AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i291_mjan_pyro_300.orf -o291_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 Purged sequences: RMJ03270 23 M_jannaschii_chromosome RMJ13401 29 M_jannaschii_chromosome Input sequences: #1 RMJ14233 69 M_jannaschii_chromosome #2 RMJ00153 62 M_jannaschii_chromosome #3 RMJ00065 39 M_jannaschii_chromosome #4 RMJ00927 156 M_jannaschii_chromosome #5 RMJ06922 26 M_jannaschii_chromosome #6 RMJ08184 47 M_jannaschii_chromosome #7 RMJ10917 47 M_jannaschii_chromosome #8 RMJ15396 94 M_jannaschii_chromosome #9 RPH01249 28 Pyrococcus_OT3 #10 RPH01250 64 Pyrococcus_OT3 #11 RPH01251 23 Pyrococcus_OT3 #12 RPH01252 44 Pyrococcus_OT3 #13 RPH01253 40 Pyrococcus_OT3 #14 RPH01256 31 Pyrococcus_OT3 #15 RPH01257 274 Pyrococcus_OT3 Motif number 1 GTTGGAGACTATAATTTCATAACAAACTTTT 1 25 1 ATATTTCATA 0.901348 -45 ATTTCATAACAAACTTTTATCAATGATTATG 1 38 1 AAATTTTATC 0.822667 -32 AAATAAAATAAAATTATTATTCTATTTTCAA 2 20 1 AAATATTATT 0.907708 -43 ATTTTCAAATAAACTTTTATTGTTGGGATT 2 43 1 AAATTTTATT 0.915176 -20 TTTTTAGGTGTAAGTTTTAAATATGACTAAC 4 35 1 TAATTTTAAA 0.79073 -122 TTATTTTAGCATAACATCATTATGGATTTTT 4 68 1 ATACATCATT 0.707332 -89 GATTTAAAAAATAATATCATTACTCAATGAA 4 120 0 ATATATCATT 0.859542 -37 GCCACCACGAAAAGTATTATTAATTAATAAT 6 16 1 AAATATTATT 0.907707 -32 TAAAAGGAATTATTATTAATTAATAATACT 6 28 0 TTATATTAAT 0.563854 -20 AATAATTTTAAACAATATCTAT 7 2 1 ATATTTTAAA 0.824044 -46 ATCTATCGGCTAAATTTCAAAGAGGGATAAT 7 27 1 TAATTTCAAA 0.821506 -21 TTTGCAGTAATAATTATTAAATATGTTAATA 8 45 0 TAATATTAAA 0.775 -50 ATTACTGCAAATATTATCATCACAGTTATGG 8 65 1 ATATATCATC 0.724618 -30 AAATCAAGGAAAAACTTTATATAAAGACTTA 10 12 1 AAACTTTATA 0.852924 -53 AACTTCATTTTTAATATTAAAAACTTTG 12 8 0 TTATATTAAA 0.637619 -37 CCCACCGCCTAAAACTTCATTTTTAATATTA 12 20 0 AAACTTCATT 0.838451 -25 AGTTGGGGGCAAAGTTTTAAATAAATTATTT 13 14 0 AAATTTTAAA 0.901651 -27 CAAAACCCATAAACTATCATTACTACAAAAG 15 92 1 AAATATCATT 0.922956 -183 TCACCTCCAATAAATTTCAAAATGTAAATAT 15 180 1 TAATTTCAAA 0.821506 -95 AATACCCCCTAAATCTTTATATACTATAAGT 15 214 0 AAACTTTATA 0.852924 -61 TTATATGAAAAAAATATCATAAATTAGGGGG 15 244 1 AAATATCATA 0.942211 -31 *** ******* Masking position 7 Map Score: 21.2835 Number of sites scoring better than the average of aligned sites = 2138 Number in coding regions = 1472 Number in noncoding regions = 666 Number of orfs with sites within 600 bp upstream = 476 Fraction of orfs with sites within 600 bp upstream = 0.0764536 Motif number 2 AAATAAAATAAATAAAATAAAATT 2 1 1 AAAAAAAATA 0.965781 -62 GTTTATTTGAAAATAGAATAATAATTTTATTTTA 2 23 0 