AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_bsub_mtub_300.orf -o300_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 yqiE 246 similar to hypothetical proteins #2 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #3 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #4 yqhZ 263 similar to transcription termination #5 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #6 spoIIIAC 22 spoIIIAC #7 spoIIIAA 75 spoIIIAA #8 yqhV 144 alternate gene name: yqgE #9 efp 24 elongation factor P #10 yqhS 86 similar to 3-dehydroquinate dehydratase #11 yqhR 226 yqhR #12 dxs 143 dxs #13 idsA 22 idsA Motif number 1 TCGGCGGACTCTCTCTTCAAAA 1 3 1 GGCGGACTCT 0.950067 -244 CCTAAAGCCAGGGCGGGTTTTCTTTAGTTA 3 83 1 GGGCGGGTTT 0.928496 -55 AATGCTTAGGAGAGGAGTTTTTAGAC 3 122 1 AGAGGAGTTT 0.819515 -16 CGGCTATGTAAGCCGGCTTTCTTCATGCTT 4 77 0 AGCCGGCTTT 0.987714 -187 CGGCTTACATAGCCGAGTTTCTTCATGAAC 4 92 1 AGCCGAGTTT 0.958437 -172 CCGCTTGTTTAGCGGGCTTTTTTCCCTCAT 5 13 0 AGCGGGCTTT 0.994511 -143 CCGCTAAACAAGCGGGCTTTTTGCGTTGCT 5 28 1 AGCGGGCTTT 0.994511 -128 ATCTTACAGGAGCGGACTTGTGAATTCAAC 5 69 0 AGCGGACTTG 0.962842 -87 TATGATGTGAGGCAGACTTTATGACAAGCC 7 16 0 GGCAGACTTT 0.944424 -60 GGTAGAAAGGAGGAGGCTCTG 7 65 1 AGGAGGCTCT 0.848639 -11 CCCAAATGGGAGCAGGCTTTTTTTGTGCCC 8 32 1 AGCAGGCTTT 0.980816 -113 CTAGAGGTTTAGCGGTGTTTCCTGTACAAT 11 62 0 AGCGGTGTTT 0.927654 -165 CTGGGCCAATGGGGGGGTTGCTGCGTACAC 12 117 1 GGGGGGGTTG 0.902406 -27 ********** Masking position 8 Map Score: 20.5591 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 577 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 ATATAAAAGGTCTTTTTGAAGAGAGAGTCCG 1 15 0 TCTTTTTGAG 0.868714 -232 TTCAAAAAGACCTTTTATATGAGCTTTGTGA 1 26 1 CCTTTTATAG 0.93681 -221 GCGCGTTTGTCTTTTTTTATGTCTGAGATTA 1 158 1 CTTTTTTTAG 0.877782 -89 ATGATACATGTCTTTTGCATGCCGAGCTGAC 1 191 0 TCTTTTGCAG 0.931817 -56 CATGTTTCATTTTTTTTCACGTCTG 2 5 0 TTTTTTTCAG 0.955565 -81 GCCCTTTGGTTTTTTTACACGTTACCCTTTA 4 41 1 TTTTTTACAG 0.976187 -223 TGAAATTTCTTTTTTTATAGGTTACTACTAA 5 116 0 TTTTTTATAG 0.969537 -40 ACAGAATCTTTCTTTTATACGGAAATGACAA 8 66 1 TCTTTTATAG 0.971829 -79 AACCTCCCATTTTTTTATATGATATGCTCTA 8 113 0 TTTTTTATAG 0.969551 -32 GAAGTGAACATTTTTTACATGAGAAACCCTC 10 48 1 TTTTTTACAG 0.976187 -39 ********* * Masking position 6 Map Score: 12.5576 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 278 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 TTATTGTCAGCTCGGCATGCAAAAGACATG 1 186 1 CTCGGCATGC 0.880145 -61 TCAACTCACTTTCAGCATGAATTTCTGCAA 