AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_ecoli_reg_300.orf -o00970_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BIME233 22 BIME Input sequences: #1 b0024 102 orf, hypothetical protein #2 ileS 42 isoleucine tRNA synthetase #3 proS 111 proline tRNA synthetase #4 rcsF 117 regulator in colanic acid synthesis; interacts with RcsB #5 yaeC 39 putative lipoprotein #6 abc 187 ATP-binding component of a transporter #7 cysS 173 cysteine tRNA synthetase #8 leuS 234 leucine tRNA synthetase #9 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #10 glnS 202 glutamine tRNA synthetase #11 lrp 300 regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system #12 ftsK 134 cell division protein #13 lolA 108 periplasmic protein effects translocation of lipoproteins from inner membrane to outer #14 serS 90 serine tRNA synthetase; also charges selenocystein tRNA with serine #15 asnS 168 asparagine tRNA synthetase #16 pncB 265 nicotinate phosphoribosyltransferase #17 tyrS 128 tyrosine tRNA synthetase #18 pdxH 58 pyridoxinephosphate oxidase #19 ydhA 178 orf, hypothetical protein #20 b1640 273 orf, hypothetical protein #21 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #22 pheM 122 phenylalanyl-tRNA synthetase (pheST) operon leader peptide #23 rplT 52 50S ribosomal subunit protein L20, and regulator #24 rpmI 96 50S ribosomal subunit protein A #25 thrS 300 threonine tRNA synthetase #26 aspS 276 aspartate tRNA synthetase #27 argS 209 arginine tRNA synthetase #28 metG 101 methionine tRNA synthetase #29 gltX 258 glutamate tRNA synthetase, catalytic subunit #30 hisS 110 histidine tRNA synthetase #31 gcpE 26 orf, hypothetical protein #32 yfgA 284 putative membrane protein #33 yfgB 149 orf, hypothetical protein #34 ndk 148 nucleoside diphosphate kinase #35 b2520 47 orf, hypothetical protein #36 alaS 128 alanyl-tRNA synthetase #37 oraA 68 regulator, OraA protein #38 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #39 ygaD 144 orf, hypothetical protein #40 mltB 255 membrane-bound lytic murein transglycosylase B #41 prfB 90 peptide chain release factor RF-2 #42 dsbC 24 protein disulfide isomerase II #43 xerD 111 site-specific recombinase #44 def 129 peptide deformylase #45 dam 106 DNA adenine methylase #46 damX 91 putative membrane protein; interferes with cell division #47 aroB 56 3-dehydroquinate synthase #48 