AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_tpal_reg_100.orf -o03010_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0060 105 ribosomal protein L9 (rplI) #2 TP0061 116 ribosomal protein S18 (rpsR) #3 TP0063 141 ribosomal protein S6 (rpsF) #4 TP0185 147 signal peptidase I (sip) #5 TP0186 54 oxygen-independent coproporphyrinogen III oxidase, putative #6 TP0187 63 translation elongation factor TU (tuf) #7 TP0188 71 ribosomal protein S10 (rpsJ) #8 TP0189 46 ribosomal protein L3 (rplC) #9 TP0192 55 ribosomal protein L2 (rplB) #10 TP0207 187 ribosomal protein L15 (rplO) #11 TP0234 234 ribosomal protein L33 (rpmG) #12 TP0237 106 ribosomal protein L11 (rplK) #13 TP0240 108 ribosomal protein L7/L12 (rplL) #14 TP0243 102 ribosomal protein S12 (rpsL) #15 TP0244 21 ribosomal protein S7 #16 TP0255 118 ribosomal protein L31 (rpmE) #17 TP0278 127 T. pallidum predicted coding region TP0278 #18 TP0279 45 ribosomal protein S1 (rpsA) #19 TP0306 164 ribosomal protein S4 #20 TP0362 75 ribosomal protein L28 (rpmB) #21 TP0607 249 T. pallidum predicted coding region TP0607 #22 TP0743 30 ribosomal protein L27 (rpl27) #23 TP0745 106 ribosomal protein L21 (rplU) #24 TP0758 118 ribosomal protein S21 (rpsU) #25 TP0807 128 ribosomal protein L32 (rpmF) #26 TP0848 32 ribosomal protein L20 (rplT) #27 TP0849 52 ribosomal protein L35 (rpmI) #28 TP0850 162 translation initiation factor 3 (infC) #29 TP0891 175 translation initiation factor 2 (infB) #30 TP0907 62 conserved hypothetical protein #31 TP0951 119 ribosomal protein L34 (rpmH) #32 TP1025 300 ribosomal protein L13 (rplM) Motif number 1 CTCTGCCTATGCACAGCAACTTCTACTGAAC 1 39 0 GCACAGCAAT 0.482533 -67 GATTTACGCTACGCTGGCGTCTCGCCGCGCG 3 46 1 ACGCTGGCGC 0.745577 -96 CGCGCGTTCTGCGCACGCTACTCCTCCTTGT 3 71 1 GCGCACGCTC 0.980722 -71 GCTGCACTAGACTCACCCGACAAGGAGGAGT 3 90 0 ACTCACCCGC 0.707363 -52 GCCATGAGGGGCACAGGAACCCATCTCATTG 4 43 0 GCACAGGAAC 0.849965 -105 GCCCCTCATGGCGCCGGATGCTACCGGATAG 4 62 1 GCGCCGGATC 0.95177 -86 TGTGTAGGCGCCGCATTTGTGGTGCGTG 5 8 1 GCGCCGCATT 0.76496 -47 ACAGCACGATGCGCAGCACGCACCACAAATG 5 24 0 GCGCAGCACC 0.647174 -31 AACACACTCCGCGCCGCAAACGC 7 3 0 GCGCCGCAAC 0.939711 -69 CAGCCTAAAACCGCACCCACCTTGCAAAATA 7 40 0 CCGCACCCAC 0.964854 -32 TACGCAGCTACCGCAGCTTACCG 9 3 0 CCGCAGCTTC 0.881702 -53 TTCGGTCACCGCTCTGGCACCTTACGCAGCT 9 25 0 GCTCTGGCAC 0.72604 -31 CCAGCGTTATACGCACCCTCTTTGTCATGC 10 10 0 ACGCACCCTT 0.682872 -178 ACCGTCCGACGCACCGGCTCCCTCTGACCGA 10 53 0 GCACCGGCTC 0.977138 -135 CCTAACTCCTCCACCCGCACCAGGTGCGAAA 10 164 0 CCACCCGCAC 0.938767 -24 CCATGGTTGCGCTCTGCCAACTGAGCTACAG 11 148 0 GCTCTGCCAC 0.792346 -87 AAACAACAAAACACCCGAAACCAACGCGTAA 12 62 0 ACACCCGAAC 0.633419 -45 GCCGCACACAGCACACGCGGCTAGGATACTC 14 36 0 GCACACGCGC 0.94775 -67 GGTGTAACCGACACACGTTCCAGTCTCCTTA 16 12 0 ACACACGTTC 0.546896 -107 AAGGTTACATCCACCCTCTTCCAGAAGGCTC 16 53 0 CCACCCTCTC 0.685484 -66 CGCTTATTTGCCACAGTCTTCCGAGGAAGAC 17 