AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_bsub_reg_300.orf -o00970_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: yacF 23 similar to transcriptional regulator (nitrogen regulation protein) Input sequences: #1 serS 300 seryl-tRNA synthetase #2 metS 300 methionyl-tRNA synthetase #3 spoIIE 300 serine phosphatase #4 yabS 84 similar to hypothetical proteins #5 yabT 88 yabT #6 yacA 103 similar to cell-cycle protein #7 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #8 yacB 194 similar to hypothetical proteins #9 yacC 85 similar to hypothetical proteins #10 yacD 46 similar to protein secretion PrsA homolog #11 cysK 75 cysteine synthetase A #12 pabB 166 para-aminobenzoate synthase (subunit A) #13 lysS 91 lysyl-tRNA synthetase #14 ctsR 300 transcriptional regulator #15 sms 91 DNA repair protein homolog #16 yacL 115 similar to hypothetical proteins #17 gltX 90 glutamyl-tRNA synthetase #18 cysE 300 serine acetyltransferase #19 trpS 300 tryptophanyl-tRNA synthetase #20 ileS 300 isoleucyl-tRNA synthetase #21 yloB 115 similar to calcium-transporting ATPase #22 yloC 82 similar to hypothetical proteins #23 yloD 233 similar to guanylate kinase #24 yloI 80 similar to pantothenate metabolism flavoprotein #25 def 26 polypeptide deformylase #26 flgB 300 flagellar basal-body rod protein #27 fliF 45 flagellar basal-body M-ring protein #28 fliH 117 flagellar assembly protein #29 fliK 160 fliK #30 flgE 21 flagellar hook protein #31 fliL 251 flagellar protein #32 fliM 33 flagellar motor switch protein #33 cheY 25 two-component response regulator #34 flhA 32 flagella-associated protein #35 cheW 21 cheW #36 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #37 ylxL 28 ylxL #38 rpsB 143 ribosomal protein S2 #39 tsf 101 elongation factor Ts #40 smbA 145 uridylate kinase #41 yluA 130 similar to hypothetical proteins #42 yluB 61 similar to hypothetical proteins #43 proS 32 prolyl-tRNA synthetase #44 asnS 143 asparaginyl-tRNA synthetase #45 aspB 22 aspartate aminotransferase #46 ypmA 142 ypmA #47 dinG 125 ATP-dependent helicase #48 panB 245 ketopantoate hydroxymethyltransferase #49 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #50 ypjD 300 alternate gene name: jojD #51 glyQ 296 glycyl-tRNA synthetase (alpha subunit) #52 yqxN 300 alternate gene name: yqfI; similar to hypothetical proteins #53 alaS 300 alanyl-tRNA synthetase #54 hisS 300 histidyl-tRNA synthetase #55 valS 300 valyl-tRNA synthetase #56 pheS 300 phenylalanyl-tRNA synthetase (alpha subunit) #57 thrS 300 threonyl-tRNA synthetase #58 tyrS 300 tyrosyl-tRNA synthetase #59 leuS 300 leucyl-tRNA synthetase #60 ywiB 300 ywiB #61 thrZ 300 threonyl-tRNA synthetase #62 ywaE 150 alternate gene name: ipa-10r; similar to transcriptional regulator (MarR family) #63 tyrZ 248 tyrosyl-tRNA synthetase Motif number 1 GTTTTCAATCAGGGTGGCAACGCGAGAGCTCTCG 1 213 1 AGGGGGAACG 0.996154 -88 CCGCCCTTTCACGGCGGTAACACGGGTTCGAATC 3 66 1 ACGGGGAACG 0.932845 -235 CTACTCTCACAGGGGGAAACCCCCGACTACCATC 14 24 0 