AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_bsub_reg_300.orf -o03010_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: rplB 31 ribosomal protein L2 (BL2) rpmF 21 ribosomal protein L32 rpsN 22 ribosomal protein S14 rplF 29 ribosomal protein L6 (BL8) rplR 32 ribosomal protein L18 rpsE 24 ribosomal protein S5 rpsM 22 ribosomal protein S13 cheW 21 cheW Input sequences: #1 cysE 300 serine acetyltransferase #2 sigH 62 RNA polymerase sigma-30 factor (sigma-H) #3 rpmG 92 ribosomal protein L33 #4 secE 33 preprotein translocase subunit #5 nusG 178 transcription antitermination factor #6 rplK 167 ribosomal protein L11 (BL11) #7 rplA 93 ribosomal protein L1 (BL1) #8 rplJ 251 ribosomal protein L10 (BL5) #9 rplL 46 ribosomal protein L12 (BL9) #10 ybxB 89 alternate gene name: ybaA; similar to hypothetical proteins #11 rpoB 245 RNA polymerase (beta subunit) #12 rpoC 61 RNA polymerase (beta' subunit) #13 ybxF 180 alternate gene name: ybaB; similar to ribosomal protein L7AE family #14 rpsL 113 ribosomal protein S12 (BS12) #15 rpsG 41 ribosomal protein S7 (BS7) #16 fus 53 elongation factor G #17 tufA 119 elongation factor Tu #18 ybaC 98 ybaC #19 rpsJ 235 ribosomal protein S10 (BS13) #20 rplC 39 ribosomal protein L3 (BL3) #21 rplD 27 ribosomal protein L4 #22 rpsS 57 ribosomal protein S19 (BS19) #23 rpsQ 22 ribosomal protein S17 (BS16) #24 rplN 40 ribosomal protein L14 #25 rplX 37 ribosomal protein L24 (BL23) (histone-like protein HPB12) #26 rplE 26 ribosomal protein L5 (BL6) #27 rpsH 31 ribosomal protein S8 (BS8) #28 rplO 30 ribosomal protein L15 #29 infA 300 initiation factor IF-I #30 rpmJ 33 ribosomal protein L36 (ribosomal protein B) #31 rpoA 176 RNA polymerase (alpha subunit) #32 rplQ 77 ribosomal protein L17 (BL15) #33 ybxA 127 alternate gene name: ybaD; similar to ABC transporter (ATP-binding protein) #34 rplM 162 ribosomal protein L13 #35 ylbN 209 ylbN #36 rpmB 276 ribosomal protein L28 #37 ylxM 176 similar to hypothetical proteins #38 rpsP 105 ribosomal protein S16 (BS17) #39 ylqD 121 ylqD #40 rplS 130 ribosomal protein L19 #41 flgB 300 flagellar basal-body rod protein #42 fliF 45 flagellar basal-body M-ring protein #43 fliH 117 flagellar assembly protein #44 fliK 160 fliK #45 flgE 21 flagellar hook protein #46 fliL 251 flagellar protein #47 fliM 33 flagellar motor switch protein #48 cheY 25 two-component response regulator #49 flhA 32 flagella-associated protein #50 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #51 ylxL 28 ylxL #52 rpsB 143 ribosomal protein S2 #53 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #54 nusA 34 nusA #55 truB 81 tRNA pseudouridine 55 synthase #56 rpsO 156 ribosomal protein S15 (BS18) #57 ypfD 232 alternate gene name: jofD; similar to ribosomal protein S1 homolog #58 cmk 78 cytidylate kinase #59 ypfB 44 alternate gene name: jofB #60 ypfA 92 alternate gene name: jofA #61 ypeB 34 alternate gene name: joeB, yzuA; similar to hypothetical proteins #62 sleB 138 spore cortex-lytic enzyme #63 ypdC 119 similar to hypothetical proteins #64 