17 0 CCACAGTCTC 0.647576 -111 GATCACCAGCGCACTCCCTTCCCCACATGGA 17 52 0 GCACTCCCTC 0.948792 -76 GGTTTTGTTTGCGCGCGCTCCGATGCGGTTG 19 82 1 GCGCGCGCTC 0.822539 -83 GTTCATGTCTCCGCCGCCGATGATAAAGAAA 20 54 0 CCGCCGCCGT 0.803216 -22 CAGGGGCCGTCCGCCCGCTCTCCTTCAGCAG 21 12 0 CCGCCCGCTT 0.831509 -238 CCCCGCGCCTACGCTCCTTCCAGTCAAGCTG 21 49 0 ACGCTCCTTC 0.510936 -201 GGATTTGAACCCACCGCCTTTGGCTCCGGAG 21 115 1 CCACCGCCTT 0.828086 -135 ACCGCCTTTGGCTCCGGAGGCCAACGCTCTA 21 127 1 GCTCCGGAGC 0.717305 -123 CTTCCCAGGCCCGCAGCAGGTTACAGAGCAG 21 178 0 CCGCAGCAGT 0.496968 -72 GCACAGAGACGCTCACCAAGCACGAACGACA 23 13 0 GCTCACCAAC 0.737473 -94 AACCACGCAGACGCAGCCATCCCTCGCACCG 23 54 0 ACGCAGCCAC 0.91509 -53 TCCCCTGCACGCACACCCTACGTGTC 24 6 0 GCACACCCTC 0.979387 -113 TCTTCCGAAAGCACTCCTGCCTCCCCTGCAC 24 27 0 GCACTCCTGC 0.591604 -92 CCTGAAAAAAACACAGCCTACCAGGGGTAGG 24 89 0 ACACAGCCTC 0.927371 -30 AGGGTGCGCTCCTTTCTGCGCAAGAA 25 113 0 GCGCTCCTTC 0.802478 -16 ACCGGTGAACGCACAGCCTGCTCACTAGCAA 29 58 0 GCACAGCCTC 0.980252 -118 AACCCACCACACACCGCCTGCAACAAGGCCG 30 30 0 ACACCGCCTC 0.940564 -33 GATCTTGACGCCTCCGGTACCTTTGGTACAG 31 60 1 CCTCCGGTAC 0.450621 -60 CGATTTCTCCTCCCCCTGCTAAGAACACG 31 101 0 CCTCCCCCTC 0.935529 -19 ACCGCGCCCACCACCGCCTCCCGCGCAAAAT 32 52 0 CCACCGCCTC 0.976816 -249 CCCATCAGCAGCACACCAACCAAAACCGCGC 32 76 0 GCACACCAAC 0.886427 -225 GCGAAAACCGCCGCTCCCATCAGCAGCACAC 32 91 0 CCGCTCCCAC 0.914568 -210 CATCCTGCGCCCACCCGAGACCACAACCGTA 32 141 0 CCACCCGAGC 0.822 -160 TCTCGGGTGGGCGCAGGATGCACTGCGGTTC 32 152 1 GCGCAGGATC 0.941 -149 GTGCGCCCACGCGCAAGCTACCGGAGCGTGT 32 262 1 GCGCAAGCTC 0.647978 -39 GCTCCTTTATCCACACGCTCCGGTAGCTTGC 32 274 0 CCACACGCTC 0.957609 -27 ********* * Masking position 4 Map Score: 50.8391 Number of sites scoring better than the average of aligned sites = 3658 Number in coding regions = 3333 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 2 GTCTCTTTCCCCACAAGGAGCATGCAT 2 5 1 CTCCCCCAAG 0.924934 -112 TAAAACCGCACCCACCTTGCAAAATAACTCCAA 7 33 0 CCCCTTCAAA 0.652395 -39 CACCTACCTCTTCCGTATCGCAACG 8 32 0 CCCCTCTCCG 0.937621 -15 CCTAACTCCTCCACCCGCACCAGGTGCGAAACA 10 162 0 CCCCGCCCAG 0.976417 -26 AGCCAACCAGCCTGCCCCAGAAAGAAAGGCGCG 11 15 0 CCCCCCGAAA 0.933813 -220 TGTATAACGCCTCACCTCACACATCAAGCACGA 11 67 0 CTCCTCCACA 0.758676 -168 ACCACCCCTCCTCACATCCACAGACGGA 11 217 0 CCCCTCCATC 0.839459 -18 CGCATGATTGCCTGCCGCTTACGCGTTGGTTTC 12 44 1 CCCCGCTACG 0.975635 -63 CCGCCTAACACATACCCCGTAACTAAGTTACAA 13 18 0 CACCCCTAAC 0.451705 -91 CCCCAGAAGCCTGACCGCCTAACACATACCCCG 13 32 0 CTCCGCTAAC 0.701699 -77 CACCGTAAACCTTGCCGCACACAGCACACGCGG 14 47 0 CTCCGCCACA 0.862822 -56 ACCAACTCCTCTCCCCAGCCC 15 1 0 CTCCCCGCCC 0.754347 -21 GTCGGTTACACCCGGCGTGTACGAGCCTTCTGG 16 31 1 CCGCGTTACG 0.485698 -88 AAGGTTACATCCACCCTCTTCCAGAAGGCTCGT 16 51 0 CCCCTCTCCA 0.888791 -68 CTACAGCGCGCCGCGCCCTTAAAAAGGTTACAT 16 74 0 CCGCCCTAAA 0.803258 -45 CAGCGCACTCCCTTCCCCACATGGACTGCCGCT 17 44 0 CCCCCCCATG 0.9609 -84 CAAACAAAACCCGCACGCCCACACAAAGCTCTT 