AGGGGAACCC 0.938833 -277 TCCCCCTGTGAGAGTAGGACGCCGCCAAGCAAGC 14 41 1 AGAGAGACCG 0.77654 -260 CTTTTCAAACAGAGTGGAACCGCGCGGTTAAAGC 18 200 1 AGAGGGACCG 0.990135 -101 TGGAATAATCAGGGTGGTACCACGGTTCATTCGT 19 212 1 AGGGGGACCG 0.998397 -89 TTTTTCTAAAAGGGTGGTACCGCGAGATAAGCTT 20 212 1 AGGGGGACCG 0.998397 -89 GGAGGGAGGGGAGGCGAGTAATCGCT 31 3 1 AGGGGGGACG 0.953891 -249 CTAGTATCACAGAGCGGGAAATCCGCTTTTAAAT 46 58 0 AGAGGGAACC 0.891963 -85 ACTGGGACAGAGGGATGAAACTCGCCGAACTTTA 48 128 1 AGGGTGAACG 0.899681 -118 CTCAGCAACTAGGGTGGAACCGCGGGAGAACTCT 51 181 1 AGGGGGACCG 0.998397 -116 GCCCGTAATCAGGGTGGTACCGCGAGACAGCTCT 53 188 1 AGGGGGACCG 0.998397 -113 TATTCCAACTAGGGTGGCACCACGGGTATAACTC 54 177 1 AGGGGGACCG 0.998396 -124 AGGCGCATGCAGAGAGAGAAGCCGTTTGCTGAAA 55 60 1 AGAGGAAACG 0.838843 -241 TTCATGAAAAAAGGTGGTACCGCGAAAGAGCTTT 55 207 1 AAGGGGACCG 0.975447 -94 ACTGCTTTCCAGGGAGAAAATGCCGCTGACTGAG 56 37 1 AGGGGAAACC 0.864591 -264 GTCTGAAATAAGGGTGGTACCGCGGCCACAACTC 56 199 1 AGGGGGACCG 0.998397 -102 ACCGGCTCAAAGAGAGGGAAGCCCTGGTGCAAGC 57 54 1 AGAGGGAACC 0.891963 -247 CTGAAGTTCAAAGGCGGTAAAGCGAATGGTCCTT 57 97 0 AAGGGGAACG 0.942945 -204 TGCGGAAAAAAGGGTGGAACCACGATTCCGTTTA 57 216 1 AGGGGGACCG 0.998397 -85 TCTTATTAGTAGGGTGGTACCGCGATAATCAATC 58 218 1 AGGGGGACCG 0.998397 -83 CGCGCTAACGAGGGTGGTACCGCGGGAAAACGAA 59 151 1 AGGGGGACCG 0.998397 -150 GTCGGGAACTTGGGTGGAACCACGGGTTAATCAC 61 209 1 TGGGGGACCG 0.971059 -92 TCTCTGAAACAGGGAGACAAACCGCTACTGGATT 63 22 0 AGGGGAAACG 0.969962 -227 GTCTTCAACCAGGGTGGTACCGCGTGCATTGAGC 63 172 1 AGGGGGACCG 0.998397 -77 **** ** ** ** Masking position 4 Map Score: 79.5756 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 23 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 TCAATCAGGGTGGCAACGCGAGAGCTCTCGTC 1 217 1 TGGAACGCGG 0.982828 -84 CCTTTCACGGCGGTAACACGGGTTCGAATCCC 3 70 1 CGGAACACGG 0.806072 -231 TCAAACAGAGTGGAACCGCGCGGTTAAAGCGT 18 204 1 TGGACCGCGG 0.99826 -97 ATAATCAGGGTGGTACCACGGTTCATTCGTCC 19 216 1 TGGACCACGT 0.970774 -85 TCTAAAAGGGTGGTACCGCGAGATAAGCTTTC 20 216 1 TGGACCGCGG 0.99826 -85 GCAACTAGGGTGGAACCGCGGGAGAACTCTCG 51 185 1 TGGACCGCGG 0.99826 -112 GTAATCAGGGTGGTACCGCGAGACAGCTCTCG 53 192 1 TGGACCGCGG 0.99826 -109 CCAACTAGGGTGGCACCACGGGTATAACTCTC 54 181 1 TGGACCACGG 0.994042 -120 TGAAAAAAGGTGGTACCGCGAAAGAGCTTTTC 55 211 1 TGGACCGCGA 0.987609 -90 GAGTTGTCGCCGGGACCGCGTACACTGCGCGT 56 109 1 CGGACCGCGA 0.952157 -192 GAAATAAGGGTGGTACCGCGGCCACAACTCGT 56 203 1 TGGACCGCGC 0.985292 -98 GAAAAAAGGGTGGAACCACGATTCCGTTTATT 57 220 1 TGGACCACGT 0.970774 -81 ATTAGTAGGGTGGTACCGCGATAATCAATCGT 58 222 1 TGGACCGCGT 0.99132 -79 CTAACGAGGGTGGTACCGCGGGAAAACGAAAG 59 155 1 TGGACCGCGG 0.99826 -146 GGAACTTGGGTGGAACCACGGGTTAATCACAC 61 213 1 TGGACCACGG 0.994042 -88 TCAACCAGGGTGGTACCGCGTGCATTGAGCCA 63 176 1 TGGACCGCGG 0.99826 -73 *** ****** * Masking position 5 Map Score: 52.702 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 CATCCCCATAAAGGGACGAGAGCTCTCGCG 1 233 0 AAGGGACGAG 0.995305 -68 GCTCCCGCCCAAAGGACGAGAGCGGCGATA 2 251 0 AAAGGACGAG 0.968538 -50 TGATTGTTGACAGGGAAGAGTATAAAGCTT 18 