1 221 0 TTCAGCATGA 0.940476 -26 ATCTCCCTCTTCAAGCTTTGATACAA 2 70 0 CTCTTCAAGC 0.852726 -16 CGATACCCGCTTCTTCAGGCTCCTAAAGCC 3 62 1 TTCTTCAGGC 0.925212 -76 TAAGCCGGCTTTCTTCATGCTTTGAAATAA 4 69 0 TTCTTCATGC 0.966436 -195 ATAGCCGAGTTTCTTCATGAACGTGAAATC 4 100 1 TTCTTCATGA 0.919603 -164 AAACCTTGATTTCAATATGCGGATACGAAA 4 178 1 TTCAATATGC 0.723417 -86 ACAAGTCCGCTCCTGTAAGATGAACATAGT 5 78 1 TCCTGTAAGA 0.632763 -78 ACAAGACTACTTCAGCAAGCTAGAGCATAT 8 93 1 TTCAGCAAGC 0.940638 -52 ATAATCCTTTTCCAGTATGATAAAATGTTC 10 14 1 TCCAGTATGA 0.769008 -73 ACCTGCCTATTTCTTTAGGATTGCTAACCA 11 18 1 TTCTTTAGGA 0.585517 -209 GCCTTGCTTTTCCTACATGCATTATACCCG 11 118 1 TCCTACATGC 0.901174 -109 CCCCCATTGGCCCAGCATGCGGCCGCCGAT 12 102 0 CCCAGCATGC 0.936493 -42 ********** Masking position 7 Map Score: 8.54655 Number of sites scoring better than the average of aligned sites = 1916 Number in coding regions = 1774 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 ACGCGCTTTTCCTTTTCATTTTTCATATAAAC 1 132 0 CCTTTTTTTT 0.807497 -115 ATGTCATGTTTCATTTTTTTTCACGTCTG 2 8 0 TCATTTTTTC 0.480543 -78 GGGCCGCCCTCCCCTTGGTTTCGTGTTAAGCC 4 13 0 CCCCTTTTTC 0.978913 -251 GGGAGGGCGGCCCTTTGGTTTTTTTACACGTT 4 32 1 CCCTTTTTTT 0.829327 -232 TTTACACGTTACCCTTTATTTCAAAGCATGAA 4 54 1 ACCCTTTTTC 0.865769 -210 ACGCAAAAAGCCCGCTTGTTTAGCGGGCTTTT 5 22 0 CCCGCTTTTA 0.696132 -134 CAGAGCCTCCTCCTTTCTACCGATTGG 7 59 0 CCTCCTTTTC 0.979881 -17 TTGGGAACAGACTTCTTTTTTCCTTT 8 5 0 ACTTCTTTTC 0.780597 -140 ACTCTCCCAACCTCCCATTTTTTTATATGATA 8 120 0 CCTCCCTTTT 0.816921 -25 GTTTAATGTCCTCCTATATTCCAA 9 4 0 CCTCCTATTC 0.827393 -21 ACAATCTCTCCTTTTCGCGAGGGTTT 10 71 0 TCTCTCTTTC 0.719281 -16 ATTATCAACCTGCCTATTTCTTTAGGATTG 11 9 1 CCTGCCTTTC 0.920321 -218 GGATTGCTAACCATTTCCTTTCACTCTATTGT 11 35 1 CCATTTTTTC 0.86942 -192 ATGCATTATACCCGTTATTTTCAAATTTTACT 11 134 1 CCCGTTTTTC 0.959877 -93 ****** **** Masking position 10 Map Score: 8.27382 Number of sites scoring better than the average of aligned sites = 1425 Number in coding regions = 1099 Number in noncoding regions = 326 Number of orfs with sites within 600 bp upstream = 374 Fraction of orfs with sites within 600 bp upstream = 0.0600707 Motif number 5 AAAGGGCCGCCCTCCCCTTGGTTTCGTGTTA 4 17 0 CCCCCCTTGG 0.989878 -247 AAGGGGAGGGCGGCCCTTTGGTTTTTTTACA 4 29 1 CGCCCTTTGG 0.994039 -235 CTCCTCCTTTCTACCGATTGGCTTCTTTAAA 7 49 0 CTCCGATTGG 0.948747 -27 AAAAAGCCTGCTCCCATTTGGGAACAGACTT 8 23 0 CTCCATTTGG 0.905664 -122 ACTCTCCCAACCTCCCATTTTTTTATATGAT 8 121 0 CCCCCATTTT 0.919094 -24 