AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_mjan_reg_100.orf -o054_mjan_100.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 RMJ14902 160 M_jannaschii_chromosome #2 RMJ08360 300 M_jannaschii_chromosome #3 RMJ07567 167 M_jannaschii_chromosome #4 RMJ10911 194 M_jannaschii_chromosome #5 RMJ08527 300 M_jannaschii_chromosome #6 RMJ05443 300 M_jannaschii_chromosome #7 RMJ09985 300 M_jannaschii_chromosome Motif number 1 AAAATCTTAATTTTTATTAATTACCTTAGTT 1 62 1 TTTTTATTAT 0.655925 -99 ACGGCTTCTATTATTTAAAGTTATTGTTTGA 1 93 1 TTATTTAAAT 0.822896 -68 GTTTGATAAATTTTAAATAATTCCTTTATCC 1 118 1 TTTTAAATAT 0.931288 -43 GTGTTTCATTTTTTATATATTCTTTTTATAT 2 13 1 TTTTATATAT 0.957289 -288 TATATATTCTTTTTATATATTCCCACAATAC 2 26 1 TTTTATATAT 0.957289 -275 GGATACCATATTATATATTATTTTCGGTTTT 2 74 1 TTATATATTT 0.899458 -227 GTTGAAGTATTTATATCTAATCCTTAAAATA 2 137 1 TTATATCTAT 0.517418 -164 TTTAAATGCCTTTAATAAAATATACAAACTG 2 227 1 TTTAATAAAT 0.72162 -74 ATTTTTAAATTTTTATATTGTAATAGAACTT 2 261 0 TTTTATATTT 0.915974 -40 AATATAAAAATTTAAAAATTTATGCTGATGG 2 273 1 TTTAAAAATT 0.432768 -28 TATTAGCAGTTTATATATAATAGGTGAGTTA 3 55 1 TTATATATAT 0.948433 -113 AATAGGTGAGTTATATATACTCCAAAACTAT 3 73 1 TTATATATAT 0.948439 -95 TTACATAAAATTATAAATCCTTAAACTTTTT 3 118 0 TTATAAATCT 0.695875 -50 CACAAAATATTTTTATATCTTACATAAAATT 3 137 0 TTTTATATCT 0.821716 -31 GAAAGTATTTTTATTAATATTGCTATAATTA 4 29 0 TTATTAATAT 0.892041 -166 TTATAAGTATTTATATTTTGTGTTGTTTTTT 4 118 0 TTATATTTTT 0.628911 -77 AAAAGTTTTATTTTTAATTTTAAAATCATTT 4 164 1 TTTTTAATTT 0.830414 -31 CCAACTATTCTTTAATTTTTTGTATGGTGCC 5 38 1 TTTAATTTTT 0.4126 -263 TTCTAATAAGTTAAAAATTTTAACATATATA 5 149 0 TTAAAAATTT 0.647989 -152 CTTATTAGAATTTTTAATAATAAAACAATTA 5 170 1 TTTTTAATAT 0.909545 -131 AATAATTTACTTTTTTAAAGTTATAATTGTT 5 193 0 TTTTTTAAAT 0.849882 -108 TATAAAATAGTTAAAAATAATTTACTTTTTT 5 208 0 TTAAAAATAT 0.790982 -93 TTTTTAACTATTTTATAATTTTATATCAAAA 5 222 1 TTTTATAATT 0.787596 -79 ATTGATTATGTTATATTTCATTTTTTGATAT 5 244 0 TTATATTTCT 0.417439 -57 TTAATCGTGTTTAAATAATATTGATTATGTT 5 263 0 TTAAATAATT 0.508612 -38 TATTATTGTATTTTTTATAATAAATTAACTG 6 19 0 TTTTTTATAT 0.943258 -282 TAAGAACTGTTTTATTATTGTATTTTTTATA 6 31 0 TTTATTATTT 0.733586 -270 TTGTAATTCTTTTTATTTATTAACTTTGTGT 6 88 0 TTTTATTTAT 0.80937 -213 ACATCAAATATTATTAATAGTTAATTGTTAA 6 121 1 TTATTAATAT 0.892041 -180 TTGCCCTTATTTATTTAATTTCATTCAATAA 6 164 1 TTATTTAATT 0.693239 -137 TCATGAGCCATTATTTATATTGTTGTAGTTT 6 241 0 TTATTTATAT 0.931786 -60 TTAAAAACTATTTTATATTATCATGAGCCAT 6 261 0 TTTTATATTT 0.915964 -40 TATAAAATAGTTTTTAATAGTATAAAAGGTG 6 275 1 TTTTTAATAT 