AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i003_aful_mthe_300.orf -o003_aful_mthe_300.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 Purged sequences: RTH01593 16 M.thermo Input sequences: #1 RAG48365 300 Archaeoglobus_fulgidus #2 RAG47506 300 Archaeoglobus_fulgidus #3 RAG34801 24 Archaeoglobus_fulgidus #4 RTH00932 171 M.thermo #5 RTH01922 86 M.thermo #6 RTH01025 167 M.thermo #7 RTH00920 57 M.thermo #8 RTH01635 269 M.thermo #9 RTH01077 52 M.thermo #10 RTH01429 102 M.thermo #11 RTH00820 18 M.thermo #12 RTH00464 300 M.thermo #13 RTH02128 102 M.thermo Motif number 1 TCGCGTGTCCTCTCTGCAAGTCGGAATTGG 1 157 1 TCTCTGCAAG 0.858139 -144 GAGGAGATTATATCTGGAAAGCTCGTTTGC 1 213 1 TATCTGGAAA 0.69921 -88 AGATTTGCGCCCTCCGGAGTTGAGACA 1 284 1 CCTCCGGAGT 0.67976 -17 ACGATAAAGGTATCAGCAATTCCATATTA 2 10 0 TATCAGCAAT 0.720879 -291 GAACTTCTTACATCTGGAGTGTTCACATTA 2 84 1 CATCTGGAGT 0.950387 -217 GTTGCGGGGGCCTCTGAAAGGATAATATAT 4 57 0 CCTCTGAAAG 0.855452 -115 GATGTGAGGATATCAGCAGATCTCAGAGGA 6 11 0 TATCAGCAGA 0.823254 -157 CATCTGGAGGTATCAGAAATCAAAAAACCG 6 40 0 TATCAGAAAT 0.667337 -128 CATAGCCCACCATCTGGAGGTATCAGAAAT 6 50 0 CATCTGGAGG 0.968525 -118 TCAGGATCAGCCTCAGAAGTATCC 7 5 0 CCTCAGAAGT 0.916253 -53 TGCAAGACATCCTCTGAAGTAGATAACCAT 8 91 0 CCTCTGAAGT 0.916253 -179 GGAACCCTGTCCTCAGAAGGACCGAACCAC 8 212 0 CCTCAGAAGG 0.950314 -58 TATCGGAACTTATCAGGAGGAGAAACG 9 36 1 TATCAGGAGG 0.964713 -17 CCATGATTTTTACCAGGAGGTTATAGA 10 86 1 TACCAGGAGG 0.876121 -17 TGAATAATCATATCTGGAGAGTAGCAGATG 12 60 0 TATCTGGAGA 0.887936 -241 AAACACTCCTTCCCCGCAGGAAGATGTATA 12 112 1 TCCCCGCAGG 0.716441 -189 ********** Masking position 8 Map Score: 13.7706 Number of sites scoring better than the average of aligned sites = 1266 Number in coding regions = 1177 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 TTCGTTCTCCTCAACCACTTCAACTTCCAATTCCGA 1 177 0 TACCCAACTT 0.982485 -124 CAATGGGAAATTCAGCACGACAACTGCTGCAAACGA 1 235 0 TACCCAACTG 0.991008 -66 AAAACTTGTTTTCATCACATCAACTTAGGGTTTGGC 2 150 1 TACCCAACTT 0.982485 -151 ATTCTGATGATTCACCCCTGCCCCTGTAGTAGCCGA 5 35 0 TACCCCCCTG 0.986905 -52 TGGATAAATTCATAGCCCACCATCTGGAGGTATCAG 6 54 0 CACCCATCTG 0.951843 -114 GTCTCTCCCTTGCAAGACATCCTCTGAAGTAGATAA 8 95 0 TAGCCCTCTG 0.920348 -175 CCTGCTTATCTGAATCTCTGCCTCTTCAAGGAACCC 8 235 0 TACCCCTCTT 0.972628 -35 TTTTAATTTATCTAGCACAGCACCTTTTTATACCTT 10 16 0 TACCCACCTT 0.978949 -87 TACCAGAACATAGAAAGCGACAACTGCAAGGACGAG 12 185 1 TAACCAACTG 0.924848 -116 * * * * ****** Masking position 4 Map Score: 8.13976 