19 60 0 CCACGCCACA 0.574853 -105 AAACGGATATCCACTCCCTCAAACCTGCAACCG 19 107 0 CCTCCCCAAA 0.71293 -58 CATGCCGCATCCCTCCCCACAAAACGGATATCC 19 128 0 CCCCCCCAAA 0.980178 -37 CAGGGGCCGTCCGCCCGCTCTCCTTCAGCAGG 21 10 0 CCCCGCCTCC 0.775538 -240 TAAACGGGCGCCCCGCGCCTACGCTCCTTCCAG 21 57 0 CCGCGCTACG 0.880556 -193 CCCGCATCTTCCATCCTCTTACCCACGTAAACG 21 84 0 CCCCTCTACC 0.934948 -166 AATACGGTTGCCCGCCTCTTCTGTGGACCTTCC 21 204 0 CCCCTCTCTG 0.710357 -46 GCAGACGCAGCCATCCCTCGCACCGTTAGTGGA 23 46 0 CCCCCTGCAC 0.647047 -61 AGCACTCCTGCCTCCCCTGCACGCACACCCTAC 24 16 0 CCCCCTCACG 0.950726 -103 CGACCCTCCCCTGAAAAAAACACAGC 24 103 0 CCCCCCGAAA 0.933813 -16 CCACGCTCCTCCGTCCTCTCACGCTTGCCAC 26 9 0 CCCCTCCACG 0.978083 -24 CAGGAAATCACCATCCCCATCACAACCCCAATT 28 63 0 CCCCCCTCAC 0.957436 -100 ACGTCAACATCCGCCCGTGTACGAGAGGTAGTT 29 101 0 CCCCGTTACG 0.836855 -75 CTATCCATAACCCACCACACACCGCCTGCAACA 30 36 0 CCCCACCACC 0.834765 -27 CGATTTCTCCTCCCCCTGCTAAGAACACGAG 31 99 0 CCCCCCGCTA 0.736843 -21 CCCACCACCGCCTCCCGCGCAAAATCTCCCGAT 32 44 0 CCCCGCCAAA 0.96701 -257 CCAACCAAAACCGCGCCCACCACCGCCTCCCGC 32 59 0 CCGCCCCCAC 0.902288 -242 GCGAAAACCGCCGCTCCCATCAGCAGCACACCA 32 89 0 CCTCCCTCAG 0.611377 -212 GCAGTGCATCCTGCGCCCACCCGAGACCACAAC 32 145 0 CTGCCCCCCG 0.733991 -156 CGCATGTTTGCCACCCCTACAAGGAGAGATATA 32 224 0 CCCCCTCAAG 0.922562 -77 ** **** **** Masking position 6 Map Score: 48.6966 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1151 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 CACCCGACAAGGAGGAGTAGCGTGCGCAGAAC 3 76 0 GGGGAGAGCG 0.96436 -66 TGCCGTGTCTGGGAGGGACGCCGTTTT 4 131 1 GGAGGGCGCC 0.810864 -17 GGAGAAAGACGGGAGTCCTGCCGTCTTGGGGA 10 120 1 GGAGTCTGCC 0.807339 -68 CTGCCGTCTTGGGGATGGTGCGAGCTGTTTCG 10 137 1 GGGATGTGCG 0.957188 -51 GCGCAACCATGGTAAGGTTGAGGTCAGCGGTT 11 167 1 GGAAGGTGAG 0.913079 -68 GTAAGCGGCAGGCAATCATGCGCATTGCAACA 12 34 0 GGAATCTGCG 0.956062 -73 GATTTTTTTGGGGAAGTGAGCGAAAAGA 14 85 1 GGAAGTAGCG 0.932661 -18 CTGTAGAATGGGGAAAGGAGCGATTCAG 16 101 1 GGAAAGAGCG 0.972818 -18 AGTCTTCCGAGGAAGACGAGCGC 17 2 0 GGAGACAGCG 0.963537 -126 GGAAGACTGTGGCAAATAAGCGGCAGTCCATG 17 26 1 GGAAATAGCG 0.885771 -102 AGTCCATGTGGGGAAGGGAGTGCGCTGGTGAT 17 50 1 GGAAGGAGTG 0.825035 -78 CCGTTTTGTGGGGAGGGATGCGGCATGCAGGG 19 134 1 GGAGGGTGCG 0.986795 -31 GCGGCATGCAGGGAGTTATGCG 19 153 1 GGAGTTTGCG 0.860077 -12 CCTGCTGAAGGAGAGCGGGCGGACGGCCCCT 21 10 1 GGGAGCGGCG 0.875074 -240 AACGGTGCGAGGGATGGCTGCGTCTGCGTGGT 23 52 1 GGATGGTGCG 0.867181 -55 GCCTACCAGGGGTAGGCTAGCGCAAAAGACGT 24 73 0 GGAGGCAGCG 0.979238 -46 CATGCACAATGGCGAGCCTGTGTGTTGCGGTC 25 62 1 GGGAGCTGTG 0.765551 -67 GTGGCAAGCGTGAGAGGACGGAGG 26 3 1 GGAAGCTGAG 0.887874 -30 AGCGTGAGAGGACGGAGGAGCGTGGT 26 17 1 GAGGAGAGCG 0.47316 -16 GCCGCAAGACGGAAAAGGAGCCG 30 2 0 GGAAAGAGCC 0.87619 -61 CGGCTCCTCGGGAGGAGCCGCGTCAGCACCT 31 10 0 GGGGAGCGCG 0.903639 -110 CCCTACAAGAGGGGATCTTGACGCCTCCGGTA 31 47 1 GGGATCTGAC 0.314503 -73 GAGACGATCGGGAGATTTTGCGCGGGAGGCGG 32 38 1 