0.909648 -26 TTCTTTTATTTTTTAAACTGAAAATATTA 7 9 1 TTTTTTAAAT 0.849882 -292 ATAGATGCTCTTTATAATATTTTCAGTTTAA 7 23 0 TTTATAATAT 0.77399 -278 TTTATTAGTTTTTAATAAACTTTTTGTAAAA 7 88 0 TTTAATAAAT 0.721701 -213 TTCAAAGGTTTTATAAAAAATCTTAAATTAT 7 175 1 TTATAAAAAT 0.790982 -126 CAGACTTAACTTAATTATAATTCTCAATGTA 7 205 0 TTAATTATAT 0.822815 -96 TCTGGAAATATTATTAATATTAATTAGGATA 7 232 1 TTATTAATAT 0.892041 -69 ACCAATTTTCTTTTTATTATTAGGATTTTCT 7 274 0 TTTTTATTAT 0.656025 -27 ********* * Masking position 2 Map Score: 47.2931 Number of sites scoring better than the average of aligned sites = 3043 Number in coding regions = 2183 Number in noncoding regions = 860 Number of orfs with sites within 600 bp upstream = 579 Fraction of orfs with sites within 600 bp upstream = 0.0929971 Motif number 2 TCGTTTTATCTAAAATCTTAATTTTTATTAA 1 51 1 TAAAATTTAA 0.857945 -110 AACTAAGGTAATTAATAAAAATTAAGATTTT 1 62 0 ATTAATAAAA 0.746786 -99 TTATCAAACAATAACTTTAAATAATAGAAGC 1 96 0 ATAACTTAAA 0.858078 -65 TTATTGTTTGATAAATTTTAAATAATTCCTT 1 113 1 ATAAATTTAA 0.891676 -48 TATCCACTCATAAACTTAAAAGGTTTT 1 144 1 TAAACTAAAA 0.80335 -17 TATGGTATCCATTAATCATAACGTTGAGTAT 2 53 0 ATTAATATAA 0.814109 -248 ATTACAATATAAAAATTTAAAAATTTATGCT 2 268 1 AAAAATTAAA 0.857954 -33 ATATCTTACATAAAATTATAAATCCTTAAAC 3 123 0 TAAAATATAA 0.848164 -45 TTATAGCAATATTAATAAAAATACTTTCACA 4 32 1 ATTAATAAAA 0.746786 -163 ACAAAATATAAATACTTATAATGCATTACTT 4 128 1 AATACTATAA 0.837193 -67 AATTAAAAATAAAACTTTTAAGGGAAGTAAT 4 152 0 AAAACTTTAA 0.906884 -43 AAGTTTTATTTTTAATTTTAAAATCATTTTG 4 166 1 TTTAATTTAA 0.729571 -29 AATTTACTATTTAACTTTAAATCATAATATA 5 119 0 TTAACTTAAA 0.774507 -182 CTAATAAGTTAAAAATTTTAACATATATAAT 5 147 0 AAAAATTTAA 0.899685 -154 TATTAGAATTTTTAATAATAAAACAATTATA 5 172 1 TTTAATATAA 0.746778 -129 TAAAACAATTATAACTTTAAAAAAGTAAATT 5 190 1 ATAACTTAAA 0.858078 -111 TTTTTTGATATAAAATTATAAAATAGTTAAA 5 224 0 TAAAATATAA 0.848164 -77 CACAAAGTTAATAAATAAAAAGAATTACAAA 6 89 1 ATAAATAAAA 0.837839 -212 GAATTAACAATTAACTATTAATAATATTTGA 6 124 0 TTAACTTTAA 0.857302 -177 TATCACCTTTTATACTATTAAAAACTATTTT 6 278 0 TATACTTTAA 0.789206 -23 TTTTATTTTTTAAACTGAAAATATTATAAAG 7 14 1 TAAACTAAAA 0.80335 -287 AAGTTTATTAAAAACTAATAAAATCTAAACG 7 97 1 AAAACTATAA 0.900086 -204 AGGTTTTATAAAAAATCTTAAATTATACATT 7 180 1 AAAAATTTAA 0.899694 -121 TGGAAATATTATTAATATTAATTAGGATATT 7 234 1 ATTAATTTAA 0.825631 -67 AGAAAATCCTAATAATAAAAAGAAAATTGGT 7 274 1 AATAATAAAA 0.761269 -27 ****** **** Masking position 6 Map Score: 30.7186 Number of sites scoring better than the average of aligned sites = 2080 Number in coding regions = 1367 