AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i105_mjan_pyro_300.orf -o105_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 RPH00576 154 Pyrococcus_OT3 #2 RPH00575 113 Pyrococcus_OT3 #3 RPH00574 83 Pyrococcus_OT3 #4 RPH00573 43 Pyrococcus_OT3 #5 RPH01519 185 Pyrococcus_OT3 Motif number 1 TTAGTATGGAAGGGCTAGAAGTTATTATAATTTTC 1 118 0 ACTAGAAGTT 0.968835 -37 ATTAGGCTACAAAACTAGCACCTAAGGAAAAATAA 2 20 0 ACTAGCACTA 0.897723 -94 AAGTGTATTAATGTCACGAAAATTTTTAACGATTT 2 68 0 ACACGAAATT 0.960885 -46 ACAAAAATAAAAAACTAGACCTTATT 3 2 0 ACTAGACCTT 0.923117 -82 TTTGTATAGTAAGTCTAGAAAGTGTTATAACACCT 3 32 1 ACTAGAAATT 0.991565 -52 TTTACTCACCACTAGAAATTTTAAGAGAGGTG 3 62 0 ACTAGAAATT 0.991565 -22 CAACTTAGGGAACCCAAGCAATTTTATAGGT 4 7 0 ACAAGCAATT 0.992225 -37 GTTTAAATTTAAGTTAAGCAAATATTAGCATGGTG 5 18 0 ATAAGCAATT 0.917693 -168 ATTCGACAATAATTCAAGAAATTGTGGAGTTTTAT 5 103 0 ACAAGAAATT 0.991582 -83 AGGAAGTATTAAGGCAACCAAATTTTGGCGAGGGA 5 160 1 ACAACCAATT 0.942937 -26 * ******* * * Masking position 13 Map Score: 12.2738 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 88 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 ATAATAATCTTTTTCTGGGCTTAGGTATATATC 1 45 1 TTTCTGCTTA 0.89605 -110 TTAAGGGATATTTAGAATCCTTAGATATATACC 1 68 0 TTTGACCTTA 0.978964 -87 TAGGTGCTAGTTTTGTAGCCTAATAAAACCTCA 2 31 1 TTTGTCCTAA 0.991596 -83 CGTTAAAAATTTTCGTGACATTAATACACTTAT 2 72 1 TTTGTCATTA 0.969869 -42 AGTTTTTTATTTTTGTATAGTAAGTCTAGAAAG 3 21 1 TTTGTAGTAA 0.880539 -63 ATAAAATTGCTTGGGTTCCCTAAGTTGTGGGGG 4 15 1 TTGGTCCTAA 0.964054 -29 CATGCTAATATTTGCTTAACTTAAATTTAAACC 5 21 1 TTTCTACTTA 0.936269 -165 CTTTTAGACGTTTTGAAAACTCACAGAGGATAA 5 74 1 TTTGAACTCA 0.848144 -112 TTGTCGAATGTTCAGTTACATAACCTTTTTAAG 5 129 1 TTCGTCATAA 0.858847 -57 CTCGCCAAAATTTGGTTGCCTTAATACTTCCTT 5 159 0 TTTGTCCTTA 0.993902 -27 *** ** ***** Masking position 11 Map Score: 8.45522 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 154 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TTAGTATGGAAGGGCTAGAAGTTATTATAATT 1 121 0 AGGGCTAGGT 0.825973 -34 TTTTTCCTTAGGTGCTAGTTTTGTAGCCTAAT 2 23 1 GGTGCTAGTT 0.964593 -91 AATAAGGTCTAGTTTTTTATTTTTGT 3 5 1 AGGTCTAGTT 0.975626 -79 TGTTATAACACTTTCTAGACTTACTATACAAA 3 32 0 CTTTCTAGTT 0.943497 -52 CTCTCTTAAAATTTCTAGTGGTGAGTAAA 3 65 1 ATTTCTAGGT 0.97089 -19 ACCTATAAAATTGCTTGGGTTCCCTAAGTTG 4 10 1 ATTGCTTGTT 0.964081 -34 AAACTCCACAATTTCTTGAATTATTGTCGAAT 5 106 1 ATTTCTTGTT 0.948433 -80 ******** ** Masking position 6 Map Score: 3.97975 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 3 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 GCCCCTCCCCTCTTAGTATGGAAGGG 1 139 0 CTCCCCCTAG 0.996974 -16 CTTATCACCCCACCCAGGGATAAGTGT 2 97 