AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_mjan_pyro_300.orf -o221_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 RMJ13714 300 M_jannaschii_chromosome #2 RMJ06988 57 M_jannaschii_chromosome #3 RMJ01689 25 M_jannaschii_chromosome #4 RMJ08498 23 M_jannaschii_chromosome #5 RMJ13016 22 M_jannaschii_chromosome #6 RMJ00809 60 M_jannaschii_chromosome #7 RMJ06364 110 M_jannaschii_chromosome #8 RMJ03227 146 M_jannaschii_chromosome #9 RPH01502 121 Pyrococcus_OT3 #10 RPH01503 58 Pyrococcus_OT3 #11 RPH01506 155 Pyrococcus_OT3 #12 RPH01507 26 Pyrococcus_OT3 #13 RPH01510 101 Pyrococcus_OT3 #14 RPH01511 63 Pyrococcus_OT3 Motif number 1 TGGGATCTCCAGTCCCACGCCTTGGCCGGGC 1 165 0 ATCCCACGCC 0.984552 -136 CGCGGGGCAAAGCCCCATGGGATCTCCAGTC 1 182 0 ACCCCATGGG 0.874301 -119 GGGGATTTGAACCCCCGCGGGGCAAAGCCCC 1 197 0 ACCCCGCGGG 0.996562 -104 GGGGTTCAAATCCCCCCCTCCGCGCCACTTC 1 213 1 TCCCCCCTCC 0.910641 -88 ATAGCCAAGCTACCCCACGGCCCCACTTAAA 9 27 0 TCCCCACGGC 0.979088 -95 TAGCTTGGCTATCCTCCCGGCCTGGGGCGCC 9 46 1 ACCTCCCGGC 0.953329 -76 TGAACCCGGGTCTCCGGCGCCCCAGGCCGGG 9 61 0 TTCCGGCGCC 0.947958 -61 CCGGGTTCAAATCCCGGCGGCCCCACCAAAA 9 83 1 ACCCGGCGGC 0.994112 -39 AGGCTCGGCAACCCCCGCTCAAT 11 3 0 ACCCCGCTCA 0.893205 -153 CGGGACCCTAAATCCCGCGCCTTTGACCAGG 11 31 0 ATCCCGCGCC 0.995457 -125 GAACCCCGGAACCCCTACGGGACGGGACCCT 11 53 0 ACCCTACGGG 0.826943 -103 CGGGGTTCAAATCCCCGCCCCCGCACCAAAA 11 76 1 ACCCCGCCCC 0.99059 -80 TTGCAGTTAAATTCTCGCTGGAGACAAGATA 11 118 0 ATCTCGCTGG 0.715786 -38 CGGGCTCTCAAGGCCCGCGCCCTACCAGG 13 9 0 AGCCCGCGCC 0.992005 -93 CGGCGGGCAAACGCCCACGGGCTCTCAAGGC 13 26 0 AGCCCACGGG 0.942948 -76 GGGGATTTGAACCCCGGCGGGCAAACGCCCA 13 40 0 ACCCGGCGGG 0.988452 -62 CGGGGTTCAAATCCCCGTCCCGGCGCCAGAA 13 55 1 ACCCCGTCCC 0.896593 -47 ATTGAGTGAAATTCTGGCGCCGGGACGGGGA 13 66 0 ATCTGGCGCC 0.890207 -36 TTTATCCCCCTCCAGATTGAGTG 13 89 0 TTCCCCCTCC 0.778862 -13 * ********* Masking position 4 Map Score: 38.4927 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 25 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 GCCTAGCCCGGCCAAGGCGTGGGACTGGAGAT 1 160 1 GCAGGCGTGG 0.945678 -141 ATGGGGCTTTGCCCCGCGGGGGTTCAAATCCC 1 195 1 GCCGCGGGGG 0.886229 -106 AAAATAAAAAGAAGTGGCGCGGAGGGGGGGAT 1 222 0 GAGGGCGCGG 0.987668 -79 ATTATAAAAGGGGATGTGGCGGCAATGCTGAA 8 106 1 GGAGTGGCGG 0.946823 -41 