AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_bsub_mtub_300.orf -o117_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 yjaX 164 similar to 3-oxoacyl- acyl-carrier protein synthase #2 yjaY 22 similar to 3-oxoacyl- acyl-carrier protein synthase #3 yjaZ 75 yjaZ #4 appD 191 oligopeptide ABC transporter (ATP-binding protein) #5 appA 87 oligopeptide ABC transporter (oligopeptide-binding protein) #6 appB 75 oligopeptide ABC transporter (permease) #7 oppA 300 oligopeptide ABC transporter (binding protein) #8 oppB 107 oligopeptide ABC transporter (permease) #9 ykeA 168 alternate gene name: yzcA; similar to pyrroline-5-carboxylate reductase #10 dppA 128 dipeptide ABC transporter #11 oppB 206 oppB #12 dppA 300 dppA Motif number 1 TCAAGCCAAACCGGCTGCCCTTAAAG 3 5 1 GCCACCGGCT 0.97571 -71 TGCCCTTAAAGGGTAGCCGGTTTTTTTTGTGT 3 26 1 GGGACCGGTT 0.927236 -50 ATTCGCAAACCCCCTAATAATAATT 7 286 0 CGCACCCCCT 0.790704 -15 CGTGAAAACTGGGTAACCGGTTGTTAAAATTC 11 67 0 GGGACCGGTT 0.927243 -140 CCGGTTGATGGGGTCACCCGTGATCCGGATGG 11 122 0 GGGCCCCGTG 0.897928 -85 CCCATCAACCGGCGCGCTGGCGGCACGCCATC 11 142 1 GGCCCTGGCG 0.841255 -65 GGACAGGGTAGCGAGCCCGGCGATGGCGTGCC 11 163 0 GCGGCCGGCG 0.977617 -44 GCCCAACCACCGCGTCGCATTG 11 195 0 GCCACCACCG 0.933555 -12 GTGGCGAGGAAGGCAGCCCGCGCGA 12 4 0 AGGACCCGCG 0.666068 -297 CGCCACAGCGCCGACACCACCGGTCCTCCTCG 12 30 1 CCGCCCACCG 0.764568 -271 GAAGACCTCGCCCGACCGGGCGCTGTTGGCGT 12 72 0 CCCACGGGCG 0.89513 -229 ATCCGGTGTTGGCTACCCACCGCGACTGCGCT 12 112 0 GGCACCACCG 0.959624 -189 CACCGTCGTTCGCGATCCGGTGTTGGCTACCC 12 126 0 CGCACCGGTG 0.985 -175 CCAGAGTGCCGGCGAACCGGTGGGACGATGTT 12 171 0 GGCACCGGTG 0.989494 -130 TTAGCTACCACGCCACCCAGAGTGCCGGCGAA 12 187 0 CGCACCAGAG 0.800036 -114 TGGTAGCTAACGGTCACCGGCGAGTGTGTCGG 12 209 1 CGGCCCGGCG 0.980884 -92 GTGAAGTGCGGCCTGGCCAGCGCAGCCGACAC 12 234 0 GCCGCCAGCG 0.950547 -67 CAGTCCGGCTCCCCAGCCGGTGAAGTGCGGCC 12 253 0 CCCACCGGTG 0.974151 -48 AGCCTTCTTGTGCAGTCCGGCTCCCCAGCCGG 12 265 0 TGCGCCGGCT 0.694067 -36 *** * ****** Masking position 7 Map Score: 26.0815 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1478 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 AGTATGGTATATGGAAAGGAGGCGT 1 4 0 ATAAAGGAGG 0.943415 -161 TGCATAGGATTAAAAGAGGAGGCGATCAC 3 57 1 TAAGAGGAGG 0.994119 -19 AACGTTTGACAACAAGAGGGGGGAAAGGGGAG 4 165 1 AAAGAGGGGG 0.986325 -27 CCCGCACAGCTTTGAGAGGGGGTATGCACACT 5 16 1 TTAGAGGGGG 0.98795 -72 GAACGAACATTTCAAGAGGGGGAATATCTA 5 68 1 