AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i275_mjan_pyro_300.orf -o275_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ15218 300 M_jannaschii_chromosome #2 RMJ10665 165 M_jannaschii_chromosome #3 RMJ08964 300 M_jannaschii_chromosome #4 RPH00884 300 Pyrococcus_OT3 #5 RPH01143 300 Pyrococcus_OT3 #6 RPH01145 147 Pyrococcus_OT3 #7 RPH01150 235 Pyrococcus_OT3 #8 RPH01151 78 Pyrococcus_OT3 #9 RPH01152 38 Pyrococcus_OT3 #10 RPH01153 136 Pyrococcus_OT3 Motif number 1 TAATACGGTATTTCCATTCCCCGAGGGATCTGA 3 36 0 TTTCCACCCG 0.984019 -265 TTATTTAAGATTTCCATTCCCTGAGGGATCTGA 3 102 0 TTTCCACCTG 0.935631 -199 TGTCGATTTATTTCCATTCCCCGAGGGATCTGA 3 171 0 TTTCCACCCG 0.984019 -130 TCATCTGTTGTTTCCATTCCCTGAGGGATCTGA 3 239 0 TTTCCACCTG 0.935631 -62 TTCTAATGAGTTTCCATTCCCTTCTCCCTATTC 3 270 0 TTTCCACCTT 0.9632 -31 ACTTCGCCAATTGCCGACGCCCTTTCCGACACT 4 22 1 TTGCCGGCCT 0.914983 -279 CACTTGCCTGTTTCCGTAGAACTCAGTAGTGTG 4 51 1 TTTCCGGACT 0.981404 -250 CCCAGAGGTCTTTCCACACTACTGAGTTCTACG 4 65 0 TTTCCACACT 0.985704 -236 ACCACCTCCGTTTCCGTAGAACTTAGTAGTGTG 4 118 1 TTTCCGGACT 0.981404 -183 ACTGGTTCTCTTTCCACACTACTAAGTTCTACG 4 132 0 TTTCCACACT 0.985704 -169 GGCAGCTGGGTTTCCGTAGAACTTAGTAGTGTG 4 186 1 TTTCCGGACT 0.981404 -115 AGAGTTTGGCTTTCCACACTACTAAGTTCTACG 4 200 0 TTTCCACACT 0.985704 -101 CTCTTCCTTGTTTTCAAGCTCCTTCTCAATGGT 4 229 1 TTTTCACCCT 0.917097 -72 CTCAATGGTGTTTCCGTAGAACTAAATAGTGCC 4 253 1 TTTCCGGACT 0.981404 -48 TTTTTAGAGTTTTCCGATCTCATAAACTTAACT 5 88 1 TTTCCGCCAT 0.90929 -213 TATCGAATAATTTTCGGTGCATTGTT 5 285 1 TTTTCGGATT 0.554184 -16 ****** * *** Masking position 2 Map Score: 32.5507 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 62 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 TATGGTAAAATCAGATCCCTCGGGGAATGG 3 26 1 TCAGATCCCT 0.982926 -275 ATACGGTATTTCCATTCCCCGAGGGATCTG 3 37 0 TCCATTCCCC 0.986237 -264 TGACGTAAAATCAGATCCCTCAGGGAATGG 3 92 1 TCAGATCCCT 0.982926 -209 ATTTAAGATTTCCATTCCCTGAGGGATCTG 3 103 0 TCCATTCCCT 0.994035 -198 GAATGTAAAATCAGATCCCTCGGGGAATGG 3 161 1 TCAGATCCCT 0.982926 -140 TCGATTTATTTCCATTCCCCGAGGGATCTG 3 172 0 TCCATTCCCC 0.986237 -129 CTCCGTAAAATCAGATCCCTCAGGGAATGG 3 229 1 TCAGATCCCT 0.982926 -72 ATCTGTTGTTTCCATTCCCTGAGGGATCTG 3 240 0 TCCATTCCCT 0.994035 -61 CTAATGAGTTTCCATTCCCTTCTCCCTATT 3 271 0 TCCATTCCCT 0.994035 -30 CAACACCACCTCCGTTTCCGTAGAACTTAG 4 114 1 TCCGTTTCCG 0.905359 -187 TATCAGAACTTCCTTTTCCTCGTTCTCATA 6 56 0 TCCTTTTCCT 0.86365 -92 ********** Masking position 6 Map Score: 24.8114 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 