0 CACCCCCCAG 0.998048 -17 AGTGTTATAACACCTCTCTTAAAATTTCTAGT 3 52 1 CACCTCCTAA 0.981755 -32 TTACTCCCCCCACAACTTAGGGAAC 4 29 0 CTCCCCCCAA 0.996985 -15 ****** * *** Masking position 11 Map Score: 2.93523 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 ACGATTTTCATTGAGGTTTTATTAGGCTACA 2 44 0 TGAGGTTTTA 0.855637 -70 TTATCCCTGGGTGGGGTGATAAG 2 101 1 GGGGGTGATA 0.988064 -13 GAAATTTTAAGAGAGGTGTTATAACACTTTC 3 49 0 GGAGGTGTTA 0.991258 -35 AAAATTTCTAGTGGTGAGTAAA 3 72 1 GGGTGAGTAA 0.948641 -12 CCTAAGTTGTGGGGGGAGTAA 4 33 1 GGGGGAGTAA 0.989732 -11 TCAAGAAATTGTGGAGTTTTATCCTCTGTGA 5 94 0 GGGAGTTTTA 0.956 -92 * ********* Masking position 11 Map Score: 2.96751 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 98 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTATAATTTTCTCTTCCATACCAAAGAATT 1 99 0 CTCTTCCATA 0.904801 -56 TAACTTCTAGCCCTTCCATACTAAGAGGGG 1 129 1 CCCTTCCATA 0.965668 -26 GCCCCTCCCCTCTTAGTATGGA 1 143 0 CCCTCCCCTC 0.995085 -12 CTTATCACCCCACCCAGGGATAAGTGT 2 97 0 CCCCACCCAG 0.958257 -17 TTACTCCCCCCACAACTTAGGGA 4 31 0 CTCCCCCCAC 0.982674 -13 ATCCCTCGCCAAAATTTGGTTG 5 174 0 CCCTCGCCAA 0.977275 -12 ********** Masking position 7 Map Score: 2.8062 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 163 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 TAAGCCCAGAAAAAGATTATTATACGGTCTTT 1 36 0 AAAAGAATTA 0.883242 -119 CCAAAGAATTAAGGGATATTTAGAATCCTTAG 1 77 0 AAGGGATTTA 0.964625 -78 TTTGGTATGGAAGAGAAAATTATAATAACTTC 1 104 1 AAGAGAATTA 0.980024 -51 ACTAGCACCTAAGGAAAAATAAATTAAAGGA 2 10 0 AAGGAAATAA 0.945483 -104 AATTTAAGTTAAGCAAATATTAGCATGGTGAT 5 16 0 AAGCAAATTA 0.963268 -170 TAACCTTTTTAAGGAAGTATTAAGGCAACCAA 5 149 1 AAGGAAATTA 0.985974 -37 ****** **** Masking position 6 Map Score: 2.77564 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 229 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 GAAAATTATAATAACTTCTAGCCCTTCCAT 1 118 1 ATAACTTCTA 0.919326 -37 GTAGCCTAATAAAACCTCAATGAAAATCGT 2 45 1 AAAACCTCAA 0.969356 -69 CTTATCACCCCACCCAGGGATAA 2 101 0 ATCACCCCAC 0.882697 -13 AAAGTGTTATAACACCTCTCTTAAAATTTC 3 50 1 AACACCTCTC 0.970988 -34 CACCTCTCTTAAAATTTCTAGTGGTGAGTA 3 62 1 AAAATTTCTA 0.772614 -22 GTGAGTTTTCAAAACGTCTAAAAGGATTGC 5 68 0 AAAACGTCTA 0.938829 -118 CACAGAGGATAAAACTCCACAATTTCTTGA 5 95 1 AAAACTCCAC 0.942355 -91 ********** Masking position 4 Map Score: 2.61731 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 531 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ********** No masking Map Score: 1.5372e-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: 1.5372e-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: 1.5372e-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