CTCTGTTTAAGTGGGGCCGTGGGGTAGCTTGG 9 22 1 GGGGCCGTGG 0.971656 -100 CTATCCTCCCGGCCTGGGGCGCCGGAGACCCG 9 54 1 GCCGGGGCGC 0.976479 -68 AAGTATTTTGGTGGGGCCGCCGGGATTTGAAC 9 87 0 GGGGCCGCCG 0.983202 -35 CAAAATACTTGAGGTGGTGCTGA 9 109 1 GGGGGTGCTG 0.901968 -13 GAAGACAAGTGGGGTGGGTCCC 10 47 1 GGGGGGTCCC 0.850664 -12 ATTGAGCGGGGGTTGCCGAGCCTGG 11 4 1 GGCGGGGTTG 0.931587 -152 CCGCGCCTTTGACCAGGCTCGGCAACCCCCGC 11 16 0 GCCGGCTCGG 0.967218 -140 GAACCCCTACGGGACGGGACCCTAAATCCCGC 11 44 0 GGAGGGACCC 0.670214 -112 GTCCCGTCCCGTAGGGGTTCCGGGGTTCAAAT 11 56 1 GAGGGTTCCG 0.454687 -100 GTAAATTTTGGTGCGGGGGCGGGGATTTGAAC 11 80 0 GGCGGGGCGG 0.997412 -76 CCTGGTAGGGCGCGGGCCTTGAGAG 13 4 1 GTAGGCGCGG 0.943353 -98 CGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCC 13 21 1 GGACCCGTGG 0.706717 -81 ACGGGGATTTGAACCCCGGCGGGCAAACGCCC 13 41 0 GACCCGGCGG 0.847626 -61 TGAAATTCTGGCGCCGGGACGGGGATTTGAAC 13 59 0 GGCGGGACGG 0.982687 -43 * ** ******* Masking position 1 Map Score: 21.4471 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 85 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TTTATATATTCTTTTTATATATTCCCACAATAC 1 99 0 CTTTTTTATT 0.972116 -202 ACGTGTTTCATTTTTTATATATTCTTTTTATAT 1 112 0 TTTTTTTATT 0.773657 -189 ACTTCTTTTTATTTTTTAATATCTATTTACTAT 1 239 1 ATTTTATATC 0.891037 -62 AAGATATTATCTTTTCTTTTATTTTGGGTGAGA 6 32 1 CTTTTTTATT 0.972119 -29 TAGTTGTTATCTTTTTGAATATTGTCGGGGATT 7 79 0 CTTTTATATT 0.987177 -32 GTGATTACAACTTTTCAAATAACCGTTAAATTA 8 32 1 CTTTTATAAC 0.95866 -115 CTATAGACAACTATTATATTAATTTAACGGTTA 8 51 0 CTATTATAAT 0.750737 -96 GCCACATCCCCTTTTATAATATCAAAGCTTTAG 8 93 0 CTTTTATATC 0.988155 -54 ATTTTAAAAACTTTTTTATTATCGAAGACAAGT 10 24 1 CTTTTATATC 0.988155 -35 TTACGTCAAGCTTTTTAACTATTTTGGAGCTTG 14 32 1 CTTTTATATT 0.98718 -32 ***** * **** Masking position 5 Map Score: 12.9489 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 218 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 ATCTCCAGTCCCACGCCTTGGCCGGGCTAG 1 162 0 CCACGCCTTG 0.768643 -139 ATTTGAACCCCCGCGGGGCAAAGCCCCATG 1 194 0 CCGCGGGGCA 0.831913 -107 ATCCCCCCCTCCGCGCCACTTCTTTTTATT 1 222 1 CCGCGCCACT 0.983321 -79 CCAAGCTACCCCACGGCCCCACTTAAACAG 9 24 0 CCACGGCCCC 0.983932 -98 CCCGGGTCTCCGGCGCCCCAGGCCGGGAGG 9 58 0 CGGCGCCCCA 0.985978 -64 GTTCAAATCCCGGCGGCCCCACCAAAATAC 9 87 1 CGGCGGCCCC 0.984678 -35 GGGACCCACCCCACTTGTCTTCGAT 10 44 0 