AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_mjan_reg_100.orf -o111_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 RMJ07139 300 M_jannaschii_chromosome #2 RMJ17018 68 M_jannaschii_chromosome #3 RMJ13056 60 M_jannaschii_chromosome #4 RMJ03208 57 M_jannaschii_chromosome #5 RMJ10366 79 M_jannaschii_chromosome #6 RMJ14894 19 M_jannaschii_chromosome #7 RMJ03938 66 M_jannaschii_chromosome Motif number 1 TTATATCAAAAAATGAAATATAACATAATCAAT 1 12 0 AATAAATTAA 0.799798 -289 CATTTTTTGATATAAAATTATAAAATAGTTAAA 1 30 1 TAAAATTTAA 0.980662 -271 AATTATAAAATAGTTAAAAATAATTTACTTTTT 1 45 1 TATAAAATAA 0.905972 -256 CAATTATAACTTTAAAAAAGTAAATTATTTTTA 1 59 0 TTAAAAATAA 0.940607 -242 TTTTAATAATAAAACAATTATAACTTTAAAAAA 1 73 0 AAAAATTTAA 0.921843 -228 TGTTTTATTATTAAAAATTCTAATAAGTTAAAA 1 90 1 TTAAATTTAA 0.957727 -211 TTCTAATAAGTTAAAAATTTTAACATATATAAT 1 107 1 TTAAATTTAA 0.70067 -194 TATAATTTACTATTTAACTTTAAATCATAATAT 1 134 1 TATAACTTAA 0.821022 -167 TTCCACATTTTTCACAAATGTAATAATACAAAA 1 176 0 TTAAAATTAA 0.965973 -125 AGGGGCACCATACAAAAAATTAAAGAATAGTTG 1 215 1 TAAAAAATAA 0.957148 -86 ATGTTTTTCTTTTTTAATTTTAATAATTTTTTG 2 13 1 TTTAATTTAA 0.933382 -56 TTATATCACCTAAAAAATATCAAAAAATTATTA 2 33 0 TAAAATACAA 0.762216 -36 AACACTATACTATACAATAATGATGATAAAATA 3 11 1 TAAAATATGA 0.869108 -50 AATGATGATAAAATAAATAATAACTTTAACAAT 3 29 1 AATAATATAA 0.739416 -32 AATAATAACTTTAACAATTGTGAAACC 3 44 1 TTAAATTTGA 0.894032 -17 AATACAATCATTGAAAAATCTAATAGGTGATAC 4 33 1 TTAAAATTAA 0.96594 -25 TAAAGCTTTATATACAAATATAAGCTTAAGCTT 7 24 0 TAAAAATTAA 0.975633 -43 ** * **** *** Masking position 7 Map Score: 27.0678 Number of sites scoring better than the average of aligned sites = 1240 Number in coding regions = 783 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 381 Fraction of orfs with sites within 600 bp upstream = 0.061195 Motif number 2 TTTTATAATTTTATATCAAAAAATGAAATATAAC 1 21 0 TTTACAAAAT 0.823673 -280 AGTAAATTATTTTTAACTATTTTATAATTTTATA 1 40 0 TTTACTTTTA 0.857349 -261 AATAAAACAATTATAACTTTAAAAAAGTAAATTA 1 65 0 TTTACTAAAA 0.747774 -236 GTTATAATTGTTTTATTATTAAAAATTCTAATAA 1 82 1 TTTATAAAAA 0.492764 -219 TTATTAAAAATTCTAATAAGTTAAAAATTTTAAC 1 97 1 TTTATATTAA 0.907715 -204 AAGTTAAAAATTTTAACATATATAATTTACTATT 1 114 1 TTTACATATA 0.985321 -187 TAACTTTAAATCATAATATATATAGAGGTTTTGT 1 148 1 TCTATATATA 0.805037 -153 TCTTTTTTAATTTTAATAATTTTTTGATATTTTT 2 20 1 TTTATATTTT 0.795641 -49 TTATCACCCATTATATCACCTAAAAAATATCAAA 2 42 0 TTTACATAAA 0.978369 -27 TTATTATTTATTTTATCATCATTATTGTATAGTA 3 18 0 TTTACAATTA 0.929283 -43 TATTTGTTACTTCAACTATTTAAATC 4 3 0 TTAATATAAA 0.621347 -55 TAGTATCACCTATTAGATTTTTCA 4 44 0 TATACATATT 0.640343 -14 CTGCACTAATTCCAACAGTTATATTTGGTTTGT 5 10 1 TTCACATATA 0.907523 -70 TATATTTGGTTTGTATCAACTATACAGTGTATTA 5 30 1 TTTACATATA 0.985353 -50 TTCCCTCATTTTATAGTAACTTTAATACACTGTA 5 52 0 TTTATATTTA 0.935131 -28 ** ** ** **** Masking position 5 Map Score: 13.5646 Number of sites scoring