28 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CACACTACTGAGTTCTACGGAAACAGGCAAG 4 53 0 AGTTCTAGGA 0.992459 -248 CGTAGAACTCAGTAGTGTGGAAAGACCTCTG 4 65 1 AGTAGTGGGA 0.978634 -236 CACACTACTAAGTTCTACGGAAACGGAGGTG 4 120 0 AGTTCTAGGA 0.992459 -181 CGTAGAACTTAGTAGTGTGGAAAGAGAACCA 4 132 1 AGTAGTGGGA 0.978634 -169 CACACTACTAAGTTCTACGGAAACCCAGCTG 4 188 0 AGTTCTAGGA 0.992459 -113 CGTAGAACTTAGTAGTGTGGAAAGCCAAACT 4 200 1 AGTAGTGGGA 0.978634 -101 GGCACTATTTAGTTCTACGGAAACACCATTG 4 255 0 AGTTCTAGGA 0.992459 -46 GTGAGTGGGTAGATCTAGGGAAGTTCCTCCA 6 15 1 AGATCTAGGA 0.954016 -133 AAGTTTTTTAAGTTCTGACGACTAATGGTAG 8 31 1 AGTTCTGCGA 0.960966 -48 ******* *** Masking position 6 Map Score: 18.6183 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 5 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 ACTTTTCAATCTTTACTTTATTTTCATATACT 1 79 1 CTTTATTATT 0.778311 -222 TACATATAAATGTTAGTTTATTTATTTAAATC 1 125 1 TGTTATTATT 0.873143 -176 ACAAATTTAATTTTAAATAATAGATATTTTGA 1 191 0 TTTTATAATA 0.687754 -110 AGATATGACTTTTTAACAAATTTAATTTTAAA 1 206 0 TTTTAAAATT 0.882332 -95 GTATTCTTTGTTTTATAAAATTATCAAGAGGT 1 263 0 TTTTAAAATT 0.882332 -38 AGAATACTTTTTTTACCATTTAT 1 288 1 TTTTAATTTA 0.697928 -13 AATTTTATGTTACTTCGAAGATAC 2 3 1 TTTTATTACT 0.873143 -163 ATGAGTTATGTTTTATTTAATTTGGTGATACT 2 144 1 TTTTATAATT 0.905198 -22 AGGGATCTGATTTTACCATATTGCTCTTCCCC 3 14 0 TTTTAATATT 0.958604 -287 AAATAAGATTTTTTATCTTATTTTTTTTTATT 3 129 1 TTTTATTATT 0.967204 -172 ATCTGACCATTTTTAGAATATTGGTTTTTAAA 5 46 0 TTTTAATATT 0.958604 -255 ATTACAGATTTTTTAGAGTTTTCCGATCTCAT 5 79 1 TTTTAGTTTT 0.726258 -222 ACTAACTACTTGTTATTATTTTGCAAAAAGTT 5 166 0 TGTTAATTTT 0.699813 -135 GAGAGTAATTTTTTAAATTTTATTAAGTAA 7 9 0 TTTTATTTTA 0.746361 -227 ATTTTCGTATTTTTAGGTTATTATGATTCAAG 7 44 1 TTTTATTATT 0.967204 -192 CATTTATATCTTTTAACTTTTTCTTGAATCAT 7 66 0 TTTTATTTTT 0.927123 -170 TTATTCTTTTTTTTAATATACTTATTCG 9 21 1 TTTTAATACT 0.843859 -18 ***** ***** Masking position 5 Map Score: 15.3503 Number of sites scoring better than the average of aligned sites = 1065 Number in coding regions = 702 Number in noncoding regions = 363 Number of orfs with sites within 600 bp upstream = 315 Fraction of orfs with sites within 600 bp upstream = 0.0505943 Motif number 5 AGCAATATGGTAAAATCAGATCCCTCGGGG 3 21 1 TAAAATCAGA 0.97317 -280 GAAGATGACGTAAAATCAGATCCCTCAGGG 3 87 1 TAAAATCAGA 0.97317 -214 AATGGAAATCTTAAATAAGATTTTTTATCT 3 117 1 TTAAATAAGA 0.798563 -184 TTCAATAAAAAAAAATAAGATAAAAAATCT 3 134 0 AAAAATAAGA 0.950603 -167 TTATTGAATGTAAAATCAGATCCCTCGGGG 