15 1 CAGGGAAGAG 0.782662 -286 CCCTGTAAAAAAGGGACGAATGAACCGTGG 19 231 0 AAGGGACGAA 0.959418 -70 CTCATCCCATAAGGGACGAGAAAGCTTATC 20 237 0 AAGGGACGAG 0.995305 -64 CTCGTCCCTTATGGGATGAGAGGGCTTTTT 20 247 1 ATGGGATGAG 0.848112 -54 ATAGCATGAAATGGGACGAGTCAGAATAAG 21 44 1 ATGGGACGAG 0.973216 -72 CGGTGTAAGCTAAGGATGAGCACGCAACGA 51 107 1 TAAGGATGAG 0.637077 -190 GCCGCAAACATAGGGACGAGAGTTCTCCCG 51 203 0 TAGGGACGAG 0.987446 -94 AACGTTTACACAGGGACGAGAGCTGTCTCG 53 210 0 CAGGGACGAG 0.987196 -91 TACATGATAGTAGGGACGAGAGTTATACCC 54 200 0 TAGGGACGAG 0.987446 -101 CATCCCTGTAAAAGGACGAAAAGCTCTTTC 55 230 0 AAAGGACGAA 0.774436 -71 CGTCCTTTTACAGGGATGAAGAGCTCTTTT 55 242 1 CAGGGATGAA 0.569224 -59 TCCCTTGTACAAGGGACGAGTTGTGGCCGC 56 220 0 AAGGGACGAG 0.995305 -81 TCCCTTGTACAAGGGACGGGTTTTTTTTAT 56 234 1 AAGGGACGGG 0.955185 -67 CCCCCTATGAAAGGGACGAGGTTGAATAAA 57 246 0 AAGGGACGAG 0.995305 -55 CGTTTACACGAAGGGACGATTGATTATCGC 58 239 0 AAGGGACGAT 0.903444 -62 TCATCCCAAAAAGGGACGAGAGACTTTCGT 59 180 0 AAGGGACGAG 0.995305 -121 TCGTCCCTTTTTGGGATGAGGGAGTTTTTT 59 191 1 TTGGGATGAG 0.674477 -110 GGAATGATGAAAAGGACGTGTCAGA 60 286 1 AAAGGACGTG 0.786445 -15 GTCCCGCAGATAGGGACGAGTGTGTGATTA 61 236 0 TAGGGACGAG 0.987446 -65 CCATCCCAATAAGGGACGTGGCTCAATGCA 63 196 0 AAGGGACGTG 0.962061 -53 ********** Masking position 6 Map Score: 48.6942 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 40 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TATCGAAAATAAAAAGAGCCCTCATCCCCAT 1 254 0 AAAAAGACCC 0.907596 -47 TCAGAATGTCAAAAAGCTCCCGCCCAAAGGA 2 265 0 AAAAAGCCCC 0.936212 -36 TTTCTTTCTAAAAAAACTGCCGGCTGACGCT 8 16 1 AAAAAACGCC 0.855935 -179 CATTTACATAAAAAAACTGCCAGCGTCAGCC 8 37 0 AAAAAACGCC 0.855935 -158 AAAAAGCCAAAACTCCCGGTTCGCCGG 12 7 1 CCAAAACCCC 0.701552 -160 ACGAAATATAAAAAAACTCCCGGCGAACCGG 12 26 0 AAAAAACCCC 0.984354 -141 AAACCAAAATACAAAAAACCCAGCTCATTGA 14 86 0 ACAAAAACCC 0.870852 -215 TTCAGAAAATAAAAAAAGCCCTCTCATCCCA 20 258 0 AAAAAAACCC 0.976799 -43 AGTATTAACAAAAAAACCCCCTGTAAACATG 41 52 0 AAAAAACCCC 0.984354 -79 AAGAAAAGCCCCCTTTATCGG 47 1 1 AAGAAAACCC 0.881053 -125 AAAATCTTAAAAGAAAACCCCCGATAAAGGG 47 21 0 AAGAAAACCC 0.881053 -105 CCAAGCATCACACAAAACCCCTTTTCCTTCC 50 164 1 CACAAAACCC 0.715671 -137 AGTTGCTGAGAACAAAATCCCAGCCTCTTTT 51 160 0 AACAAAACCC 0.915177 -137 GGCAGCAACCAAAAAACTCCCGTCTCTATGC 51 239 0 AAAAAACCCC 0.984354 -58 TCAGTGACAGCAAAAAAGCCCTCCCCCTATG 53 246 0 CAAAAAACCC 0.907596 -55 ATGAAAATGAAAAAAACTCCCGCCCCTACTA 54 230 0 AAAAAACCCC 0.984354 -71 TTTGGAAAATAAAAAAAACCCGTCCCTTGTA 56 241 0 AAAAAAACCC 0.976799 -60 TTTTTTGCATATAAAAACCCCGCCCCCTATG 57 267 0 ATAAAAACCC 0.711995 -34 TAATTAAAATAAAAAACGCCCCTTCGTTTAC 58 262 0 AAAAAACCCC 0.984354 -39 CCCAAACTAAAAAAAACTCCCTCATCCCAAA 59 200 0 AAAAAACCCC 0.984354 -101 TTCAAATAAAAAAACACACCC 61 1 0 AAAACACCCC 0.906049 -300 TGTATATAAAAAAACACACCCGTCCCGCAGA 61 256 0 AAAACACCCC 0.906049 -45 CGCCAAAATAAACAAAAACCCGAAAACGGGG 62 19 0 AACAAAACCC 0.915177 -132 TCGGTTGAATAAAAAAAGCCCAAACAACGCC 62 46 0 AAAAAAACCC 0.976799 -105 TACAAACACAAAAAAGAGCCCATCCCAATAA 63 214 0 AAAAAGACCC 0.907596 -35 ******* *** Masking position 4 Map Score: 49.43 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 89 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 AATGTCAAAAAGCTCCCGCCCAAAGGACGA 2 262 0 AGCTCCCGCC 0.841584 -39 TTTCTAAAAAAACTGCCGGCTGACGCTGGC 8 20 1 AACTGCCGGC 0.97432 -175 TACATAAAAAAACTGCCAGCGTCAGCCGGC 8 34 0 AACTGCCAGC 0.835183 -161 AAAAAGCCAAAACTCCCGGTTCGCCGGGAG 12 11 1 AACTCCCGGT 0.959523 -156 AATATAAAAAAACTCCCGGCGAACCGGGAG 12 23 0 AACTCCCGGC 0.988633 -144 AAAGCAGAAAAACTGCCAGCGTAAAACTAG 13 37 0 AACTGCCAGC 0.835183 -55 CACAGGGGGAAACCCCCGACTACCATCGGC 14 21 0 AACCCCCGAC 0.914172 -280 TCAACCCCCTCCTTTACTGACT 14 289 0 AACCCCCTCC 0.812748 -12 GTTAACCCCCGGTCATTCCACTC 27 33 0 AACCCCCGGT 0.954324 -13 CAGTTTTGAAAACTCCTGGCTACTTTTCAT 29 61 0 AACTCCTGGC 0.784442 -100 TTTTGTACAGAACTGCCGCCTGCAGCACCC 38 78 0 AACTGCCGCC 0.958416 -66 TTAACAAAAAAACCCCCTGTAAACATGAGA 41 49 0 AACCCCCTGT 0.660716 -82 CTTAAAAGAAAACCCCCGATAAAGGGGGCT 47 17 0 AACCCCCGAT 0.743782 -109 GCTGAGAACAAAATCCCAGCCTCTTTTTTA 51 157 0 AAATCCCAGC 0.578224 -140 GCAACCAAAAAACTCCCGTCTCTATGCTTG 51 236 0 AACTCCCGTC 0.923575 -61 AAATGAAAAAAACTCCCGCCCCTACTATAC 54 227 0 AACTCCCGCC 0.981425 -74 TCCAGGGAGAAAATGCCGCTGACTGAGAGC 56 44 1 AAATGCCGCT 0.425727 -257 GGCTGACGGGAACTCCCGTTACAGAGCTTA 57 160 1 AACTCCCGTT 0.767095 -141 TTGCATATAAAAACCCCGCCCCCTATGAAA 57 264 0 AAACCCCGCC 0.846053 -37 GGCTCGCACCTACCGCCGGCTCTCTGAAAC 63 46 0 TACCGCCGGC 0.694062 -203 ********** Masking position 6 Map Score: 20.1377 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 283 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 CACCAACCATCGGCTCTCTTAGAAAGAGAG 1 73 0 CGGCTCTCTT 0.622588 -228 GCGAAACACTCCTTTTTTTATTGATTTA 1 283 0 CTCCTTTTTT 0.966867 -18 CCTCTATCACCACTTTTGAATAGTTTC 8 178 0 CACCACTTTT 0.542573 -17 GGCAGTTTTTCTGCTTTTTTCATGAAACAA 13 50 1 CTGCTTTTTT 0.945091 -42 ACCCCCACCTCCTTTTTTAACATTTTAA 16 98 0 CTCCTTTTTT 0.966867 -18 GAAACGTGTACTACTCTTTTTCATAGCAAG 19 41 0 CTACTCTTTT 0.705192 -260 CCGGCTGAGCCTACTTTTTTCCAGTTCGGT 19 142 0 CTACTTTTTT 0.772173 -159 CATTCCTCCACTGCATTTTTTCAGAAAATA 20 278 0 CTGCATTTTT 0.810807 -23 GTCCACTCCCCTGCTCTCTTATAGAGATAT 21 89 0 CTGCTCTCTT 0.775435 -27 CCTTTCTTTTCGGCATTTTTGAAACTTTTT 26 55 0 CGGCATTTTT 0.671848 -246 TCTGTTTTTTCTCCTTTCTTTTCGGCATTT 26 67 0 CTCCTTTCTT 0.892416 -234 AACAGAAATTCTGCTATTTTCAGGCTTATA 26 91 1 CTGCTATTTT 0.611751 -210 TGCCTTTTATCACCTTTTTTCAAGAAAAAT 39 37 1 CACCTTTTTT 0.870966 -65 GCGGCTAAGTCGGCTCTTTTCAGGCAGTAT 40 26 1 CGGCTCTTTT 0.853012 -120 TTCAAGCACCTCCACTTTTCTTTCATAAG 51 278 0 CTCCACTTTT 0.836814 -19 TCTCTGCATGCGCCTTTTTTGTACTCTTCC 55 45 0 CGCCTTTTTT 0.93307 -256 TTCGCGGTACCACCTTTTTTCATGAACTCA 55 203 0 CACCTTTTTT 0.870966 -98 TTTGCATCCTCCTTTTATGTAAACAAAC 56 283 0 CTCCTTTTAT 0.653045 -18 CTTTGTCACTCCTTTTTTTGCATATAAA 57 283 0 CTCCTTTTTT 0.966867 -18 AAGATAAAGCTCCTTTTTTAATTAAAATA 58 282 0 CTCCTTTTTT 0.966867 -19 TTTTCCTCCTTTTTTACAAACACAA 63 234 0 CTCCTTTTTT 0.966867 -15 ********** Masking position 7 Map Score: 21.2565 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 