better than the average of aligned sites = 1287 Number in coding regions = 1036 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 3 TAATACAAAACCTCTATATATATTATGATT 1 156 0 CCTCTATATA 0.981713 -145 AATAATAGGGGCACCATACAAAAAATTAAA 1 209 1 GCACCATACA 0.960821 -92 CACTGGCTCAGCTCCATATAGGGAGCGTCA 1 252 0 GCTCCATATA 0.979362 -49 GTATTATCACCCATTATATCACCTAAAAAA 2 49 0 CCATTATATC 0.860001 -20 TGGTTTGTATCAACTATACAGTGTATTAAA 5 36 1 CAACTATACA 0.78256 -44 ATAAGCTTAAGCTTTATATATAGATTT 7 8 0 GCTTTATATA 0.971532 -59 AACATCTAAAGCTTTATATACAAATATAAG 7 33 0 GCTTTATATA 0.971532 -34 ********** Masking position 6 Map Score: 4.76507 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 157 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TTGTATGGTGCCCCTATTATTTTCCACATT 1 200 0 CCCCTATTAT 0.974236 -101 ATTGCCACCTCTTAAGGTGGTTGTG 1 286 0 CACCTCTTAA 0.947306 -15 CCCATTATATCACCTAAAAAATATCAAAAA 2 40 0 CACCTAAAAA 0.960077 -29 GTATTATCACCCATTATATCACCTAAA 2 52 0 CACCCATTAT 0.919677 -17 TAGTATCACCTATTAGATTTTTCAAT 4 42 0 CACCTATTAG 0.963395 -16 AAATTCCCCCTAAGAATTT 6 4 0 CCCCTAAGAA 0.960642 -16 AGACTTCCCCAAAAAACATCTAAAGC 7 51 0 CCCCAAAAAA 0.877519 -16 ********** Masking position 9 Map Score: 4.17672 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 142 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TATTGATTATGTTATATTTCATTTTT 1 6 1 ATTATTTATA 0.910285 -295 ATTATTTTTAACTATTTTATAATTTTATATC 1 38 0 ACTATTTATA 0.975755 -263 ACTTTAAAAAAGTAAATTATTTTTAACTATT 1 53 0 AGTAATTATT 0.773644 -248 AAAGTTAAATAGTAAATTATATATGTTAAAA 1 124 0 AGTAATTATA 0.93616 -177 GTCATCGCCAACTATTCTTTAATTTTTTGTA 1 225 0 ACTATCTTTA 0.891893 -76 AACACTATACTATACAATAATGAT 3 4 1 ACTATCTATA 0.970958 -57 ***** ***** Masking position 4 Map Score: 1.1474 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 56 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TAACTATTTTATAATTTTATATCAAAAAAT 1 31 0 ATAATTTTAT 0.685853 -270 TAAAACAATTATAACTTTAAAAAAGTAAAT 1 67 0 ATAACTTTAA 0.979824 -234 AAAAATTCTAATAAGTTAAAAATTTTAACA 1 102 1 ATAAGTTAAA 0.941255 -199 AGTAAATTATATATGTTAAAATTTTTAACT 1 115 0 ATATGTTAAA 0.697708 -186 AATTTACTATTTAACTTTAAATCATAATAT 1 137 1 TTAACTTTAA 0.926106 -164 TTTTTCTTTTTTAATTTTAATAATTTTTTG 2 16 1 TTAATTTTAA 0.815433 -53 CACCCATTATATCACCTAAAAAATATCAAA 2 42 0 ATCACCTAAA 0.705252 -27 AAAATAAATAATAACTTTAACAATTGTGAA 3 38 1 ATAACTTTAA 0.979824 -23 TCATTTTATAGTAACTTTAATACACTGTAT 5 51 0 GTAACTTTAA 0.939168 -29 ATATACAAATATAAGCTTAAGCTTTATATA 7 18 0 ATAAGCTTAA 0.6718 -49 ********** Masking position 7 Map Score: 10.6559 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 623 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 7 ********** No masking Map Score: 1.58694e-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 8 ********** No masking Map Score: 1.58694e-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: 1.58694e-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