3 156 1 TAAAATCAGA 0.97317 -145 TTCAACTCCGTAAAATCAGATCCCTCAGGG 3 224 1 TAAAATCAGA 0.97317 -77 AAAAAATTTCAAAAATAAGAAGTTAAGTTT 5 111 0 AAAAATAAGA 0.950603 -190 ATAGGCCCAATAAAAATAGACTTCATCAGA 6 83 1 TAAAAATAGA 0.658951 -65 ATAATAACCTAAAAATACGAAAATAAAGAG 7 38 0 AAAAATACGA 0.800531 -198 TAAGTATATTAAAAAAAAGAATAATAAAGA 9 15 0 AAAAAAAAGA 0.842506 -24 ********** Masking position 5 Map Score: 13.2519 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 107 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CATAACTCATAACAACCTATTTATACACTTCTATCTTTTAAC 1 36 1 AAAACTTTAT 0.959196 -265 ATACTTTATATATAAGCTTTACATATAAATGTTAGTTTATTT 1 106 1 TAAACTCTAT 0.956342 -195 AACGTATCGATATAATCTAGATTTAAATAAATAAACTAACAT 1 134 0 TAAACTTTAT 0.978089 -167 GATATTTTGAAATAACCTATATATAAACGTATCGATATAATC 1 159 0 AAAACTTTAT 0.959194 -142 ATGACTTTTTAACAAATTTAATTTTAAATAATAGATATTTTG 1 192 0 AAAATTTTAT 0.697389 -109 TATTGGTTTTTAAACACTAAATATGAAGAGCTGAGTGTTATG 5 18 0 TAACCTTTAT 0.91282 -283 TTGCAAGGGTTATAAGCTCTATTTCAAACTCTACTTCATACA 7 130 0 TAAACTTTAT 0.978173 -106 TCCATACCTTTAAAACCTAGGTATTAACTTTTACCGATGGTG 10 16 0 TAAACTTTAT 0.978171 -121 CCTAAGGATTTATAAACTTCTCGTTGAACGTTGTATCAATGT 10 79 0 TAAACTCTAT 0.956342 -58 ** ** ** * * * * Masking position 14 Map Score: 5.91561 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 119 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 AAGGGAATGGAAACTCATTAGAAGATAATCA 3 280 1 AAACTATTAG 0.879469 -21 TGTTTCCGTAGAACTCAGTAGTGTGGAAAGA 4 59 1 GAACTAGTAG 0.992586 -242 CGTTTCCGTAGAACTTAGTAGTGTGGAAAGA 4 126 1 GAACTAGTAG 0.992586 -175 GGTTTCCGTAGAACTTAGTAGTGTGGAAAGC 4 194 1 GAACTAGTAG 0.992586 -107 TGTTTCCGTAGAACTAAATAGTGCCTAAATC 4 261 1 GAACTAATAG 0.974386 -40 ***** ***** Masking position 5 Map Score: 5.30921 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 TCATACTACATAACTCATAACAACCTATTT 1 28 1 TAACTCATAA 0.933106 -273 TTTGTTTTATAAAATTATCAAGAGGTATAG 1 259 0 AAAATTATCA 0.819727 -42 AAATAAAACATAACTCATAATAAGCACAAT 2 132 0 TAACTCATAA 0.933106 -34 TACGGAGTTGAAGCTCATAAAATTGTCCAA 3 206 0 AAGCTCATAA 0.80061 -95 AAGGGAATGGAAACTCATTAGAAGATAATC 3 280 1 AAACTCATTA 0.839317 -21 AAATAGTGCCTAAATCATAATTTAGGTGAC 4 276 1 TAAATCATAA 0.82052 -25 ACTTCATACATAAATTATCACTAATTCAAG 7 110 0 TAAATTATCA 0.786817 -126 AGAACTTAAAAAACTTATCATCCCACAAAT 8 17 0 AAACTTATCA 0.93277 -62 CACCTAATTGAAACTTATCAACTACCATTA 8 53 0 AAACTTATCA 0.93277 -26 ********** Masking position 5 Map Score: 4.96954 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 230 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 