CCACCCCACT 0.803556 -15 ACCCTAAATCCCGCGCCTTTGACCAGGCTC 11 28 0 CCGCGCCTTT 0.946151 -128 GTTCAAATCCCCGCCCCCGCACCAAAATTT 11 80 1 CCGCCCCCGC 0.96488 -76 CTCTCAAGGCCCGCGCCCTACCAGG 13 6 0 CCGCGCCCTA 0.990064 -96 GGGCAAACGCCCACGGGCTCTCAAGGCCCG 13 23 0 CCACGGGCTC 0.849017 -79 ATCCCCGTCCCGGCGCCAGAATTTCACTCA 13 65 1 CGGCGCCAGA 0.904065 -37 ********** Masking position 4 Map Score: 13.7697 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 14 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 CGGAGGGGGGGATTTGAACCCCCGCGGGGC 1 205 0 GATTTGAACC 0.9933 -96 GGGCCGCCGGGATTTGAACCCGGGTCTCCG 9 76 0 GATTTGAACC 0.9933 -46 CGGGGGCGGGGATTTGAACCCCGGAACCCC 11 69 0 GATTTGAACC 0.9933 -87 CCGGGACGGGGATTTGAACCCCGGCGGGCA 13 48 0 GATTTGAACC 0.9933 -54 ********** Masking position 5 Map Score: 11.8612 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 ATTATATATTATTTTCGGTTTTTAGTAAGGT 1 42 0 ATTTCGGTTT 0.488125 -259 AACGTTGAGTATTGTGGGAATATATAAAAAG 1 91 1 ATTTGGGAAT 0.69639 -210 AAAACACGAAATTATGGAGGTGCAACCTTGA 1 272 1 ATTTGGAGGT 0.962856 -29 ATTCTCGGTCAAGGTTGCACC 1 290 0 ATTTCGGTCA 0.847255 -11 CTTTTCTTTTATTTTGGGTGAGAAACATG 6 42 1 ATTTGGGTGA 0.954625 -19 CTTTTTGAATATTGTCGGGGATTTAAAAATT 7 71 0 ATTTCGGGGA 0.974455 -40 TCACAAGTAGATTGTGGTGAAACTT 8 5 0 ATTTGGTGAA 0.869561 -142 CACCTCAAGTATTTTGGTGGGGCCGCCGGGA 9 94 0 ATTTGGTGGG 0.942872 -28 AAACTTTTTTATTATCGAAGACAAGTGGGGT 10 31 1 ATTTCGAAGA 0.79267 -28 ATTAATGTAAATTTTGGTGCGGGGGCGGGGA 11 87 0 ATTTGGTGCG 0.894798 -69 TCATTTTCCCATTTTGGAGGAA 12 15 1 ATTTGGAGGA 0.974327 -12 CTTTTTAACTATTTTGGAGCTTGATGTTTTT 14 42 1 ATTTGGAGCT 0.930357 -22 *** ******* Masking position 1 Map Score: 8.73042 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 265 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 CGCTCTGAAACGTGTTTCATTTTTTATATA 1 124 0 CGTGTTTCAT 0.988179 -177 TCCATAATTTCGTGTTTTATAGTAAATAGA 1 260 0 CGTGTTTTAT 0.95799 -41 TGTTATGCTAAGTGTTTCATTTAATAAT 2 9 0 AGTGTTTCAT 0.95799 -49 AGTGTTTCACCTTTAATTTA 3 16 0 AGTGTTTCAC 0.93044 -10 CGTGTTTTAATCCAGTTTAT 5 13 0 CGTGTTTTAA 0.95799 -10 GTAGGGGTTCCGGGGTTCAAATCCCCGCCC 11 66 1 CGGGGTTCAA 0.974261 -90 GTTTGCCCGCCGGGGTTCAAATCCCCGTCC 13 45 1 CGGGGTTCAA 0.974261 -57 ********** Masking position 9 Map Score: 8.19879 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AACATCAAATTAATAACTATCCTTTAACCT 1 