482 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 7 AAAAATGAAAAAAATCGGCTTCTGCAAGAG 3 129 0 AAAATCGGCT 0.808526 -172 GGATGATTGTAAAAGCCGCAGCTGAGCCAA 8 69 0 AAAAGCCGCA 0.879837 -126 TCTCAAATTAAAAACCCGCTAAAGAGC 10 8 0 AAAACCCGCT 0.791743 -39 TTAATTTGAGAAAAGGGGCTGAAAGCAGGT 10 27 1 AAAAGGGGCT 0.97372 -20 ACCCAATAAAAAAAGCGTCTCTGCATGTAA 18 247 0 AAAAGCGTCT 0.798459 -54 CAGATCAAAAAGCGGCTGACAGAAAAG 44 8 1 AAAAGCGGCT 0.987637 -136 AATGCAGATAAAAAGCGGCTTTTCTGTCAG 44 26 0 AAAAGCGGCT 0.987637 -118 CCCACACCGCAAAAGCCGCTTTATGCGGCT 46 12 0 AAAAGCCGCT 0.979809 -131 TGTTTTATTTAAAAGCGGATTTCCCGCTCT 46 52 1 AAAAGCGGAT 0.818848 -91 AACCCCCGATAAAGGGGGCTTTTCTT 47 7 0 AAAGGGGGCT 0.824528 -119 TAATGGAAGGAAAAGGGGTTTTGTGTGATG 50 169 0 AAAAGGGGTT 0.787094 -132 GCAATTTTAAAAAAGAGGCTGGGATTTTGT 51 150 1 AAAAGAGGCT 0.851458 -147 AAGAGTACAAAAAAGGCGCATGCAGAGAGA 55 47 1 AAAAGGCGCA 0.772521 -254 TCCAGGGAGAAAATGCCGCTGACTGAGAGC 56 44 1 AAATGCCGCT 0.805912 -257 CTTTGTTTGCAAAAGCGGTTCATGAGTGTA 58 112 0 AAAAGCGGTT 0.888525 -189 TTTTAATTAAAAAAGGAGCTTTATCTT 58 284 1 AAAAGGAGCT 0.744864 -17 TGCAGCGGTGAAAAGCCGCTGACGCATAAC 59 87 1 AAAAGCCGCT 0.979809 -214 ********** Masking position 3 Map Score: 17.6444 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 685 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 TTGTTTTTAATTGTAAAGCAATGTTGTTAGT 12 117 0 TTGTAAGCAA 0.603144 -50 GAAACAATATCTGTAATGGAGTGATAACA 13 73 1 CTGTAAGGAG 0.967165 -19 TAGTCAAAGTCAGTAAAGGAGGGGGTTGA 14 282 1 CAGTAAGGAG 0.778942 -19 CAACTTCAGCCTGTAACGGCGGCGGCCGCCT 18 153 0 CTGTAAGGCG 0.728537 -148 TCCACTCTGTTTGAAAAGCAGACTTCTGCTC 18 187 0 TTGAAAGCAG 0.867267 -114 ACTCTGACGTTTGTAACGGAGACTGCTCCGG 19 168 0 TTGTAAGGAG 0.93758 -133 AGTGATTCCATTTTAATGGAATAATCAGGGT 19 196 1 TTTTAAGGAA 0.391499 -105 GTGAAAAAAACTGAAATGGAGGTAAGTGGAT 26 280 1 CTGAAAGGAG 0.948428 -21 ATTTTTCGATTTAAAAGGAGAGAAAAAACA 34 10 1 TTTAAAGGAG 0.734468 -23 ATGGCGTGTCCTGAAATGGAGTATGACTAAC 46 93 1 CTGAAAGGAG 0.948428 -50 ACGTTTTGTACGGAAATGGAGCGGCAAAACC 47 63 0 CGGAAAGGAG 0.649015 -63 ATCCTTCTCGTTGTAACGGAAGGTTTTTTGG 48 173 1 TTGTAAGGAA 0.685664 -73 TTTGTTTAACATGAAATGGAGGACATCTGGT 52 36 1 ATGAAAGGAG 0.699415 -265 ACCTTTAACCCTGTAACGCAGGATAAGCGGC 53 142 0 CTGTAAGCAG 0.953537 -159 CCGCTCGATCCTTTAACGCAGGTTCACGTTC 54 135 0 CTTTAAGCAG 0.858222 -166 CATTTTCTCCCTGGAAAGCAGTTGATCAGAA 56 28 0 CTGGAAGCAG 0.749609 -273 CTGAGAGCATTTTTAACGCAGCCGGAAATTG 56 66 1 TTTTAAGCAG 0.755308 -235 GGTTTGTTTACATAAAAGGAGGATGCAAA 56 282 1 CATAAAGGAG 0.393533 -19 TGTGAACCTCTTGAAAAGGAACAGTAATGGC 57 132 1 TTGAAAGGAA 0.57661 -169 CACTTGATACTTTTAACGCAGTTATGCGTCA 59 106 0 TTTTAAGCAG 0.755308 -195 CGGCTCGGTGCTGTAACGCAGCATAGACGGC 61 164 0 CTGTAAGCAG 0.953537 -137 GATTCTGATAATTTAAGGCAGGCCTAAAAA 62 131 1 ATTTAAGCAG 0.433713 -20 ****** **** Masking position 6 Map Score: 14.818 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 299 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 9 AAAAAAACTGCCAGCGTCAGCCGGCAGTTTTT 8 27 0 CCGCTCAGCC 0.877574 -168 ACCTGCTTTCAGCCCCTTTTCTCA 10 33 