ypdA 108 similar to thioredoxin reductase #65 ypcA 155 similar to glutamate dehydrogenase #66 ypbH 158 similar to negative regulation of competence MecA homolog #67 ypbG 85 similar to hypothetical proteins #68 ypbF 62 ypbF #69 ypbD 59 ypbD #70 ypbB 265 ypbB #71 rpsU 163 ribosomal protein S21 #72 rpsT 203 ribosomal protein S20 (BS20) #73 rplU 146 ribosomal protein L21 (BL20) #74 spoIVFA 150 inhibitor of SpoIVFB #75 minC 52 minC #76 mreC 30 cell-shape determining protein #77 mreB 90 cell-shape determining protein #78 ysxA 36 similar to DNA repair protein #79 maf 152 maf #80 spoIIB 133 spoIIB #81 comC 139 DNA-binding protein #82 folC 59 folyl-polyglutamate synthetase #83 valS 300 valyl-tRNA synthetase #84 rplT 31 ribosomal protein L20 #85 infC 171 initiation factor IF-3 #86 rpsD 294 ribosomal protein S4 (BS4) #87 rpmE 118 ribosomal protein L31 #88 rho 300 transcriptional terminator Rho #89 yybT 36 yybT #90 yybS 300 yybS #91 rpsR 37 ribosomal protein S18 #92 ssb 40 single-strand DNA-binding protein #93 rpsF 110 ribosomal protein S6 (BS9) #94 yyaF 126 similar to hypothetical proteins #95 yyaE 300 similar to formate dehydrogenase #96 rpmH 217 ribosomal protein L34 Motif number 1 CTAAAACCAAATGCGGGGAGGGAAGGACTGG 5 143 1 AGCGGGGAGG 0.753235 -36 CGCTATAACCACATAAGGAGGAAATTTTAAA 7 73 1 AATAAGGAGG 0.506444 -21 TTAAGCCATGAAAAAAGGAGGTTCTAATA 10 71 1 AAAAAGGAGG 0.882852 -19 ATCCGAAGATAAAAAGGGAGGTAGGCCCC 12 43 1 AAAAGGGAGG 0.935346 -19 ATAAAACGTAATGAAGGGAGGAAAAATTC 14 95 1 AGAAGGGAGG 0.987359 -19 CGCATAATTAATGAAGGGAGGATATTCAG 15 23 1 AGAAGGGAGG 0.987359 -19 ATTTCCTAATAAGGAAGGAGAAATTACCCA 16 34 1 AGGAAGGAGA 0.722335 -20 GTGATGTAGGCGAAAAGGAGGGAAAATA 19 218 1 CAAAAGGAGG 0.799148 -18 TTCTCTTAGGAAAGGAGGAAATTGATT 21 8 1 AGAAAGGAGG 0.976013 -20 TAGTGCAATCACGAAGGGAGGTTCCAAA 22 40 1 AGAAGGGAGG 0.987359 -18 TCACTGAGGGGAGGTCGTGAGC 23 4 1 CGAGGGGAGG 0.952781 -19 AATTCTTTTTCCGAAGGGAGGTAACAAATA 24 21 1 CGAAGGGAGG 0.976325 -20 TATTAAAAGGAAGGGAGGTCTATCTC 26 8 1 AGAAGGGAGG 0.987359 -19 TCCCCAAGAAAGGGAAGGAGGTAATTATATA 27 11 1 AGGAAGGAGG 0.951539 -21 TACTGATTTGAAGAAGGGAGAACACTTGA 29 282 1 AGAAGGGAGA 0.911886 -19 CACTCCGGAAACTGAAGGAGGTTGGAAACAC 30 13 1 ATGAAGGAGG 0.534712 -21 ACAGCATTCCAATAAAGGAGGGGACATCAC 32 58 1 ATAAAGGAGG 0.704271 -20 TGTGTATCTAAAGAAGGGCGGGACAGTTTCT 33 22 1 AGAAGGGCGG 0.893377 -106 AGAGCATTAGCTGAGAGGAGGCCGGTTTTCC 33 107 1 CGAGAGGAGG 0.913127 -21 TAAACATAGCAAGAAAGGCGGAAAAAAT 35 8 0 AGAAAGGCGG 0.813597 -202 TGTTTTGTGCAAGTGAGGAGGGAAACAA 36 259 1 AGTGAGGAGG 0.730513 -18 TTTGACTTAACAAAGGGGAGAGCTCAA 37 160 1 CAAGGGGAGA 0.331171 -17 TGCGTGTAAAAAAAGGGGAGGTGCCGGCCCT 39 18 0 AAAGGGGAGG 0.876217 -104 AAATGCCGAAAAGAAAGGAGAAAAAACAGAA 41 67 1 AGAAAGGAGA 0.843529 -234 GGAGGGAGGGGAGGCGAGTAATCG 46 4 1 GGAGGGGAGG 0.745666 -248 CAAATGTTTTAAGGGGGGAGACCGTTAA 54 17 1 AGGGGGGAGA 0.7096 -18 ATTGGTGTATTCGGAGGGAGGGAAAGAGA 71 145 1 TGGAGGGAGG 0.661122 -19 GGTCAAGCAAATGAAGGGAGGAAGCGGAA 80 115 1 AGAAGGGAGG 0.987359 -19 CTCTCTGCTGCTGGAGCGAGGATACATGAAA 86 199 1 CGGAGCGAGG 0.567679 -96 CAAAAATAAAACCAAAGGAGGAGTCACATT 86 275 