AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_aful_mthe_100.orf -o056_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG48429 192 Archaeoglobus_fulgidus #2 RAG21207 31 Archaeoglobus_fulgidus #3 RAG50420 80 Archaeoglobus_fulgidus #4 RAG21288 173 Archaeoglobus_fulgidus #5 RAG22420 300 Archaeoglobus_fulgidus #6 RAG45771 182 Archaeoglobus_fulgidus #7 RAG45588 64 Archaeoglobus_fulgidus #8 RAG35664 297 Archaeoglobus_fulgidus #9 RAG49289 45 Archaeoglobus_fulgidus #10 RTH00661 61 M.thermo #11 RTH01407 25 M.thermo #12 RTH01538 300 M.thermo #13 RTH01353 75 M.thermo #14 RTH00151 64 M.thermo #15 RTH00311 135 M.thermo #16 RTH00569 142 M.thermo Motif number 1 TATTTGAAAAAAGGTTTTTAAATCGGTGGCTTTAGCCTTAAAAC 1 14 0 ATTTTTACTA 0.968652 -179 AACCTTTTTTAATTCCGCCCCTACTTAGCTC 2 2 1 ATTTTTACTT 0.983492 -30 GAAAGCTGATAACTTTTTTAATCCACCGGCTGTTCAGGTTTC 4 142 1 ATTTTTACTT 0.983492 -32 GAAGTGCTTCATTATTTTTTAAGTTTTGGTTGGATGGTGTGAAG 5 260 0 ATTTTTATTA 0.689167 -41 ACAAAGGTAAGTAGTTTTTAAAACTTAGCTTGCAGCAGTGCAAT 6 17 1 GTTTTTACTA 0.914597 -166 GGGCGAACCAAAACTTTTTAAAGCGCATGCTGGTGGTGGGAGTG 6 71 1 ATTTTTACTT 0.983492 -112 GTTAAGTTTAAAATTTTTTCATTCATTTAATGATTGG 7 4 0 ATTTTTACTT 0.983489 -61 TCGAAGCATGGTTATTTTAGAAGCGTTAAGTTTAAAATTTTTTC 7 28 0 GTTTTAACTA 0.79199 -37 GCCTACCAGCAAAGTTTTTATCACCCCCAATTTTGGCTTTAAC 8 265 1 ATTTTTTCTT 0.87343 -33 GAGCTCACCAAGTCTTTTATAGACGGGGCGTGATATTATTAATC 12 23 0 ATTTTAACTT 0.954918 -278 CACTTGCTGGAACCTTTATGAACCCTTCAATTATTCTGCTAAAG 12 256 1 ATTTATACTT 0.873427 -45 CTACAATTAAAAGCTTTTACACACAGTATGTTATAAGTTATATC 16 62 0 ATTTTAACTT 0.954918 -81 * ***** * * * * Masking position 7 Map Score: 10.1089 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 38 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 AAATCCCTCCAATTTTTGTT 3 1 1 AAATCCCTCC 0.979708 -80 CCTTCCCTCACTCTCCCTCC 4 1 0 CTCTCCCTCC 0.974116 -173 TTTCAGCCTACTATCCCTCCTAATTTTTGC 4 64 1 CTATCCCTCC 0.987178 -110 GTAATGATGCAAATCCCGTCACGTTTACGA 5 163 1 AAATCCCGTC 0.859029 -138 ACTTTTTCATCACTCCCACCACCAGCATGC 6 95 0 CACTCCCACC 0.902767 -88 GCTTTGGTTTATATCCCTACTCATTTTTTA 8 93 0 ATATCCCTAC 0.825575 -205 CAAAGCATTCAAGTCCCGCCTCCCGGATTT 8 117 1 AAGTCCCGCC 0.942888 -181 AGTAAGCTATCGAACCCGCCTTAGCTCAGA 8 210 0 CGAACCCGCC 0.920402 -88 TTGATTAATAATATCACGCCCCGTCTATAA 12 21 1 ATATCACGCC 0.844493 -280 CGATCCCTCCTGAGGGCCTG 15 1 1 CGATCCCTCC 0.984575 -135 ********** Masking position 5 Map Score: 9.05887 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 410 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 CTTTTTTAATCCACCGGCTGTTCAGGTTTC 4 154 1 CCACCGGCTG 0.947858 -20 AAAAAGAACTCCACCACCCGTACCGGCAAT 5 74 1 CCACCACCCG 0.981578 -227 TTCATCACTCCCACCACCAGCATGCGCTTT 6 90 0 CCACCACCAG 0.930769 -93 CATTCAAGTCCCGCCTCCCGGATTTGAACC 