AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_mjan_reg_300.orf -o00051_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0399 89 phosphomannomutase (pmmA) #2 MJ1113 300 N-acetylglucosamine-1-phosphate transferase #3 MJ1418 300 fuculose-1-phosphate aldolase (fucA) Motif number 1 TAAAACAATAAAAATTTGTAAATGTGAGAAT 1 9 0 AAAATTTAAT 0.967762 -81 TTTCTATATTAAAACTTTAACATTAATATCAAA 1 42 0 AAAATTAAAT 0.800242 -48 ATTGATATCTGATATTTCTATATTAAAACTTTA 1 56 0 GATATTTAAT 0.833355 -34 TATTAATTAGGATATTTTTATATTTCATAATT 2 10 0 GATATTTAAT 0.833355 -291 AAAATCAGTAAAAAGATATTAATTAGGATATTT 2 26 0 AAAAATTTAT 0.783434 -275 AAAATATTTAAAAACAAATAGATAGTATGGTAA 2 81 0 AAAAAATAAT 0.960414 -220 AAATATTTTGAAAAGTATTTTATGATGGACTTT 2 105 1 AAAATATTAT 0.892361 -196 AAGGATAACTAAAACTATTAAAAAAATTGCACC 2 147 0 AAAATATAAA 0.97361 -154 TTCCCTAAGCAATAAAAGTAGATTAATAATGGC 2 180 0 AATAAATAAT 0.872287 -121 GGGAAGTAAGGAAAATAATAAAAGAATTTCTAT 2 208 1 GAAATATAAA 0.956201 -93 TTTTTTGCTAAAAAATTATAGAAATTCTTTTAT 2 225 0 AAAATTTAAA 0.964422 -76 TTTTTAGCAAAAAACATATATATCCTAAACTTT 2 244 1 AAAAATTAAT 0.946882 -57 TAATGAAGATAAAAGAAGTTAAAGTTTAGGATA 2 264 0 AAAAAATTAA 0.816385 -37 TATTGAGTAAAAAAATTTTAGAATTAGAGAAGA 3 43 1 AAAATTTAAA 0.964423 -258 GAGTAGATGCAAAACTAAAAGAAAATGAGAAAA 3 76 1 AAAATAAAAA 0.831179 -225 AAGAAAATGAGAAAAAATTAGATGAAAAAACTA 3 94 1 GAAAAATAAT 0.934882 -207 ATTAGATGAAAAAACTAATAAAATATTAAAACA 3 110 1 AAAATATAAA 0.97361 -191 TATATAAAGAAATACAATTAAAATCCCTAAGAT 3 228 0 AATAAATAAA 0.860483 -73 TCTTGATGTTGAAACTAATAAAAATATTTTAAG 3 271 1 GAAATATAAA 0.956201 -30 **** ** ** ** Masking position 4 Map Score: 31.9097 Number of sites scoring better than the average of aligned sites = 1547 Number in coding regions = 1043 Number in noncoding regions = 504 Number of orfs with sites within 600 bp upstream = 401 Fraction of orfs with sites within 600 bp upstream = 0.0644073 Motif number 2 TTATTGTTTTATTTGATATTAATGTTAAAGT 1 31 1 ATTGATATTA 0.589963 -59 ATATCTGATATTTCTATATTAAAACTTTAAC 1 54 0 TTTTATATTA 0.860017 -36 AAATTTTAAATATTGATATCTGATA 1 75 0 TTTAATATTG 0.93609 -15 AAGATATTAATTAGGATATTTTTATATTTCA 2 16 0 TTAGATATTT 0.970743 -285 AATATCCTAATTAATATCTTTTTACTGATTT 2 27 1 TTATATCTTT 0.77688 -274 TTACTGATTTTTTGGATATTTTTGGCTTATC 2 48 1 TTTGATATTT 0.979983 -253 TCTATTTGTTTTTAAATATTTTGAAAAGTAT 2 92 1 TTTAATATTT 0.976885 -209 GGTGCAATTTTTTTAATAGTTTTAGTTATCC 2 147 1 TTTAATAGTT 0.860431 -154 ATAGAAATTCTTTTATTATTTTCCTTACTTC 2 210 0 TTTATTATTT 0.794491 -91 AATAAAAGAATTTCTATAATTTTTTAGCAAA 2 224 1 TTTTATAATT 0.653194 -77 AAGTTAAAGTTTAGGATATATATGTTTTTTG 2 251 0 TTAGATATAT 0.752295 -50 ACGCCTCTTGTTTTAATATTTTATTAGTTTT 3 120 0 TTTAATATTT 0.976871 -181 ATCCCTAAGATTATGATATTAATGCGGATTA 3 208 0 TTAGATATTA 0.914154 -93 TATATAACGGTTATAATCTTGATGTTGAAAC 3 255 1 TTAAATCTTG 0.727125 -46 AATCTCACTTAAAATATTTTTATTAGTTT 3 282 0 TTAAATATTT 0.966263 -19 *** ******* Masking position 7 Map Score: 17.5107 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 899 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 278 Fraction of orfs with sites within 600 bp upstream = 0.0446515 Motif number 3 ACAAATTTTTATTGTTTTATTTGATATTAA 1 23 1 ATTGTTTTAT 0.855735 -67 TCCTAATTAATATCTTTTTACTGATTTTTT 2 31 1 TATCTTTTTA 0.651603 -270 TATCTTTTTACTGATTTTTTGGATATTTTT 2 41 1 CTGATTTTTT 0.423992 -260 ATACTATCTATTTGTTTTTAAATATTTTGA 2 86 1 TTTGTTTTTA 0.8784 -215 AATTGCACCAATGCTTTTAAAGTCCATCAT 2 126 0 ATGCTTTTAA 0.925959 -175 CATTGGTGCAATTTTTTTAATAGTTTTAGT 2 143 1 ATTTTTTTAA 0.872938 -158 AATTATAGAAATTCTTTTATTATTTTCCTT 2 215 0 ATTCTTTTAT 0.910545 -86 TAGGATATATATGTTTTTTGCTAAAAAATT 2 241 0 ATGTTTTTTG 0.521893 -60 TAAACTTTAACTTCTTTTATCTTCATTATA 2 269 1 CTTCTTTTAT 0.850532 -32 TAATTCTAAAATTTTTTTACTCAATACTTC 3 39 0 ATTTTTTTAC 0.56404 -262 TTTTTCTCATTTTCTTTTAGTTTTGCATCT 3 80 0 TTTCTTTTAG 0.827971 -221 AACAACGCCTCTTGTTTTAATATTTTATTA 3 125 0 CTTGTTTTAA 0.888049 -176 TAAATCCTCCATGGTTTTTATGTATATTCC 3 162 0 ATGGTTTTTA 0.866758 -139 TATTTTTAGGTTTCTTTTTAAATCCTCCAT 3 180 0 TTTCTTTTTA 0.925349 -121 ATTAATGCGGATTATTTTTAGGTTTCTTTT 3 192 0 ATTATTTTTA 0.859791 -109 TTTAATTGTATTTCTTTATATAACGGTTAT 3 239 1 TTTCTTTATA 0.4989 -62 AACTAATAAAAATATTTTAAGTGAGATT 3 283 1 AATATTTTAA 0.508981 -18 ********** Masking position 5 Map Score: 11.2521 Number of sites scoring better than the average of aligned sites = 2771 Number in coding regions = 2284 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 4 TCAGATATCAATATTTAAAATTT 1 77 1 ATATTTAAAA 0.681889 -13 AATTATGAAATATAAAAATATCCTAAT 2 8 1 AAATATAAAA 0.933839 -293 ACTTTTCAAAATATTTAAAAACAAATAGAT 2 91 0 ATATTTAAAA 0.681889 -210 TTTTAAAGTCCATCATAAAATACTTTTCAA 2 112 0 CATCATAAAA 0.788131 -189 AATGGCAAGGATAACTAAAACTATTAAAAA 2 156 0 ATAACTAAAA 0.757864 -145 AAGTAAGGAAAATAATAAAAGAATTTCTAT 2 211 1 AATAATAAAA 0.774815 -90 TTTGCTAAAAAATTATAGAAATTCTTTTAT 2 225 0 AATTATAGAA 0.522807 -76 CTTTTATCTTCATTATAAAGGGGATAGTT 2 282 1 CATTATAAAG 0.654881 -19 TCTCTTCTCTAATTCTAAAATTTTTTTACT 3 48 0 AATTCTAAAA 0.887102 -253 GAGTAGATGCAAAACTAAAAGAAAATGAGA 3 76 1 AAAACTAAAA 0.836441 -225 AAAACTAATAAAATATTAAAACAAGAGGCG 3 120 1 AAATATTAAA 0.563743 -181 TTTTATGTATATTCCTAAAGCTAACAACGC 3 147 0 ATTCCTAAAG 0.731277 -154 CTTTAGGAATATACATAAAAACCATGGAGG 3 157 1 ATACATAAAA 0.89799 -144 ATTTAAAAAGAAACCTAAAAATAATCCGCA 3 187 1 AAACCTAAAA 0.928993 -114 ATTATAACCGTTATATAAAGAAATACAATT 3 242 0 TTATATAAAG 0.325024 -59 TTATTAGTTTCAACATCAAGATTATAACCG 3 262 0 CAACATCAAG 0.314247 -39 ********** Masking position 6 Map Score: 7.90466 Number of sites scoring better than the average of aligned sites = 3165 Number in coding regions = 2304 Number in noncoding regions = 861 Number of orfs with sites within 600 bp upstream = 563 Fraction of orfs with sites within 600 bp upstream = 0.0904272 Motif number 5 AAAAATTTGTAAATGTGAGAAT 1 2 0 AAATTGAGAA 0.913662 -88 AGATAGTATGGTAAAAGATAAGCCAAAAATA 2 64 0 GTAAAGATAA 0.797252 -237 GGGAAGTAAGGAAAATAATAAAAGAATTTCT 2 208 1 GAAATAATAA 0.822416 -93 TTTTGCTAAAAAATTATAGAAATTCTTTTAT 2 225 0 AAATATAGAA 0.628407 -76 GGATGAAAAGGAAATAGAGGAGAGGTTTGAA 3 11 1 GAAAAGAGGA 0.95993 -290 AAAAATTTTAGAATTAGAGAAGAGAGTAGAT 3 53 1 GAATAGAGAA 0.975478 -248 AAAACTAAAAGAAAATGAGAAAAAATTAGAT 3 86 1 GAAATGAGAA 0.975479 -215 AAATGAGAAAAAATTAGATGAAAAAACTAAT 3 98 1 AAATAGATGA 0.764351 -203 TCTTGATGTTGAAACTAATAAAAATATTTTA 3 271 1 GAAATAATAA 0.822412 -30 **** ****** Masking position 8 Map Score: 3.35061 Number of sites scoring better than the average of aligned sites = 1284 Number in coding regions = 1183 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 ********** No masking Map Score: 6.63809e-14 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 7 ********** No masking Map Score: 6.63809e-14 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 8 ********** No masking Map Score: 6.63809e-14 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