1 ACAAAGGAGG 0.786494 -20 TGAGTTTTGAAGGAAGCGAGGACAAAAACAT 88 119 0 AGAAGCGAGG 0.837504 -182 TAAAATGAAAAAGAAAGGAGGGAA 91 24 1 AGAAAGGAGG 0.976013 -14 GCCGCTTAGTCCAAAAGGAGGTGCAAACAG 93 91 1 CAAAAGGAGG 0.799148 -20 TTCATATAGAAGGTAAGGAGAAGACGGCG 95 282 1 AGTAAGGAGA 0.423305 -19 ACAGCTATTCCTCGAGGGAGGTGTCATAA 96 199 1 CCGAGGGAGG 0.643066 -19 * ********* Masking position 8 Map Score: 52.9196 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 143 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 GAGACACACCTCCTTAAGTCCGTGAT 6 152 0 CACCTCCTTA 0.9857 -16 TGATAATATACACCTCGGTAGGATAATTAA 8 99 0 CACCTCGGTA 0.765165 -153 GGTTACACCTCCTGTAGATTCTTGT 8 237 0 CACCTCCTGT 0.94229 -15 TATTAGAACCTCCTTTTTTCATGGCT 10 74 0 AACCTCCTTT 0.872024 -16 TCGTCACACCTCCTATTAAGATCATT 20 24 0 CACCTCCTAT 0.970934 -16 TAGGACACCTCCTTATCCGATCAAA 28 16 0 CACCTCCTTA 0.9857 -15 GTGATGTCCCCTCCTTTATTGGAATGC 32 61 0 CCCCTCCTTT 0.947926 -17 TGAATTTCCCCTCCTAAATGATCTGTC 34 146 0 CCCCTCCTAA 0.882981 -17 TTTACTAGCACCTCCGAAAATATTTCAA 38 88 0 CACCTCCGAA 0.892786 -18 GATCAATACGCACCTCTTGTATAGAAAGTT 43 58 0 CACCTCTTGT 0.703372 -60 TTTCCTCACCTCCGTATTCTGTCAAA 47 18 0 CACCTCCGTA 0.948926 -16 CCTGTTTCACCTCCAAATCATATTTAG 56 140 0 CACCTCCAAA 0.841163 -17 TGGAGCACCTCCATTACAAATAGTA 59 30 0 CACCTCCATT 0.927408 -15 TTATCACACCTCTTTTTATGCTTTCT 61 19 0 CACCTCTTTT 0.915424 -16 GTATAAAAATAACCTCGTTACAGAAAATAC 62 81 1 AACCTCGTTA 0.524985 -58 GTGTTTCACCTCCTAAGATACAACCT 72 188 0 CACCTCCTAA 0.968647 -16 TCTCTGCACCTCCTATTAGACTAAGA 73 131 0 CACCTCCTAT 0.970934 -16 TGATAATCCCCTCTTTTATAAGACAAG 82 43 0 CCCCTCTTTT 0.725544 -17 CTGATAAATACACCTGCTTAGAACGGGAAG 83 20 1 CACCTGCTTA 0.772262 -281 GAGCCACCTCCATAGTTTCTTCGA 85 158 0 CACCTCCATA 0.921971 -14 AATGTGACTCCTCCTTTGGTTTTATTT 86 278 0 CTCCTCCTTT 0.820843 -17 TTAGTCACCTCGTATCATCCTGAAC 90 286 0 CACCTCGTAT 0.854188 -15 CTGTTTGCACCTCCTTTTGGACTAAGC 93 94 0 CACCTCCTTT 0.98676 -17 TTTTCCAGTGAACCTCCTTATAATTGCTCT 94 55 1 AACCTCCTTA 0.863052 -72 CAAGACCCTTCACCTCTTTTCCTAAACTGC 95 27 0 CACCTCTTTT 0.915424 -274 ********** Masking position 5 Map Score: 33.9242 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 88 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 ATGAGGCGAGCTTTTTCTTTGCCATTCTTT 10 43 1 CTTTTTCTTT 0.883089 -47 TAGAACCTCCTTTTTTCATGGCTTAAAGAA 10 67 0 TTTTTTCATG 0.877991 -23 TTAGAAACCCTTTTTTCTTTTGTCTTGTAA 11 157 1 TTTTTTCTTT 0.858097 -89 CATAGAGTGACTTTTTCATAAATATATCTG 13 55 0 CTTTTTCATA 0.866775 -126 GTTTGCTTATCTTTTTCTTGTATAATAGGA 18 52 1 CTTTTTCTTG 0.880942 -47 GATTGATATTCTTTTTCTTAGGAGAATGAA 29 153 0 CTTTTTCTTA 0.842658 -148 TTTGTCAATATTTTTTCTTTACAGCATAAT 35 139 0 TTTTTTCTTT 0.858097 -71 TTGTAAAGTGTTTTTTCTTAACAACGGTTT 38 27 0 TTTTTTCTTA 0.810874 -79 TCTTTTGAGTTTTTTTCTTATAAACGAAGA 55 47 0 TTTTTTCTTA 0.810874 -35 ATTTTTCACCCTTTTTCATAAAGTTCGTGA 58 21 1 CTTTTTCATA 0.866775 -58 GTCTTTTCCTTTTTTTCATTACGTGCTTTA 60 33 1 TTTTTTCATT 0.880184 -60 TTCAGCAGTTTTTTTTCGTTAAAAAACATG 65 34 1 TTTTTTCGTT 0.77172 -122 AGAAAAATAACTTTTTCATGACAAAATAAA 79 53 0 CTTTTTCATG 0.899888 -100 ACGAGTATCTTTTTTTCTTAAGCAAACCCT 79 118 