8 122 1 CCGCCTCCCG 0.987578 -176 CATGGGATCTCCGCCTGCCGCGGAGTGGCG 8 158 1 CCGCCTGCCG 0.97289 -140 GCCCCATGGACCACTTGCTGGAACCTTTAT 12 245 1 CCACTTGCTG 0.907654 -56 CGATCCCTCCTGAGGGCCTGCGGCC 15 6 1 CCTCCTGAGG 0.828484 -130 CCGGCCACATCCACCTGAGGGAACTTGCAG 15 99 1 CCACCTGAGG 0.959594 -37 ********** Masking position 4 Map Score: 6.99272 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 218 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 GATAGTAGGCTGAAAAATAAGGGTTTACATGAC 4 46 0 TAAAATAGGG 0.869089 -128 TGGTGGGGCAGCAAAAATTAGGAGGGATAGTAG 4 71 0 GAAAATAGGA 0.869089 -103 GCTTTTGCATGTCAAAATTCCGGAAAGGAAAGC 4 115 1 GAAAATCCGG 0.982254 -59 CAATACATCCGGACAAATAAGAGCAACCGGACT 5 17 0 GCAAATAGAG 0.915602 -284 ATGGTCCCCGGTTCAAATCCGGGAGGCGGGACT 8 128 0 GCAAATCGGG 0.98131 -170 GTTAAAGCCAAAATTGGGGGTGATAAAAA 8 279 0 GAAAATGGGG 0.968219 -19 GGGGCAGTCTGTGAAAATTAGAGCCTCTTTAAC 12 217 0 GAAAATAGAG 0.956885 -84 TGCTCAATGCGGAAAAATTCCGGATCAGACCGG 13 11 1 GAAAATCCGG 0.982255 -65 AATTTAAGCAGATAAAATGCCAGACCACGGGGA 16 114 1 GAAAATCCAG 0.947759 -29 * ***** **** Masking position 7 Map Score: 6.21951 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 142 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ACATTAGGCTAAGCTGTAAATCGTTTTCGG 1 165 0 AAGCTGTAAA 0.96318 -28 GAGGGATAGTAGGCTGAAAAATAAGGGTTT 4 53 0 AGGCTGAAAA 0.884407 -121 CCGGAAAGGAAAGCTGATAACTTTTTTAAT 4 134 1 AAGCTGATAA 0.902916 -40 TCCCATAAACAGGAAGTAAAAAGAACTCCA 5 57 1 AGGAAGTAAA 0.775946 -244 TCCTTTAGAAAAGAAGTAAAAGCTGTACTA 6 146 0 AAGAAGTAAA 0.808053 -37 CTGTTAATCTGGATGTTAAAATGCA 11 7 0 TGGATGTTAA 0.707339 -19 CTTTGATAATAAGATTTAAATATATAGTAA 12 85 0 AAGATTTAAA 0.621952 -216 GGTGAAAATATAGATGTAAAATTCAGACGA 12 129 1 TAGATGTAAA 0.74606 -172 TATTTTAAATGAGCTGTTAATTAGAAC 13 59 1 GAGCTGTTAA 0.845091 -17 GAACTTGCAGAGGCTGTTAAGGAGGGT 15 119 1 AGGCTGTTAA 0.955595 -17 CTGTGTGTAAAAGCTTTTAATTGTAGCCCA 16 80 1 AAGCTTTTAA 0.78423 -63 ACAGAAATTTAAGCAGATAAAATGCCAGAC 16 109 1 AAGCAGATAA 0.767797 -34 ********** Masking position 9 Map Score: 7.01883 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 504 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 AGGAGTACACAAACAAAAATTGGAGGGATTT 3 11 0 AAACAAAAAT 0.879883 -70 TCCTCTTTCAAACCAAAAAGCTTATTATTTC 3 41 1 AACCAAAAAC 0.887976 -40 TTTTGACAAAAAACAAAACATTTATTTGTTT 5 205 0 AAACAAAACT 0.955906 -96 CACACCATCCAACCAAAACTTAAAAAATAAT 5 263 1 AACCAAAACT 0.984652 -38 TGCCTGGGCGAACCAAAACTTTTTAAAGCGC 6 66 1 AACCAAAACT 0.984652 -117 TAGGGATATAAACCAAAGCATTCAAGTCCCG 8 104 1 AACCAAAGCT 0.959114 -194 ********* * Masking position 6 Map Score: 3.18515 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 14 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TACAAAGCCTATGCTGAAGGACATTGCAAAAACA 5 110 1 ATTAAGGACT 0.965113 -191 AACTTAAAAAATAATGAAGCACTTCTAAAACC 5 279 1 ATTAAGCACT 0.957144 -22 TTTTACTTCTTTTCTAAAGGAGTTAGAGGTGGTT 6 155 1 TTTAAGGAGT 0.87647 -28 CTAAAATCGAATAATGAATGAGGTTTGTGGAATT 8 55 0 ATTAATGAGT 0.958174 -243 TAGGCACAAGATTTTTAAGCAGATTCGCTCAGTA 8 236 0 ATTAAGCAGT 0.973216 -62 GGGGCGTGATATTATTAATCAAGTGAGGGACC 12 9 0 ATTAATCAAT 0.741008 -292 CATAAATTTTATTTTAAATGAGCTGTTAATTAGA 13 50 1 ATTAATGAGT 0.958174 -26 ATCTGTCATTATTATTAATGACATATTTCCTATA 14 31 0 ATTAATGACT 0.933689 -34 TAGCCCACAGAAATTTAAGCAGATAAAATGCCAG 16 103 1 AATAAGCAGT 0.851369 -40 ** * ****** * Masking position 7 Map Score: 3.63051 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 87 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ACAAGAATACGTATTTGATTTGTAGCAGTTG 1 93 1 GTATTGATTT 0.886866 -100 TTGACGGAAATAATAAGCTTTTTGGTTTGAA 3 47 0 TAATAGCTTT 0.819972 -34 CACCATGATGGTATATGCTTTTGCATGTCAA 4 99 1 GTATAGCTTT 0.960304 -75 ATTAAAAAAGTTATCAGCTTTCCTTTCCGGA 4 133 0 TTATCGCTTT 0.838977 -41 TACTTCCTGTTTATGGGATTTACATCAATAC 5 44 0 TTATGGATTT 0.856956 -257 ATGTCCTTCAGCATAGGCTTTGTAGCTATTA 5 103 0 GCATAGCTTT 0.884296 -198 ATCCCGTCACGTTTACGATTTTTGTGATTAA 5 175 1 GTTTAGATTT 0.723997 -126 AACAAAACATTTATTTGTTTTAATCACAAAA 5 194 0 TTATTGTTTT 0.79126 -107 CTTCATTATTTTTTAAGTTTTGGTTGGATGG 5 267 0 TTTTAGTTTT 0.55917 -34 CCCACCACCAGCATGCGCTTTAAAAAGTTTT 6 80 0 GCATGGCTTT 0.766695 -103 ACCTCATTCATTATTCGATTTTAGAGTATAA 8 65 1 TTATTGATTT 0.878438 -233 TAGTAATAACTTATTAGTTTTCAGGAGCTCA 12 60 0 TTATTGTTTT 0.79126 -241 AATACTTTGATAATAAGATTTAAATATATAG 12 88 0 TAATAGATTT 0.739965 -213 GGGTTATAACTTATAAGATATAACTTATAAC 16 46 1 TTATAGATAT 0.56053 -97 CATACTGTGTGTAAAAGCTTTTAATTGTAGC 16 76 1 GTAAAGCTTT 0.688917 -67 ***** ***** Masking position 9 Map Score: 4.786 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 103 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 TAAAAAGTTTTGGTTCGCCCAGGCAAGGTA 6 61 0 TGGTTCGCCC 0.867194 -122 AATTTGAAGAGGGTTCGCTGAAAGGCGAAA 8 29 0 GGGTTCGCTG 0.93765 -269 GGAGATCCCATGGTCCCCGGTTCAAATCCG 8 140 0 TGGTCCCCGG 0.979334 -158 AAAATTTATGGGAGTCCCGGTCTGATCCGG 13 30 0 GGAGTCCCGG 0.9398 -46 TACACTGACATAGTTCCCGGCCACATCCAC 15 83 1 TAGTTCCCGG 0.952329 -53 GTTATAACCCGGGTTCCCGGGTGCCAGGTA 16 26 0 GGGTTCCCGG 0.994652 -117 CTTGATTCCCCGTGGTCTGGCA 16 131 0 TGATTCCCCG 0.956445 -12 ********** Masking position 6 Map Score: 2.79804 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 91 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 10 TTAAGGCTAAAGCCACCGATTTAAAAACCTTTTT 1 17 1 AGCACGTTAA 0.832119 -176 GAGCTAAGTAGGGGCGGAATTAAAAAAGGTT 2 9 0 AGGGGGTTAA 0.988088 -23 TTGGTTTGAAAGAGGAGGAGTACACAAACAAAAA 3 23 0 AGGGGGTACA 0.97122 -58 AGGGAGAGTGAGGGAAGGTATTAAACTTTAATTG 4 13 1 AGGAGGTTAA 0.96452 -161 AAACCTGAACAGCCGGTGGATTAAAAAAGTTATC 