0 CTCTTCAGCC 0.969258 -14 GGCTCATGGATCTCTCTCAGCCAATGAAGATC 18 62 0 TCCTTCAGCC 0.935391 -239 TTCTGCTCTCCCAACTTCAGCCTGTAACGGCG 18 163 0 CCACTCAGCC 0.895051 -138 GACAGTCATGTTTCCTTCAGGCCTTCATAGCG 20 50 1 TTCCTCAGGC 0.781035 -251 CGGATGATTTCGATTGTCAGCCCGGAGTCTGC 23 138 1 CGTTTCAGCC 0.813955 -96 AGAAATTCTGCTATTTTCAGGCTTATATCAGG 26 94 1 CTTTTCAGGC 0.754722 -207 GCGCTCCGGGTTCTCTTCAGCCTGCAAAAGGT 28 94 0 TTTCTCAGCC 0.85421 -24 GCTAAGTCGGCTCTTTTCAGGCAGTATAGGGG 40 29 1 CTTTTCAGGC 0.754722 -117 GAGATTCCTCCGTCACCCAAAAAGGTTA 41 113 0 CCCCTCACCC 0.806946 -18 AAAAGCGGCTTTTCTGTCAGCCGCTTTTTGAT 44 14 0 TTCTTCAGCC 0.908717 -130 TATGCCCTTTTCCACATCAGCCCCTC 50 5 0 TCACTCAGCC 0.729199 -296 ACCTGTAAAACCGCCCTCAGCCAGATTGTTCT 50 52 1 CCCCTCAGCC 0.985381 -249 TGAACGAAACCTCCTATCATCCTCTTACATGT 50 279 0 CTCTTCATCC 0.56881 -22 TCTGATAAAGCTCCTTTCAGCTTATGGAGCTT 53 72 0 CTCTTCAGCT 0.778584 -229 GCAATGGGATCCGCTTTCAGCCTGGGGCGGGT 54 39 0 CCCTTCAGCC 0.978657 -262 AGCTCTTTTTTCGTTCTCAGCCATTTTTAAAC 55 263 1 TCTTTCAGCC 0.85287 -38 CAGACTGATGCTGTCGTCAGCTTCATTGACAT 56 168 0 CTTCTCAGCT 0.67423 -133 GTAACGGGAGTTCCCGTCAGCCATTACTGTTC 57 150 0 TTCCTCAGCC 0.936036 -151 TGATTTTCACCGGCCATCAGCTCTCTGGAACG 58 60 0 CGCCTCAGCT 0.641766 -241 CGGACCTGATCCGTTATCAGGCAAAGTGATAA 58 169 1 CCTTTCAGGC 0.817351 -132 ** ** ****** Masking position 7 Map Score: 18.7991 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 778 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 GGCTCTCTTAGAAAGAGAGGCTCCCTACTAG 1 61 0 GAAGAGAGGC 0.946378 -240 AACAGGTGGGAGATGAGAGGA 3 290 1 AGAGAGAGGA 0.582092 -11 TACTGTGGGAGGAGGTAAGGA 7 87 1 GGAGTAAGGA 0.752818 -11 TATAGAAGACGGAAATGAGGCATACAGCATG 15 11 1 GGAATGAGGC 0.621668 -81 TTCTTGATATGAAAGTGAGGCATACACTTAC 15 41 0 GAAGTGAGGC 0.879139 -51 GTCCCTTATGGGATGAGAGGGCTTTTTTTAT 20 250 1 GGAGAGAGGG 0.901758 -51 AATGCAGGAAGAATGAGAGGGTGTA 21 5 0 GAAGAGAGGG 0.861957 -111 GCAGGGGAGTGGACGAGCGGA 21 105 1 GGAGAGCGGA 0.967882 -11 ACGATTTAGAGAAAGAGTGGAATGACCGGGG 27 19 1 GAAGAGTGGA 0.695978 -27 GGAGGGAGGGGAGGCGAGTAATCGC 31 5 1 GGAGGGAGGC 0.766909 -247 AATGGATCAAGGAATAGAGGAACCGGA 31 235 1 GGATAGAGGA 0.631945 -17 GACAGAATACGGAGGTGAGGAAA 32 21 1 GGAGTGAGGA 0.938083 -13 ACATGTAAGAGGATGATAGGAGGTTTCGTTC 50 279 1 GGAGATAGGA 0.645771 -22 CCTTCCTCAAGCAGGAGCGGCCAAGAGGTTT 52 273 0 GCAGAGCGGC 0.712953 -28 CCTGCTTGAGGAAGGTGCGGAA 52 289 1 GAAGTGCGGA 0.89417 -12 CTGTAACGCAGGATAAGCGGCAGTGATTAAC 53 132 0 GGAAAGCGGC 0.765717 -169 GGACGAGGTTGAATAAACGGAATCGTGGTTC 57 232 0 GAAAAACGGA 0.387731 -69 CAGCTCTCTGGAACGTAAGGATATTCTACTT 58 44 0 GAAGTAAGGA 0.67446 -257 TTTCAGTAGTGAAAGAACGGACCTGATCCGT 58 152 1 GAAGAACGGA 0.804723 -149 GTATTGACGGGAAGGAGAGGATTATATTCAG 59 237 0 GAAGAGAGGA 0.961549 -64 GAATACATGCGAAGAAAAGGACATGAATGAT 61 34 1 GAAAAAAGGA 0.435821 -267 ACCGTTATTCGAATGAGCGGAAGACAATGTC 63 144 1 GAAGAGCGGA 0.953489 -105 *** ******* Masking position 3 Map Score: 15.9442 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 414 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 11 CATTCTGATTAGGAGGTTTCAAG 2 288 1 AGGAGGTTTC 