TTAGAGGGGG 0.98795 -20 ATTTCCCTTAAAGGGGAGGGAGAGCGTTT 6 8 1 TTAGGGGAGG 0.94478 -68 TCCTTATTAAAAACAGAAGAGGGAGAAAACGC 6 34 0 AAAGAAGAGG 0.924134 -42 TTAATAAGGAAAGTAAAGGGGGACAAGTAT 6 56 1 AAAAAGGGGG 0.958785 -20 CAAATTATATTAAAAAAAGAGGAAAAATGCAA 10 69 0 TAAAAAGAGG 0.883385 -60 CATAATTTAGTAAAAAAGGAGGAGCGTT 10 111 1 TAAAAGGAGG 0.981989 -18 CACACCGCGATACCCGAGGAGGCCCGC 11 6 0 TACGAGGAGG 0.983217 -201 GCGTGCGGCATCCTCGAGGAGGACCGGTGGTG 12 44 0 TCCGAGGAGG 0.939614 -257 ** ******** Masking position 9 Map Score: 20.366 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 117 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 CTCAGATCGACGCCGCGGTGAATTTTAACA 11 48 1 CGCCGCGGTG 0.956638 -159 CCCCATCAACCGGCGCGCTGGCGGCACGCC 11 141 1 CGGCGCGCTG 0.951602 -66 GTAGCGAGCCCGGCGATGGCGTGCCGCCAG 11 158 0 CGGCGATGGC 0.92798 -49 TGTCCCAATGCGACGCGGTGGTTGGGC 11 190 1 CGACGCGGTG 0.987838 -17 CCGGTGGTGTCGGCGCTGTGGCGAGGAAGG 12 23 0 CGGCGCTGTG 0.995469 -278 TCGCCCGACCGGGCGCTGTTGGCGTGCGGC 12 67 0 GGGCGCTGTT 0.967269 -234 GCGCCCGGTCGGGCGAGGTCTTCCCTTGGG 12 81 1 GGGCGAGGTC 0.961667 -220 TGGGAAGCGCAGTCGCGGTGGGTAGCCAAC 12 107 1 AGTCGCGGTG 0.86765 -194 GGATCGCGAACGACGGTGTGAGCGTTCCCA 12 140 1 CGACGGTGTG 0.913488 -161 CGAACCGGTGGGACGATGTTTTGGGAACGC 12 161 0 GGACGATGTT 0.705829 -140 AGTGTGTCGGCTGCGCTGGCCAGGCCGCAC 12 231 1 CTGCGCTGGC 0.788671 -70 AAGGCTTTAGGGTCGCTGTC 12 291 1 GGTCGCTGTC 0.952392 -10 ********** Masking position 4 Map Score: 13.4879 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 649 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TGTTGCCCGCACAGCTTTGAGAGGG 5 5 1 GCCCGCACGC 0.993712 -83 GTGTACCGTTTTCCGCACTTTTTCACAATTT 9 119 0 TTCCGCACTT 0.68937 -50 GAGTAGCAAAGTCCACACCGCGATACCCGAG 11 20 0 GTCCACACGC 0.924047 -187 CCGGCGCGCTGGCGGCACGCCATCGCCGGGC 11 150 1 GGCGGCACCC 0.991943 -57 TCGCCACAGCGCCGACACCACCGGTCCTCCT 12 29 1 GCCGACACAC 0.942314 -272 TCCTCGAGGATGCCGCACGCCAACAGCGCCC 12 56 1 TGCCGCACCC 0.984838 -245 CCACCGGTTCGCCGGCACTCTGGGTGGCGTG 12 180 1 GCCGGCACCT 0.990627 -121 GGCCAGCGCAGCCGACACACTCGCCGGTGAC 12 221 0 GCCGACACCT 0.967552 -80 GCGCTGGCCAGGCCGCACTTCACCGGCTGGG 12 243 1 GGCCGCACTC 0.984328 -58 TCTTGTGCAGTCCGGCTCCCCAGCCGGTGAA 12 261 0 TCCGGCTCCC 0.936988 -40 ******** ** Masking position 6 Map Score: 10.8583 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 472 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TATATTGCCATGTGAAAAAAAATAGGATAG 1 69 1 TGTGAAAAAA 0.934529 -96 