AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_mjan_reg_300.orf -o070_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 RMJ03213 300 M_jannaschii_chromosome #2 RMJ01903 20 M_jannaschii_chromosome #3 RMJ08949 251 M_jannaschii_chromosome #4 RMJ13850 17 M_jannaschii_chromosome #5 RMJ13412 101 M_jannaschii_chromosome #6 RMJ10489 300 M_jannaschii_chromosome #7 RMJ05083 300 M_jannaschii_chromosome Motif number 1 GATGAAAACTAAGAAAAATTATATTTCACTATT 1 21 1 AAAAATTATA 0.744159 -280 TACTAAAAATATTTGAAAAAATAGTGAAATATA 1 40 0 ATAAAAAATA 0.933744 -261 TTTTAGTATAAAGAATAAAAATAATTAAACTTC 1 65 1 AATAAAAATA 0.913328 -236 AGTTTTAATCAAATTTAAAAATAGAACATTATA 1 122 1 ATTAAAAATA 0.972985 -179 TTAGCTTATGAACTAAAAATATAAAAGGTTAAT 1 163 1 ATAAAATATA 0.928305 -138 AATAAAGAAAAATTTTAAATATACATGGTCTAA 1 227 1 ATTAAATATA 0.964626 -74 AACTTACACCAAAAATTATTTTATAATTGA 1 281 0 AAAAATTATT 0.457563 -20 ATAATTCCTTATATTGAATTATAAAACTGTGAA 3 144 1 ATGAATTATA 0.75527 -108 GTGATGAATATTATGAAAAAATAATCCTATAAT 3 207 1 TTAAAAAATA 0.696675 -45 GACACCAAAAAACTTTAATTATAGGATTATTTT 3 224 0 ATTAATTATA 0.962774 -28 TTCCTTAAAAATTTTTAAAAATTTTATTTTACT 5 45 0 ATTAAAAATT 0.905776 -57 GAATTTCCTAAATTCTAAATATATGAAATTTTT 5 75 1 ATTAAATATA 0.970838 -27 TAAATTTAAAACCTCTAAATAAATAAATAATTC 6 24 1 ATTAAATAAA 0.672926 -277 TAATTATAGTTTGTTTAATAATATTCTATCGTT 6 161 0 TTTAATAATA 0.821332 -140 GTCTGTAGATAATTTTAATTATAGTTTGTTTAA 6 176 0 ATTAATTATA 0.956551 -125 TGTAATAATTAGTTGTAATAATAGGATAATTGA 6 248 0 ATTAATAATA 0.965766 -53 TTTTTATCTTAGTTGTAATAATTAGTTGTAATA 6 261 0 ATTAATAATT 0.891062 -40 TATTACAACTAAGATAAAAAATACTGCTGGTGA 6 274 1 AAAAAAAATA 0.80342 -27 AAAATTTAGAATCTATAAATAGAGTAAACACGA 7 16 0 ATTAAATAGA 0.753043 -285 CCTAATATTTAGCATTAAAAATTTAGAATCTAT 7 33 0 AATAAAAATT 0.753898 -268 TATTAGGTATTGCTATAAATATTTAATGCATAA 7 59 1 TTTAAATATT 0.612664 -242 TAATGCATAAAGATTTAATAATACATGGTTACA 7 82 1 ATTAATAATA 0.965769 -219 ACATAGTGGCATGTTTAATAATATGTAGCATTT 7 112 1 ATTAATAATA 0.965755 -189 * * ******** Masking position 7 Map Score: 29.3623 Number of sites scoring better than the average of aligned sites = 1626 Number in coding regions = 1098 Number in noncoding regions = 528 Number of orfs with sites within 600 bp upstream = 412 Fraction of orfs with sites within 600 bp upstream = 0.0661741 Motif number 2 AAAACTAAGAAAAATTATATTTCACTATTTT 1 25 1 AAAATTATTT 0.584291 -276 CTATTTAGGAAAAGCTTTCTCTTAAAGAAGT 1 93 0 AAAGCTTTTC 0.566618 -208 AAGAGAATATAATGTTCTATTTTTAAATTTG 1 131 0 AATGTTCTTT 0.518211 -170 TGTATATTTAAAATTTTTCTTTATTGGGGAG 1 221 0 AAATTTTTTT 0.839847 -80 TACATGGTCTAAAATTTTGTGTGGTTAATCT 1 248 1 AAAATTTTTG 0.886105 -53 ACTTACACCAAAAATTATTTTATAATTGATA 1 279 0 AAAATTATTT 0.571321 -22 TGGTTACTTCAAATCTCTATTAAAGTGGGGT 3 27 1 AAATCTCTTT 0.847201 -225 TATTCCTGTGAAAGTCCTGTGGTATACCCAA 3 78 0 AAAGTCCTTG 0.923313 -174 TCACAGGAATAAATTTCTTATTGAACATAAT 3 98 1 AAATTTCTAT 