1 TTTTTTCTTA 0.810874 -35 GTCTTGTTCTTTTTTTCTTTGCCTGTGCTA 80 55 1 TTTTTTCTTT 0.858097 -79 ATTCTGCCGTTTTTTTCATGTGTAAAATTG 81 42 1 TTTTTTCATG 0.877991 -98 CGGTACCACCTTTTTTCATGAACTCAATCA 83 199 0 TTTTTTCATG 0.877991 -102 TGAAGAGCTCTTTTTTCGTTCTCAGCCATT 83 258 1 TTTTTTCGTT 0.77172 -43 CCTTGTTTTTCTTTTTCGTTTTTCTGACAT 90 23 0 CTTTTTCGTT 0.808531 -278 ATGTCTTTTCCTTTTTCATGTTTCACATGA 90 110 1 CTTTTTCATG 0.899888 -191 TCCCTCCTTTCTTTTTCATTTTAGGCGATA 91 17 0 CTTTTTCATT 0.901731 -21 ATGGATGCGGTTTTTTCATTTCTACGATAT 95 82 0 TTTTTTCATT 0.880184 -219 GACACTCATGCTTTTTCATATAGAAGGTAA 95 268 1 CTTTTTCATA 0.866775 -33 ********** Masking position 5 Map Score: 28.7654 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 706 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 4 CATGCAGAGACGCTTTTTTTATTGGGTAGAGGA 1 250 1 CGCTTTTTTT 0.849581 -51 ACCCGTTCAGCGGGTTTTTTATTGTGGCTTAAA 5 57 1 CGGTTTTTTT 0.785312 -122 CCCTGTGGGTCTCGTTTTTTGTTTGCTTATCTT 18 32 1 CTCTTTTTTT 0.857943 -67 ATCATTTGCACACTTTTTTTATTATACAGGGGT 19 34 0 CACTTTTTTT 0.910478 -202 GGGCCGGCACCTCCCCTTTTTTTACACGCAAAA 39 19 1 CTCCCTTTTT 0.821453 -103 TCCGGTTCCTCTATTCCTTGATCCA 46 237 0 CGGTCCTTTT 0.449994 -15 AATCTATCTCTCTCCTTGTGTTTCG 48 4 0 CTCCCTTTTT 0.821453 -22 TTGCCTTTCACTCCTTCTTTTGAGTTTTTTT 55 61 0 CACCCTTTTT 0.885684 -21 CTTGACAAACCTGTCCTTTTATTAGAAGTTAAT 57 64 1 CTGCCTTTTT 0.748721 -169 TTTTTGTGTGCAGTTTTTATGTTCTGAGGGATA 62 35 1 CAGTTTTTTT 0.868191 -104 CATTCGTATGCTCTTTTTGTTTTTTTAAGTGCA 63 30 1 CTCTTTTTTT 0.857943 -90 CGTTGATTTGCTCTTTTTATTTTAACAGATTTC 70 212 0 CTCTTTTTTT 0.857943 -54 TATGCTGTGTCAGGTTTTTTTTTGTTTTTGCCT 74 46 1 CAGTTTTTTT 0.868191 -105 CGTGTTACACCTCTTCTATTGAACTCCCGA 76 11 0 CACTCTTTTT 0.898752 -20 GCACTCCTTTTCTTTCCCTTCCCG 78 23 0 CACCCTTTTT 0.885684 -14 TTATAATGCCCACACTTTTTGTTTGCCTGCAAA 85 97 1 CACCTTTTTT 0.898752 -75 TGAAATATTGCAGCCTTTTTGTTCAGCTTCTAT 86 126 1 CAGCTTTTTT 0.851828 -169 CCTTTTTGTTCAGCTTCTATGTTTTCATTTTGT 86 139 1 CAGTTCTTTT 0.627969 -156 TTCGACCATGCACATTTTGTTTTCATGTATCCT 86 217 0 CACTTTTTTT 0.910478 -78 ATAGAGCAGACGGTTTTTATTTTCCACAAAAAT 86 249 1 CGGTTTTTTT 0.785312 -46 AAATTCGCAGCACTCTTTATTTTTACCT 88 6 0 CACCTTTTTT 0.898752 -295 TCCGCCAAAGCACATTCTTTTTTTAACATAAAG 88 211 0 CACTTCTTTT 0.722708 -90 GCATAAACGACTGCTCTTTTGTTCATCGCTGCA 90 234 0 CTGTCTTTTT 0.773441 -67 *** **** * ** Masking position 8 Map Score: 20.7592 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 402 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 5 GCGCACTTCTAAAACCCGGCTCATGGATCTC 1 80 0 AAAACCGGCT 0.887656 -221 TTGGGAGAGCAGAAGTCTGCTTTTCAAACAG 1 181 1 AGAATCTGCT 0.521366 -120 GTAAAAGACCTCCACAATTTAAAA 4 20 0 AAAGCCTCCA 0.735116 -14 ATTCCATATAAAAAGCCTCCATGAGACATGG 8 165 0 AAAACCTCCA 0.926835 -87 TGGCAAAGAAAAAGCTCGCCTCATAAAAGCG 10 36 0 AAAGTCGCCT 0.701238 -54 TCTAAAATCCTCCTTAAGAGCTTT 17 106 0 AAAACCTCCT 0.976776 -14 TACTTAAAACCCTCCTTCAAAACGTC 31 161 0 AAAACCTCCT 0.976776 -16 GGAAAACCGGCCTCCTCTCAGCT 33 115 0 AAAACGGCCT 0.783531 -13 AAAAATCCTCCTTAAAATAGGG 37 2 1 AAAACCTCCT 0.976776 -175 TCTTGGCCACAAAAACCGGCACAGCGGAACA 40 93 0 AAAACCGGCA 0.70412 -38 GTTCGTGTAAAAAAATGTCCTCACAATTATC 41 177 0 AAAATGTCCT 0.69493 -124 ATGTCGAGACAAAATTCTCCTGTTCAATACA 53 183 0 AAAATCTCCT 0.943946 -118 ACTCTGCATAAAAACCCTGCTTCAAAAGAGC 53 239 0 AAAACCTGCT 0.92548 -62 TTGAATAACCTCCTTGGTCCAAAC 57 219 0 AATACCTCCT 0.760938 -14 CATAAAAATAAAAAATCTCCTATGATAAAAT 64 23 1 AAAATCTCCT 0.943946 -86 TTCCGAATAAAAAAATCTCCTATTTTATCAT 64 44 0 AAAATCTCCT 0.943946 -65 AAAAAACTCTCCATTCTTTTTAG 67 73 0 AAAATCTCCA 0.83531 -13 CGGTTTCTAGAGAAACCGCCTTGTCTTATAA 82 24 1 AGAACCGCCT 0.854274 -36 **** ****** Masking position 1 Map Score: 14.4401 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 249 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 6 AAACCTTGAGTGGGAGGGTTTACCCTATTAC 6 118 1 TGGGAGGTTT 0.877416 -50 CCCTTATTCGTGGGAGGTTATCCGCTATAAC 7 51 1 TGGGAGGTAT 0.817146 -43 ATAACCACATAAGGAGGAAATTTTAAA 7 77 1 AAGGAGGAAT 0.861725 -17 TCCATGTCTCATGGAGGCTTTTTATATGGAA 8 164 1 ATGGAGGTTT 0.885985 -88 TTAAAACAAAATGGAGGAATTACAA 9 32 1 ATGGAGGATT 0.750397 -15 GCCATGAAAAAAGGAGGTTCTAATA 10 75 1 AAGGAGGTCT 0.790075 -15 ACCTGTTACTTTGGAGGATATGTTT 13 166 1 TTGGAGGTAT 0.738042 -15 TAATTAATGAAGGGAGGATATTCAG 15 27 1 AGGGAGGTAT 0.884997 -15 CCTAATAAGGAAGGAGAAATTACCCA 16 38 1 AAGGAGAATT 0.591765 -16 AAAAGCTCTTAAGGAGGATTTTAGA 17 105 1 AAGGAGGTTT 0.962687 -15 TCTCTTAGGAAAGGAGGAAATTGATT 21 12 1 AAGGAGGAAT 0.861725 -16 CAAGAAAGGGAAGGAGGTAATTATATA 27 15 1 AAGGAGGAAT 0.861725 -17 CGACGTTTTGAAGGAGGGTTTTAAGTA 31 160 1 AAGGAGGTTT 0.962687 -17 ACCCTATTTTAAGGAGGATTTTT 37 3 0 AAGGAGGTTT 0.962687 -174 ACCATTATATTAGGAGGAAATAAC 52 130 1 TAGGAGGAAT 0.783502 -14 TGCTCTTTTGAAGCAGGGTTTTTATGCAGAG 53 238 1 AAGCAGGTTT 0.591656 -63 GGTTTGGACCAAGGAGGTTATTCAA 57 218 1 AAGGAGGTAT 0.941549 -15 AAATTTGCAGTAGGAGGCTTGAAAAG 62 123 1 TAGGAGGTTG 0.577183 -16 TATTTTATCATAGGAGATTTTTTATTTTTAT 64 24 0 TAGGAGATTT 0.685122 -85 TATGATAAAATAGGAGATTTTTTTATTCGGA 64 43 1 TAGGAGATTT 0.685122 -66 TCTAAAAAGAATGGAGAGTTTTTT 67 72 1 ATGGAGATTT 0.530186 -14 AAGAACAATCTGGGAGGTTTTATTC 70 5 0 TGGGAGGTTT 0.877416 -261 ******* *** Masking position 5 Map Score: 21.4566 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 163 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 7 CACTCTGTTTGAAAAGCAGACTTCTGCTCTC 1 185 0 GAAAAGCGAC 0.949907 -116 TGATGTAGGCGAAAAGGAGGGAAAATA 19 219 1 GAAAAGGGGG 0.833983 -17 AGCAGACGGAGAAAAGCGTACATTTCATTCT 29 130 1 GAAAAGCTAC 0.824476 -171 TTAATAGAGAGAAAAGCAGAGCATTAGCTGA 33 90 1 GAAAAGCGAG 0.957657 -38 AGGCAAAATAGAAAAGCCTGGACGAGTAAAA 39 75 1 GAAAAGCTGG 0.914202 -47 GTAAAAGTTTTAAAAGCGGGGAGCTTGGTGC 39 100 1 TAAAAGCGGG 0.868888 -22 CATATTCGGCTAAAAGCGGGCATGTTATATG 57 153 1 TAAAAGCGGC 0.847478 -80 TGTGTAGCATGAAAAGCCGACAAGAACGGTC 80 88 1 GAAAAGCGAC 0.949907 -46 TGAAAAGCCGGGGCGGTTTCTA 82 2 1 GAAAAGCGGG 0.977281 -58 TATTGACTATGAAAAGCGTGGTGTTTTT 88 283 1 GAAAAGCTGG 0.914202 -18 CACTGGAAAAGACAAGCTGACAAAAAAGCAT 94 34 0 GACAAGCGAC 0.781234 -93 ******* *** Masking position 5 Map Score: 7.93718 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 292 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 CCTCCTTATGTGGTTATAGCGGATAACCTCCC 