GGGATTTGCG 0.828913 -263 TACTCCATAGGGGAAAGAAGAGCGAAAACCGC 32 111 0 GGAAAGAGAG 0.831271 -190 TTGTAGGGGTGGCAAACATGCGTGATCGTGCG 32 235 1 GGAAACTGCG 0.967856 -66 ** **** **** Masking position 10 Map Score: 32.8928 Number of sites scoring better than the average of aligned sites = 938 Number in coding regions = 861 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 CTGGTATACAGCGGTTGTTTTTCCTAGTTC 1 13 1 GCGGTTGTTT 0.918233 -93 AAAAAGCCTTGCGGTTCTTTGCAATGAGAT 4 22 1 GCGGTTCTTT 0.928795 -126 CAAGGTGGGTGCGGTTTTAGGCTGATGGAG 7 47 1 GCGGTTTTAG 0.750193 -25 GTCGGACGGTTCGGTCTTTGGGTTTGAGGA 10 74 1 TCGGTCTTTG 0.638082 -114 GCGGTTGTTGTAACTTAGTT 13 1 1 GCGGTTGTTG 0.974407 -108 GCGCTCGTCTTCCTCGGAAG 17 1 1 GCGCTCGTCT 0.71765 -127 GAGACTGTTTGCGCTCCTCGTCTGTTGTCT 17 83 0 GCGCTCCTCG 0.909169 -45 ACACTCATGGGCGGATGATGGA 17 116 1 GCGGATGATG 0.662805 -12 GTGTGGGCGTGCGGGTTTTGTTTGCGCGCG 19 69 1 GCGGGTTTTG 0.943716 -96 GCGCGCACGCGCGCTTTATGGCATA 20 6 0 GCGCTTTATG 0.696987 -70 AAGCGCGCGTGCGCGCCTTTACTCTGGCGG 20 20 1 GCGCGCCTTT 0.759536 -56 CTTTACTCTGGCGGACCTTTTCTTTATCAT 20 36 1 GCGGACCTTT 0.83893 -40 GATGGAAGATGCGGGATTTGAACCCACCGC 21 102 1 GCGGGATTTG 0.773989 -148 GTAACCTGCTGCGGGCCTGGGAAGGTCCAC 21 185 1 GCGGGCCTGG 0.867322 -65 CCTGTGTGTTGCGGTCGACGGTCCGAAGCG 25 78 1 GCGGTCGACG 0.794385 -51 AGGGTGCGCTCCTTTCTGCGCAAGA 25 114 0 GCGCTCCTTT 0.868624 -15 TCGTACACGGGCGGATGTTGACGTAAAGGA 29 110 1 GCGGATGTTG 0.91979 -66 TTTCTTTGCGCGCACTTTGATTGTCTTCT 29 157 0 GCGCACTTTG 0.842722 -19 GGTGGTGGGCGCGGTTTTGGTTGGTGTGCT 32 68 1 GCGGTTTTGG 0.891201 -233 GATGGGAGCGGCGGTTTTCGCTCTTCTTTC 32 101 1 GCGGTTTTCG 0.940019 -200 AGGATGCACTGCGGTTCTTGCGTGGTGCTG 32 166 1 GCGGTTCTTG 0.977888 -135 GCGCCAGTCGGCGGTATTTTTGCTGGTTTT 32 195 1 GCGGTATTTT 0.678904 -106 ********** Masking position 3 Map Score: 25.6684 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 428 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 AACAACCGCTGTATACCAGCG 1 1 0 GTTACCAGCG 0.859151 -105 TTTTATTCCTGCGTAGGAGGGGACAAAACGT 1 85 1 GCTAGGAGGG 0.980716 -21 CTACGCTGGCGTCTCGCCGCGCGTTCTGCGC 3 54 1 GTTCGCCGCG 0.848641 -88 AGGCTGCCGTGTCTGGGAGGGACGCCGTTTT 4 127 1 GTTGGGAGGG 0.93141 -21 TACCTCTTCCGTATCGCAACGCACAGACAAA 8 22 0 GTTCGCAACG 0.748171 -25 GGGAGCCGGTGCGTCGGACGGTTCGGTCTTT 10 62 1 GCTCGGACGG 0.930867 -126 TTGGCTGCCTGTTTAGGGAGGTGTTTCGTGC 11 42 1 GTTAGGGAGG 0.585648 -193 ATGCGGGCCGGCCTCCGGGCGGCTCGGGGAG 11 100 1 GCTCCGGGCG 0.915035 -135 ACAGACGGAAGCTTCCGAGCGGGATTGAACC 11 195 0 GCTCCGAGCG 0.973728 -40 ACCTGCAACCGCATCGGAGCGCGCGCAAACA 19 87 0 GCTCGGAGCG 0.986498 -78 ACTGGAAGGAGCGTAGGCGCGGGGCGCCCGT 21 56 1 GCTAGGCGCG 0.929526 -194 CGGGGCGCCCGTTTACGTGGGTAAGAGGATG 21 75 1 GTTACGTGGG 0.751042 -175 CCTGCTGCGGGCCTGGGAAGGTCCACAGAAG 21 189 1 GCTGGGAAGG 0.769791 -61 GTGGTTAGAGGTGTAGCTGGGTGTTTTTTGG 23 79 1 GTTAGCTGGG 0.716665 -28 AAAAAACACAGCCTACCAGGGGTAGGCTAGC 24 84 0 GCTACCAGGG 0.916686 -35 AGAACTGTGCGCTTCGGACCGTCGACCGCAA 25 86 0 GCTCGGACCG 