GCAAAATGATTGTAATAATATACAACTATA 4 73 1 TGTAATAATA 0.448685 -119 AAAACAGAAGAGGGAGAAAACGCTCTCCCT 6 27 0 AGGGAGAAAA 0.852188 -49 ATTATGTTCATGGAAGAAAAACTAACGAAG 7 70 1 TGGAAGAAAA 0.73391 -231 GTAACAATAGAGTGAACAAGTTCATTATAA 7 151 0 AGTGAACAAG 0.84398 -150 TGATTATTTTTGTAAAAAAGCTGTAACAAT 7 173 0 TGTAAAAAAG 0.906013 -128 ATACTCCATCAGTAAGAAAGGTATATGGGG 8 57 0 AGTAAGAAAG 0.825802 -51 AGAGAAACGGAGTGAACATG 9 1 0 AGTGAACATG 0.673355 -168 TAAATAGACATGTGAAAATAGAGAAACGGA 9 20 0 TGTGAAAATA 0.844708 -149 ACAAAAACTGTGGGATAAAAATGAAAAGAT 9 83 1 TGGGATAAAA 0.806505 -86 TATGGGAAATTGTGAAAAAGTGCGGAAAAC 9 113 1 TGTGAAAAAG 0.958171 -56 TCAATCATTCAGTGATAAAAAAAGAATCCT 10 22 0 AGTGATAAAA 0.816987 -107 GCAATATAACTGGGAAAAATCTCAATCATT 10 43 0 TGGGAAAAAT 0.677517 -86 TTAAAAAAAGAGGAAAAATGCAATATAACT 10 62 0 AGGAAAAATG 0.726334 -67 TTCATAATTTAGTAAAAAAGGAGGAGCGTT 10 109 1 AGTAAAAAAG 0.894512 -20 ********** Masking position 5 Map Score: 8.83425 Number of sites scoring better than the average of aligned sites = 1827 Number in coding regions = 1506 Number in noncoding regions = 321 Number of orfs with sites within 600 bp upstream = 329 Fraction of orfs with sites within 600 bp upstream = 0.0528429 Motif number 6 TCATAGAGTATGGTATATGGAAAGGAGGCG 1 12 0 TGGTATATGG 0.967813 -153 TTCTAGGCTGTTGTTTATGTAGTGTGCATA 5 38 0 TTGTTTATGT 0.784141 -50 GAAGGATATTATGTTCATGGAAGAAAAACT 7 63 1 ATGTTCATGG 0.834305 -238 AAAGACCTCAAGGTATATGGGGAGAAAAGC 8 28 1 AGGTATATGG 0.967813 -80 TCAGTAAGAAAGGTATATGGGGCTTTTCTC 8 49 0 AGGTATATGG 0.967813 -59 TTATATTGATAGGTTTATGACTTGAGTTTA 9 47 1 AGGTTTATGA 0.935728 -122 CCCACAGTTTTTGTTTATGATAAACTCAAG 9 67 0 TTGTTTATGA 0.901755 -102 ACACTTCATATTGTATATGAAAGGACTGAG 9 146 1 TTGTATATGA 0.901744 -23 ********** Masking position 7 Map Score: 6.38568 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 108 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 GATAAAATAATGGAATTTCATTAATAATATTA 4 14 1 TGAATTTATT 0.897661 -178 TTAGGATAAATGTAATATTATTAATGAAATTC 4 26 0 TGAATATATT 0.97933 -166 TTCTTGATTTTGCAAAATGATTGTAATAATAT 4 62 1 TGAAAATATT 0.897661 -130 AATTTTATAGTTGTATATTATTACAATCATTT 4 76 0 TTTATATATT 0.774195 -116 TTTTCGATAATTCAATATTATTTATTATTTCT 4 107 1 TTAATATATT 0.950325 -85 AATAATTTATTGCAATATTATTTTATCAATTT 7 112 0 TGAATATATT 0.979954 -189 AGAGGAAAAATGCAATATAACTGGGAAAAATC 10 52 0 TGAATATACT 0.928461 -77 TTCCTCTTTTTTTAATATAATTTGTTAGAATA 10 77 1 TTAATATATT 0.950311 -52 ** ***** *** Masking position 5 Map