AACTTTTCAATCTTTACTTTATTTTCATAT 1 78 1 TCTTTACTTT 0.818076 -223 AATGTTAGTTTATTTATTTAAATCTAGATT 1 133 1 TATTTATTTA 0.552423 -168 AAAAAAGTATTCTTTGTTTTATAAAATTAT 1 271 0 TCTTTGTTTT 0.931059 -30 AGTTATGTTTTATTTAATTTGGTGATACT 2 147 1 TATTTAATTT 0.620056 -19 CGTCATCTTCTATTTGTTGTATGTATTTTA 3 67 0 TATTTGTTGT 0.802413 -234 TTTTTTATCTTATTTTTTTTTATTGAATGT 3 137 1 TATTTTTTTT 0.763261 -164 GCCAAACTCTTCCTTGTTTTCAAGCTCCTT 4 223 1 TCCTTGTTTT 0.680519 -78 CAGCTCTTCATATTTAGTGTTTAAAAACCA 5 27 1 TATTTAGTGT 0.713347 -274 GATAAAATACTATTTATTTTGTAACTTTTT 5 144 1 TATTTATTTT 0.920624 -157 AAAATTACTCTCTTTATTTTCGTATTTTTA 7 29 1 TCTTTATTTT 0.955679 -207 ATTGAGGCTTTCTTTAGTGTGCTTTCTTAG 7 195 1 TCTTTAGTGT 0.822269 -41 GTTATCTTTATTATTCTTTTTTTT 9 5 1 TCTTTATTAT 0.75211 -34 TCTTTATTATTCTTTTTTTTAATATACTTA 9 15 1 TCTTTTTTTT 0.857019 -24 ********** Masking position 5 Map Score: 6.48826 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 580 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 10 ACTTTTCAATCTTTACTTTATTTTCATATAC 1 79 1 CTTACTTTAT 0.609942 -222 GATATGCTCACTATACCTCTTGATAATTTTA 1 249 1 CTTACCTCTT 0.970539 -52 TTTGCAGAAGCAATGCCTCTTAGCTCACTTT 2 39 0 CATGCCTCTT 0.894147 -127 ACCCAGGATGCATTGCTTCTTTGCAGAAGCA 2 58 0 CATGCTTCTT 0.867745 -108 ATCTCATAAACTTAACTTCTTATTTTTGAAA 5 104 1 CTAACTTCTT 0.930664 -197 TTGGGCCTATCAGAACTTCCTTTTCCTCGTT 6 62 0 CAAACTTCCT 0.720238 -86 TCTTTCCTAGCTTTACCTCATGAACCTCTAT 6 125 0 CTTACCTCAT 0.953565 -23 CTATTTCAAACTCTACTTCATACATAAATTA 7 123 0 CTTACTTCAT 0.941005 -113 TAAAGAAAGCCTCAATCTCTTGTTCCCTCTG 7 180 0 CTAATCTCTT 0.628825 -56 ** ******** Masking position 8 Map Score: 1.63544 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 305 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TACCATAGGGCTTCGCCCTATTGGGATACC 2 86 0 CTTCGCCCTA 0.979806 -80 CCATATTGCTCTTCCCCATC 3 1 0 CTTCCCCATC 0.921891 -300 TTTCCATTCCCTTCTCCCTATTCATCTGTT 3 263 0 CTTCTCCCTA 0.969104 -38 TGAATGTACTCTTCTCTCTCGCTTGGCATG 5 206 0 CTTCTCTCTC 0.956314 -95 TTCCCTAGATCTACCCACTCACTTTC 6 7 0 CTACCCACTC 0.91144 -141 AACAAGCCTCCTACGCTCTAAGAAAGCACA 7 212 0 CTACGCTCTA 0.920265 -24 ********** Masking position 2 Map Score: 0.841213 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ********** No masking Map Score: -2.81132e-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 13 ********** No masking Map Score: -2.81132e-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 14 ********** No masking Map Score: -2.81132e-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