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 90 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ATTTATCCATTCATGATCTGTTTCATCGATCCG 6 81 1 TCATATTGTT 0.843593 -87 AGCTGATCTCCTGTTTAAACCTTCTA 7 42 0 TGATTCTGTT 0.963376 -16 GGAACATAACTGATATTATGGTTATCTACTTCA 8 74 1 TGATTTTGTT 0.9305 -196 TGATGAAGAGTCATGCTGTGGTTCGGTCCTTCT 8 195 1 TCATCTTGTT 0.936352 -75 GCTTCCTGTCCTGCTTATCTGAATCT 8 254 0 TCCTTCTGTT 0.976799 -16 AAAAAAATTATCATATCATGTTTCTTGGGATAT 10 48 1 TCATTCTGTT 0.980785 -55 CTTGGGATATTCATTCCATGATTTTTACCAGGA 10 71 1 TCATCCTGTT 0.966559 -32 CTCAAGCTGATGCTATCCTGAATAATCATATCT 12 75 0 TGCTTCTGAT 0.773774 -226 TCTCCTCTTCTGATTCTGAAAAGCT 12 286 0 TCCTTTTGTT 0.955415 -15 **** ** ** ** Masking position 9 Map Score: 6.40375 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 32 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 AAATTTTTCTTTCGTGAAATCCATGCTGGTAG 1 36 1 TTCTGAAACC 0.944261 -265 AAGCTTCCTTTTCATGAATGCTGTTGGAGGTA 1 115 0 TTCTGAATCT 0.937504 -186 AAAAGGAAGCTTCTGGAAATCCTCGCGTGTCC 1 135 1 TTCGGAAACC 0.985589 -166 AGGAGATTATATCTGGAAAGCTCGTTTGCAGC 1 214 1 ATCGGAAACT 0.95305 -87 GAGGGCGCAAATCTGGAATCCCATCCTCAATG 1 266 0 ATCGGAATCC 0.970034 -35 CGATAAAGGTATCAGCAATTCCATATTA 2 7 0 ATCGCAATCC 0.807385 -294 ATGTAAGAAGTTCAGGAATTCTATATTAATAT 2 65 0 TTCGGAATCT 0.983756 -236 TACCACTCAGTTCGGGTAATGTGAACACTCCA 2 98 0 TTCGGTAAGT 0.750828 -203 TTTATCACCTTCTTGAATCCTTCTAAAGTAA 4 151 0 TTCTGAATCT 0.937504 -21 GCTTTCTATGTTCTGGTATGGCTGCTACCCGT 12 171 0 TTCGGTATGC 0.827744 -130 CCTCTTCTGATTCTGAAAAGCTATTTATATTT 12 276 0 TTCGAAAACT 0.816596 -25 *** ***** ** Masking position 8 Map Score: 9.44795 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 410 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 GAAACGATAAAGGTATCAGCAATTCCATAT 2 13 0 AGGTATCAGC 0.963635 -288 ACCGATGTGAGGATATCAGCAGATCTCAGA 6 14 0 GGATATCAGC 0.987717 -154 CACCATCTGGAGGTATCAGAAATCAAAAAA 6 43 0 AGGTATCAGA 0.77463 -125 GGTTTAAACAGGAGATCAGCT 7 47 1 GGAGATCAGC 0.981729 -11 AATCATATCTGGAGAGTAGCAGATGCGCAA 12 55 0 GGAGAGTAGC 0.894498 -246 TGATTATTCAGGATAGCATCAGCTTGAGTA 12 80 1 GGATAGCATC 0.926469 -221 CCACTAACACGGGTAGCAGCCATACCAGAA 12 163 1 GGGTAGCAGC 0.991547 -138 ********** Masking position 5 Map Score: 5.45751 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 212 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 AAAAAGCCTACCAGCATGGATTTCACGAAA 1 45 0 CCAGCATGGA 0.954568 -256 TTAGGAGGAGTTATCATGGAAATACCACTC 2 122 0 TTATCATGGA 0.73134 -179 TGCGGGGGCCTCTGAAAGGATAATATATGT 4 55 0 TCTGAAAGGA 0.853006 -117 