0.923836 -43 TAGGCGTATTGTCTCGTAGGGTCATAGCTCT 29 12 0 GTTCGTAGGG 0.770089 -164 ACATCCGCCCGTGTACGAGAGGTAGTTTGAC 29 97 0 GTTACGAGAG 0.584116 -79 ** ******** Masking position 4 Map Score: 16.5362 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 280 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GTGCATAGGCAGAGTGGCTCTGCGTGGACTTTTA 1 56 1 AGAGTCTGCG 0.806267 -50 ACGCCAGCGTAGCGTAAATCTGTGTGCCGCATCA 3 32 0 AGCGTCTGTG 0.967296 -110 AGTCTAGTGCAGCCTGATAAGGTGAGCCGTCCAT 3 108 1 AGCCTAGGTG 0.77011 -34 CAGACACGGCAGCCTAACACGGCGATAATCGAAT 4 108 0 AGCCTCGGCG 0.974841 -40 GTTTTGTCTGTGCGTTGCGATACGGAAGAGGTAG 8 20 1 TGCGTATACG 0.503145 -27 ACAAAGAGGGTGCGTATAACGCTGGTGAGGAGTA 10 16 1 TGCGTCGCTG 0.870685 -172 AGGGAGCCGGTGCGTCGGACGGTTCGGTCTTTGG 10 61 1 TGCGTCGGTT 0.50299 -127 CCCGCTCGGAAGCTTCCGTCTGTGGATGTGAGGA 11 203 1 AGCTTCTGTG 0.58009 -32 CAGGGTGGAGAGTGTTGCAATGCGCATGATTGCC 12 22 1 AGTGTATGCG 0.79462 -85 TTAGGCGGTCAGGCTTCTGGGGTGCTGTCTTCCT 13 43 1 AGGCTGGGTG 0.528777 -66 GAAAGAGCTTTGTGTGGGCGTGCGGGTTTTGTTT 19 58 1 TGTGTGTGCG 0.816356 -107 CGTTCATGTCTCCGCCGCCGATGATAAAGA 20 56 0 TGTCTCGCCG 0.580333 -20 TGGCCTCCGGAGCCAAAGGCGGTGGGTTCAAATC 21 116 0 AGCCACGGTG 0.602015 -134 ATTCGGATAGAGCGTTGGCCTCCGGAGCCAAAGG 21 131 0 AGCGTCTCCG 0.947743 -119 GTGCTTGGTGAGCGTCTCTGTGCGTTCCACTAAC 23 21 1 AGCGTGTGCG 0.96644 -86 GTGCGAGGGATGGCTGCGTCTGCGTGGTTAGAGG 23 56 1 TGGCTCTGCG 0.810956 -51 TGAACGGTCAAGGGTGCTCATGTGTGCTTCTTAG 25 20 0 AGGGTATGTG 0.587559 -109 GTGGCAAGCGTGAGAGGACGGAGGAGCGTG 26 7 1 AGCGTGGACG 0.754575 -26 CAACACGGGAAGTGTCTTTAGGCGTATTGTCTCG 29 27 0 AGTGTAGGCG 0.841442 -149 GAGCAGGCTGTGCGTTCACCGGTGACGTCTGGTC 29 66 1 TGCGTCGGTG 0.96692 -110 AAAATCATTCTGTGTCAAGCTGCG 32 1 0 TGTGTCTGCG 0.923977 -300 GGGAAAGAAGAGCGAAAACCGCCGCTCCCATCAG 32 99 0 AGCGACGCCG 0.720347 -202 CTGCGGTTCTTGCGTGGTGCTGCGCCAGTCGGCG 32 174 1 TGCGTCTGCG 0.982677 -127 GTGGCAAACATGCGTGATCGTGCGCCCACGCGCA 32 243 1 TGCGTGTGCG 0.954018 -58 ***** ***** Masking position 2 Map Score: 23.922 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 1008 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 CTTTCCCCACAAGGAGCATGCATAATGAATA 2 15 1 AAGGAGATGC 0.332189 -102 GGACCTCAGAAAGGAATTGGGCGTGCTAATT 2 74 1 AAGGAATGGG 0.769674 -43 ACCCGACAAGGAGGAGTAGCGTGCGCAGAAC 3 76 0 GAGGAGAGCG 0.869421 -66 GGTTCTTTGCAATGAGATGGGTTCCTGTGCC 4 34 1 AATGAGTGGG 0.664482 -114 TTGCGATACGGAAGAGGTAGGTG 8 34 1 GAAGAGTAGG 0.544806 -13 GCGGTGACCGAAGGAGACGGGG 9 44 1 AAGGAGCGGG 0.989976 -12 GATCGGTCAGAGGGAGCCGGTGCGTCGGACG 10 51 1 AGGGAGCGGT 0.719689 -137 GGTGCGGGTGGAGGAGTTAGGTTA 10 174 1 GAGGAGTAGG 0.949389 -14 TTTCGCATACAAGGAGAAGATAAT 13 95 1 AAGGAGAGAT 0.571639 -14 GGGCTGGGGAGAGGAGTTGGT 15 11 1 GAGGAGTGGT 0.932755 -11 GTAAGGAGACTGGAACGTGTGTC 16 3 1 AAGGAGCTGG 0.957719 -116 GAGAAGGACAGAGGAGTCTAGAAAAAATACC 19 19 0 GAGGAGCTAG 0.883923 -146 CCTGCTGAAGGAGAGCGGGCGGACGGCC 21 8 1 AAGGAGGCGG 0.741929 -242 GCTTGACTGGAAGGAGCGTAGGCGCGGGGCG 21 51 