aroK 199 shikimate kinase I #49 yrfD 68 orf, hypothetical protein #50 glyQ 300 glycine tRNA synthetase, alpha subunit #51 lysU 236 lysine tRNA synthetase, inducible; heat shock protein #52 yjdL 58 putative peptide transporter #53 cadA 79 lysine decarboxylase 1 #54 cadB 300 transport of lysine/cadaverine #55 yjeA 294 putative lysyl-tRNA synthetase #56 holC 52 DNA polymerase III, chi subunit #57 pepA 266 aminopeptidase A/I Motif number 1 AAATCACTTTTTTTTGTCCCAGGCTCGCCTTGAG 3 55 1 TTTGTCCGGC 0.935172 -57 CTGTTGTCCGTTTTAGCATCGGGCAGGAAAAGCC 12 91 1 TTTGCACGGC 0.876842 -44 TACTGTATCCCTGTGGTCGCAGGCTGTGGCCACA 14 34 1 CTTGTCCGGC 0.981457 -57 GGGGGGATACCTATGTTACCTGGCATCTGCAATC 15 92 0 CTTTTACGGC 0.936766 -77 TTCTATGTCTCTTTCGCATCTGGCGAAAAGTCGT 17 64 1 CTTGCACGGC 0.963131 -65 TTACTTGCCATTTTGGTCCCGGGCTGTGCTCGAA 21 193 0 TTTGTCCGGC 0.935172 -91 GACTTAGAGCCTATCCCATCAGGCTATTTTACTT 21 221 0 CTTCCACGGC 0.84881 -63 GACTAGCTCCCTCTTTCAACTGGC 22 1 0 CTTTCACGGC 0.92886 -122 TTATTACACGTTATGGCCCCTGGAGGGTTGAAAA 33 109 0 TTTGCCCGGA 0.600079 -41 AATTATTCGACGTTGCTAACGGGCCATTGTGGCA 35 14 1 CGTCTACGGC 0.727514 -34 ATTGACTATCCGGTATTACCCGGCATGACAGGAG 38 51 1 CGTTTACGGC 0.861291 -29 GACGAAAGTGCTATCTTGTCCGGCATAAATTTTT 39 104 1 CTTTTGCGGC 0.755469 -41 CACAAGGAAGCGGTAGTCACTGCCCGATACGGAC 40 175 0 CGTGTCCGCC 0.923625 -81 ATCAGAATCGCTTTAGTCACGGCACAATAAGGCA 43 54 1 CTTGTCCGCA 0.772986 -58 GCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTG 45 67 1 CTTTCCCGCC 0.927062 -40 TGAGAGTTGGTGCTCTTCGCTGCCTGCGTTCCAT 48 99 1 TGTTTCCGCC 0.622272 -101 GATCGGTACACTGTATTATCTGCCTCGACTATTA 51 165 0 CTTTTACGCC 0.889812 -72 TGGGAGGGGCCTTTTTTACCTGGAGATATGACT 53 57 1 CTTTTACGGA 0.636142 -23 ATCGTGCTTTTTTTAGTCACTGCCCACCGCTGTT 55 223 1 TTTGTCCGCC 0.887178 -72 GCAATTCTATCTGTAGCCACCGCCGTTGTCTTTA 57 224 1 CTTGCCCGCC 0.962163 -43 ** * *** * *** Masking position 4 Map Score: 18.7979 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 789 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 GCTCAAGCGTCGCATCAGGCATAAAGCAGA 10 8 0 CGCACAGGAA 0.980929 -195 CACGGAACAGGTGCAAAATCGGCGT 12 3 1 CGGACAGGGA 0.942133 -132 GCGCGATTTACGCAACAGGAATAGACTGAACAC 16 42 0 CGCACAGGAA 0.980929 -224 ATGTCTCTTTCGCATCTGGCGAAAAGTCGTGTA 17 68 1 CGCACTGGGA 0.94454 -61 TGATTAAAGGCGCTACAGCCGGAGAGAAGGACC 19 143 0 CGCTCAGCGA 0.864449 -36 AAAAGCCTGTCTCATCAGGTGTAATTGTCGCAG 21 104 1 CTCACAGGGA 0.913245 -180 