AAAAAAATAA 0.733403 -40 AAACAAAAATAATAAATTAATTATTTTG 3 5 1 AAAAAAAATT 0.765757 -35 CCTAAAAATAATAGATAGTAAATAGAGGAAGT 4 9 0 ATAAGAAATA 0.969373 -148 ATGAATTAATAAAAAAAGCAAAAACAAAAAATCC 4 91 0 AAAAGAAAAA 0.978343 -66 CACCTTTTTAAGATTTAAAAAATAATATCATTAC 4 128 0 AGAAAAAATA 0.882303 -29 AATAACTTATAAACTTAGCAAAAAGTTTTAGGTT 8 15 0 AAAAGAAAAA 0.978343 -80 ATTTGCAGTAATAATTATTAAATATGTTAATAAC 8 43 0 ATAATAAATA 0.804127 -52 AAAAACCTCCAAAAAGAGGAAAGAAA 9 3 0 AAAAGAAAGA 0.942914 -26 TAAATCAAGGAAAAACTTTATATAA 10 2 1 AAAAGAAAAA 0.978343 -63 GTTTTAATAATGAGAAAAAAGGG 11 4 0 ATAAGAAAAA 0.963813 -20 GGGGGTATTTATATGAAAAAAATATCATAAATTA 15 236 1 ATAAAAAATA 0.943313 -39 *** ** ***** Masking position 7 Map Score: 13.0062 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 768 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 ATCAATGATTATGGAGGGAGAGTT 1 56 1 ATGGAGGGAG 0.947527 -14 TAAATTAATTATTTTGGGTGAAAAATC 3 23 1 ATTTTGGGTG 0.868481 -17 TATAAATCGTAAGGAGGTGGCTTGAT 10 49 1 AAGGAGGTGG 0.962987 -16 GCTCAAAGTTGGGGGCAAAGTTTTA 13 26 0 AAGTTGGGGG 0.990837 -15 AATTAAACCGAAGGTGGGGAGA 14 20 1 AAGGTGGGGA 0.964805 -12 AGAGCTTACCAAGGAGGGTAGAGC 15 5 0 AAGGAGGGTA 0.922798 -270 TTTGGGACAAAATTACGGGGAAGGAGTACT 15 66 0 AATTACGGGG 0.938442 -209 GTATATAAAGATTTAGGGGGTATTTATATG 15 221 1 ATTTAGGGGG 0.982155 -54 AAATATCATAAATTAGGGGGTGAAAACTAT 15 255 1 AATTAGGGGG 0.990559 -20 ********** Masking position 1 Map Score: 11.0981 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 167 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AACTCTCCCTCCATAATCATTGATAA 1 54 0 CCCTCCATAA 0.846894 -16 GATTTTTCACCCAAAATAATTAATTT 3 24 0 TCACCCAAAA 0.930397 -16 TTTAAAACTTACACCTAAAAATAATAGATA 4 26 0 ACACCTAAAA 0.922271 -131 CAAAAACAAAAAATCCATAATGATGTTATG 4 77 0 AAATCCATAA 0.83884 -80 ATTATTTTTTAAATCTTAAAAAGGTGAAAC 4 136 1 AAATCTTAAA 0.485504 -21 CTAAAACCTAAAACTTTTTGCTA 8 4 1 AAACCTAAAA 0.754656 -91 GGTTATCACCCATAACTGTGATGAT 8 80 0 TCACCCATAA 0.884045 -15 GGAAAAACCTCCAAAAAGAGGAAAGA 9 13 0 ACCTCCAAAA 0.982607 -16 ATCAAGCCACCTCCTTACGATTTATATC 10 47 0 ACCTCCTTAC 0.743497 -18 CTTCCCCACCGCCTAAAACTTCATTTT 12 28 0 ACCGCCTAAA 0.908379 -17 TTTTGTCCCAAAACCCATAAACTATCATTA 15 84 1 AAACCCATAA 0.906338 -191 CATCTAAGTCACCTCCAATAAATTTCAAAA 15 172 1 ACCTCCAATA 0.847567 -103 TCATATAAATACCCCCTAAATCTTTATATA 15 222 0 ACCCCCTAAA 0.983581 -53 ATAGTTTTCACCCCCTAATTTATGATATT 15 256 0 ACCCCCTAAT 0.864403 -19 ********** Masking position 5 Map Score: 11.7851 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 607 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 