1 AAGGAGGTAG 0.638849 -199 TCCGGAGCCAAAGGCGGTGGGTTCAAATCCC 21 114 0 AAGGCGTGGG 0.927374 -136 AAGGTCCACAGAAGAGGCGGGCAACCGTATT 21 206 1 GAAGAGCGGG 0.903994 -44 TGTGCGTGCAGGGGAGGCAGGAGTGCTTTCG 24 22 1 GGGGAGCAGG 0.838407 -97 TGAGAGGACGGAGGAGCGTGGT 26 21 1 GAGGAGGTGG 0.921562 -12 ACATGTAAATAAGGAATTGGGGTTGTGATGG 28 49 1 AAGGAATGGG 0.769674 -114 TGTTGACGTAAAGGAGAAAAGACTCGTAATA 29 125 1 AAGGAGAAAG 0.643455 -51 GGCTCCTCGGGAGGAGCCGCGTCAGCACCT 31 10 0 GAGGAGCGCG 0.949498 -110 GGCTCCTCCCGAGGAGCCGGTTCCCCCTACA 31 23 1 GAGGAGCGGT 0.96158 -97 AAAGGTACCGGAGGCGTCAAGATCCCCTCTT 31 53 0 GAGGCGCAAG 0.639835 -67 TTTTGCGCGGGAGGCGGTGGTGGGCGCGGTT 32 53 1 GAGGCGTGGT 0.763927 -248 CGTGTGGATAAAGGAGCAGAGGG 32 288 1 AAGGAGAGAG 0.887243 -13 ****** **** Masking position 4 Map Score: 24.7198 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 510 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 ATAACTCCTATGGACGGCTCACCTTATCAG 3 121 0 TGGACGGCTC 0.812031 -21 GCCGGTGCGTCGGACGGTTCGGTCTTTGGG 10 66 1 CGGACGGTTC 0.830044 -122 CCAAGACGGCAGGACTCCCGTCTTTCTCCA 10 119 0 AGGACTCCCG 0.340157 -69 TTATACAATGCGGGCCGGCCTCCGGGCGGC 11 93 1 CGGGCCGGCC 0.948129 -142 GGCCGGCCTCCGGGCGGCTCGGGGAGTCCT 11 105 1 CGGGCGGCTC 0.95473 -130 CAACACAGACAGGACTCCCCGAGCCGCCCG 11 115 0 AGGACTCCCC 0.386372 -120 CTTCCCCACATGGACTGCCGCTTATTTGCC 17 36 0 TGGACTGCCG 0.718041 -92 AGAACACTCATGGGCGGATGATGGA 17 113 1 TGGGCGGATG 0.718798 -15 GAGCTTTGTGTGGGCGTGCGGGTTTTGTTT 19 62 1 TGGGCGTGCG 0.682067 -103 GTTTTGTTTGCGCGCGCTCCGATGCGGTTG 19 83 1 CGCGCGCTCC 0.649195 -82 ATAAAGCGCGCGTGCGCGCCTTTACTCTGG 20 17 1 CGTGCGCGCC 0.6076 -59 CGCCTTTACTCTGGCGGACCTTTTCTTTAT 20 33 1 CTGGCGGACC 0.602868 -43 GGAGAGCGGGCGGACGGCCCCTGAGTTGCC 21 20 1 CGGACGGCCC 0.977646 -230 CCCACGTAAACGGGCGCCCCGCGCCTACGC 21 66 0 CGGGCGCCCC 0.671541 -184 GCCTCTTCTGTGGACCTTCCCAGGCCCGCA 21 194 0 TGGACCTTCC 0.268377 -56 CTGTGCGCTTCGGACCGTCGACCGCAACAC 25 83 0 CGGACCGTCG 0.856036 -46 CTCTCGTACACGGGCGGATGTTGACGTAAA 29 107 1 CGGGCGGATG 0.864246 -69 TGGTACAGAGTGGACCCTCGTGTTCTTAGC 31 83 1 TGGACCCTCG 0.604717 -37 GTTGTGGTCTCGGGTGGGCGCAGGATGCAC 32 145 1 CGGGTGGGCG 0.6636 -156 AGCTTGCGCGTGGGCGCACGATCACGCATG 32 251 0 TGGGCGCACG 0.846408 -50 ********** Masking position 5 Map Score: 11.5625 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 659 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 GCGGTGACCGAAGGAGACGGGG 9 44 1 AAGGAGACGG 0.790423 -12 TCAATGGTGGAGAAAGACGGGAGTCCTGCC 10 112 1 AGAAAGACGG 0.89209 -76 TCGCACCATCCCCAAGACGGCAGGACTCCC 10 130 0 CCCAAGACGG 0.838772 -58 GAGCTACAGAAGCAACACAGACAGGACTCC 11 127 0 AGCAACACAG 0.860069 -108 ATAAACGGACAGGAAGACAGCACCCCAGAA 13 57 0 AGGAAGACAG 0.91585 -52 CAGTCTTCCGAGGAAGACGAGCGC 17 5 0 AGGAAGACGA 0.900969 -123 TCGTCTTCCTCGGAAGACTGTGGCAAATAA 17 15 1 CGGAAGACTG 0.813687 -113 AAGTACAGGGCAGAAAACGGAAG 18 4 0 CAGAAAACGG 0.774284 -42 CATCCCTCCCCACAAAACGGATATCCACTC 19 124 0 CACAAAACGG 0.774284 -41 CTCCCCTGAAAAAAACACAGCCTACCAGGG 