GCCCCCGCAACCATCAAGGAAACTTTAATT 4 76 1 CCATCAAGGA 0.975602 -96 GCATGACTCTTCATCAAGGACTCTGTATTC 8 181 0 TCATCAAGGA 0.979575 -89 AATCTCTGCCTCTTCAAGGAACCCTGTCCT 8 229 0 TCTTCAAGGA 0.973602 -41 GAAAGCGACAACTGCAAGGACGAGTGCAAC 12 197 1 ACTGCAAGGA 0.9315 -104 ********** Masking position 6 Map Score: 3.73577 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 304 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 GCTGTTGGAGGTATGAGTAAATAACGATTTCCGC 1 94 0 GAGTAAATAA 0.904356 -207 GATAGTTAACGATGGGGTAAATATTAATATAGAA 2 45 1 GTGTAAATAT 0.934863 -256 TCAACTTAGGGTTTGGCTAAATAAATTTTAATCT 2 169 1 GTGTAAATAA 0.920945 -132 TGCAATTCCAGCTAAGTTAAAAATGGTTATATTT 2 224 1 GTATAAAAAT 0.846118 -77 TTTTTGAGGATAAAAAATAAATATAACCATTTTT 2 242 0 TAATAAATAT 0.580635 -59 AAAACTTGTTGGTGAATTAAATAAAGGTAATTTT 2 273 0 GTATAAATAA 0.933876 -28 ATAGGATTAAGCAGACTTAAATATAGAATACACA 6 114 1 GAATAAATAT 0.933876 -54 TGCTGTGCTAGATAAATTAAAAAAATTATCATAT 10 30 1 GTATAAAAAA 0.81695 -73 ATATTTTACCGAATAATTAAATATTATGGAGGCA 12 248 0 GAATAAATAT 0.933876 -53 * * * ******* Masking position 8 Map Score: 2.25962 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 15 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ACGAGCTTTCCAGATATAATCTCCTCTTCG 1 209 0 CAGATATAAT 0.875456 -92 GTGAACACTCCAGATGTAAGAAGTTCAGGA 2 80 0 CAGATGTAAG 0.901603 -221 AATCAAAAAACCGATGTGAGGATATCAGCA 6 23 0 CCGATGTGAG 0.977077 -145 TTTCATCGATCCGATAGGATTAAGCAGACT 6 101 1 CCGATAGGAT 0.964438 -67 CTGATAAGTTCCGATAGGAGCATCTGTAAT 9 22 0 CCGATAGGAG 0.977077 -31 TGCTACTCTCCAGATATGATTATTCAGGAT 12 64 1 CAGATATGAT 0.95413 -237 ********** Masking position 5 Map Score: 2.17395 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 33 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 CAGATGTAAGAAGTTCAGGAATTCTATATT 2 70 0 AAGTTCAGGA 0.98407 -231 TAAGGACATAAAGTTCAGTAGAGTCGATTT 4 17 0 AAGTTCAGTA 0.922101 -155 CCTTCTAAGCATGTTCAGGATCAGCCTCAG 7 19 0 ATGTTCAGGA 0.988829 -39 GTCGCTTTCTATGTTCTGGTATGGCTGCTA 12 176 0 ATGTTCTGGT 0.891038 -125 CATCTATTTAATGTTAAGGATGGACGGTGT 13 49 0 ATGTTAAGGA 0.944326 -54 ********** Masking position 5 Map Score: 1.68707 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 80 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 10 CCAGATATAATCTCCTCTTCGTTCTCCTCA 1 200 0 TCTCCTCTTC 0.971028 -101 TTTATCACCTTCTTGAATCCTT 4 160 0 TATCACCTTC 0.861676 -12 TTCTGATGATTCACCCCTGCCCCTGTAGTA 5 40 0 TCACCCCTGC 0.977027 -47 CCGTGCAGTCTCTCCCTTGCAAGACATCCT 8 108 0 TCTCCCTTGC 0.969412 -162 TGGCCCTGGATATCCCGTGCAGTCTCTCCC 8 122 0 TATCCCGTGC 