7 62 0 TGGTAAGCGG 0.826196 -32 ATAATACGCATGATTTGAGGGGTGAATCAG 11 226 1 TGATTAGGGG 0.936975 -20 TAGTTATACTTGAGTTAAGCGGCAAAATCAA 17 10 0 TGATTAGCGG 0.974469 -110 ATACTACTTGTGGCTTAAGCGGGCTTATCCGC 40 44 1 TGGTTAGCGG 0.973961 -87 CTACTTTTCATGTTTTTAGCGGCAGAACCCGT 44 40 0 TGTTTAGCGG 0.959665 -121 TGTACAAAAATGACCTAAGCGGAGGAAAAAAA 52 99 1 TGACTAGCGG 0.959849 -45 TGAATACAAATGTTTTAAGGGGGGAGACCGTT 54 11 1 TGTTTAGGGG 0.902602 -24 GGAAAACTGCTGATTTCAGCAGTTTTTTTTCG 65 20 1 TGATTAGCAG 0.750464 -136 TCTTAACACCTGTACTGAGCGGTTGTAGCAAT 73 70 0 TGTCTAGCGG 0.937114 -77 CACCTCCTTTTGGACTAAGCGGCCCATAATGG 93 82 0 TGGCTAGCGG 0.95907 -29 TCCACATGCGTGATTTTAGGGGCAAATTGTTT 96 12 1 TGATTAGGGG 0.936975 -206 *** ** ***** Masking position 8 Map Score: 10.5357 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 79 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TGTGAAAAAACTTGAAATTGCTATATA 6 3 1 TGAAAAGAAA 0.935949 -165 AACTCTCTGCTGAAAGACTGCAAAAACAGTCTTGC 13 18 1 TGAAGAAAAA 0.866275 -163 ATGTATAGAGTGATAGGAAGTGAAAGAAAGCTTTC 17 62 0 TGAAGGGAAA 0.643722 -58 TAGATCCTTGATAAATAAGAAAAACCCCTGTAT 19 9 1 TGAAAAAAAA 0.946839 -227 ACTTGCTTTCTGACAAATTTCAAAAGAAGTTTGTC 29 247 0 TGAAAAAAAA 0.946839 -54 TGAATTTTCTTGAAAGATGATGAAACAATAGTTGC 36 144 1 TGAAGAGAAA 0.841641 -133 ATATTGAGGGTGAAAAAAACTGAAATGGAGGTAAG 41 271 1 TGAAAAGAAA 0.935949 -30 CTATCTTCGTTGAAAAATTCAAAAAAAGTGGCATT 57 19 0 TGAAAAAAAA 0.946839 -214 ACGAACTTTATGAAAAAGGGTGAAAAATTGATGAA 58 14 0 TGAAAAGAAA 0.935949 -65 AAGCACGTAATGAAAAAAAGGAAAAGACATTTAGT 60 26 0 TGAAAAAAAA 0.946839 -67 CAGATATGAGAAAGCATAAAAAGAGGTGTGA 61 7 1 TGAAAAAAAA 0.946839 -28 TCCGTCTTATTGATAAGTTCTAAAAAGAATGGAGA 67 54 1 TGAAAGAAAA 0.858251 -32 AACTTTTTCATGACAAAATAAAAAAAGCCTGTCAC 79 40 0 TGAAAAAAAA 0.946839 -113 TCTTCATCCCTGTAAAAGGACGAAAAGCTCTTTCG 83 229 0 TGTAAAGAAA 0.75957 -72 TACACCTTATTGATAAGGAACAAAATGAAAACATA 86 156 0 TGAAAGAAAA 0.858255 -139 TTCGTTTTTCTGACATACATAAAAATTA 90 4 0 TGAATAAAAA 0.619842 -297 TAATGTTTCATGTGAAACATGAAAAAGGAAAAGAC 90 112 0 TGTAAAAAAA 0.793844 -189 TTTGGACTTATGTTAAAATATAAAAGTAAAATTTA 90 165 1 TGTAAAAAAA 0.793794 -136 *** *** **** Masking position 1 Map Score: 18.1283 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 249 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 CTGAAAGACTGCAAAAACAGTCTTGCAGCA 13 27 1 GCAAAAACAG 0.935315 -154 GGAATCTGACGCAAAAACAAAAGTACG 14 8 0 GCAAAAACAA 0.590618 -106 CTGACAAATTTCAAAAGAAGTTTGTCACAC 29 243 0 TCAAAAGAAG 0.704506 -58 TTTTTTGCGTGTAAAAAAAGGGGAGGTGCC 39 24 0 GTAAAAAAAG 0.492963 -98 TTTTTTACACGCAAAAAAAGGGTAAACTGA 39 36 1 GCAAAAAAAG 0.936552 -86 AAAGAAAGGAGAAAAAACAGAAATTCTGCT 41 76 1 GAAAAAACAG 0.706437 -225 TAAAAGGAGAGAAAAAACAGC 49 22 1 GAAAAAACAG 0.706437 -11 AGAAAAAAACTCAAAAGAAGGAGTGAAAGG 55 59 1 TCAAAAGAAG 0.704506 -23 GTTGAAAAATTCAAAAAAAGTGGCATTTGC 57 16 0 TCAAAAAAAG 0.811075 -217 ATATGAGAAAGCATAAAAAGAGGTGTGATA 61 14 1 GCATAAAAAG 0.558113 -21 AACAAAGCAGGCAAAAACAAAAAAAAACCT 74 57 0 GCAAAAACAA 0.590618 -94 ACTCATTTCGTCAAAAAAAGATAAAATCCT 75 13 0 TCAAAAAAAG 0.811075 -40 TTAATTCGACGAAAAAAAAGTG 77 3 0 GAAAAAAAAG 0.710697 -88 TCCGGCAGAATCAAAAAAAGATTCTGCCGT 81 22 1 TCAAAAAAAG 0.811075 -118 ATTGTATTTGCAAAAGAAGTAAATCACTG 87 10 1 GCAAAAGAAG 0.891274 -109 CGGATGTTGTGCAAAAGCAGCAGATGACAT 88 240 1 GCAAAAGCAG 0.889259 -61 ********** Masking position 5 Map Score: 11.3747 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 535 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 11 TTTTTGCGCTTTTAAATTGTGGA 4 4 1 TTGCGCTTTT 0.765877 -30 CGATTATTGCCTGGTCTTTTCATAATGGAA 36 61 0 CTGGTCTTTT 0.802071 -216 AACAGAAATTCTGCTATTTTCAGGCTTATA 41 91 1 CTGCTATTTT 0.7322 -210 GTGGGGAAACCCGCTCTTTTGTATTGAACA 53 164 1 CCGCTCTTTT 0.877691 -137 TTTTTAGCCCCTGCTCTTTTGAAGCAGGGT 53 227 1 CTGCTCTTTT 0.974428 -74 ATTCCTCTCCTTGCTCTTTTCTCCTCTAAG 58 58 0 TTGCTCTTTT 0.904205 -21 ATGCATTCGTATGCTCTTTTTGTTTTTTTA 63 27 1 ATGCTCTTTT 0.788835 -93 AATCGTTGATTTGCTCTTTTTATTTTAACA 70 218 0 TTGCTCTTTT 0.904205 -48 TAAAAACCGTCTGCTCTATTCGACCATGCA 86 238 0 CTGCTCTATT 0.815281 -57 CACCCATGATCGGCGCTTTTGTTAAAAGGA 88 159 0 CGGCGCTTTT 0.71322 -142 GCATAAACGACTGCTCTTTTGTTCATCGCT 90 237 0 CTGCTCTTTT 0.974428 -64 GTCGTTTATGCTGCTCTTTTCTATTCGTAT 90 256 1 CTGCTCTTTT 0.974428 -45 ********** Masking position 7 Map Score: 11.4871 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 135 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 TAAATGATTGTTGACAGGGAAGAGTATAA 1 8 1 TTTTGACAGG 0.816385 -293 GAAAGGATCTTCATTGGCTGAGAGAGATCCAT 1 57 1 TCTTGGCTGG 0.903886 -244 TGTATGTTGGTCTTTGACTGCGATGAAGTGAG 19 116 1 TCTTGACTGG 0.962574 -120 TCATAACCCATTATTGACAGGGACACAAAATC 31 23 0 TTTTGACAGG 0.816385 -154 ATGCACCGACTCGTTGCCTGAGCACATACGGG 31 75 1 TCTTGCCTGG 0.970685 -102 GTATAATATTTCTTTGACAGAGTCTGCATAAA 34 18 1 TCTTGACAGG 0.962574 -145 CATTGAAGTATCGTTGACAGCGGAATATGCTA 35 102 0 TCTTGACAGG 0.962574 -108 GTTTCCCCACTCTTTGCCTCGGTAATCGTTAG 53 142 0 TCTTGCCTCG 0.810882 -159 GTTCTTTTTTTCTTTGCCTGTGCTAAAGTGTG 80 60 1 TCTTGCCTGG 0.970685 -74 TGTCAGCTTGTCTTTTCCAGTGAACCTCCTTA 94 43 1 TCTTTCCAGG 0.743126 -84 ** ******* * Masking position 5 Map Score: 6.46654 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 82 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 13 TAAAAGTATTTTCTTTCTTTGGAAGAAATG 11 184 1 TTCTTTCTTT 0.505998 -62 TGGGTAATTTCTCCTTCCTTATTAGGAAAT 16 34 0 CTCCTTCCTT 0.743962 -20 TATTTTCCCTCCTTTTCGCCTACA 19 222 0 TTCCCTCCTT 0.743962 -14 ATCAATTTCCTCCTTTCCTAAGAGAA 21 7 0 TCCTTTCCTA 0.239382 -21 GAGATAGACCTCCCTTCCTTTTAATA 26 7 0 TCCCTTCCTT 0.743962 -20 ATATAATTACCTCCTTCCCTTTCTTGGGGA 27 11 0 CTCCTTCCCT 0.68408 -21 GTGATGTCCCCTCCTTTATTGGAATG 32 62 0 TCCCCTCCTT 0.786054 -16 TTGAGCTCTCCCCTTTGTTAAGTCA 37 162 0 CTCTCCCCTT 0.387059 -15 GAGGTGCCGGCCCTCTCCCTT 39 2 0 CCCTCTCCCT 0.896653 -120 CTGTTTTTTCTCCTTTCTTTTCGGCATTTT 41 66 0 TCCTTTCTTT 0.564299 -235 AGAACTACATTTCTCGCCCTGATATAAGCC 41 113 0 TTCTCGCCCT 0.271226 -188 GGTCATTCCACTCTTTCTCTAAATCGTCAG 42 16 0 CTCTTTCTCT 0.491138 -30 GTATTGATCATTCTCACCTTTTGCAGGCTG 43 79 1 TTCTCACCTT 0.372715 -39 ATTAGGAGTTCCCTTTCCTTGTTCTGAAAG 44 119 0 CCCTTTCCTT 0.902033 -42 ATTACTCGCCTCCCCTCCCTCC 46 3 0 TCCCCTCCCT 0.732477 -249 AATCTATCTCTCTCCTTGTGTTTCG 