0.980569 -13 GGAAGTGTATAGGAGGTTTAGTA 9 73 1 AGGAGGTTTA 0.969258 -13 CGATGGTAGTCGGGGGTTTCCCCCTGTGAG 14 23 1 CGGGGGTTTC 0.809585 -278 AAAAGTAGCCAGGAGTTTTCAAAACTGGCT 29 64 1 AGGAGTTTTC 0.783588 -97 CCATTCGAGGAGGTGTCTCAC 35 8 1 AGGAGGTGTC 0.888383 -14 TCATGTTTACAGGGGGTTTTTTTGTTAATA 41 51 1 AGGGGGTTTT 0.770129 -80 AGAGGATGATAGGAGGTTTCGTTCA 50 286 1 AGGAGGTTTC 0.980569 -15 AGGAGCGGCCAAGAGGTTTATAAAATTGGA 52 262 0 AAGAGGTTTA 0.674971 -39 ATAAGCTGAAAGGAGCTTTATCAGAAGATC 53 79 1 AGGAGCTTTA 0.860539 -222 AACAACACTCCGGAGGTTTCCTGCTGAACG 54 82 1 CGGAGGTTTC 0.936093 -219 GGAATACATAAGGAGGTCTACCT 54 288 1 AGGAGGTCTA 0.832574 -13 TAATTAAAAAAGGAGCTTTATCTT 58 287 1 AGGAGCTTTA 0.860539 -14 TTCAATCAGAAGGAGGTTTTTACT 59 287 1 AGGAGGTTTT 0.920269 -14 AATGCTTTTTATGAGGTTTATCTTCAAATC 60 183 1 ATGAGGTTTA 0.674971 -118 ********** Masking position 7 Map Score: 11.5627 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 69 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 12 TGTGGACCGGGAAAATGGAAATAATGAAGGATAGAGC 14 192 1 GAAAATGAAA 0.74285 -109 CACCCTTTTAGAAAAAGCAAGCATACACTTTTTCCTC 20 191 0 GAAAAAGAAA 0.921319 -110 GTTCTCATAATAAAAGGGCAATAGACACGCTATTACC 22 33 0 TAAAAGGAAA 0.869227 -50 ACTTTTTGAAGAAAAATGCAAAATTTATTAAAATTAT 26 25 0 GAAAAATAAA 0.642984 -276 TATTTCTCCACAAAAGGAAAAAAGAAAACTTTCTATA 28 32 1 CAAAAGGAAA 0.87768 -86 TTTTTCGATTTAAAAGGAGAGAAAAAACAGC 34 12 1 TAAAAGGAAA 0.869227 -21 ACGAAAAGTAAATCAATCAGAGGTGCGAA 43 3 1 GAAAAGTAAA 0.849375 -30 GGCTGATGTGGAAAAGGGCATAAAGCAAAAGTGTAAT 50 15 1 GAAAAGGAAA 0.973449 -286 TATAGTGGATGAAAAAGAAAACAGCAAACGTGCTTAA 50 213 1 GAAAAAGAAA 0.921319 -88 TAAAGAACTGGAAAAAGAGAACATGGAAAGACCCGAA 52 193 1 GAAAAAGAAA 0.921319 -108 CACACGTATTGATAAGGACACGAAGGAATGATACCGG 57 22 1 GATAAGGAAA 0.758282 -279 AGCTTCATATGAAAAGGTAAAGATTGAGACAAGTAGA 58 14 1 GAAAAGGAAA 0.973449 -287 TCCCTCATCCCAAAAAGGGACGAGAGACTTTCGTTTT 59 177 0 CAAAAAGAAA 0.696203 -124 AGTTTTAAGATAAAAGTACAACATAGATCTGCTAGAA 60 24 0 TAAAAGTAAA 0.505521 -277 AAAAAAATGTGAAAAGGAAATGATAGATTTCGGAAAA 60 92 1 GAAAAGGAAA 0.973449 -209 TACATGCGAAGAAAAGGACATGAATGATAGTTACGGT 61 37 1 GAAAAGGAAA 0.973449 -264 ******* * * * Masking position 10 Map Score: 13.5056 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 137 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 ATGATTTGCACTTATCGCCGCTCTCGTCCTTTG 2 239 1 CATGCCGCTC 0.961351 -62 GATCCCCTCCGCCGCTACCATATTTGT 3 5 1 CTCGCCGCTA 0.540535 -296 GAATATCTTTAAAATACCTGCTCATTGTGAGGA 6 74 1 AATCCTGCTC 0.647373 -30 ATACCATACACGATCAGCGGCTCATTTGTAAAC 8 116 0 CTCGCGGCTC 0.889083 -79 TACTCACCTCTATTTGCTGCTCACTGCTAGTT 13 10 1 CTTGCTGCTC 0.941008 -82 TCATTATTTCCATTTTCCCGGTCCACAAAACCT 14 186 0 CTTCCCGGTC 0.665066 -115 GTTTGAAAAGCAGACTTCTGCTCTCCCAACTTC 18 177 0 CACTCTGCTC 0.583223 -124 TCCACATTGCCCGTTATCTGCTCCCAGCACCGC 19 90 0 CTTTCTGCTC 0.760523 -211 TTTTCCAGTTCGGTCAGCTGCTCCAAAGTCCAT 19 123 0 CTCGCTGCTC 0.918421 -178 TCCGCTCGTCCACTCCCCTGCTCTCTTATAGAG 21 93 0 CTCCCTGCTC 0.900482 -23 AGCGGCTTTTCTGTCAGCCGCTTTTTGATCTG 44 10 0 CTCGCCGCTT 0.540535 -134 