0.957882 -148 ATGTAAATTATATCCACTGCCTCCATAATA 12 231 1 TATCCACTGC 0.950018 -70 TCTCCTCTTCTGATTCTGAA 12 291 0 TCTCCTCTTC 0.971028 -10 ********** Masking position 8 Map Score: 4.45161 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 315 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ATTTATTTTTTATCCTCAAAAAATTACCTT 2 254 1 TATCCTCAAA 0.805148 -47 ATGGTTGCGGGGGCCTCTGAAAGGATAATA 4 60 0 GGGCCTCTGA 0.946289 -112 GATCTGCTGATATCCTCACATCGGTTTTTT 6 19 1 TATCCTCACA 0.859635 -149 TGTTCAGGATCAGCCTCAGAAGTATCC 7 8 0 CAGCCTCAGA 0.971188 -50 CCTTGCAAGACATCCTCTGAAGTAGATAAC 8 94 0 CATCCTCTGA 0.926413 -176 GGGATATCCAGGGCCACAGAGAAGATACTC 8 136 1 GGGCCACAGA 0.896098 -134 CCACAGAGAAGATACTCAGAGCCGCAGGAC 8 149 1 GATACTCAGA 0.848342 -121 CAAGGAACCCTGTCCTCAGAAGGACCGAAC 8 215 0 TGTCCTCAGA 0.968968 -55 ********** Masking position 10 Map Score: 2.43152 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 202 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ********** No masking Map Score: -7.23089e-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 CTGGAAAGCTCGTTTGCAGCAGTTGTCGTGCT 1 226 1 CGTTGCACAG 0.958916 -75 TTGATGGTTGCGGGGGCCTCTGAAAGGATAAT 4 61 0 CGGGGCCCTG 0.953258 -111 TGATGATTCACCCCTGCCCCTGTAGTAGCCGA 5 35 0 CCCTGCCCTG 0.875491 -52 CTTTGAGGTACGATGGCATCAG 5 75 1 CGTGGCACAG 0.988411 -12 GACTATTAATAGTTGTCAGCAGCCCTGAGAAA 8 40 0 AGTGTCACAG 0.755117 -230 CACGGGATATCCAGGGCCACAGAGAAGATACT 8 133 1 CCGGGCCCAG 0.979101 -137 CTTCAAGGAACCCTGTCCTCAGAAGGACCGAA 8 216 0 CCTGTCCCAG 0.973922 -54 ** ***** *** Masking position 7 Map Score: 0.739416 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 163 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 TGCAAGCAACTGAAATTTTTCTTTCGTGAAAT 1 24 1 TGAAATTTCT 0.879155 -277 ATAACTCCTCCTAAAACTTGTTTTCATCACAT 2 138 1 CTAAACTTTT 0.780315 -163 CAGTCCAAGATTAAAATTTATTTAGCCAAACC 2 178 0 TTAAATTTTT 0.921921 -123 GGTTAAAACTTGTTGGTGAATTAA 2 287 0 TTAAACTTTT 0.938276 -14 CTGATCTAAATTAAAGTTTCCTTGATGGTTGC 4 82 0 TTAAATTTCT 0.938202 -90 TACCTCAATTTTAAAGTTTACTTTAGAAGGAT 4 134 1 TTAAATTTCT 0.938202 -38 GATCTCCTGTTTAAACCTTCTAAGCATGTTCA 7 32 0 TTAAACTTTA 0.705579 -26 CAGCACCTTTTTATACCTTTCTTT 10 3 0 TTATACTTCT 0.860818 -100 AAACATGATATGATAATTTTTTTAATTTATCT 10 39 0 TGATATTTTT 0.645809 -64 ***** *** ** Masking position 5 Map Score: 1.21727 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 46 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 15 ********** No masking Map Score: -7.23089e-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