AAGTTTGTTATGAAATTATAGTCTCCAACT 1 24 0 TGAAATTATA 0.758804 -46 ATAAAATAAATAAAATAAAATTATTATTCT 2 13 1 TAAAATAAAA 0.809153 -50 TATTTGAAAATAGAATAATAATTTTATTTT 2 24 0 TAGAATAATA 0.8626 -39 AAACAAAAATAATAAATTAATTAT 3 5 1 AAAAATAATA 0.935753 -35 ATTTTTCACCCAAAATAATTAATTTATTAT 3 19 0 CAAAATAATT 0.816047 -21 ACTTACACCTAAAAATAATAGATAGTAAAT 4 20 0 AAAAATAATA 0.935753 -137 GATGTTATGCTAAAATAATTGTTAGTCATA 4 56 0 TAAAATAATT 0.949914 -101 CATTACTCAATGAATTAATAAAAAAAGCAA 4 104 0 TGAATTAATA 0.758921 -53 TTAAGATTTAAAAAATAATATCATTACTCA 4 125 0 AAAAATAATA 0.935753 -32 AAAAGTATTATTAATTAATAATAATTCCTT 6 25 1 TTAATTAATA 0.535777 -23 AGATATTGTTTAAAATTATT 7 1 0 TAAAATTATT 0.807857 -47 ATAAAATAATTTATTTAAAAC 13 2 1 TAAAATAATT 0.949914 -39 ********** Masking position 4 Map Score: 12.0335 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 536 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 6 AACTCTCCCTCCATAATCATTG 1 58 0 CTCTCCCTCC 0.854864 -12 TTTATGCCACCACGAAAAGTA 6 2 1 TTATGCCACC 0.94717 -46 ATCAAGCCACCTCCTTACGAT 10 54 0 TCAAGCCACC 0.936662 -11 CTTCCCCACCGCCTAAAACT 12 35 0 CTTCCCCACC 0.983115 -10 TTATTTAAAACTTTGCCCCCAACTTTGAGC 13 21 1 CTTTGCCCCC 0.961416 -20 TCTCCCCACCTTCGGTTTAA 14 22 0 TCTCCCCACC 0.973893 -10 GCTCTACCCTCCTTGGTAAGCT 15 3 1 TCTACCCTCC 0.911665 -272 TAAAACCCATCTAAGTCACCTCCAATAAAT 15 165 1 CTAAGTCACC 0.69352 -110 ATAGTTTTCACCCCCTAATTTATGA 15 260 0 TTTCACCCCC 0.853623 -15 ********** Masking position 7 Map Score: 4.20456 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 173 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 ATTAAACATATATAGTTGGAGACT 1 5 1 AACATATATA 0.854267 -65 AAATAAAATAAATAAAATAAAATTAT 2 7 1 AATAAATAAA 0.78567 -56 CACCCAAAATAATTAATTTATTATTTTTGT 3 13 0 AATTAATTTA 0.755189 -27 TTACTCAATGAATTAATAAAAAAAGCAAAA 4 102 0 AATTAATAAA 0.818717 -55 TAAAAACACATTAATGGTGATGCA 5 5 1 AACACATTAA 0.876866 -22 ATATGTTAATAACTTATAAACTTAGCAAAA 8 26 0 AACTTATAAA 0.913665 -69 ATAAGTTATTAACATATTTAATAATTATTA 8 39 1 AACATATTTA 0.854372 -56 ATAAAATAATTTATTTAAAACTTTGCC 13 8 1 AATTTATTTA 0.755186 -33 TGTATAACTAATTAAACCGAAGGTG 14 6 1 AACTAATTAA 0.913665 -26 TTTGTCCCAAAACCCATAAACTATCATTAC 15 85 1 AACCCATAAA 0.762358 -190 ********** Masking position 6 Map Score: 4.61414 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 533 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 8 ********** No masking Map Score: 3.16435e-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: 3.16435e-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: 3.16435e-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