TGGTCACCTGCGCAGCAGGGGGCATCCGCCGGC 26 233 1 CGCACAGGGC 0.987498 -44 AAAAATTGCCCGCACCAGTTAAAGAAATTAGGG 27 159 0 CGCACAGTAA 0.786805 -51 ACACAAGGGTCGCATCTGCGGCCCTTTTGCTTT 37 25 1 CGCACTGCGC 0.826821 -44 CATCACGCCCCGCACAAGGAAGCGGTAGTCACT 40 188 0 CGCAAAGGAC 0.892996 -68 ATACACTAGCCGCAAAAGCCACAGCAGAATCGA 43 23 0 CGCAAAGCAA 0.806715 -89 CAGCATCCAGCGCTTCAGGCAACTCCCGCAACG 45 38 0 CGCTCAGGAC 0.861432 -69 TCTCCACAGCCGGAGAAGGTGTAATTAGTTAGT 45 80 1 CGGAAAGGGA 0.779183 -27 CCCTTTTTTGCTCATAAGGAGAACAC 52 43 1 CTCAAAGGGA 0.695235 -16 GATTTAAATACGCATCAGGTATACACCGCAGC 56 10 0 CGCACAGGAA 0.980929 -43 ACGAAGTCATCGCAACAGCGGACATGAGTTACG 57 184 1 CGCACAGCGC 0.967296 -83 **** **** * * Masking position 8 Map Score: 17.9487 Number of sites scoring better than the average of aligned sites = 958 Number in coding regions = 724 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 GTGGGTAATTGAGTTGCGTATAATACCCAT 7 132 0 GAGTTGCGTA 0.528365 -42 GTTTCATCTCCCGGGTCGTTAACTGACTAT 8 12 1 CCGGGTCGTT 0.86543 -223 GGTGAGAAGACCGTTGCCTTGTGGCAGCTA 11 156 0 CCGTTGCCTT 0.753965 -145 CGTCCTCGTACAGGAGCGTTTAGTACAATA 16 233 0 CAGGAGCGTT 0.818351 -33 AGGGATGCTTGCGTGGCGTTTCATGGTGAA 20 25 0 GCGTGGCGTT 0.959555 -249 CGCGGAGAAACCGGAGCGTATTTAAGTACG 21 156 1 CCGGAGCGTA 0.948154 -128 ACTTTTATCGCCGTAGCCTTTTCAATAAAG 22 69 1 CCGTAGCCTT 0.799611 -54 AGCAACGTGCGCGTGGCGTATTGCCGTTTT 27 98 0 GCGTGGCGTA 0.954276 -112 CATAAAGTAACCGTGGCGTAATGGCTA 32 8 0 CCGTGGCGTA 0.97826 -277 ACTTTATGTACCGTGGCGTAATGTTTTATG 32 30 1 CCGTGGCGTA 0.97826 -255 CAGCCGCTCACCGGGGCGTTTCTTTTTTCA 33 85 1 CCGGGGCGTT 0.984722 -65 GCTTCCTTGTGCGGGGCGTGATGCTTTACC 40 198 1 GCGGGGCGTG 0.874761 -58 CTGCTTTTTCCCGTTTCGTACTGTATATCT 50 220 1 CCGTTTCGTA 0.526539 -81 CATGTGTTGGGAGGGGCCTTTTTTACCTGG 53 50 1 GAGGGGCCTT 0.610405 -30 ATTTGTCTCGCCGTCGCGTTGCGAGTAGAC 55 272 1 CCGTCGCGTT 0.881412 -23 CTTTAAGATTCAGGAGCGTAGTGC 57 253 1 CAGGAGCGTA 0.798509 -14 ********** Masking position 9 Map Score: 13.023 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 1050 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 ATTTCATTGACGGCGTTGCCCGTTTCAGGCATT 6 124 1 CGCGTTCCGT 0.986505 -64 TAAGATCATACGCCGTTATACGTTGTTTACGCT 10 166 1 CGCGTTACGT 0.91845 -37 CATGTAAATACCATGTTTACCGTGCTAGTGAAA 11 84 1 CCTGTTCCGT 0.950802 -217 TGGCGTCTGTCCACGCCATACGTAGATTTCACT 11 110 0 CCCGCCACGT 0.908708 -191 CACTGTTCAGAGTCGCTACCCGTCACGATAGAC 11 227 0 AGCGCTCCGT 0.885452 -74 ATTTTTCTTACCGCGTCTGCCGTTACACTTGGA 19 27 1 CCCGTCCCGT 0.979652 -152 GGCTTTCAGGCGCTGTTTTCCGTTTCTCTTCTC 21 30 0 CGTGTTCCGT 0.91845 -254 TCCGGTTTCTCCGCGCTGGCCGTGTCCAGTCTG 21 138 0 CCCGCTCCGT 0.994095 -146 ATGGGAAGCGCCTCGCTTCCCGTGTATGATTGA 30 18 1 CCCGCTCCGT 0.994095 -93 GAAAAATCTCCCGCGTTACCCGTCTG 31 4 0 CCCGTTCCGT 0.992088 -23 AACTCATTCCCCTCGCTATCCTTTTATTCAAAC 40 130 0 CCCGCTCCTT 0.929896 -126 ** **** **** Masking position 13 Map Score: 13.4726 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 194 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTTTTACAAGCTCCTGATTCAATATTGACG 4 72 1 CTCCTGATTC 0.935398 -46 GTCGGATTGACGCCTGTCTGCGCAAATCCA 9 39 0 CGCCTGTCTG 0.883267 -262 TCCTTCCCTACTCCTGTCTGACCCTGAAAC 11 262 0 CTCCTGTCTG 0.861609 -39 GTACTAAACGCTCCTGTACGAGGACGCTAC 16 237 1 CTCCTGTACG 0.685517 -29 ATCGCTGGTACTCCTGATTCTGGCACTTTA 17 34 1 CTCCTGATTC 0.935398 -95 CTTAAATACGCTCCGGTTTCTCCGCGCTGG 21 152 0 CTCCGGTTTC 0.731671 -132 ATGTGCTCTCCTGTATCTATATTCTAA 23 36 0 CTCCTGTATC 0.882488 -17 TCAGACTCTACGCCAGTTTGCTATAAAGGT 26 75 0 CGCCAGTTTG 0.849615 -202 CTATCACTCCCGCCTGATTCCTCAATGTAG 29 171 0 CGCCTGATTC 0.946229 -88 AGCAAAATGCCGCCTGAATGATAAATCATC 48 136 0 CGCCTGAATG 0.901253 -64 AACGTTTTGCCGCCTGATCCTTGCATAACG 50 41 0 CGCCTGATCC 0.836278 -260 GTAATCTTATCGCCAGTTTGGTCTGGTCAG 54 222 1 CGCCAGTTTG 0.849615 -79 GACATTCCTCCAGATTGTTTTTATCCC 55 8 1 CTCCAGATTG 0.822964 -287 GCACTACGCTCCTGAATCTTAAAGACAA 57 249 0 CTCCTGAATC 0.882488 -18 ********** Masking position 4 Map Score: 11.1873 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 327 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GGGCATATTCCTCGGCCTTTGAATTGTCCATAT 1 34 0 CTCGCCTGAA 0.795256 -69 CTTATTTGCACAAATCCATTGACAAAAGAAGGC 1 72 0 CAATCCTGAC 0.769923 -31 TCACGGCGCGCAATGCCTGGGTCTACGGTGAGA 11 179 0 CAAGCCGGTC 0.909358 -122 GAGATGTGGCCACAGCCTGCGACCACAGGGATA 14 39 0 CACGCCGGAC 0.992135 -52 GAATTTCGAGCACAGCCCGGGACCAAAATGGCA 21 189 1 CACGCCGGAC 0.992135 -95 CAAAGGCGAACAAAGCCTGTGAAGCCCGAAGGC 24 37 0 CAAGCCGGAA 0.943847 -60 TAATGAGCAACAGGGCCGTTGACTATTGATGAA 34 66 0 CAGGCCTGAC 0.947766 -83 AAGCGGTAGTCACTGCCCGATACGGACTTTACA 40 169 0 CACGCCGTAC 0.892579 -87 GAGCTTTCTCCACAGCCGGAGAAGGTGTAATTA 45 74 1 CACGCCGGAA 0.985477 -33 AAATCGACGTCACCGCCTTCGAACAGTTCCAGG 50 89 1 CACGCCTGAA 0.973333 -212 CGCCTTCGAACAGTTCCAGGGAAGCTATGAAAT 50 102 1 CAGTCCGGAA 0.783194 -199 AGTGGCAAGCCACTTCCCTTGTACGAGCTAA 