24 94 0 AAAAACACAG 0.461599 -25 CCCTTTATCCAACAACACGAACTGCAGTTA 27 23 0 AACAACACGA 0.784464 -30 CACGCTAAAAAACAAGACTGGGCCCCAATC 28 131 0 AACAAGACTG 0.805146 -32 CCTGCTCACTAGCAACACGGGAAGTGTCTT 29 43 0 AGCAACACGG 0.95953 -133 ACTCGTAATAAAGAAGACAATCAAAGTGCG 29 146 1 AAGAAGACAA 0.625566 -30 GCAACAAGGCCGCAAGACGGAAAAGGAGCC 30 12 0 CGCAAGACGG 0.969167 -51 TCCCCCTGCTAAGAACACGAGGGTCCACTC 31 90 0 AAGAACACGA 0.784464 -30 ********** Masking position 5 Map Score: 9.68969 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 255 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 GAGTGTGTTTGGAGTTATTTTGCAAGGTGGGT 7 25 1 GGAGTTTTTG 0.965787 -47 GGCGTGTGTGTTTTGTCTGTGCGTT 8 4 1 GTGTGTTTTG 0.743057 -43 GCCTGTTTAGGGAGGTGTTTCGTGCTTGATGT 11 48 1 GGAGGTTTTG 0.973221 -187 TCCGTTTATAGGGGTTATTTCGCATACAAGGA 13 78 1 GGGGTTTTTG 0.973221 -31 ACGGTGTTGAGGATTTTTTTGGGGAAGTGAGC 14 74 1 GGATTTTTTG 0.946801 -29 GTGGGCGTGCGGGTTTTGTTTGCGCGCGCTCC 19 71 1 GGGTTTGTTG 0.842605 -94 AGGTGTAGCTGGGTGTTTTTTGGAGGTTTT 23 87 1 GGGTGTTTTG 0.967212 -20 AGGGGAGGCAGGAGTGCTTTCGGAAGAAACGA 24 31 1 GGAGTGTTTG 0.868344 -88 GATTGACAGGGGACGTCTTTTGCGCTAGCCTA 24 61 1 GGACGTTTTG 0.911675 -58 ****** *** * Masking position 9 Map Score: 4.76938 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 39 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 CCTCTGACCGATCGTACTCCTCACCAGCGT 10 34 0 ATCGTACTCC 0.932115 -154 AATCCTCAACACCGTAAACCTTGCCGCACA 14 59 0 ACCGTAAACC 0.957154 -44 GAGGCGGGCAACCGTATTCCATACGTCTGA 21 219 1 ACCGTATTCC 0.957154 -31 AGCACCCTTGACCGTTCACCGAAGAACATG 25 36 1 ACCGTTCACC 0.964256 -93 TGCGCTTCGGACCGTCGACCGCAACACACA 25 80 0 ACCGTCGACC 0.937168 -49 CGAGACCACAACCGTACTCCATAGGGGAAA 32 127 0 ACCGTACTCC 0.988858 -174 ********** Masking position 5 Map Score: 2.16944 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 42 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GTGCAGCCTGATAAGGTGAGCCGTCCATAG 3 114 1 ATAAGGTGAG 0.713108 -28 AATCGAATTGACAAGGGAAGTGCCTATCCG 4 86 0 ACAAGGGAAG 0.947132 -62 AGCCTGCCCCAGAAAGAAAGGCGCGTCAC 11 10 0 AGAAAGAAAG 0.521334 -225 TTTTTACGTCATAAGGAGAGGCCAGT 12 91 1 ATAAGGAGAG 0.922916 -16 TATTTCGCATACAAGGAGAAGATAAT 13 93 1 ACAAGGAGAA 0.619588 -16 TGAAAAACGAAGAAGGGAAGTACAGGGCAG 18 21 0 AGAAGGGAAG 0.963592 -25 CAACCGGCTGAGAAGGACAGAGGAGTCTAG 19 29 0 AGAAGGACAG 0.85808 -136 CCTGCTGAAGGAGAGCGGGCGGACG 21 6 1 TGAAGGAGAG 0.921435 -244 CAGGTTACAGAGCAGGGAAGATTAGCTCAT 21 163 0 AGCAGGGAAG 0.930366 -87 AGGGTGTGCGTGCAGGGGAGGCAGGAGTGC 24 18 1 TGCAGGGGAG 0.904548 -101 CTGTGTTTTTTTCAGGGGAGGGTCG 24 104 1 TTCAGGGGAG 0.756442 -15 CTCACTAGCAACACGGGAAGTGTCTTTAGG 29 39 0 ACACGGGAAG 0.738604 -137 TGCCACCCCTACAAGGAGAGATATAAAACC 32 219 0 ACAAGGAGAG 0.961132 -82 ********** Masking position 9 Map Score: 7.50972 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 202 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 ACAGCACGATGCGCAGCACGCACCACAAAT 5 25 0 GCGCAGCACG 0.825288 -30 