AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i195_dna_replication1_mjan_reg_300.orf -o195_mjan_300.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 RMJ16446 239 M_jannaschii_ECEL #2 RMJ16608 74 M_jannaschii_ECEL #3 RMJ10805 28 M_jannaschii_chromosome #4 RMJ04288 67 M_jannaschii_chromosome #5 RMJ16676 62 M_jannaschii_chromosome #6 RMJ01438 300 M_jannaschii_chromosome #7 RMJ03243 87 M_jannaschii_chromosome Motif number 1 CAGATATTCGATTTTAGTTATCTCCTAAACT 1 27 0 ATTTTAGTAT 0.965026 -213 TTACAAATATATTTAAATATTAGTTAATGAT 1 98 0 ATTTAAATTT 0.940376 -142 CTTTCTATTCATTTAAGTTATAGGATTTTTA 1 126 0 ATTTAAGTAT 0.884667 -114 CACCATATACATTGTAATTTTTAGTGTATCT 1 212 0 ATTGTAATTT 0.922074 -28 CGGGAGTTTTATTTTAGTTTTAGGACATT 2 56 1 ATTTTAGTTT 0.975845 -19 TAGGTAGATAATTTTAATTTAATCTACCTAT 4 29 0 ATTTTAATTA 0.899442 -39 AGGCGTTCAAATTTTCATTATGAATTTTAAT 6 26 1 ATTTTCATAT 0.889862 -275 TTCATTATGAATTTTAATGACTTTTGCAAAA 6 39 1 ATTTTAATAC 0.900546 -262 TTTTTGTAGTATTTTAATATTCTTTAAAAAA 6 79 1 ATTTTAATTT 0.982643 -222 TTAGATAGTTATTTTAATGTTTTCACTATGT 7 55 0 ATTTTAATTT 0.98268 -33 ******** ** Masking position 8 Map Score: 12.2215 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 170 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 2 ACAAATCTCTTTACATAGAGAGGTTATGGCA 1 65 0 TTACATAGGA 0.993878 -175 CCATACAAAATTAGGTAGATAATTTTAATTT 4 40 0 TTAGGTAGTA 0.962867 -28 GTAGAAATTATTATATAGAGATAAACTTATG 6 139 1 TTATATAGGA 0.976124 -162 TCTAAAAGTATTACATAGCTAAATTGGACAT 6 254 0 TTACATAGTA 0.990409 -47 CTACATCCAATTACATAGTGAAAACATTAAA 7 43 1 TTACATAGGA 0.993815 -45 TATCACCAACTTAGATAGTTATTTTAATGTT 7 65 0 TTAGATAGTA 0.986093 -23 ******** ** Masking position 6 Map Score: 8.44096 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 23 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 TTCCATTCCTAGTATCCGCAGAAAGATACA 1 189 1 AGTATCCGCA 0.960497 -51 TGTATCACCATACAAAATTA 4 58 0 TGTATCACCA 0.974355 -10 GAGGTGTTAGGGTATCCCAATAGGGTTTCC 5 41 1 GGTATCCCAA 0.993419 -22 ATGGACGTCGGGTATCCCAATAGGGCGGAG 6 198 0 GGTATCCCAA 0.993419 -103 GGTATCACCAACTTAGATAG 7 78 0 GGTATCACCA 0.993419 -10 ********** Masking position 5 Map Score: 6.43945 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 8 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AGTTATCTCCTAAACTATACCAAGTAATTTTT 1 11 0 TAAATAACCA 0.909498 -229 AGGAGATAACTAAAATCGAATATCTGTTAGGA 1 32 1 TAAATCAATA 0.751973 -208 TTGTTTATCATTAACTAATATTTAAATATATT 1 92 1 TTAATATATT 0.454485 -148 AACTAACCTCTAATTTAATCCTAAGCTTTCTA 1 150 0 TAATTATCCT 0.873322 -90 AGGAATGGAATAATATAAACTAACCTCTAATT 1 167 0 TAATTAACTA 0.890784 -73 GTCCTAAAACTAAAATAAAACTCCCGATTTCA 2 50 0 TAAATAAACT 0.923753 -25 TACCTATCTCTTATATATACTTTAT 4 4 0 TTATTAACTT 0.789497 -64 ATAGGTAGATTAAATTAAAATTATCTACCTAA 4 29 1 TAAATAAATT 0.912676 -39 AAATAATTTACACCTCCGAGCGTAA 5 4 1 TAATTAACCT 0.950955 -59 TAAAGAATATTAAAATACTACAAAAACCTATA 6 73 0 TAAATATACA 0.690742 -228 CTCTATATAATAATTTCTACTTAGTTTAAGCA 6 127 0 TAATTCACTT 0.903456 -174 CAGCCCCAATTAATGTCCAATTTAGCTATGTA 6 242 1 TAATTCAATT 0.853947 -59 **** ** **** Masking position 3 Map Score: 6.77191 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 303 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 ATTTAAGTTATAGGATTTTTACAAATATATT 1 116 0 TAGATTTTTA 0.949015 -124 AATTTAATCCTAAGCTTTCTATTCATTTAAG 1 140 0 TAGCTTTCTA 0.965715 -100 AAATTTTCATTATGAATTTTAATGACTTTTG 6 34 1 TAGAATTTTA 0.950091 -267 AAGCATTTTATATGCTTTTTTAAAGAATATT 6 94 0 TAGCTTTTTT 0.953617 -207 GTTTAAGCAGTAAGCATTTTATATGCTTTTT 6 105 0 TAGCATTTTA 0.975619 -196 ** ******** Masking position 7 Map Score: 1.96986 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 48 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GAAAGATACACTAAAAATTACAATGTATAT 1 209 1 CTAAAAATTA 0.644093 -31 TATAATACCAAATCAACATAATACA 2 6 1 TACCAAATCA 0.734288 -69 AATGTCCTAAAACTAAAATAAAACT 2 60 0 CCTAAAACTA 0.715517 -15 TGTATCACCATACAAAATTAGGTAGATAAT 4 48 0 TACAAAATTA 0.814515 -20 ATGACTTTTGCAAAAAACTATAGGTTTTTG 6 55 1 CAAAAAACTA 0.918185 -246 TAAAATACTACAAAAACCTATAGTTTTTTG 6 65 0 CAAAAACCTA 0.902505 -236 GGGCTGAAAGCCCCAACTTAATGGACGTCG 6 218 0 CCCCAACTTA 0.930605 -83 TCTCTCACCAAACCACAACCTTTAT 7 6 1 CACCAAACCA 0.947556 -82 GGTATCACCAACTTAGATAGTTATT 7 73 0 CACCAACTTA 0.959484 -15 ********** Masking position 5 Map Score: 1.80988 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 355 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 AGATAACTAAAATCGAATATCTGTTAGGAGTG 1 35 1 AACAATATCT 0.960806 -205 AGTTAATGATAAACAAATCTCTTTACATAGAG 1 76 0 AACAATCTCT 0.980631 -164 TATTTGTAAAAATCCTATAACTTAAATGAATA 1 120 1 AACTATAACT 0.701909 -120 GGAATAATATAAACTAACCTCTAATTTAATCC 1 161 0 AACAACCTCT 0.966299 -79 TTCTGCTCATAAGTTTATCTCTATATAATAAT 6 145 0 AATTATCTCT 0.944779 -156 TATGGATAGGAAATGCATTTCTGCTCATAAGT 6 163 0 AATCATTTCT 0.835282 -138 AATTGCACCTCTTTTTTAAAAC 6 289 0 AATCACCTCT 0.937445 -12 GAAAACATTAAAATAACTATCTAAGTTGGTGA 7 62 1 AATACTATCT 0.804092 -26 ** * ******* Masking position 2 Map Score: 1.56606 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 313 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 AGGGAAACCCTATTGGGATACCCTAA 5 47 0 ACCCTATTGG 0.988926 -16 ATAGGGCGGAGCCCTATGGATAGGAAATGC 6 179 0 GCCCTATGGA 0.97872 -122 ATAGGGCTCCGCCCTATTGGGATACCCGAC 6 192 1 GCCCTATTGG 0.995574 -109 ********** Masking position 6 Map Score: 0.97164 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 2 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAATAATTTACACCTCCGAGCGTAAGC 5 8 1 TTACACCTCC 0.994254 -55 TGGGATACCCTAACACCTCCTCGCTTACGC 5 30 0 TAACACCTCC 0.989912 -33 AATTGCACCTCTTTTTTAAAAC 6 289 0 TTGCACCTCT 0.981592 -12 ********** Masking position 5 Map Score: 0.578165 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 1 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ********** No masking Map Score: 6.20604e-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 11 ********** No masking Map Score: 6.20604e-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 12 ********** No masking Map Score: 6.20604e-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