TCATCACTTTATTATACCCGCTCTTAACTAACC 44 61 0 AATCCCGCTC 0.820956 -83 ATTTAAAAGCGGATTTCCCGCTCTGTGATACTA 46 58 1 GTTCCCGCTC 0.831704 -85 AGAGTAAAACGGTTTTGCCGCTCCATTTCCGTA 47 53 1 GTTGCCGCTC 0.860115 -73 GCCAAATGAAAAAATTGCCGCTCCGATTAAAAT 50 103 1 AATGCCGCTC 0.850856 -198 TTTTATAAACCTCTTGGCCGCTCCTGCTTGAGG 52 267 1 CTTGCCGCTC 0.975514 -34 GGAATACGTTCATATTCCCGCTCGATCCTTTAA 54 150 0 CATCCCGCTC 0.952363 -151 ACACGAAGGAATGATACCGGCTCAAAGAGAGGG 57 39 1 AATCCGGCTC 0.566562 -262 ACTTCAGTTCCCCAATGCTGCTCCAAGGCGGTA 61 124 0 CAAGCTGCTC 0.476908 -177 GACAAATACTATGTTGTCGGCTCGGTGCTGTAA 61 179 0 ATTTCGGCTC 0.341499 -122 ATTCGAATAACGGTTTCCCGTTCTTTGCTACTA 63 125 0 CTTCCCGTTC 0.572603 -124 * ** ******* Masking position 12 Map Score: 12.6458 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 664 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 14 CTACTCTCACAGGGGGAAACCCCCGACTAC 14 28 0 AGGGGGAAAC 0.782723 -273 CCTTTTTTACAGGGGAAGAATGAGCCTTTT 19 247 1 AGGGGAAGAA 0.69368 -54 TACGATGCTCAAGAGGAAAAAGTGTATGCT 20 179 1 AAGAGGAAAA 0.664454 -122 TAAAGTGCAGAGGGGGAGAATTCA 24 67 1 AGGGGGAGAA 0.947568 -14 CCGAAAAGAAAGGAGAAAAAACAGAAATTC 26 72 1 AGGAGAAAAA 0.750792 -229 GGCTTATATCAGGGCGAGAAATGTAGTTCT 26 113 1 AGGGCGAGAA 0.736089 -188 AAGGATATTGAGGGTGAAAAAAACTGAAAT 26 267 1 AGGGTGAAAA 0.739192 -34 TTAAGGTATTAGGGGGATAACA 36 11 1 AGGGGGATAA 0.736552 -12 ATGACCTAAGCGGAGGAAAAAAACCATTAT 38 108 1 CGGAGGAAAA 0.718269 -36 CCATTATATTAGGAGGAAATAAC 38 131 1 AGGAGGAAAT 0.838658 -13 TAAACATATAAGGAGGAATACAA 39 89 1 AGGAGGAATA 0.762385 -13 TCTATTATGCAAGAGAAAAAAAGGTTTGTA 40 96 0 AAGAGAAAAA 0.198804 -50 GACGAATTAGGGGGAGTTCAAG 45 9 1 AGGGGGAGTT 0.342715 -14 TTCAAACTGGAGGATGAAAAA 46 132 1 AGGATGAAAA 0.705784 -11 TCTAAACATGAGGAGGAGAAAAC 48 233 1 AGGAGGAGAA 0.938636 -13 ATTTTTATAGAGGAGGAAATACA 53 288 1 AGGAGGAAAT 0.838658 -13 TCCCTGTAAAAGGACGAAAAGCTCTTTCGC 55 228 0 AGGACGAAAA 0.787714 -73 ACTGCTTTCCAGGGAGAAAATGCCGCTGAC 56 37 1 AGGGAGAAAA 0.61646 -264 TTTGTAAAAAAGGAGGAAAA 63 239 1 AGGAGGAAAA 0.960068 -10 ********** Masking position 7 Map Score: 10.5439 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 332 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 15 TATACATACGCCCTGAAAAAGAATAATTAA 2 144 0 CCCTGAAAAA 0.879675 -157 TTATACTCTTCCCTGTCAACAATCATTTA 18 10 0 CCCTGTCAAC 0.900206 -291 CTCATTCTTCCCCTGTAAAAAAGGGACGAA 19 241 0 CCCTGTAAAA 0.967175 -60 TCTACGTTCCCCCTGTAAAATAGACGTCTC 23 55 0 CCCTGTAAAA 0.967175 -179 ACTACAATTACTCTGTCAAATGGTAAGAAG 31 131 1 CTCTGTCAAA 0.781066 -121 CAAAAAAACCCCCTGTAAACATGAGAGGGT 41 45 0 CCCTGTAAAC 0.948598 -86 AAAGTGTAATACCTGTAAAACCGCCCTCAG 50 42 1 ACCTGTAAAA 0.698943 -259 TACGCCGAAGCCCTGTTAAAGAGAGAAGCT 53 47 1 CCCTGTTAAA 0.903016 -254 AGCTCTTCATCCCTGTAAAAGGACGAAAAG 55 237 0 CCCTGTAAAA 0.967175 -64 TTCCTTCCCTCTCTGAAAACCGTAACTATC 61 62 0 CTCTGAAAAC 0.531446 -239 TCACACCAGACTCTGTTAAAATTCGTTTCA 62 93 1 CTCTGTTAAA 0.697556 -58 ********** Masking position 8 Map Score: 9.38994 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 58 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911