AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_ecoli_reg_100.orf -o02010_ecoli_100.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: BIME185 97 BIME Input sequences: #1 tbpA 163 thiamin-binding periplasmic protein #2 yabN 83 putative transport protein #3 BIME8 209 BIME #4 fhuA 219 outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80 #5 fhuC 50 ATP-binding component of hydroxymate-dependent iron transport #6 yaeC 39 putative lipoprotein #7 abc 187 ATP-binding component of a transporter #8 insA_2 300 IS1 protein InsA #9 tauA 300 taurine transport system periplasmic protein #10 ybbL 145 putative ATP-binding component of a transport system #11 fepA 300 outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D #12 fepD 110 ferric enterobactin (enterochelin) transport #13 fepB 300 ferric enterobactin (enterochelin) binding protein; periplasmic component #14 gltJ 169 glutamate/aspartate transport system permease #15 ybeJ 249 putative periplasmic binding transport protein #16 modA 166 molybdate-binding periplasmic protein; permease #17 glnP 138 glutamine high-affinity transport system; membrane component #18 glnH 300 periplasmic glutamine-binding protein; permease #19 ybiK 203 putative asparaginase #20 potF 300 periplasmic putrescine-binding protein; permease protein #21 artJ 173 arginine 3rd transport system periplasmic binding protein #22 artP 217 ATP-binding component of 3rd arginine transport system #23 ycbP 300 orf, hypothetical protein #24 potA 249 ATP-binding component of spermidine/putrescine transport #25 oppA 300 oligopeptide transport; periplasmic binding protein #26 oppB 85 oligopeptide transport permease protein #27 sapA 248 homolog of Salmonella peptide transport periplasmic protein #28 ycjM 185 putative polysaccharide hydrolase #29 ycjQ 30 putative oxidoreductase #30 b1329 300 putative transport periplasmic protein #31 b1440 244 putative transport protein #32 b1488 257 orf, hypothetical protein #33 b1513 248 putative ATP-binding component of a transport system #34 btuE 62 vitamin B12 transport #35 btuC 100 vitamin B12 transport permease protein #36 ydjX 118 orf, hypothetical protein #37 yebL_yebM 24 yebL: putative adhesin, yebM: putative ATP-binding component of a transport system #38 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #39 araG 69 ATP-binding component of high-affinity L-arabinose transport system #40 araF 300 L-arabinose-binding periplasmic protein #41 fliY 87 putative periplasmic binding transport protein #42 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #43 yehZ 143 putative transport system permease protein #44 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #45 mglB 279 galactose-binding transport protein; receptor for galactose taxis #46 rtn 180 orf, hypothetical protein #47 yejA 75 orf, hypothetical protein #48 ccmC 41 heme exporter protein C #49 napF 300 ferredoxin-type protein: electron transfer #50 hisQ 89 histidine transport system permease protein #51 hisJ 220 histidine-binding periplasmic protein of high-affinity histidine transport system #52 argT 265 lysine-, arginine-, ornithine-binding periplasmic protein #53 cysW 300 sulfate transport system permease W protein #54 cysP 300 thiosulfate binding protein #55 yphD 24 putative transport system permease protein #56 yphE 22 putative ATP-binding component of a transport system #57 yphF 96 putative LACI-type transcriptional regulator #58 proV 300 ATP-binding component of transport system for glycine, betaine and proline #59 proX 57 high-affinity transport