AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_mjan_reg_300.orf -o047_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 Purged sequences: RMJ01128 21 M_jannaschii_chromosome RMJ02772 29 M_jannaschii_chromosome Input sequences: #1 RMJ15817 120 M_jannaschii_chromosome #2 RMJ08873 166 M_jannaschii_chromosome #3 RMJ09513 108 M_jannaschii_chromosome #4 RMJ07037 64 M_jannaschii_chromosome #5 RMJ03862 33 M_jannaschii_chromosome #6 RMJ14786 89 M_jannaschii_chromosome #7 RMJ06121 273 M_jannaschii_chromosome #8 RMJ14683 177 M_jannaschii_chromosome #9 RMJ10436 145 M_jannaschii_chromosome #10 RMJ15659 136 M_jannaschii_chromosome Motif number 1 AAATTAAGAAAATTTAAAATAATGTTAA 1 9 1 AAAATTTAAA 0.932759 -112 AAATATTGTGAATTTTATAAAGTTATGAAA 1 57 1 AATTTTATAA 0.643129 -64 ATCTATAATGAATTATATAAATTAATGCTT 2 33 1 AATTATATAA 0.659575 -134 AGATAAAGAAAAAGCTAAAAAATACTCCAA 2 74 1 AAAGCTAAAA 0.807864 -93 ATGGAAAGTTAGTAATTAAAGCTGATTAG 2 148 1 AGTAATTAAA 0.733354 -19 GGGGATAATCATAATTAAAAAACTAATTGA 3 31 1 ATAATTAAAA 0.825961 -78 GAAGATTTTAAAATATTAAAAATTATAGAG 3 83 1 AAATATTAAA 0.941025 -26 TTTATAGCAAAAAAATTAAATAATATGATT 4 27 1 AAAAATTAAA 0.937162 -38 AATTTCACCAAATCTTTAAATCATATTAT 4 46 0 AAATCTTTAA 0.787119 -19 CAAAAGGTTAAAAAATTAAAGAAAT 5 6 0 AAAAATTAAA 0.937162 -28 ATTAAACTGTATTTCTAAAAACACAATAAA 6 11 1 ATTTCTAAAA 0.630187 -79 TTAGAGGGACAGATTTTAAATAAAAGAACA 7 18 1 AGATTTTAAA 0.860876 -256 AATTAGTGTTAATTTTAAAAAAACAAACAT 7 112 1 AATTTTAAAA 0.845888 -162 TACTGCAAAAAATAATAAAAAATGTTTGTT 7 133 0 AATAATAAAA 0.846523 -141 ATTAGGATTGAGATATAAAACATTACTACT 7 159 0 AGATATAAAA 0.847624 -115 CAATGTTGGTATTTTTAAAAAGATTTTCCA 7 202 0 ATTTTTAAAA 0.691907 -72 ACATTGATTTAGAATTAAAAGATGCATTTT 7 226 1 AGAATTAAAA 0.828651 -48 TATATTAAAAATATATTAAAAATGCATCTT 7 244 0 ATATATTAAA 0.867119 -30 TGAAAGATAATATATTAAAAATATATTAA 7 255 0 ATATATTAAA 0.867119 -19 AACTATATTGAATACTTAAACTATAAATAT 8 18 1 AATACTTAAA 0.823184 -160 ATGTAATAATAAAGTTTAAAGTTAGTGACA 8 119 0 AAAGTTTAAA 0.868888 -59 TAAGTTTTTTAAAATTAAAAATGAATGTAA 8 143 0 AAAATTAAAA 0.920629 -35 TTAATTTTAAAAAACTTAAAACAGAGTGAA 8 155 1 AAAACTTAAA 0.913239 -23 AAAACATATCAAAAATTTAATTGGGTATTG 9 39 0 AAAAATTTAA 0.830414 -107 ATTAAATTTTAAATATTAAACTTGAATAGT 9 92 1 AAATATTAAA 0.941025 -54 TTAAACTTGAATAGTTATAATTTATAGTTA 9 107 1 ATAGTTATAA 0.426738 -39 TTATTAAATTATAACTATAAATTATAACTA 9 118 0 ATAACTATAA 0.541777 -28 GTTCTAAATTATTAAATTATAACTAT 9 130 0 AATTATTAAA 0.875891 -16 AAAATAAGGTATATTTAAAAAT 10 3 0 ATATTTAAAA 0.835459 -134 TGTGTTAGCTAATATTAAAAAATAAGGTAT 10 21 0 AATATTAAAA 0.836875 -116 AAATATTTGCAAAATTTTAATTTAAATATC 10 68 1 AAAATTTTAA 0.819968 -69 