GCCTGGTCGGCGACTCATTGTCATCCAACTC 12 22 0 CGCTCATTGT 0.847238 -122 CAAAGTGGTTCGGCCCTTTTGATCGGCGGCC 12 81 1 CGCCCTTTTG 0.974453 -63 ACGCAGCAACCCCCCCATTGGCCCAGCATGC 12 112 0 CCCCCATTGG 0.995405 -32 ** ******** Masking position 8 Map Score: 6.40693 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 102 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 CAATTAAATCACAAAGCTCATATAAAAGGT 1 35 0 ACAAAGCTCA 0.94883 -212 CCGAGCTGACAATAATCTCAGACATAAAAA 1 171 0 AATAATCTCA 0.729528 -76 AAGCTTTGATACAATGCTCTCAAGCCCTTT 2 54 0 ACAATGCTCT 0.842043 -32 CCTATTACCGAATATTTTCACACACCTTAA 4 142 0 AATATTTTCA 0.731758 -122 AAAAGTACATACTATGTTCATCTTACAGGA 5 88 0 ACTATGTTCA 0.921201 -68 CCAGTATGATAAAATGTTCACGAGAAGTGA 10 25 1 AAAATGTTCA 0.950331 -62 TCTCATGTAAAAAATGTTCACTTCTCGTGA 10 42 0 AAAATGTTCA 0.950331 -45 AATGTCAATAAAAAAGCTCACACTTTTTGG 11 174 0 AAAAAGCTCA 0.949794 -53 ********** Masking position 4 Map Score: 4.43605 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 352 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TCTTTTGCATGCCGAGCTGACAATAATCTCA 1 181 0 GCCGAGCGAC 0.890803 -66 CTAAAGAAAACCCGCCCTGGCTTTAGGAGCC 3 79 0 CCCGCCCGGC 0.968792 -59 AAACCAAAGGGCCGCCCTCCCCTTGGTTTCG 4 22 0 GCCGCCCCCC 0.996176 -242 AGCACTCTCCCAACCTCCCATTTTTTTAT 8 126 0 CCCAACCCCC 0.958385 -19 ACAATGAGTCGCCGACCAGGCTTCCCGGCGC 12 32 1 GCCGACCGGC 0.976076 -112 AGCGTCGGTGGCCGGCGCGCCGGGAAGCCTG 12 48 0 GCCGGCGGCC 0.638895 -96 AGTGTACGCAGCAACCCCCCCATTGGCCCAG 12 117 0 GCAACCCCCC 0.917474 -27 ******* *** Masking position 2 Map Score: 2.64211 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 365 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 TGAGCACGATACCCGCTTCTTCAGGCTCCT 3 56 1 ACCCGCTTCT 0.963891 -82 GATCCTCTTTATCCGCTTGTCGTTAAGCCA 4 230 0 ATCCGCTTGT 0.845057 -34 AACGCAAAAAGCCCGCTTGTTTAGCGGGCT 5 25 0 GCCCGCTTGT 0.976321 -131 GAATTCACAAGTCCGCTCCTGTAAGATGAA 5 72 1 GTCCGCTCCT 0.989885 -84 CAGAGCCTCCTCCTTTCTACCGAT 7 62 0 GCCTCCTCCT 0.949529 -14 GAAAAAAGAAGTCTGTTCCCAAATGGGAGC 8 15 1 GTCTGTTCCC 0.805282 -130 CACAAAAAAAGCCTGCTCCCATTTGGGAAC 8 29 0 GCCTGCTCCC 0.985036 -116 ********** Masking position 7 Map Score: 2.48749 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 834 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 AGTTTATATGAAAAATGAAAAGGAAAAGCG 1 131 1 AAAAATGAAA 0.962687 -116 CTCAGACATAAAAAAAGACAAACGCGCTTT 1 155 0 AAAAAAGACA 0.916621 -92 AGACGTGAAAAAAAATGAAACATGACATTT 2 12 1 AAAAATGAAA 0.962687 -74 AGGATCAAAGGAGAAAGAAA 4 254 1 GAGAAAGAAA 0.744892 -10 GTAACCTATAAAAAAAGAAATTTCATACAT 5 122 1 AAAAAAGAAA 0.976409 -34 AAAGGAAAAAAGAAGTCTGTTCCCA 8 6 1 AAAAAAGAAG 0.916621 -139 TCATTTCCGTATAAAAGAAAGATTCTGTTT 8 64 0 ATAAAAGAAA 0.881197 -81 AGTGTGCCCAAAAAATGAAATGTCAATAAA 11 192 0 AAAAATGAAA 0.962687 -35 ********** Masking position 5 Map Score: 9.16323 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 320 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 ACGAGGGTATGGTAAAATGTAAGCAGTTTA 1 107 1 GGTAAAATGT 0.923873 -140 TGAAGAAGCGGGTATCGTGCTCATATTCAA 3 49 0 GGTATCGTGC 0.973509 -89 GTTTTCTTTAGTTATGGTGCAGGAATGCTT 3 99 1 GTTATGGTGC 0.789017 -39 CCCTCCCCTTGGTTTCGTGTTAAGCCAT 4 9 0 GGTTTCGTGT 0.870447 -255 TGAAATAAAGGGTAACGTGTAAAAAAACCA 4 47 0 GGTAACGTGT 0.974021 -217 TTTCCAGTATGATAAAATGTTCACGAGAAG 10 22 1 GATAAAATGT 0.65247 -65 GAAAATAACGGGTATAATGCATGTAGGAAA 11 126 0 GGTATAATGC 0.922452 -101 GGCACCTCCAGTTAAAGTGTGCCCAAAAAA 11 207 0 GTTAAAGTGT 0.894398 -20 ********** Masking position 3 Map Score: 2.94109 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 104 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 TTACCATACCCTCGTGCAGCCGCTTCAAATT 1 91 0 CTCGTCAGCC 0.972581 -156 TTGATACAATGCTCTCAAGCCCTTTCATCGC 2 48 0 GCTCTAAGCC 0.94867 -38 CTTCTTCAGGCTCCTAAAGCCAGGGCGGGTT 3 71 1 CTCCTAAGCC 0.980572 -67 CCCTTGGTTTCGTGTTAAGCCAT 4 3 0 CGTGTAAGCC 0.950525 -261 TTATCCGCTTGTCGTTAAGCCACAAAGAGAT 4 221 0 GTCGTAAGCC 0.985985 -43 TGGCCGGCGCGCCGGGAAGCCTGGTCGGCGA 12 40 0 GCCGGAAGCC 0.973204 -104 ***** ***** Masking position 8 Map Score: 1.02179 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 148 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 ACAATCGCACTCCTATGTATGAA 5 143 0 ATCGCACTCC 0.99061 -13 ATCGAACTCCGGAGTTGGAT 12 1 1 ATCGAACTCC 0.992096 -143 ACTCATTGTCATCCAACTCCGGAGTTCGAT 12 11 0 ATCCAACTCC 0.98555 -133 ********** Masking position 6 Map Score: 0.641082 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 7 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 AAAGAAGTCTGTTCCCAAATGGGAGCAGGC 8 19 1 GTTCCCAAAT 0.928752 -126 GGCTTTTTTTGTGCCCAAAAACAGAATCTT 8 46 1 GTGCCCAAAA 0.992416 -99 TTACTCGCAGCTGCCAAAAAGTGTGAGCTT 11 161 1 CTGCCAAAAA 0.924739 -66 CAGTTAAAGTGTGCCCAAAAAATGAAATGT 11 199 0 GTGCCCAAAA 0.992416 -28 ********** Masking position 7 Map Score: 1.18231 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: 2.53196e-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 15 ********** No masking Map Score: 2.53196e-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