52 9 0 CACTCCTGTA 0.699962 -50 TATCTGTAGCCACCGCCGTTGTCTTTAAGATTC 57 231 1 CACGCCTGTC 0.956112 -36 *** *** * *** Masking position 7 Map Score: 11.9508 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 429 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ATTCACGCCCTTCTCTTTTGACATTTCT 3 3 1 TCCGCCTTCT 0.952174 -109 GATCGGATCATCACGCAATGTATGCTGATTCGCGCG 7 90 1 TCCGCATATT 0.796151 -84 AAACAGCCTTTCGCGCACTCGACGTTGAAATGATGC 8 117 0 TCCGCCTACT 0.931005 -118 GGAGATCTTCTCTGCCGCTTTTTTTTTCATCAATCA 10 66 1 TCGCCCTTTT 0.758552 -137 TACTCCTGATTCTGGCACTTTATTCTATGTCTCTTT 17 42 1 TCGGCCTATT 0.861012 -87 GTTTCTCTTCTCACGCGCTAGCCTCCTGGAT 21 6 0 TCCGCCTCCC 0.756612 -278 TGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTC 21 32 0 TCGGCCTTTC 0.872502 -252 AGGGAGCTAGTCTCCCTCTTTTCGTTTCAACGCCAT 22 23 1 TCCCCCTTCT 0.872502 -100 TGCAGTATACTCCCGCCCTAATTTCTTTAACTGGTG 27 144 1 TCCGCCTTTT 0.963757 -66 TGATAGAATATCGCCCACTTAATTTTTCCAGGATTT 29 195 1 TCCCCCTATT 0.861012 -64 TGTACCCAATCCACGCTCTTTTTTATAGAGAAGATG 41 14 0 CCCGCCTTTT 0.771286 -77 TTGGGTACAATCCCGCTCTTATCACCGCATTTTGAC 41 41 1 TCCGCCTTCC 0.937132 -50 TCTAGACAAATCCCCCTCTGATTGACAGCATCACTG 44 57 0 TCCCCCTTTC 0.872502 -73 CAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGA 45 12 1 TCCGCATTTT 0.852125 -95 CGCTCTGGCGATAAATCACCGGGTAAGAT 48 181 0 TCGGCATATC 0.501272 -19 CCAGAGAATGTCACGCAATCCATTGTAAACATTAAA 54 64 1 TCCGCATATT 0.796151 -237 ** *** ** ** * Masking position 9 Map Score: 10.0594 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 309 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 TATCATTCAGGACGGGCGCTTGCCCGTCTTGTCAT 4 38 1 GACGGCGCCC 0.960954 -80 AGGTCGGATTGACGCCTGTCTGCGCAAATCCAGGT 9 36 0 GACGCTGCGC 0.962345 -265 CCTGTACGAGGACGCTACTGCGCACCT 16 249 1 GACGCTGCAC 0.690672 -17 GTCAGTGGGTGACGCTATTGTGCGCCGCCCCTGGA 18 17 0 GACGCTGCGC 0.962345 -42 TCCTGGTCTGGAGGGCAATACGCCCTCCCTAACGT 19 60 0 GAGGGTGCCC 0.891487 -119 CTTTGACCATGAGGGATGCTTGCGTGGCGTTTCAT 20 31 0 GAGGGCGCGT 0.887655 -243 CCTCCACTGGGAGGCTTTCAGGCGCTGTTTTCCGT 21 40 0 GAGGCCGCGC 0.990409 -244 GAAACGAAAAGAGGGAGACTAGCTCCCTCTTTCAA 22 16 0 GAGGGCGCTC 0.912833 -107 AAGTGGTAACGAGGCGTTCCAGCGCGGGCCAGGCT 26 121 1 GAGGCCGCGC 0.99041 -156 GGCTGTTTTCGTCAGCAACGTGCGCGTGGCGTATT 27 106 0 GTCAGCGCGC 0.727431 -104 GCGTGCAAACGTGGCATCCGTGCGCCAGAATTTGT 33 27 1 GTGGCCGCGC 0.954737 -123 CTATTTACAAGAGGGGGGCGTGAGCTTCCCTCTGG 39 