4 149 0 AGCGTGTTAA 0.847203 -25 ACTCTTTTCCAGAGAACTTTTTCATCACTCCCAC 6 106 0 AGGACTTTCA 0.709157 -77 TAAAGGAGTTAGAGGTGGTTTTAA 6 169 1 AGGGGGTTAA 0.988088 -14 CCTGCCGCGGAGTGGCGGACTACAGTCCCACGCT 8 171 1 AGGGGGTACA 0.971219 -127 TGTAAAATTCAGACGAGTTTTTCAGTATGAAGGC 12 143 1 AGCGGTTTCA 0.915518 -158 ** ** ** **** Masking position 11 Map Score: 3.58715 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 273 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 AAATCGGTGGCTTTAGCCTTAAAACTGG 1 9 0 CTTTAGCCTT 0.985352 -184 AAGCAGCCTCTTTTCGCCTTTCAGCGAACC 8 18 1 TTTTCGCCTT 0.963221 -280 GGATAACTGTCTTTCGCCTTCATACTGAAA 12 162 0 CTTTCGCCTT 0.990481 -139 ATTAGAGCCTCTTTAACCTTCTGATGTCCC 12 204 0 CTTTAACCTT 0.944232 -97 ********** Masking position 4 Map Score: 1.37604 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 GGAGGGAGAGTGAGGGAAGGTATTAAACT 4 10 1 GTGAGGGAAG 0.947048 -164 ATTACCTTGCCTGGGCGAACCAAAACTTTT 6 59 1 CTGGGCGAAC 0.918316 -124 CGCTCTACCTCTGAGCTAAGGCGGGTTCGA 8 201 1 CTGAGCTAAG 0.805512 -97 CGATAGCTTACTGAGCGAATCTGCTTAAAA 8 228 1 CTGAGCGAAT 0.964179 -70 TATTAATCAAGTGAGGGACC 12 1 0 GTGAGGGACC 0.962398 -300 AAAAGACTTGGTGAGCTCCTGAAAACTAAT 12 49 1 GTGAGCTCCT 0.673281 -252 CGATCCCTCCTGAGGGCCTGCGGCCTGAC 15 10 1 CTGAGGGCCT 0.937483 -126 CCACATCCACCTGAGGGAACTTGCAGAGGC 15 103 1 CTGAGGGAAC 0.976952 -33 ********** Masking position 2 Map Score: 2.42783 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 281 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ATTTTACGTATTCTTGCAGTTCTATTTGAA 1 50 0 TTCTTGCAGT 0.925402 -143 ATACGTATTCTTGTTGCAATTACTTGGATT 1 77 0 TTGTTGCAAT 0.965251 -116 CGTATTTGATTTGTAGCAGTTGCCGAGAAT 1 102 1 TTGTAGCAGT 0.977618 -91 AGCATAGGCTTTGTAGCTATTATTGCCGGT 5 95 0 TTGTAGCTAT 0.872659 -206 CTTATAACTGTTTTTGCAATGTCCTTCAGC 5 122 0 TTTTTGCAAT 0.841845 -179 AAAACTTAGCTTGCAGCAGTGCAATTACCT 6 36 1 TTGCAGCAGT 0.941076 -147 ********** Masking position 2 Map Score: 0.89988 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 84 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 ********** No masking Map Score: -2.42052e-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 15 TTTTTTAATTCCGCCCCTACTTAGCTC 2 15 1 CCGCCCCTAC 0.918513 -17 CTAATTTTTGCTGCCCCACCATGATGGTAT 4 83 1 CTGCCCCACC 0.993906 -91 GTAAAAAGAACTCCACCACCCGTACCGGCA 5 72 1 CTCCACCACC 0.895327 -229 GGACTGTAGTCCGCCACTCCGCGGCAGGCG 8 169 0 CCGCCACTCC 0.96608 -129 TTAACGGACGCTGCAACACGGAGC 9 32 1 CTGCAACACG 0.900894 -14 TTTTCACAGACTGCCCCATGGACCACTTGC 12 233 1 CTGCCCCATG 0.958772 -68 ACATAGTTCCCGGCCACATCCACCTGAGGG 15 90 1 CGGCCACATC 0.923199 -46 ********** Masking position 4 Map Score: 1.30308 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 472 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665