ATCTTTATTAAGATATTTAAATTAAAATTT 10 79 0 AGATATTTAA 0.685957 -58 ATATCTTAATAAAGATTAAATCAATTTATT 10 93 1 AAAGATTAAA 0.876922 -44 ********** Masking position 6 Map Score: 38.9838 Number of sites scoring better than the average of aligned sites = 5056 Number in coding regions = 3660 Number in noncoding regions = 1396 Number of orfs with sites within 600 bp upstream = 693 Fraction of orfs with sites within 600 bp upstream = 0.111307 Motif number 2 CTTTAACATTATTTTAAATTTTCTTAATTT 1 6 0 ATTTATTTTT 0.479892 -115 ATGCATCAACTTTTTCTTTAACATTATTTTAAATT 1 21 0 TTTTTTACTT 0.74328 -100 CTTATGTTATTTTTCATAACTTTATAAAATTCACA 1 63 0 TTTTTATTAT 0.902712 -58 CGGTTTTGGTGAAATCATGAGTATCTAT 2 4 1 TTTTTAATAT 0.769566 -163 CAAGCATTAATTTATATAATTCATTATAGATACTC 2 29 0 TTTATATCTT 0.441132 -138 ATTTTTTAGCTTTTTCTTTATCTTTAACTTATTCA 2 62 0 TTTTTTTCTT 0.889432 -105 TCAACTATTATTTTGGAGTATTTTTTAGCTTTTTC 2 81 0 TTTTATTTTT 0.909987 -86 CTTCAATTAGTTTTTTAATTATGATTATCCCCTCC 3 28 0 TTTTATATAT 0.649138 -81 ATTTTTAATATTTTAAAATCTTCATCCTGTGCCTG 3 71 0 TTTTATTTAT 0.837143 -38 CTTTAAATCATATTATTTAATTTTTTTGCTATAAA 4 27 0 TATTTATTTT 0.771385 -38 ATTTCTTTAATTTTTTAACCTTTTG 5 1 1 ATTTTATTTT 0.624839 -33 TATTTATGTTTTTTATTGTGTTTTTAGAAATACAG 6 17 0 TTTTTTTTTT 0.944362 -73 CTCTTATTGTTTTTATTGAATTGATAATTAGGTAT 6 49 0 TTTTTATTAT 0.902712 -41 CAAAAGAAACTATTGTTCTTTTATTTAAAATCTGT 7 26 0 TATTTTTTTT 0.758359 -248 CAATAGTTTCTTTTGTTATATCGTTGGGCATAATT 7 46 1 TTTTTTTCTT 0.889432 -228 TTGGGCATAATTTTATACATATTATCAAAAATTGA 7 69 1 TTTTAAATAT 0.665453 -205 AAACAAACATTTTTTATTATTTTTTGCAGTAGTAA 7 132 1 TTTTTATTTT 0.948048 -142 ATGTTGGTATTTTTAAAAAGATTTTCCAACGATAA 7 195 0 TTTTAAATTT 0.796417 -79 AAAGATGCATTTTTAATATATTTTTAATATATTAT 7 243 1 TTTTTTTTTT 0.944362 -31 TGGATTATTCTTTTATAAAGTCGTTAAAGAGTGTA 8 47 1 TTTTAATCTT 0.83743 -131 TGATATTCCTTTTTTATTAGTTCTTTACTACACTC 8 75 0 TTTTTATTTT 0.948048 -103 TAAACTTTATTATTACATTCATTTTTAATTTTAAA 8 131 1 TATTATATTT 0.402193 -47 CCAATTAAATTTTTGATATGTTTTTGATTTGATGT 9 45 1 TTTTTTTTTT 0.944362 -101 TCAAGTTTAATATTTAAAATTTAATTAAGGTCTTA 9 82 0 TATTAATTAT 0.5054 -64 ATTTTTAAATATACCTTATTTTTTAAT 10 3 1 TTTTAAACTT 0.649618 -134 AAAATTTTAATTTAAATATCTTAATAAAGATTAAA 10 78 1 TTTATTTTAT 0.440386 -59 CTAAGGTTATTTATAATAAATTGATTTAATCTTTA 10 102 0 TTATTATTAT 0.316006 -35 **** * * ** ** Masking position 15 Map Score: 34.0254 Number of sites scoring better than the average of aligned sites = 3705 Number in coding regions = 2833 Number in noncoding regions = 872 Number of orfs with sites within 600 bp upstream = 494 Fraction of orfs with sites within 600 bp upstream = 0.0793447 Motif number 3 CGGTTTTGGTGAAATCATGAGTATC 2 6 1 TTGGTGAAAT 