11 1 GAGGGCGAGC 0.887655 -134 AGAAAGCTCCGACAGCATCCAGCGCTTCAGGCAAC 45 48 0 GACAGCGCGC 0.92891 -59 ***** * **** Masking position 12 Map Score: 13.0665 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 545 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TTTTGATCATACATTGAGGAAATACT 4 102 1 ACTTGAGGAA 0.977919 -16 CGTTGTTTACGCTTTGAGGAATCCACG 10 186 1 GCTTGAGGAA 0.902307 -17 GCTAATAATCAGCTTGAGGAAAGAAGAAAAT 13 33 0 AGTTGAGGAA 0.865501 -76 GGAGTGACGTAATTTGAGGAATA 13 96 1 AATTGAGGAA 0.812795 -13 ATATACTTTGACCATGAGGGATGCTTGCGTG 20 40 0 ACATGAGGGA 0.896079 -234 TTTCGTGAATACCATGCGGAATGACCGATTT 20 204 0 ACATGCGGAA 0.80703 -70 CACCACTGACACAATGAGGAAAACC 21 269 1 ACATGAGGAA 0.952503 -15 GGAATACCTTACATTGATGAAGCGAGCAAAA 27 188 0 ACTTGATGAA 0.794632 -22 AACCCGAACTACATTGAGGAATCAGGCGGGA 29 163 1 ACTTGAGGAA 0.977919 -96 GGCTCCCGAAACATTGAGGGAAGCGTTGAGG 30 59 1 ACTTGAGGGA 0.950107 -52 ** ******** Masking position 5 Map Score: 6.84059 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 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 10 TGCTGATTCGCGCGGGAAATATGGGTATTA 7 112 1 CGCGGGAAAT 0.956239 -62 CAGTTAACGACCCGGGAGATGAAACG 8 7 0 CCCGGGAGAT 0.662225 -228 CCCAAACGTCCGCGTCAAAACAGCCTTTCG 8 140 0 CGCGTCAAAA 0.782669 -95 AGGAGGCTAGCGCGTGAGAAGAGAAACGGA 21 15 1 CGCGTGAGAA 0.853101 -269 GCTCTTACGGTGCGGCAGAATTTCCAGTAT 26 153 1 TGCGGCAGAA 0.860939 -124 CATCAGAAGCGGCGTGAAATCAGCGGTTGG 27 60 0 GGCGTGAAAT 0.706435 -150 AAGAAATTAGGGCGGGAGTATACTGCAAAT 27 141 0 GGCGGGAGTA 0.578716 -69 CTTTAACTGGTGCGGGCAATTTTTGCTCGC 27 168 1 TGCGGGCAAT 0.668276 -42 AGACGGGTAACGCGGGAGATTTTTC 31 12 1 CGCGGGAGAT 0.965895 -15 TCGTAAATGCCGCGTGCAAACGTGGCATCC 33 16 1 CGCGTGCAAA 0.495363 -134 GATAAACCATTGCGGGAGATAACCTTGA 45 9 0 TGCGGGAGAT 0.92259 -98 GGTTTATCGTTGCGGGAGTTGCCTGAAGCG 45 31 1 TGCGGGAGTT 0.720414 -76 AATACCTGCGCGCGTCAAATAGATGAAACA 48 47 0 CGCGTCAAAT 0.847837 -153 GCAAGGATCAGGCGGCAAAACGTTATAACA 50 47 1 GGCGGCAAAA 0.797578 -254 AATGGCCATCCGCGTCAAAAGAACAGACAA 50 164 0 CGCGTCAAAA 0.782669 -137 TACTAATAGTCGAGGCAGATAATACAGTGT 51 162 1 CGAGGCAGAT 0.51531 -75 ATAATATGTTGCGGCAATTTATTTGCCGC 54 10 1 TGCGGCAATT 0.61507 -291 ATAAAAATTATGCGGCAAATAAATTGCCGC 54 21 0 TGCGGCAAAT 0.880822 -280 ********** Masking position 4 Map Score: 9.95529 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1507 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 11 