Score: 6.20153 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GCTAGCTCCCCTTTCCCCCCT 4 181 0 GCTAGCTCCC 0.963763 -11 GAGGGAGAGCGTTTTCTCCCTCTTCTGTTTT 6 26 1 GTTTTCTCCT 0.631627 -50 TTTTTCATGTGTTTTCTGCCCA 7 2 0 GTTTTCTCCC 0.951517 -299 GTATATGGGGCTTTTCTCCCCATATACCTTG 8 36 0 CTTTTCTCCC 0.94271 -72 AAAGTCCACACCGCGATACCCGAGGAGGCCC 11 13 0 CCGCGATCCC 0.765084 -194 GCGGTGTGGACTTTGCTACTCAGATCGACGC 11 30 1 CTTTGCTCTC 0.839596 -177 CCATCGCCGGGCTCGCTACCCTGTCCCAATG 11 169 1 GCTCGCTCCC 0.987455 -38 CCCACCGCGACTGCGCTTCCCAAGGGAAGAC 12 98 0 CTGCGCTCCC 0.985073 -203 GCGATCCGGTGTTGGCTACCCACCGCGACTG 12 116 0 GTTGGCTCCC 0.972746 -185 GCCGGTGACCGTTAGCTACCACGCCACCCAG 12 199 0 GTTAGCTCCA 0.787685 -102 AGTGTGTCGGCTGCGCTGGCCAGGCCGCACT 12 231 1 CTGCGCTGCC 0.885149 -70 ******* *** Masking position 7 Map Score: 7.5715 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 391 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 TAGGGAAGACTCCTTTATATCT 1 153 0 GGGAAGACTC 0.937274 -12 GTGATCGCCTCCTCTTTTAA 3 66 0 GTGATCGCCT 0.83603 -10 TCTGAATAAAGGGATTGCTTTCTCTTGAAA 4 136 1 GGGATTGCTT 0.857762 -56 TTTCAAGAGGGGGAATATCTA 5 77 1 GGGAATATCT 0.738179 -11 GGGGGAACACCTCCATGGTTTT 8 96 0 GGGAACACCT 0.986713 -12 GCCGGTTGATGGGGTCACCCGTGATCCGGA 11 125 0 GGGGTCACCC 0.92338 -82 CGCTTCCCAAGGGAAGACCTCGCCCGACCG 12 86 0 GGGAAGACCT 0.974956 -215 ACGATGTTTTGGGAACGCTCACACCGTCGT 12 149 0 GGGAACGCTC 0.965502 -152 ********** Masking position 3 Map Score: 2.60013 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 257 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 ATGAAATTCCATTATTTTATCCTT 4 5 0 ATTATTTTAT 0.88323 -187 ATAATTCAATATTATTTATTATTTCTGAAT 4 113 1 ATTATTTATT 0.841724 -79 TTATTGCAATATTATTTTATCAATTTAAAA 7 108 0 ATTATTTTAT 0.88323 -193 ATTGCAATAAATTATTTGTTTCATTATAAT 7 128 1 ATTATTTGTT 0.935566 -173 GTCTTTTCTGATTATTTTTGTAAAAAAGCT 7 181 0 ATTATTTTTG 0.843499 -120 TTGAAAGAGGATTCTTTTTTTATCACTGAA 10 15 1 ATTCTTTTTT 0.843499 -114 TTTTTTTAATATAATTTGTTAGAATATTCA 10 83 1 ATAATTTGTT 0.750902 -46 ********** Masking position 1 Map Score: 0.644461 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 124 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 11 ********** No masking Map Score: 2.44017e-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: 2.44017e-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 13 ********** No masking Map Score: 2.44017e-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