16 1 TAATAACTAT 0.965587 -285 TTTTATTTTTTAATATCTATTTACTATAAA 1 245 1 TAATATCTAT 0.911258 -56 AAAGAAAAGATAATATCTTTCCAAAAATTG 6 21 0 TAATATCTTT 0.864796 -40 TTCAAAAAGATAACAACTATTTTTAAAG 7 93 1 TAACAACTAT 0.971333 -18 CTACTTGTGATTACAACTTTTCAAATAACC 8 26 1 TTACAACTTT 0.814293 -121 AAATAACTATAGACAACTATTATATTAATT 8 60 0 AGACAACTAT 0.792394 -87 GCTTTAGAGTAAATAACTATAGACAACTAT 8 70 0 AAATAACTAT 0.911258 -77 CCGTTAATTTTAAAAACTTTTTTATTATCG 10 18 1 TAAAAACTTT 0.841673 -41 ********** Masking position 5 Map Score: 4.22154 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 198 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 TAATAACTATCCTTTAACCTTACTAAAAACCG 1 26 1 CCTTAACTTA 0.982701 -275 AATATGGTATCCATTAATCATAACGTTGAGTA 1 70 1 CCTTAACATA 0.921835 -231 AGTGTTTCACCTTTAATTTATATTT 3 5 0 CCTTAATTAT 0.899016 -21 TTTATATACTCCCTTATACTTATTTCTATCCT 7 21 1 CCTTATCTTA 0.921835 -90 GGGGAAACAACCACTAATTTTTAAATCCCCGA 7 56 1 CCCTAATTTT 0.862955 -55 TTTCAAATAACCGTTAAATTAATATAATAGTT 8 44 1 CCTTAATTAA 0.953411 -103 ATATATTCCGTTAATTTTAAAAACTTTTT 10 8 1 CCTTAATTTA 0.979185 -51 ** **** **** Masking position 6 Map Score: 3.27687 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 122 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TCAGAGCGGAGGTAGCCTAGCCCGGCCAAGG 1 146 1 GGTAGCCAGC 0.898207 -155 AGGCCGGGAGGATAGCCAAGCTACCCCACGG 9 38 0 GATAGCCAGC 0.931925 -84 ATTGAGCGGGGGTTGCCGAGCCTGGTCAAAG 11 11 1 GGTTGCCAGC 0.979576 -145 ******* *** Masking position 9 Map Score: 0.988568 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ATACCATATTATATATTATTTTCGGTTTTT 1 50 0 ATATATTATT 0.735922 -251 TATTCTTTTTATATATTCCCACAATACTCA 1 96 0 ATATATTCCC 0.980652 -205 TTCATTTTTTATATATTCTTTTTATATATT 1 109 0 ATATATTCTT 0.935661 -192 GATAAAATTTATATACTCCCTTATACTTAT 7 14 1 ATATACTCCC 0.958041 -97 ATATATTCCGTTAATTTTAA 10 1 1 ATATATTCCG 0.964963 -58 ********** Masking position 5 Map Score: 0.216551 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 88 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ********** No masking Map Score: 3.29935e-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 13 ********** No masking Map Score: 3.29935e-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 14 ********** No masking Map Score: 3.29935e-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