Number in noncoding regions = 713 Number of orfs with sites within 600 bp upstream = 517 Fraction of orfs with sites within 600 bp upstream = 0.0830389 Motif number 3 TTCGGCATCTTATCTCACCAACTACCAAAAA 1 18 1 TATTCACCAA 0.983203 -143 TTTATCCCCAAAAATTTCTAT 3 1 1 TTTTCCCCAA 0.936221 -167 GGAGTATATATAACTCACCTATTATATATAA 3 65 0 TAATCACCTA 0.7068 -103 ACTTATCACCAAAAAGATTAAT 4 2 1 CTTTCACCAA 0.9588 -193 TGATATGGTTTAAGTCACCAACAAAACATTT 4 66 0 TAATCACCAA 0.960729 -129 TGACTTAAACCATATCAAAAATGATTAAAAT 4 80 1 CATTCAAAAA 0.697719 -115 TTAATCACCAAAATGATTTTA 4 184 0 TTATCACCAA 0.95483 -11 ATTTTCCACATTTTTCACAAATGTAATAATA 5 75 1 TTTTCACAAA 0.910056 -226 TTTATAATTTTATATCAAAAAATGAAATATA 5 233 1 TATTCAAAAA 0.833329 -68 TATTTCACCAATGCATTTTAA 5 290 0 TATTCACCAA 0.98305 -11 CACTGAAAAATATAACACAAAGTTAATAAAT 6 74 1 TATACACAAA 0.838483 -227 AATCCTGTTTTTTTACAAAAAGTTTATTAAA 7 78 1 TTTACAAAAA 0.44762 -223 ATTAGGATATTTATTCCCAAAGAAAATCCTA 7 254 1 TTATCCCAAA 0.743399 -47 CCTTTCACCAATTTTCTTTTT 7 290 0 CCTTCACCAA 0.877471 -11 *** ******* Masking position 11 Map Score: 12.6632 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 416 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 TTTTGGTAGTTGGTGAGATAAGATGCCGAA 1 18 0 TGGTGAGATA 0.786915 -143 GCCGTAACTAAGGTAATTAATAAAAATTAA 1 68 0 AGGTAATTAA 0.880951 -93 TAAGTTTATGAGTGGATAAAGGAATTATTT 1 132 0 AGTGGATAAA 0.795116 -29 TTGAGTATTGTGGGAATATATAAAAAGAAT 2 31 0 TGGGAATATA 0.889195 -270 GGAACTTTCGTAGGAATAAATGTTCTATGG 2 177 1 TAGGAATAAA 0.625347 -124 TAGAAATTTTTGGGGATAAA 3 1 0 TGGGGATAAA 0.97778 -167 TATATATAATAGGTGAGTTATATATACTCC 3 66 1 AGGTGAGTTA 0.615291 -102 TTAATCTTTTTGGTGATAAGT 4 2 0 TGGTGATAAG 0.799996 -193 AAAACTTTTAAGGGAAGTAATGCATTATAA 4 143 0 AGGGAAGTAA 0.845319 -52 AAAATCATTTTGGTGATTAA 4 185 1 TGGTGATTAA 0.939901 -10 TATAACACAAAGTTAATAAATAAAAAGAAT 6 84 1 AGTTAATAAA 0.6011 -217 GCAATATTTATGGGAATTAACAATTAACTA 6 138 0 TGGGAATTAA 0.939901 -163 ATAGTATAAAAGGTGATAAA 6 291 1 AGGTGATAAA 0.954173 -10 GGATTTTCTTTGGGAATAAATATCCTAATT 7 253 0 TGGGAATAAA 0.964814 -48 ********** Masking position 6 Map Score: 11.0071 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 578 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 TAAGGTAATTAATAAAAATTAAGATTTTAGA 1 59 0 AAAAAAATTA 0.454438 -102 GGAATATATAAAAAGAATATATAAAAAATGA 2 18 0 AAAGAATATA 0.785502 -283 CTAAAAACCGAAAATAATATATAATATGGTA 2 77 0 AAATAATATA 0.94608 -224 TCTAATCCTTAAAATAATTTACAATGGAACT 2 152 1 AAATAATTTA 0.860066 -149 AAATGCCTTTAATAAAATATACAAACTGCGA 2 230 1 AAAAAATATA 0.86192 -71 CGAAAGTTCTATTACAATATAAAAATTTAAA 2 258 1 