CGATCGTACTCCTCACCAGCGTTATACGCA 10 26 0 CCTCACCAGC 0.97943 -162 ACTCCTCCACCCGCACCAGGTGCGAAACAG 10 161 0 CCGCACCAGG 0.89207 -27 ACCACCCCTCCTCACATCCACAGACGGAA 11 216 0 CCTCACATCC 0.447026 -19 ACCCCAGAAGCCTGACCGCCTAACACATAC 13 36 0 CCTGACCGCC 0.631372 -73 CCAAAAAAATCCTCAACACCGTAAACCTTG 14 66 0 CCTCAACACC 0.873942 -37 TCTGTTGTCTGATCACCAGCGCACTCCCTT 17 63 0 GATCACCAGC 0.862811 -65 CTTCCCAGGCCCGCAGCAGGTTACAGAGCA 21 179 0 CCGCAGCAGG 0.86201 -71 AAGAAGCACACATGAGCACCCTTGACCGTT 25 22 1 CATGAGCACC 0.697021 -107 TCACCATCCCCATCACAACCCCAATTCCTT 28 59 0 CATCACAACC 0.680436 -104 CGCACAGCCTGCTCACTAGCAACACGGGAA 29 50 0 GCTCACTAGC 0.615079 -126 GGAGGAGCCGCGTCAGCACCT 31 2 0 CGTCAGCACC 0.861913 -118 CCAAAACCGCGCCCACCACCGCCTCCCGCG 32 58 0 GCCCACCACC 0.871515 -243 CCGCCGCTCCCATCAGCAGCACACCAACCA 32 85 0 CATCAGCAGC 0.90322 -216 CCGCCGACTGGCGCAGCACCACGCAAGAAC 32 179 0 GCGCAGCACC 0.947509 -122 ********** Masking position 5 Map Score: 6.8658 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 715 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 14 CCGAACCTGGCGTTCGCCTGGACCTCAGAA 2 55 1 CGTTCGCCTG 0.643888 -62 GCACCTTACGCAGCTACCGCAGCTTACCG 9 10 0 CAGCTACCGC 0.429944 -46 CCGTCTCCTTCGGTCACCGCTCTGGCACCT 9 34 0 CGGTCACCGC 0.974988 -22 GGAGTACGATCGGTCAGAGGGAGCCGGTGC 10 44 1 CGGTCAGAGG 0.743068 -144 CAATGCGGGCCGGCCTCCGGGCGGCTCGGG 11 98 1 CGGCCTCCGG 0.837915 -137 GGTAAGGTTGAGGTCAGCGGTTCAATCCCG 11 177 1 AGGTCAGCGG 0.502281 -58 GAACGTGTGTCGGTTACACCCGGCGTGTAC 16 23 1 CGGTTACACC 0.539323 -96 CGCTCCGATGCGGTTGCAGGTTTGAGGGAG 19 97 1 CGGTTGCAGG 0.853415 -68 ACTCAGGGGCCGTCCGCCCGCTCTCCTTCA 21 16 0 CGTCCGCCCG 0.677115 -234 CCCACGTAAACGGGCGCCCCGCGCCTACGC 21 66 0 CGGGCGCCCC 0.749422 -184 GTATGGAATACGGTTGCCCGCCTCTTCTGT 21 213 0 CGGTTGCCCG 0.73485 -37 CACCCTTGACCGTTCACCGAAGAACATGCA 25 38 1 CGTTCACCGA 0.547388 -91 CTGTGTGTTGCGGTCGACGGTCCGAAGCGC 25 79 1 CGGTCGACGG 0.832621 -50 ACACGAACTGCAGTTACCCGACACTCCA 27 9 0 CAGTTACCCG 0.702504 -44 GCAGGCTGTGCGTTCACCGGTGACGTCTGG 29 68 1 CGTTCACCGG 0.943595 -108 CCCGAGGAGCCGGTTCCCCCTACAAGAGGG 31 30 1 CGGTTCCCCC 0.65686 -90 GGTGCTGCGCCAGTCGGCGGTATTTTTGCT 32 189 1 CAGTCGGCGG 0.801847 -112 ********** Masking position 1 Map Score: 7.6856 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 561 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 15 CCCTAAACAGGCAGCCAACCAGCCTGCCCC 11 30 0 GCAGCCAACC 0.989376 -205 CGCGTAAGCGGCAGGCAATCATGCGCATTG 12 39 0 GCAGGCAATC 0.97086 -68 TTCCAGTCAAGCTGGCAACTCAGGGGCCGT 21 33 0 GCTGGCAACT 0.796529 -217 CACAGAAGAGGCGGGCAACCGTATTCCATA 21 212 1 GCGGGCAACC 0.978122 -38 CCACGCAGACGCAGCCATCCCTCGCACCGT 23 53 0 GCAGCCATCC 0.950821 -54 AAGTAAACATGCAGGAAATCACCATCCCCA 28 77 0 GCAGGAAATC 0.901028 -86 GCTCCCATCAGCAGCACACCAACCAAAACC 32 80 0 GCAGCACACC 0.886595 -221 ********** Masking position 4 Map Score: 3.18147 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 52 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274