ATTTGTAGCCGTATTGAAAACAGGACCACTGGCT 8 208 1 GATGAAAAGG 0.855294 -27 GTCGCATCCAACAATGACAAGCGGTGGAGATCTT 10 41 1 AATGACAAGG 0.817189 -162 TGAGCAAATCATAATGAAAGTAGGATCAACCAAT 20 109 1 AATGAAAGGG 0.958874 -165 CGCAAACGTCAGATTGAAAAAGGATGAACT 20 254 1 AATGAAAAGA 0.79748 -20 AGCGATGTTAACACTAAAAAAAGGGAGATTGTAC 25 113 0 AATAAAAAGG 0.651171 -188 ATGTCACAACTGAATGAAAAAAGGCGGCTATTAT 26 181 0 TATGAAAAGG 0.909717 -96 ATTAACGCTTTTACTGAAAGACGAAGA 27 4 0 TATGAAAGGA 0.535259 -206 TTCTGATGCAATAGTGAAAACGGCAATACGCCAC 27 82 1 AATGAAAAGC 0.767968 -128 TTACTTCTTAATAGTGAAAAGGGGTTAGATAGTA 28 70 0 AATGAAAAGG 0.965919 -32 GCCGGGCTGGTAACTGAAAAGTGGGAATAAGATA 36 48 0 TATGAAAAGG 0.909717 -81 TATCTACGCTAAATTGAAAGCTGGATTTAGAGGA 51 207 1 AATGAAAGGG 0.958874 -30 CACATGGGACAAAATGAAAGGAGGAGCCTCGGAA 53 22 0 AATGAAAGGG 0.958874 -58 TCCAAATTCAAAAATGAAATTAGGAGAAGAGC 54 279 1 AATGAAATGG 0.817111 -22 * * ****** ** Masking position 7 Map Score: 6.43744 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 84 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 TCCTCAATGTATGATCAAAACGTCAATATT 4 92 0 ATGATCAAAA 0.482832 -26 TTCTGGTTTAGCCAGTAAAAGGGAGTGATA 9 96 1 GCCAGTAAAA 0.67666 -205 ACGGCTTGAAACGAGCCAAATAGGGTTCTC 9 267 1 ACGAGCCAAA 0.698851 -34 GGAGAGAAGGACCGGCAAAATGATAATTAA 19 126 0 ACCGGCAAAA 0.729401 -53 TCGTTTCAACGCCATCAAAACATTGACTTT 22 44 1 GCCATCAAAA 0.901311 -79 TAGTGAGTACACCAGCAAAACGCTTAAAGA 25 45 0 ACCAGCAAAA 0.944721 -256 CATTGATGAAGCGAGCAAAAATTGCCCGCA 27 178 0 GCGAGCAAAA 0.964731 -32 CTGCCTTAAAGTCAGCAAAAACGCACCGTT 32 96 0 GTCAGCAAAA 0.875216 -189 CTTTCATTTTGCGATCAAAATAACACTTTT 40 80 0 GCGATCAAAA 0.887167 -176 GCGTAAAAAAGACAGCAAAATGCCGCCTGA 48 149 0 GACAGCAAAA 0.735161 -51 TATAACACCGGCGAGCAAAAAATCGACGTC 50 70 1 GCGAGCAAAA 0.964731 -231 CTAATAAATAACCATCAAAATGGTTTAAAT 51 85 0 ACCATCAAAA 0.830865 -152 TGTTCTCCTTATGAGCAAAAAAGGGAAGTG 52 38 0 ATGAGCAAAA 0.764593 -21 ********** Masking position 8 Map Score: 6.44043 Number of sites scoring better than the average of aligned sites = 1100 Number in coding regions = 1041 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 13 GCGTCAAAACAGCCTTTCGCGCACTCGACGTT 8 127 0 AGCTTTCCGC 0.634527 -108 TCTGCGCAAATCCAGGTTACGCTTAAAGATGC 9 21 0 TCCGGTTCGC 0.758744 -280 AACAGTTGTCAGCCTGTCCCGCTTATAAGATC 10 141 1 AGCTGTCCGC 0.966127 -62 GCATGTAAATACCATGTTTACCGTGCTAGTGA 11 83 1 ACCTGTTACC 0.700388 -218 GGACAACAGTACCAGGTTACCCCAGTACTGTT 12 68 0 