0.971837 -161 AGAAGGGTCATTGGAGATTAAAGATGGAAA 2 125 1 TTGGAGATTA 0.879683 -42 ATTTAAAGATTTGGTGAAATT 4 54 1 TTGGTGAAAT 0.971837 -11 TTTTAACCTTTTGGTGATAAT 5 23 1 TTGGTGATAA 0.991744 -11 AAGAGTGTTATTGGTGATAAA 6 79 1 TTGGTGATAA 0.991744 -11 TAAAATCTTGTTGGTGATAAAA 9 3 0 TTGGTGATAA 0.991744 -143 ********** Masking position 7 Map Score: 10.234 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 38 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 GTTATGAAAAATAACATAAGGATACATAACCT 1 78 1 ATAACAAAGA 0.95222 -43 AAATGGTTTTATAGCAAAAAAATTAAATAATA 4 20 1 ATAGCAAAAA 0.822748 -45 TGTATTTCTAAAAACACAATAAAAAACATAAA 6 18 1 AAAACAAAAA 0.976693 -72 AACACAATAAAAAACATAAATACCTAATTATC 6 30 1 AAAACAAATA 0.920941 -60 CAATTCAATAAAAACAATAAGAGTGTTATTGG 6 61 1 AAAACATAGA 0.831228 -29 CAGATTTTAAATAAAAGAACAATAGTTTCTTT 7 27 1 ATAAAAAAAA 0.918491 -247 GCCCAACGATATAACAAAAGAAACTATTGTTC 7 43 0 ATAACAAAAA 0.969531 -231 GTTAATTTTAAAAAAACAAACATTTTTTATTA 7 119 1 AAAAAAAACA 0.776152 -155 TTACTACTGCAAAAAATAATAAAAAATGTTTG 7 135 0 AAAAAAAAAA 0.936869 -139 ATTGAGATATAAAACATTACTACTGCAAAAAA 7 151 0 AAAACATATA 0.686119 -123 TAACGACTTTATAAAAGAATAATCCATATTTA 8 41 0 ATAAAAAAAA 0.918491 -137 TAAAGAACTAATAAAAAAGGAATATCATAATC 8 83 1 ATAAAAAGAA 0.780705 -95 TAAAAAACTTAAAACAGAGTGAAACA 8 162 1 AAAACAAGGA 0.89238 -16 CATCAAATCAAAAACATATCAAAAATTTAATT 9 47 0 AAAACAATAA 0.829169 -99 ****** ** ** Masking position 6 Map Score: 12.9797 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 532 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 5 AAATAATGTTAAAGAAAAAGTTGATGCATGAAA 1 27 1 AAAGAAATTG 0.944306 -94 TGAATTATATAAATTAATGCTTGAATAAGTTAA 2 41 1 AAATAATTTG 0.980504 -126 AAAATACTCCAAAATAATAGTTGAGTTAATAGA 2 92 1 AAAAAATTTG 0.96435 -75 AATCATAATTAAAAAACTAATTGAAGCATTAAG 3 37 1 AAAAACTTTG 0.822437 -72 CGATATAACAAAAGAAACTATTGTTCTTTTATT 7 36 0 AAAGAACTTG 0.90863 -238 TAATTTATCTAAATCAATTTTTGATAATATGTA 7 84 0 AAATAATTTG 0.980682 -190 CAAAAAATAATAAAAAATGTTTGTTTTTTTAAA 7 125 0 TAAAAATTTG 0.757967 -149 ATCCTAATTAAAAGTTATCGTTGGAAAATCTTT 7 181 1 AAAGTATTTG 0.831378 -93 TTTTAATTCTAAATCAATGTTGGTATTTTTAAA 7 213 0 AAATAATTGG 0.898571 -61 GGTATTGCGGATATAAAATCTTGTTGGTGATAA 9 13 0 ATATAAATTG 0.704235 -133 CGCAATACCCAATTAAATTTTTGATATGTTTTT 9 37 1 AATTAATTTG 0.920397 -109 AAGATATTTAAATTAAAATTTTGCAAATATTTA 10 67 0 AATTAAATTG 0.821617 -70 **** *** *** Masking position 11 Map Score: 7.99325 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 397 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 TAAGGATACATAACCTACAAACCTTAAGGG 1 94 1 TAACCTACAA 0.435076 -27 ATTCAAGCATTAATTTATATAATTCATTAT 2 37 0 TAATTTATAT 0.707109 -130 GACAGCTCTATAATTTTTAATATTTTAAAA 3 88 0 TAATTTTTAA 0.848395 -21 ATTAAACTGTATTTCTAAAAAC 6 3 1 TAAACTGTAT 0.627452 -87 TAAATTAGTGTTAATTTTAAAAAAACAAAC 7 110 1 TTAATTTTAA 0.688233 -164 TTTCCAACGATAACTTTTAATTAGGATTGA 7 178 0 TAACTTTTAA 0.822691 -96 TGTACTAAACTATATTGAATACTTA 8 6 1 TAAACTATAT 0.878175 -172 ATTGAATACTTAAACTATAAATATGGATTA 8 24 1 TAAACTATAA 0.943531 -154 TCACTAACTTTAAACTTTATTATTACATTC 8 121 1 TAAACTTTAT 0.878175 -57 ACATTCATTTTTAATTTTAAAAAACTTAAA 8 145 1 TTAATTTTAA 0.688233 -33 AGACCTTAATTAAATTTTAAATATTAAACT 9 84 1 TAAATTTTAA 0.936233 -62 TTTTAAATATTAAACTTGAATAGTTATAAT 9 98 1 TAAACTTGAA 0.817725 -48 ATTATAACTATAAATTATAACTATTCAAGT 9 111 0 TAAATTATAA 0.936245 -35 TCTAAATTATTAAATTATAACTATAAATTA 9 124 0 TAAATTATAA 0.936245 -22 TATAATTTAATAATTTAGAAC 9 135 1 TAATTTAGAA 0.600402 -11 TTAAGATATTTAAATTAAAATTTTGCAAAT 10 72 0 TAAATTAAAA 0.591088 -65 TAAATTGATTTAATCTTTATTAAGATATTT 10 91 0 TAATCTTTAT 0.73312 -46 ********** Masking position 6 Map Score: 16.0221 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 510 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 7 ATTAAGAAAATTTAAAATAATGTTAAAGAAA 1 13 1 TTTAAAATAT 0.657109 -108 TTGTGAATTTTATAAAGTTATGAAAAATAAC 1 62 1 TATAAAGTAT 0.855955 -59 TAATGAATTATATAAATTAATGCTTGAATAA 2 38 1 TATAAATTAT 0.923978 -129 TAAAAAATACTCCAAAATAATAGTTGAGTTA 2 89 1 TCCAAAATAT 0.810791 -78 ATTTTTTTGCTATAAAACCATTTCTAAACTT 4 12 0 TATAAAACAT 0.908964 -53 AATCTGTCCCTCTAAGTCCATC 7 2 0 TCTAAGTCAT 0.778737 -272 TGATAATATGTATAAAATTATGCCCAACGAT 7 65 0 TATAAAATAT 0.923993 -209 CACTAATTTATCTAAATCAATTTTTGATAAT 7 89 0 TCTAAATCAT 0.933754 -185 AGGATTGAGATATAAAACATTACTACTGCAA 7 155 0 TATAAAACTT 0.712895 -119 ATCTTTTAATTCTAAATCAATGTTGGTATTT 7 218 0 TCTAAATCAT 0.933754 -56 AAAAGAATAATCCATATTTATAGTTTAAGTA 8 30 0 TCCATATTAT 0.268289 -148 TTAACGACTTTATAAAAGAATAATCCATATT 8 43 0 TATAAAAGAT 0.695989 -135 GTATTGCGGATATAAAATCTTGTTGGTGATA 9 14 0 TATAAAATTT 0.751442 -132 GTTCTAAATTATTAAATTATAAC 9 133 0 TCTAAATTTT 0.810159 -13 GGTTATTTATAATAAATTGATTTAATCTTTA 10 102 0 AATAAATTAT 0.509738 -35 TTTAAAACCTCTAAGGTTATTTATAATAAA 10 117 0 TCTAAGGTAT 0.676856 -20 ******** ** Masking position 4 Map Score: 10.1826 Number of sites scoring better than the average of aligned sites = 660 Number in coding regions = 522 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 8 ********** No masking Map Score: 1.48036e-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 9 ********** No masking Map Score: 1.48036e-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 10 ********** No masking Map Score: 1.48036e-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