ATACAATATA 0.86934 -43 TATATCTTACATAAAATTATAAATCCTTAAA 3 124 0 ATAAATTATA 0.405839 -44 AACAAAAAACAACACAAAATATAAATACTTA 4 115 1 AAACAAAATA 0.789072 -80 TTAACTTTAAATCATAATATATATAGAGGTT 5 109 0 ATATAATATA 0.922489 -192 AAAATAGTTAAAAATAATTTACTTTTTTAAA 5 205 0 AAATAATTTA 0.860066 -96 TTGATATAAAATTATAAAATAGTTAAAAATA 5 220 0 ATATAAAATA 0.819344 -81 CAAAAAATGAAATATAACATAATCAATATTA 5 248 1 AAATAACATA 0.7509 -53 TGTATTTTTTATAATAAATTAACTGTTTAAG 6 13 0 ATATAAATTA 0.613592 -288 GTAAGAAACTACAACAATATAAATAATGGCT 6 236 1 ACACAATATA 0.671837 -65 ATAATGGCTCATGATAATATAAAATAGTTTT 6 258 1 ATATAATATA 0.922489 -43 TTTTAAACTGAAAATATTATAAAGAGCATCT 7 21 1 AAATATTATA 0.739205 -280 ** ******** Masking position 6 Map Score: 11.9414 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 447 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 6 ATATATTCCCACAATACTCAACGTTATGATT 2 40 1 AAATACTCAA 0.947822 -261 CTATCCTTTAACCTTACTAAAAACCGAAAAT 2 93 0 ACTTACTAAA 0.489192 -208 TGCCTTTAATAAAATATACAAACTGCGAAAG 2 233 1 AAATATACAA 0.862554 -68 AAGTTCTATTACAATATAAAAATTTAAAAAT 2 261 1 AAATATAAAA 0.860307 -40 TATAAGCAATAAAATACAAAAAGTTTAAGGA 3 101 1 AAATACAAAA 0.965396 -67 AAAAATGATTAAAATACTCAACAAAAAACAA 4 96 1 AAATACTCAA 0.947822 -99 TCAACAAAAAACAACACAAAATATAAATACT 4 113 1 AAACACAAAA 0.814821 -82 TAATAGGGGCACCATACAAAAAATTAAAGAA 5 45 0 ACATACAAAA 0.933703 -256 CACAAATGTAATAATACAAAACCTCTATATA 5 90 1 AAATACAAAA 0.965396 -211 AATGAAATATAACATAATCAATATTATTTAA 5 253 1 ACATAATCAA 0.444808 -48 TTTATTATAAAAAATACAATAATAAAACAGT 6 26 1 AAATACAATA 0.748038 -275 ATGGCTCATGATAATATAAAATAGTTTTTAA 6 261 1 AAATATAAAA 0.860307 -40 TAACTTAATTATAATTCTCAATGTATAATTT 7 199 0 AAATTCTCAA 0.659064 -102 * ********* Masking position 1 Map Score: 9.58334 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 204 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 AAATCTTAATTTTTATTAATTACCTTAGTT 1 63 1 TTTTATTAAT 0.718091 -98 TAATCATAACGTTGAGTATTGTGGGAATAT 2 42 0 GTTGAGTATT 0.692678 -259 TATTTTCGGTTTTTAGTAAGGTTAAAGGAT 2 92 1 TTTTAGTAAG 0.858559 -209 ACTTTCGCAGTTTGTATATTTTATTAAAGG 2 235 0 TTTGTATATT 0.443798 -66 AATTTTTAAATTTTTATATTGTAATAGAAC 2 263 0 TTTTTATATT 0.625497 -38 ATCCTTAAACTTTTTGTATTTTATTGCTTA 3 103 0 TTTTTGTATT 0.934982 -65 GATTTATAATTTTATGTAAGATATAAAAAT 3 130 1 TTTATGTAAG 0.430616 -38 GTGAAAGTATTTTTATTAATATTGCTATAA 4 32 0 TTTTATTAAT 0.718091 -163 GTTGTTTTTTGTTGAGTATTTTAATCATTT 4 98 0 GTTGAGTATT 0.692678 -97 ATTCTTTAATTTTTTGTATGGTGCCCCTAT 5 44 1 TTTTTGTATG 0.901467 -257 ATATATAGAGGTTTTGTATTATTACATTTG 5 92 0 GTTTTGTATT 0.865251 -209 GTTATAATTGTTTTATTATTAAAAATTCTA 