0.632434 -154 TAAAACTGTGAAAGTCCTGTGCCAATAGGGC 3 165 1 AAAGTCCTTG 0.923313 -87 CCAATAGGGCGAAGCCCTATGGTGATGAATA 3 186 1 GAAGCCCTTG 0.689365 -66 TCCTATAATTAAAGTTTTTTGGTGTCAAACT 3 231 1 AAAGTTTTTG 0.933502 -21 AAAAGAGGATGAAACTCTTTGACCTACTTCA 5 15 1 GAAACTCTTG 0.678251 -87 AAAATTTTTAAAAATTTTATTTTACTGAAGT 5 40 0 AAAATTTTTT 0.873492 -62 AAATTTTTAAAAATTTTTAAGGAATTTCCTA 5 54 1 AAATTTTTAG 0.568701 -48 CTAAATATATGAAATTTTTTGTG 5 89 1 GAAATTTTTG 0.66597 -13 TGAAAATCCTAAAACCCTAATAATGTAATGA 6 124 1 AAAACCCTAT 0.487417 -177 TTGACTTAATAAAGCTTTATTATCACAAAAT 6 221 0 AAAGCTTTTT 0.899626 -80 TATAGATTCTAAATTTTTAATGCTAAATATT 7 32 1 AAATTTTTAT 0.53927 -269 ATGTATTATTAAATCTTTATGCATTAAATAT 7 77 0 AAATCTTTTG 0.80949 -224 TTAATTCTTTAAAATTTTATTAAGTTTTTGA 7 146 0 AAAATTTTTT 0.873492 -155 TATTCTTGCGAAAGTCCTATTAGGCACTTTT 7 186 0 AAAGTCCTTT 0.914439 -115 ATAAACTGCAAAAGTCCTATTCAATGTTATG 7 270 1 AAAGTCCTTT 0.914439 -31 ******** ** Masking position 8 Map Score: 21.7262 Number of sites scoring better than the average of aligned sites = 1492 Number in coding regions = 1202 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 AATTTATTCCTGTGAAAGTCCTGTGGTATAC 3 82 0 TGGAAAGTCC 0.997255 -170 ATTATAAAACTGTGAAAGTCCTGTGCCAATA 3 161 1 TGGAAAGTCC 0.997255 -91 ATTTAGAATTTAGGAAATTCCTTAAAAATTT 5 64 0 TAGAAATTCC 0.930262 -38 ATTGTATTCTTGCGAAAGTCCTATTAGGCAC 7 190 0 TGGAAAGTCC 0.997255 -111 ATCTATAAACTGCAAAAGTCCTATTCAATGT 7 266 1 TGAAAAGTCC 0.985838 -35 ** ******** Masking position 6 Map Score: 9.00932 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 11 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AGAAAGCTTTTCCTAAATAGTTTTAATCAAA 1 104 1 TCCTAAATGT 0.953532 -197 CTCCAATAACTCCTAACTCCCCAATAAAGAA 1 205 1 TCCTAACTCC 0.958846 -96 TTAAGGAATTTCCTAAATTCTAAATATATGA 5 70 1 TCCTAAATCT 0.98895 -32 AATAAATAATTCCTAAATACTCTCATTTCTA 6 45 1 TCCTAAATCT 0.98895 -256 ATACTCTCATTTCTAAATTCCAAACTTATAC 6 61 1 TTCTAAATCC 0.959887 -240 AAATTGAAAATCCTAAAACCCTAATAATGTA 6 120 1 TCCTAAAACC 0.940192 -181 TATTTATAGATTCTAAATTTTTAATGCTAAA 7 28 1 TTCTAAATTT 0.869451 -273 AAATTTTTAATGCTAAATATTAGGTATTGCT 7 42 1 TGCTAAATTT 0.848433 -259 ******** ** Masking position 6 Map Score: 7.34685 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 136 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AAACTAAGAAAAATTATATTTCACTATTTT 1 26 1 AAATTATATT 0.70401 -275 TAAAAATAGAACATTATATTCTCTTTTTAG 1 137 1 ACATTATATT 0.939169 -164 GTCTATAGCATCATTATGTTCAATAAGAAA 3 111 0 TCATTATGTT 0.831401 -141 ACATCATAATTCCTTATATTGAATTATAAA 3 139 1 TCCTTATATT 0.94253 -113 GATTATTTTTTCATAATATTCATCACCATA 3 203 0 TCATAATATT 0.968863 -49 CGTTATTCTATCATTACATTATTAGGGTTT 6 135 0 TCATTACATT 0.909501 -166 ATAGTTTGTTTAATAATATTCTATCGTTAT 6 159 0 TAATAATATT 0.827402 -142 AAGTCAATTATCCTATTATTACAACTAATT 6 245 1 TCCTATTATT 0.828639 -56 TTATAGCAATACCTAATATTTAGCATTAAA 7 47 0 ACCTAATATT 