system for glycine betaine and proline #60 b3020 132 putative transport periplasmic protein #61 yrbF 209 putative ATP-binding component of a transport system #62 yhdW 300 putative periplasmic binding transport protein #63 yhdX 49 putative transport system permease protein #64 yhdY 98 putative transport system permease protein #65 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #66 BIME167 47 BIME #67 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #68 livH 47 high-affinity branched-chain amino acid transport system; membrane component #69 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein #70 livJ 213 high-affinity amino acid transport system; periplasmic binding protein #71 nikA 110 periplasmic binding protein for nickel #72 dppB 172 dipeptide transport system permease protein 1 #73 dppA 300 dipeptide transport protein #74 xylF 300 xylose binding protein transport system #75 xylG 77 putative ATP-binding protein of xylose transport system #76 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #77 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #78 rbsD 300 D-ribose high-affinity transport system; membrane-associated protein #79 rbsB 24 D-ribose periplasmic binding protein #80 sbp 164 periplasmic sulfate-binding protein #81 malE_malK 364 malE: periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis, malK: ATP-binding component of transport system for maltose #82 malM 104 periplasmic protein of mal regulon #83 yjcW 33 putative ATP-binding component of a transport system #84 BIME216 65 BIME #85 yjcX 58 putative LACI-type transcriptional regulator #86 rpiR 300 transcriptional repressor of rpiB expression #87 phnD 24 periplasmic binding protein component of Pn transporter #88 phnC 132 ATP-binding component of phosphonate transport #89 ytfQ 300 putative LACI-type transcriptional regulator #90 BIME228 47 BIME #91 ytfR 29 putative ATP-binding component of a transport system #92 fecB 38 citrate-dependent iron transport, periplasmic protein #93 fecA 86 outer membrane receptor; citrate-dependent iron transport, outer membrane receptor #94 fecI 291 probable RNA polymerase sigma factor Motif number 1 TCACCCTGGAAGGGAGAGGGGGCAGAACGG 13 135 0 AGGGAGAGGG 0.976832 -166 TCTCCCTTCCAGGGTGAGGGCTGGGGTGAG 13 148 1 AGGGTGAGGG 0.969711 -153 GGTGAGGGCTGGGGTGAGGGTTAATGTTCG 13 160 1 GGGGTGAGGG 0.98932 -141 GGAGAGGGTTAGGGTGAGGGGAACAGCCAG 13 198 0 AGGGTGAGGG 0.969711 -103 TCGCCCCTTTGGGGAGAGGGTTAGGGTGAG 13 210 0 GGGGAGAGGG 0.99187 -91 TCTCCCCAAAGGGGCGAGGGGACGGATTGT 13 223 1 GGGGCGAGGG 0.99202 -78 TCTCCCCATAGGGGAGAGGGAACTGCCAGT 17 33 0 GGGGAGAGGG 0.99187 -106 TCTCCCCTATGGGGAGAGGATTAGGGTGAG 17 46 1 GGGGAGAGGA 0.843378 -93 GGAGAGGATTAGGGTGAGGGGCGCAAACCC 17 58 1 AGGGTGAGGG 0.969711 -81 CAAAATAACGGGGGCGGTGGTCGGCGAGCA 22 74 0 GGGGCGGTGG 0.881176 -144 AATTTTCTCAGGGGCGAAGGTGTGCCTGCA 31 145 1 GGGGCGAAGG 0.970751 -100 GGTTACCCGAAGGGAGCGGGCTTTCTTTCA 50 21 0 AGGGAGCGGG 0.860149 -69 TGAGGGAAAATGGGAGATGGGGCACGGATA 67 66 0 TGGGAGATGG 0.641927 -173 GGTGACGGCGTGGGTGAGGGAAAATGGGAG 67 80 0 TGGGTGAGGG 0.921386 -159 GCCCCAGCGCGGAGCGGGGGCGTGATTTCT 75 18 1 GGAGCGGGGG 0.738104 -60 GTTGTTACAAAGGGAGAAGGGC 81 3 0 AGGGAGAAGG 0.918413 -362 AAAAAGCCAGGGGGTGGAGGATTTAAGCCA 81 84 0 GGGGTGGAGG 0.927022 -281 CTTTTTTATGGGGGAGGAGGCGGGAGGATG 81 108 1 GGGGAGGAGG 0.943595 -257 AAGCGACGGTGGGGCGTAGGGGCAAGGAGG 81 264 1 GGGGCGTAGG 0.765619 -101 ********** Masking position 6 Map Score: 31.7774 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 71 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 GCAGGTATAATCTGCTGGCGGGTGATTTTACA 