5 175 0 TTTTATTATT 0.738283 -126 AACTGTTTTATTATTGTATTTTTTATAATA 6 28 0 TTATTGTATT 0.657422 -273 AGTGCTATAAGTTTTTTAAGAACTGTTTTA 6 48 0 GTTTTTTAAG 0.496193 -253 ATTTATTAACTTTGTGTTATATTTTTCAGT 6 75 0 TTTGTGTTAT 0.307402 -226 ATATTTGATGTTTTTGTAATTCTTTTTATT 6 102 0 TTTTTGTAAT 0.928498 -199 TTTAATAAACTTTTTGTAAAAAAACAGGAT 7 79 0 TTTTTGTAAA 0.561028 -222 TGAACGAACCTTATAGTAAGAGGAATATAA 7 149 0 TTATAGTAAG 0.447529 -152 CCAATTTTCTTTTTATTATTAGGATTTTCT 7 274 0 TTTTATTATT 0.738283 -27 ********** Masking position 7 Map Score: 9.14494 Number of sites scoring better than the average of aligned sites = 1104 Number in coding regions = 871 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 8 AAATTTATCAAACAATAACTTTAAATAATAGA 1 99 0 AACAATACTT 0.898474 -62 ATAAATTTTAAATAATTCCTTTATCCACTCAT 1 123 1 AATAATCCTT 0.948756 -38 TCAACATCAAATTAATAACTATCCTTTAACCT 2 110 0 ATTAATACTT 0.856547 -191 TCTATGGAATAATAATGCCTTTAGGCATTTAA 2 200 1 AATAATCCTT 0.948756 -101 AATAACTGTCAATAATCAATCTAAATAGAAAT 3 24 0 AATAATAATT 0.92545 -144 ATAAACTGCTAATAATAACTGTCAATAATCAA 3 37 0 AATAATACTT 0.974278 -131 TTAATATTGCTATAATTAATCTTTTTGGTGAT 4 15 0 TATAATAATT 0.689886 -180 ATAATAAAACAATTATAACTTTAAAAAAGTAA 5 186 1 AATTATACTT 0.856547 -115 TGAAATATAACATAATCAATATTATTTAAACA 5 255 1 CATAATAATT 0.767288 -46 ****** *** * Masking position 6 Map Score: 3.93642 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 91 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TATTCCTACGAAAGTTCCATTGTAAATTAT 2 165 0 AAAGTTCCAT 0.801881 -136 CGTAGGAATAAATGTTCTATGGAATAATAA 2 185 1 AATGTTCTAT 0.950975 -116 ACAAACTGCGAAAGTTCTATTACAATATAA 2 250 1 AAAGTTCTAT 0.949732 -51 ATAAATTTTTAAATTTTTATATTGTAATAG 2 266 0 AAATTTTTAT 0.779188 -35 TTATCCCCAAAAATTTCTATTTAGATTGAT 3 12 1 AAATTTCTAT 0.947005 -156 ACTTCCCTTAAAAGTTTTATTTTTAATTTT 4 155 1 AAAGTTTTAT 0.79262 -40 TAACATATATAATTTACTATTTAACTTTAA 5 130 0 AATTTACTAT 0.832681 -171 AGTTAAAAATAATTTACTTTTTTAAAGTTA 5 201 0 AATTTACTTT 0.577483 -100 ACTATTTTATAATTTTATATCAAAAAATGA 5 228 1 AATTTTATAT 0.666798 -73 CCTTTCACCAATTTTCTTTTTATTATTAG 7 282 0 AATTTTCTTT 0.832681 -19 ********** Masking position 5 Map Score: 5.61882 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 137 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 10 ********** No masking Map Score: 3.92463e-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 11 ********** No masking Map Score: 3.92463e-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 12 ********** No masking Map Score: 3.92463e-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