48 9 0 CTCTCTCCTT 0.902033 -17 GCTGTTTTTTCTCTCCTTTTAAATCGAA 49 15 0 TTCTCTCCTT 0.879254 -18 GGTTTCCCCACTCTTTGCCTCGGTAATCGT 53 145 0 CTCTTTGCCT 0.176208 -156 TATACGCCTATCCTCTCTTTTT 55 3 0 TCCTCTCTTT 0.620876 -79 TTGCCTTTCACTCCTTCTTTTGAGTT 55 66 0 TTCACTCCTT 0.273728 -16 AATTCCTCTCCTTGCTCTTTTCT 58 66 0 TCCTCTCCTT 0.902033 -13 AGACATTTAGTCCTTTCCTCCTGTTT 60 7 0 TCCTTTCCTC 0.318083 -86 TTTTTATACACTCTTTCCTTGTTATCCCTC 62 60 0 CTCTTTCCTT 0.879254 -79 CAGGCAACCTCTTTCCTTTATATTCCTA 63 102 0 CTCTTTCCTT 0.879254 -18 CAACCCCTTTCTTTCATTATATAG 71 5 1 CCCTTTCTTT 0.620876 -159 TCTCTTTCCCTCCCTCCGAAT 71 153 0 CTCTTTCCCT 0.844395 -11 GCACTCCTTTTCTTTCCCTTCCCGTTTAT 78 18 0 TTCTTTCCCT 0.811022 -19 AGCAAACGGCTTCTCTCTCTGCATGCGCCT 83 60 0 TTCTCTCTCT 0.491138 -241 TGTATCCATCTCCTTCCGCCCTGAA 87 104 0 CCATCTCCTT 0.230594 -15 TTCCCTCCTTTCTTTTTCATTTTAG 91 23 0 TCCTTTCTTT 0.564299 -15 GACCCTTCACCTCTTTTCCTAAACTGCTGT 95 24 0 CTCTTTTCCT 0.126118 -277 CGCCGTCTTCTCCTTACCTTCTATATGAAA 95 281 0 TCCTTACCTT 0.372715 -20 ********** Masking position 3 Map Score: 17.861 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 550 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 14 TTGTAAGATGAGGAAGTGAAAGCTTTCTTTCAC 17 45 1 AGATGAAAGC 0.680245 -75 ATAGAGTGATAGGAAGTGAAAGAAAGCTTTCAC 17 60 0 AGATGAAAGA 0.925331 -60 CGAAGTTTATTGAAAATGACAGATCATTTAGGA 34 129 1 TGATGACAGA 0.81652 -34 CAAACTTCTTACCATTTGACAGAGTAATTGTAG 46 132 0 ACATGACAGA 0.901535 -120 AGCATAATTTGACAGAATACGGAGGT 47 4 1 ATATGACAGA 0.770471 -30 TTCATACCTAAGCAAGTGACAGAAACTCTAATA 53 50 0 AGATGACAGA 0.974633 -251 TGCCAATCGCAGGAGTTGACAGAA 64 95 1 AGATGACAGA 0.974633 -14 GATTATATTCAGCATATGACTGACCATGATATG 69 22 1 AGATGACTGA 0.81652 -38 ATCAAAGAGAAGAATCTGACAAAGCATATGCTG 74 20 1 AGATGACAAA 0.842228 -131 ACTGGAAAAGACAAGCTGACAAAAAAGCATTTT 94 31 0 ACATGACAAA 0.559882 -96 TTTTATATAGAGGAGATGAAAGA 94 114 1 AGATGAAAGA 0.925331 -13 TTCCGAGAAGAGAATTTGAAAGAAAACTAAAAA 95 193 1 AGATGAAAGA 0.925331 -108 ** * ******* Masking position 9 Map Score: 5.67749 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 123 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 TACTGATTTCAAAAAACGTTCTTCAAAGGTC 1 117 0 AAAAACGTTC 0.938777 -184 ATTACTTGCCAAAACCCGTTCAGCGGGTTTT 5 44 1 AAAACCGTTC 0.724696 -135 CCAAAGAAAGAAAATACTTTTACAAGACAAA 11 175 0 AAAAACTTTT 0.721926 -71 ATAGATTAACAAAACACAATTTCCTAATAAG 16 16 1 AAAAACAATT 0.455585 -38 TACCACAGCTAAAAAACGTTTGCAACTATTG 36 169 0 AAAAACGTTT 0.929735 -108 TTGATCATTCAAAAAACTTTTTTGGATGATT 57 114 1 AAAAACTTTT 0.721926 -119 GAAAAAAAGGAAAAGACATTTAGTCCTTTCC 60 19 0 AAAAACATTT 0.787391 -74 CTCGTTACAGAAAATACGATTACACTTAAAA 62 94 1 AAAAACGATT 0.747846 -45 GGACAATAAAAAAAGACGTTTCTATCGTTTG 67 26 0 AAAAACGTTT 0.928095 -60 CGCCTTGTCCAAAAAACGTTCGTCAAATTTT 80 18 0 AAAAACGTTC 0.938777 -116 ATGAAAAAGGAAAAGACATTCTTTGAAAAGA 90 98 0 AAAAACATTC 0.812225 -203 CTCTAGGTTCAAAATACGTTCATACAATGAC 94 81 1 AAAAACGTTC 0.938777 -46 **** ****** Masking position 4 Map Score: 5.18019 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 67 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