 1 GTTGCTATCC 0.923236 -22 GGCGTGGGAACCTGCTCTACCACCCGCTAT 10 89 1 CCTGCTCTAC 0.983296 -142 ********** Masking position 6 Map Score: 3.62474 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 478 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTGTTAAACTTGAGGAATGTGCAAGGCACGATAAAAA 3 192 1 TGGGAGTCGC 0.993781 -109 TCACCCGTGATCCGGATGGTTCCGCTCGGGCCGATTC 4 87 1 TCGGAGTCCC 0.993781 -120 GGTATCGCGGTGTGGACTTTGCTACTCAGATCGACGC 4 167 0 TGGGATTCCC 0.986407 -40 GCTTCAGGATTGTGCCACCCGCTTGCCAGG 6 34 0 TCGGAGTCCC 0.993781 -20 CGCCGAGGCGTGGGGGGCCTTGGCGCCTGCTCACCTA 8 46 1 TGGGGCTGGC 0.927961 -215 AGCGCTCGACTGCGGAACCTCGGTCACACGTTTTGCA 10 171 0 TGGGACTGCC 0.988169 -60 GACTGTGGTTCGTCCTCCTCGAAGGCGGCC 10 211 0 TGGGTGTCCC 0.98941 -20 ** *** ** * * * Masking position 10 Map Score: 3.3192 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 35 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 AAGAGTGGATTCCCACCCTTTTTTAAAAGA 3 127 0 TCCCACCCTT 0.950667 -174 CAGGATTGTGCCACCCGCTTGCCAGGGACA 6 30 0 CCACCCGCTT 0.985851 -24 CGCCAAGGCCCCCCACGCCTCGGCGTGTCG 8 41 0 CCCCACGCCT 0.990955 -220 TAGAGCAGGTTCCCACGCCTGTGCCTCGCC 10 78 0 TCCCACGCCT 0.985851 -153 ACCTGCTCTACCACCCGCTATGGTGTGAGG 10 98 1 CCACCCGCTA 0.945023 -133 GGAACCTCGGTCACACGTTTTGCAACCGCA 10 165 0 TCACACGTTT 0.892108 -66 ********** Masking position 6 Map Score: 3.35783 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 126 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTTCTGCCTCAATGAAAATTCGCTGAAGGT 2 82 1 AATGAAAATT 0.93532 -118 TGGAAACAAGAATGAAAGTAGAGCGGCAGA 3 38 1 AATGAAAGTA 0.903463 -263 TTTTATAACAAATGAAAAGTAAATACAACT 3 228 0 AATGAAAAGT 0.867214 -73 ATAAAATTAGAATGAGAATAAAATGAGAAT 3 252 1 AATGAGAATA 0.957304 -49 ATGAGAATAAAATGAGAATAATGATTATAT 3 263 1 AATGAGAATA 0.957304 -38 ********** Masking position 5 Map Score: 0.526893 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 107 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 TTCTTGTTTCCAGCCGGCGTCCATATTCCT 3 20 0 CAGCCGGCGT 0.774506 -281 AAGCGGATTTCTGCGGGAGCTTATTGAGAA 3 91 1 CTGCGGGAGC 0.981331 -210 CGATGGCGTGCCGCCAGCGCGCCGGTTGAT 4 53 1 CCGCCAGCGC 0.923208 -154 CCGGATGGTTCCGCTCGGGCCGATTCTGAT 4 98 1 CCGCTCGGGC 0.978892 -109 TTAAAATTCACCGCGGCGTCGATCTGAGTA 4 152 1 CCGCGGCGTC 0.801597 -55 CAGCCCGAGCCGTCAGCCTA 5 1 1 CAGCCCGAGC 0.976042 -93 TCTCGGCGGGCTGCCGGTGCGCCAGTGCGC 5 33 0 CTGCCGGTGC 0.979733 -61 GCTGTCAACGCAGCCCCATCTCGGCGGGCT 5 51 0 CAGCCCCATC 0.595309 -43 CTGGGCAATCTGGCTGGGGCCAGACCAC 7 9 0 TGGCTGGGGC 0.483918 -88 TGCCCAGCCGCTGCTGCGGCCGTGGCCTGC 7 32 1 CTGCTGCGGC 0.934519 -65 CGGCCGTGGCCTGCGCGCACGTTCTGCGTC 7 48 1 CTGCGCGCAC 0.796338 -49 TTCTGCGTCGCCGCCCGGGCCAGTATTCTA 7 69 1 CCGCCCGGGC 0.992716 -28 GTTCCCTGCGCGAGCAGTCGCAAAA 8 6 1 CTGCGCGAGC 0.978393 -255 CCGGCGGATACTCCCGGTGCCCGGTTCGCG 10 43 0 CTCCCGGTGC 0.813635 -188 ********** Masking position 4 Map Score: 15.0484 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1321 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 10 ********** No masking Map Score: -5.2337e-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: -5.2337e-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 12 ********** No masking Map Score: -5.2337e-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