AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_mjan_reg_100.orf -o006_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 RMJ14456 184 M_jannaschii_chromosome #2 RMJ02718 147 M_jannaschii_chromosome #3 RMJ10497 83 M_jannaschii_chromosome Motif number 1 TCTTATTATTATCAAAAAATCGTAATCATA 1 58 1 ATCAAAAAAT 0.845719 -127 TTAAAAATTAAGAAAACATTATAGAAATAC 1 92 0 AGAAAACATT 0.858679 -93 TTAATGGTAAATTAAAAATTAAGAAAACAT 1 103 0 ATTAAAAATT 0.971388 -82 TTAATTTACCATTAAAAATTTAATATCATA 1 118 1 ATTAAAAATT 0.971388 -67 AAGAATTAGTATTTAAAACTTTTGGTTGGG 1 155 1 ATTTAAAACT 0.832502 -30 TAGACATCCCACAAAATTATATAAA 2 6 0 ACAAAATTAT 0.643359 -142 GATGTCTATGAGAAAAATTTACCTCATCTC 2 28 1 AGAAAAATTT 0.843372 -120 TGCAAATATTATAAAATACTGCAATAGACC 2 76 1 ATAAAATACT 0.978059 -72 GAGGAGATGAATAAAACTCTAATAAAAAAT 2 119 1 ATAAAACTCT 0.921436 -29 TAAAACTCTAATAAAAAATTGGAATAAT 2 130 1 ATAAAAAATT 0.978128 -18 ACTTAAATTTATTAAATACTT 3 2 0 ATTAAATACT 0.970588 -82 AATAATAAAAACTAAAAACTTAAATTTATT 3 19 0 ACTAAAAACT 0.944966 -65 AAAACTAAAAATAAAATAATAAAAACTAAA 3 33 0 ATAAAATAAT 0.935811 -51 AAAATTTTCTATTAAAAACTAAAAATAAAA 3 47 0 ATTAAAAACT 0.981804 -37 CACCTGAATTATAAAATTTTCTATTAAAAA 3 59 0 ATAAAATTTT 0.91585 -25 ********** Masking position 5 Map Score: 23.9238 Number of sites scoring better than the average of aligned sites = 1655 Number in coding regions = 1215 Number in noncoding regions = 440 Number of orfs with sites within 600 bp upstream = 367 Fraction of orfs with sites within 600 bp upstream = 0.0589464 Motif number 2 CTATCAAAATTCATACTAAAAGGTGAGTTAA 1 13 0 TATACTAAAA 0.889797 -172 GTATGAATTTTGATAGTATTAGAATTAGCTT 1 28 1 TATAGTATTA 0.787826 -157 TACGATTTTTTGATAATAATAAGAAGCTAAT 1 51 0 TATAATAATA 0.923283 -134 TAAGAAAACATTATAGAAATACACACTATGA 1 83 0 TATAGAAATA 0.91693 -102 ATTAAATTTTTAATGGTAAATTAAAAATTAA 1 111 0 TATGGTAAAT 0.885426 -74 TATGGTATTATGATATTAAATTTTTAATGGT 1 125 0 TATATTAAAT 0.869408 -60 ATACTAATTCTTATGGTATTATGATATTAAA 1 136 0 TATGGTATTA 0.700384 -49 CAAAAGTTTTAAATACTAATTCTTATGGTAT 1 148 0 AATACTAATT 0.672071 -37 TTTATATAATTTTGTGGGATGT 2 2 1 TATATAATTT 0.608825 -146 TTGCAGTATTTTATAATATTTGCATGGTTAA 2 69 0 TATAATATTT 0.651376 -79 AATAAAACTCTAATAAAAAATTGGAATAAT 2 128 1 TATAAAAAAT 0.852645 -20 ACTAAAAATAAAATAATAAAAACTAAAAACT 3 29 0 AATAATAAAA 0.640537 -55 TTTTAGTTTTTAATAGAAAATTTTATAATTC 3 53 1 TATAGAAAAT 0.918778 -31 * ********* Masking position 8 Map Score: 11.0789 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 786 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 3 CATACTAAAAGGTGAGTTAAAC 1 2 0 GGTGAGTAAA 0.993795 -183 AATTTTTAATGGTAAATTAAAAATTAAGAAA 1 107 0 GGTAAATAAA 0.885381 -78 TAAAACTTTTGGTTGGGTGAATGTATG 1 168 1 GGTTGGTGAA 0.951469 -17 GCGTATCAGAGATGAGGTAAATTTTTCTCAT 2 35 0 GATGAGTAAA 0.986129 -113 TTCAAATGTTGAGGAGATGAATAAAACTCTA 2 109 1 GAGGAGTGAA 0.971888 -39 ****** **** Masking position 8 Map Score: 0.489182 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 169 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TAATTCTAATACTATCAAAATTCATACTAA 1 25 0 ACTATCAAAA 0.979176 -160 GCTTCTTATTATTATCAAAAAATCGTAATC 1 55 1 ATTATCAAAA 0.821738 -130 AGAAATACACACTATGATTACGATTTTTTG 1 70 0 ACTATGATTA 0.804852 -115 TTTTTAATTTACCATTAAAAATTTAATATC 1 115 1 ACCATTAAAA 0.936944 -70 TTAAAAATTTAATATCATAATACCATAAGA 1 129 1 AATATCATAA 0.741834 -56 ATATCATAATACCATAAGAATTAGTATTTA 1 140 1 ACCATAAGAA 0.909081 -45 TTGTGGGATGTCTATGAGAAAAATTTACCT 2 22 1 TCTATGAGAA 0.897913 -126 ACGCATTTTAACCATGCAAATATTATAAAA 2 62 1 ACCATGCAAA 0.874719 -86 GATGAATAAAACTCTAATAAAAAATTGGAA 2 124 1 ACTCTAATAA 0.730675 -24 TATAAAATTTTCTATTAAAAACTAAAAATA 3 50 0 TCTATTAAAA 0.852967 -34 ********** Masking position 5 Map Score: 5.30127 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 513 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 ********** No masking Map Score: -5.09159e-13 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 6 ********** No masking Map Score: -5.09159e-13 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 7 ********** No masking Map Score: -5.09159e-13 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