0.919941 -254 GAAAAATGCTACATATTATTAAACATGCCA 7 118 0 ACATATTATT 0.819889 -183 TATGCCACCTCATAACATTGAATAGGACT 7 282 0 TCATAACATT 0.922735 -19 ********** Masking position 4 Map Score: 10.3205 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 179 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 AAAGAATAAAAATAATTAAACTTCTTTAAG 1 74 1 AATAATTAAA 0.86481 -227 GTTTTAATCAAATTTAAAAATAGAACATTA 1 123 1 AATTTAAAAA 0.43757 -178 CTAACTCCCCAATAAAGAAAAATTTTAAAT 1 217 1 AATAAAGAAA 0.667734 -84 TAATCTTATCAATTATAAAATAATTTTTGG 1 273 1 AATTATAAAA 0.584443 -28 CAGTTTTATAATTCAATATAAGGAATTATG 3 143 0 ATTCAATATA 0.163421 -109 AAAATAATCCTATAATTAAAGTTTTTTGGT 3 224 1 TATAATTAAA 0.582778 -28 AGTAAAATAAAATTTTTAAAAATTTTTAAG 5 45 1 AATTTTTAAA 0.793427 -57 AAAACCTCTAAATAAATAAATAATTCCTAA 6 31 1 AATAAATAAA 0.901581 -270 ATAAGTTTGGAATTTAGAAATGAGAGTATT 6 60 0 AATTTAGAAA 0.546168 -241 ACAACAAGACAATCAATAAATCAATTAACA 6 90 1 AATCAATAAA 0.895615 -211 TCAATAAATCAATTAACAAAATTGAAAATC 6 102 1 AATTAACAAA 0.756745 -199 ATAGAATATTATTAAACAAACTATAATTAA 6 165 1 ATTAAACAAA 0.202333 -136 TTAAACAAACTATAATTAAAATTATCTACA 6 176 1 TATAATTAAA 0.582778 -125 AGGATAATTGACTTAATAAAGCTTTATTAT 6 229 0 ACTTAATAAA 0.734825 -72 TATTACAACTAATTATTACAACTAAGATAA 6 261 1 AATTATTACA 0.512961 -40 AAAAATTTAGAATCTATAAATAGAGTAAAC 7 20 0 AATCTATAAA 0.76851 -281 TTATGCATTAAATATTTATAGCAATACCTA 7 62 0 AATATTTATA 0.308218 -239 TGTAACCATGTATTATTAAATCTTTATGCA 7 85 0 TATTATTAAA 0.697044 -216 AAATGCTACATATTATTAAACATGCCACTA 7 115 0 TATTATTAAA 0.697044 -186 TTTTTCAAAAACTTAATAAAATTTTAAAGA 7 142 1 ACTTAATAAA 0.734825 -159 AATTTTAAAGAATTAATATAAGCCTAAAAG 7 161 1 AATTAATATA 0.719505 -140 AACCTTAACAAATCTATAAACTGCAAAAGT 7 255 1 AATCTATAAA 0.76851 -46 ********** Masking position 3 Map Score: 12.6384 Number of sites scoring better than the average of aligned sites = 2989 Number in coding regions = 2175 Number in noncoding regions = 814 Number of orfs with sites within 600 bp upstream = 541 Fraction of orfs with sites within 600 bp upstream = 0.0868937 Motif number 7 TTTTCTTAGTTTTCATCCTCTTAGAGG 1 8 0 TTTCATCCTC 0.95111 -293 GGGTTGCCAAAGGCAACCCCACTTTAATAG 3 43 0 AGGCAACCCC 0.97553 -209 GGGTTGCCTTTGGCAACCCCGCTCTTGGGT 3 54 1 TGGCAACCCC 0.97553 -198 TTTTCATAATATTCATCACCATAGGGCTTC 3 196 0 ATTCATCACC 0.825551 -56 GGTCAAAGAGTTTCATCCTCTTTTATCA 5 9 0 TTTCATCCTC 0.95111 -93 TATGCCACCTCATAACATTGA 7 290 0 ATGCCACCTC 0.917933 -11 ********** Masking position 4 Map Score: 0.471918 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 146 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ********** No masking Map Score: -2.75447e-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 9 ********** No masking Map Score: -2.75447e-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 10 ********** No masking Map Score: -2.75447e-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