AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -intrC_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0082 300 formate hydrogenlyase transcriptional activator (fhlA) #2 TP0227 66 cobalt ABC transporter, ATP-binding protein #3 TP0519 300 response regulatory protein (atoC) #4 TP0965 24 membrane fusion protein, putative #5 TP0966 46 T. pallidum predicted coding region TP0966 #6 TP0970 21 T. pallidum predicted coding region TP0970 #7 TP0971 155 membrane antigen, pathogen-specific (tpd) Motif number 1 ATCTTTCAATGGCTGCGGCTGAGACACAAAAAC 1 78 1 GGGCGGCGAG 0.995862 -223 GCAAGATTATTGCTGCGGGAGAGAACTGGTTCT 1 218 0 TGGCGGGGAG 0.993349 -83 TCTTGCTAACCGAAACGCCAGAGAGCAGTACGT 1 245 1 CGACGCCGAG 0.958929 -56 AGTATTCGCGTGTCGCGGGTGTGTACGCGCCAC 2 17 1 TGGCGGGGTG 0.989649 -50 TCAGTATTTCGGATACAGGAGAGGGAATTGATG 3 36 1 GGACAGGGAG 0.992489 -265 TAAAACTGAAGGTACGGGGTTAGGGTTAACCTT 3 109 1 GGCGGGGTAG 0.881684 -192 AGAACATGGCGGTGACATCAGTGTGTCCTCTAC 3 160 1 GGACATCGTG 0.770819 -141 TTTATCTATGGGTAAAAGGAGAGTAAAACACGT 3 206 0 GGAAAGGGAG 0.920285 -95 GCTTGGGACGGCTGTGTCGCGTCCTA 7 4 1 TGACGGCGTG 0.964708 -152 GCGTCCTACTGGGGCCGGGTGTGTGCTGCGCCG 7 29 1 GGCCGGGGTG 0.995221 -127 GGAAAAGAAGCGCTGGACGGGAGAAGGCGTTTT 7 95 1 CGGGACGGAG 0.918376 -61 GTTTTGAAAAGGAGGGGCGCGTGACGCCCCAGG 7 123 1 GGGGGCGGTG 0.976092 -33 GGGCGCGTGACGCCCCAGGGGAGTGAAGA 7 137 1 CGCCAGGGAG 0.98113 -19 ** ***** *** Masking position 2 Map Score: 19.6804 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 840 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TCAATGGCTGCGGCTGAGACACAAAAACCTT 1 83 1 CGGCGAGACA 0.797975 -218 CTTTCGCGCACGTGGGTGAGCAACTACCAAA 1 145 0 CGTGGTGAGC 0.859995 -156 CACCCACGTGCGCGAAAGTCCTTAAGTCGCG 1 158 1 CGCGAAGTCC 0.839856 -143 GTCCTTAAGTCGCGCGAGGTCATGACACCTC 1 175 1 CGCGGAGGTC 0.976326 -126 ATTATTGCTGCGGGAGAGAACTGGTTCTTGC 1 215 0 CGGGGAGAAC 0.987844 -86 CTAACCGAAACGCCAGAGAGCAGTACGTCTT 1 250 1 CGCCGAGAGC 0.983017 -51 ACACCCGCGACACGCGAATACTATGGCA 2 8 0 CACGGAATAC 0.6423 -59 TCGCGTGTCGCGGGTGTGTACGCGCCACAGG 2 22 1 CGGGGTGTAC 0.952852 -45 GGTGTGTACGCGCCACAGGGCACGGTGAATC 2 34 1 CGCCCAGGGC 0.948104 -33 ATTTCGGATACAGGAGAGGGAATTGATGCCC 3 41 1 CAGGGAGGGA 0.94108 -260 CCCCGTCCAACAGTAGAGGACACACTGATGT 3 174 0 CAGTGAGGAC 0.688101 -127 CCCAGTAGGACGCGACACAGCCGTCCCAAGC 7 11 0 CGCGCACAGC 0.868383 -145 CTACTGGGGCCGGGTGTGTGCTGCGCCGTGG 7 34 1 CGGGGTGTGC 0.984291 -122 AAGCGCTGGACGGGAGAAGGCGTTTTGAAAA 7 102 1 CGGGGAAGGC 0.98235 -54 AAAGGAGGGGCGCGTGACGCCCCAGGGGAGT 7 130 1 CGCGGACGCC 0.966349 -26 CGTGACGCCCCAGGGGAGTGAAGA 7 142 1 CAGGGAGTGA 0.893592 -14 **** ****** Masking position 1 Map Score: 18.5349 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1403 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 TACCAAAGAAGGTAGTGAAGAAGATAGTCG 1 122 0 GGTAGTGAAG 0.972681 -179 TTATTGCTGCGGGAGAGAACTGGTTCTTGC 1 215 0 GGGAGAGAAC 0.965393 -86 AGGGATTGTACCGTATTACTC 1 290 0 GGGATTGTAC 0.945601 -11 CGCGTGTCGCGGGTGTGTACGCGCCACAGG 2 23 1 GGGTGTGTAC 0.982754 -44 CTTCAGTTTTAGTAGTGAAGTACGGCTCAA 3 90 0 AGTAGTGAAG 0.799031 -211 ACATGGGGAGTCTGGTATCTTATGC 5 6 1 GGGAGTCTGG 0.935852 -41 TACTGGGGCCGGGTGTGTGCTGCGCCGTGG 7 35 1 GGGTGTGTGC 0.969942 -121 GACGCCCCAGGGGAGTGAAGA 7 145 1 GGGAGTGAAG 0.993617 -11 ********** Masking position 2 Map Score: 9.89229 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 218 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AATGACGCAGTGTTTCTCAGCA 1 2 0 TGTTCTCAGC 0.984428 -299 AAAAGGTTTTTGTGTCTCAGCCGCAGCCATT 1 85 0 TGTGCTCAGC 0.958514 -216 CTTCTTTGGTAGTTGCTCACCCACGTGCGCG 1 141 1 AGTTCTCACC 0.97413 -160 GAACCAGTTCTCTCCCGCAGCAATAATCTTG 1 219 1 TCTCCGCAGC 0.885824 -82 GCAGCAATAATCTTGCTAACCGAAACGCCAG 1 235 1 TCTTCTAACC 0.887466 -66 TCGGGCATCAATTCCCTCTCCTGTATCCGAA 3 43 0 ATTCCTCTCC 0.855076 -258 GGGGTACGTGTTTTACTCTCCTTTTACCCAT 3 201 1 TTTTCTCTCC 0.959921 -100 CCAGCGCTTCTTTTCCTCACCATTATAGAAA 7 80 0 TTTTCTCACC 0.984944 -76 **** ****** Masking position 3 Map Score: 5.02491 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 119 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 CGCTACCAATGACGCAGTGTTTCTCAGCA 1 9 0 GACGCAGTGT 0.950285 -292 TTACGCTCAAGACGTACTGCTCTCTGGCGTT 1 258 0 GACGTACTGT 0.988015 -43 ACACACCCGCGACACGCGAATACTATGGCA 2 10 0 GACACGCGAT 0.893121 -57 TCCTGTATCCGAAATACTGATACTGATGTGG 3 25 0 GAAATACTGT 0.949039 -276 TTTTAGTAGTGAAGTACGGCTCAAAAATATT 3 83 0 GAAGTACGGT 0.964486 -218 AACAGTAGAGGACACACTGATGTCACCGCCA 3 166 0 GACACACTGT 0.988013 -135 ACCCACCTAAGACATACGAGTAAAGAATAAG 3 272 1 GACATACGAT 0.957427 -29 ********* * Masking position 2 Map Score: 4.47392 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 105 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ACAGGGCACGGTGAATCTTCTGTGGACGC 2 48 1 GTGAATCTTC 0.940328 -19 CAAAAATATTGTGAATATTTCGGGCATCAA 3 63 0 GTGAATATTT 0.978655 -238 TCTTAGGTGGGTGGATATTTTTTCTTGTAA 3 254 0 GTGGATATTT 0.986094 -47 GTGCTGCGCCGTGGAGATTTCCATTTGTTT 7 51 1 GTGGAGATTT 0.976526 -105 ********** Masking position 5 Map Score: 0.843086 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AACCGAAACGCCAGAGAGCAGTACGTCTTG 1 252 1 CCAGAGAGCA 0.978686 -49 TGTGTACGCGCCACAGGGCACGGTGAATCT 2 36 1 CCACAGGGCA 0.996017 -31 GCGTCCACAGAAGATTCACCGTGC 2 53 0 CCACAGAAGA 0.955095 -14 ATGGAAATCTCCACGGCGCAGCACACACCC 7 45 0 CCACGGCGCA 0.983927 -111 GCGCGTGACGCCCCAGGGGAGTGAAGA 7 139 1 CCCCAGGGGA 0.986806 -17 ********** Masking position 10 Map Score: 3.34999 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 54 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TCTTCACTACCTTCTTTGGTAGTTGCTCAC 1 131 1 CTTCTTTGGT 0.951388 -170 CACGGTGAATCTTCTGTGGACGC 2 54 1 CTTCTGTGGA 0.976011 -13 AATACTGATACTGATGTGGTCAGTTTGTTT 3 14 0 CTGATGTGGT 0.89813 -287 AGTGTGTCCTCTACTGTTGGACGGGGTACG 3 179 1 CTACTGTTGG 0.918281 -122 ACTCGTATGTCTTAGGTGGGTGGATATTTT 3 263 0 CTTAGGTGGG 0.931358 -38 ACAACTTCCTTCTTGGGGTATTCT 4 7 0 CTTCTTGGGG 0.967397 -18 GTGTCGCGTCCTACTGGGGCCGGGTGTGTG 7 24 1 CTACTGGGGC 0.95604 -132 ********** Masking position 2 Map Score: 2.26605 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 184 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CGACTTAAGGACTTTCGCGCACGTGGGTGA 1 157 0 ACTTTCGCGC 0.839751 -144 GAGGTGTCATGACCTCGCGCGACTTAAGGA 1 176 0 GACCTCGCGC 0.967958 -125 GCAAGAACCAGTTCTCTCCCGCAGCAATAA 1 215 1 GTTCTCTCCC 0.873957 -86 AAGACGTACTGCTCTCTGGCGTTTCGGTTA 1 251 0 GCTCTCTGGC 0.988922 -50 GATTCACCGTGCCCTGTGGCGCGTACACAC 2 35 0 GCCCTGTGGC 0.982038 -32 GCTTGGGACGGCTGTGTCGCGTCCTACTGG 7 11 1 GCTGTGTCGC 0.955143 -145 TTTTCAAAACGCCTTCTCCCGTCCAGCGCT 7 103 0 GCCTTCTCCC 0.958557 -53 TCTTCACTCCCCTGGGGCGTCACGCGCC 7 138 0 CCCCTGGGGC 0.94035 -18 ********** Masking position 5 Map Score: 4.02871 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 487 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 ********** No masking Map Score: 4.64285e-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: 4.64285e-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: 4.64285e-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