ACCGGTTCCC 0.929274 -67 GCTGGAGTATACCTTGTTTCGCAATTTATTGA 16 185 0 ACCTGTTCGC 0.969096 -81 GCCTTTAATCAGCTGGTTGAGCGC 19 165 1 AGCGGTTAGC 0.852793 -14 TGAAAGAGGGAGCTAGTCTCCCTCTTTTCGTT 22 17 1 AGCAGTCCCC 0.648973 -106 CTCACCTTCCACCCGGTTGAGCGATGTTAACA 25 134 0 ACCGGTTAGC 0.852793 -167 TTTGTTGGCTAGATGGTTTCGCAATGAACTGT 25 213 1 AGAGGTTCGC 0.787744 -88 GCACCGTAAGAGCCTGGCCCGCGCTGGAACGC 26 134 0 AGCTGGCCGC 0.806223 -143 GCGTTAATTTACCCTGTTGCCCTGTGCCAACC 27 30 1 ACCTGTTCCC 0.928027 -180 CGCAAAACAGACCGTGTTGCGCAATTTGTCAA 29 106 1 ACCTGTTCGC 0.969096 -153 ATTTAACCAGAGAATGTCACGCAATCCATTGT 54 58 1 AGATGTCCGC 0.768124 -243 *** **** *** Masking position 12 Map Score: 5.80149 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 679 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 TATAAGCGGGACAGGCTGACAACTGTTAGTTTTTTAA 10 131 0 ACAGGACTTT 0.895313 -72 CCCCCCATTTACGGGTGGACAAGTGTTTATTTTTTCC 15 120 1 ACGGGACTTT 0.973952 -49 TGAATACCATGCGGAATGACCGATTTTTACCGTTGGT 20 193 0 GCGGGACTTT 0.989654 -81 TTAGCCGATGGCGGAACGACAAATTTTGTTAATTTTT 26 23 1 GCGGGACTTT 0.989654 -254 CGCTTGATAAGCGGCCTGACCTTTCTTGTTG 46 5 0 GCGGGACTTT 0.989654 -87 TCCGTAAAGAGCAGTTTGTCTGTTCTTTTGACGCGGA 50 149 1 GCAGGTCTTT 0.819568 -152 TTCTTTTGACGCGGATGGCCATTTTTTGCATCTTTCC 50 171 1 GCGGGCCTTT 0.967142 -130 TCGCAACGCGACGGCGAGACAAATTTTACGCAGGAAT 55 259 0 ACGGGACTTT 0.973951 -36 **** *** * ** Masking position 14 Map Score: 5.44257 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 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 15 ATGCCTGAAACGGGCAACGCCGTCAATGAA 6 126 0 CGGGCAACGC 0.98255 -62 ACGTCGAGTGCGCGAAAGGCTGTTTTGACG 8 128 1 CGCGAAAGGC 0.891554 -107 ATCTTATAAGCGGGACAGGCTGACAACTGT 10 142 0 CGGGACAGGC 0.808284 -61 AGATTCACGGCGCGCAATGCCTGGGTCTAC 11 186 0 CGCGCAATGC 0.967495 -115 TTGCGTAAATCGCGCTATGCAGAATCTTCA 16 60 1 CGCGCTATGC 0.824318 -206 TAACATACACCGCGTAATGCCATCGACCAG 16 128 1 CGCGTAATGC 0.90702 -138 TTTATGAGTTCGGGCAACACCTTTATAGCA 26 57 1 CGGGCAACAC 0.896638 -220 CGTTCCAGCGCGGGCCAGGCTCTTACGGTG 26 135 1 CGGGCCAGGC 0.948541 -142 CAGACGGGTAACGCGGGAGATTTT 31 5 1 CGGGTAACGC 0.948597 -22 CCTGTCATGCCGGGTAATACCGGATAGTCA 38 53 0 CGGGTAATAC 0.641887 -27 GAAGTCTACTCGCAACGCGACGGCGAGA 55 277 0 CTCGCAACGC 0.788131 -18 ********** Masking position 7 Map Score: 6.93414 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 605 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467