3 49 1 TCTGTGGCGG 0.890879 -161 ATGAACTAGATCTGGTTGCTGCTCAGCTAAAC 8 157 0 TCTGTTGCGC 0.538235 -144 GGAAGTGAGAGCTGGTGGCAGTCGAAACATGG 11 19 0 GCTGTGGCGT 0.949887 -282 CCAGCGTATTGCGGTTTTCAGGCCCGATGGGG 14 89 0 GCGGTTTCGG 0.839158 -81 GATAAATATTCCCGCTTGCAGGGGTAAAAGTG 24 77 0 CCCGTTGCGG 0.930904 -173 GGCGATTCAAGCGGTTTGCCGTAGAATTACCG 24 160 1 GCGGTTGCGT 0.957001 -90 GAATCGTCTGGCGGTTGCCCGGAAAGTACCAA 25 28 0 GCGGTGCCGG 0.855759 -273 TCGGAGACTTTCTGCTGTCAGGTTACTTTATC 25 203 0 TCTGTGTCGG 0.542593 -98 CACGTTCAAACCCGTTTTCGGTATCATAATCA 30 98 0 CCCGTTTCGT 0.562185 -203 ACCATAGACGGCGGCTTGCAGGCACACCTTCG 31 159 0 GCGGTTGCGG 0.972177 -86 TGTTGTTATGTCTGTTTGCAGTGTAGAGCCAT 41 54 0 TCTGTTGCGT 0.786755 -34 AAAAAACCCCGCCGGTGGCGGGGAAGCACGTT 42 34 0 GCCGTGGCGG 0.970658 -145 AACAATTAAAGCCGTTTTCTGGAGCGTTACCG 45 138 1 GCCGTTTCGG 0.778482 -142 TGAAAGCATGCCGGATTGCGGCTAATGATGAG 47 40 1 CCGGTTGCGC 0.804885 -36 TCAGCAAGGGGCTGATGCCGGTTTTACAGAAT 53 21 1 GCTGTGCCGT 0.695323 -280 TGATGATCGCGCTGATTGCCGTACCGGTAAAC 53 93 1 GCTGTTGCGT 0.932515 -208 TACTGGACATTCCGTTTGCCGTATCGCCGGTG 53 198 1 TCCGTTGCGT 0.800092 -103 GGCCCGCTCGGCGGTTGGCTCGACGAGCATAA 53 269 1 GCGGTGGCCG 0.910932 -32 CCGCCAGCGTGCTGCTTGCCGTTGCAAATCAG 62 235 1 GCTGTTGCGT 0.932489 -66 CAAATCAGGCGCTGCTGGCGCGACGCTTGATG 62 259 1 GCTGTGGCCG 0.863945 -42 AATCTGTATACCCGGTGGCGCTGTGCCTCTGC 72 35 1 CCCGTGGCCT 0.71567 -138 AGTATTGCTGCCGGATGGCGCTGCACGCAGAG 72 61 0 CCGGTGGCCT 0.788893 -112 GGTGTAAATCCCGGTTGGCTGTATTGACGTTT 73 87 1 CCGGTGGCGT 0.947387 -214 GTGTTAACGCCCGGCTTGCCGGGCTTTTAGCT 92 12 1 CCGGTTGCGG 0.949003 -27 **** **** ** Masking position 6 Map Score: 22.713 Number of sites scoring better than the average of aligned sites = 2052 Number in coding regions = 1974 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 GAAGGGAGAGGGGGCAGAACGGCGCAGGACAT 13 125 0 GGGCAGACGG 0.764186 -176 GTTAATGTTCGCACCAGTGCTGGCTGTTCCCC 13 179 1 GCCCAGGCTG 0.948661 -122 GTAATTAATGGCCCCGGAGCGGGTTTGCGCCC 17 76 0 GCCCGGGCGG 0.938408 -63 TTTTATATAGCGAGCAGTGCTGGCCGGGAGAA 20 170 1 CGGCAGGCTG 0.813904 -131 ATTAAAGCACGCTGCAGTGCGTGTCATTGTTA 27 11 0 GCGCAGGCGT 0.946799 -238 AACTTAGCGAGGAGCAGAGCGGTACGATCGTG 27 51 0 GGGCAGGCGG 0.983951 -198 AAATGAAAACCCGCGAGTGCGGGCGAGAGGAA 32 15 0 CCCGAGGCGG 0.947823 -243 AAGAAAAAAGGCCGCAGAGCGGCCTTTTTAGT 35 20 0 GCGCAGGCGG 0.994425 -81 CCAGTTTGAGCCAGGAGAGCTGCTAAA 36 6 0 CCGGAGGCTG 0.813904 -113 GTGAAAGCATGCCGGATTGCGGCTAATGATGA 47 39 1 GCGGATGCGG 0.90412 -37 AGTTTGGACACGAACAGCGCGGAGAAACCGGA 54 132 0 CGACAGGCGG 0.713001 -169 TTTGTGATGAGCGGCAGCGCGTGCCGCTCAAA 57 29 0 GCGCAGGCGT 0.946798 -68 TTTCATTTTCGCACCATTGCGGGGCGCTGTTT 62 21 1 GCCCATGCGG 0.948641 -280 GCGTTACGCCCCAGCGCGGAGCGGGGGCG 75 8 1 GCCCAGGCGG 0.991736 -70 AAAGGTAATTCCGCCATCGCGGAGTTACCTGT 85 14 1 CCCCATGCGG 0.53091 -45 CGATGACAGTGCGGGAGGGCGGGCCTCCCGGC 88 14 0 GCGGAGGCGG 0.983922 -119 ** **** **** Masking position 10 Map Score: 17.9433 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 868 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 CAAGTCCTTTGCCACTCTTTTTTGAGGTGCA 1 141 1 GCCACTTTTT 0.958619 -23 TGAATCTACAGCAGCTTTTTTTAATATGTCC 8 54 0 GCAGCTTTTT 0.622489 -247 TCTTTCCTTAGCCGTTTTTTTGCTAAGAATA 9 247 1 GCCGTTTTTT 0.857713 -54 TCATGTTTGAGCCGATTTTTTCTCCCGTAAA 15 70 0 GCCGATTTTT 0.857713 -180 TGCTTTTCCTGCCGATATTTTTTCTTATCTA 16 58 1 GCCGATTTTT 0.857713 -109 TTGCAAAACTGGCACGATTTTTTCATATATG 18 232 1 GGCACGTTTT 0.602182 -69 GCGCTTATGCGCCGTTTTTTTTTCTGTCACA 28 29 1 GCCGTTTTTT 0.857713 -157 TGCTTCCTTTGTCACTTTTTTGATGGAAGTT 30 234 1 GTCACTTTTT 0.729039 -67 CACGCTTCCCGCCACTCTTTTGATCCTGCTA 49 144 1 GCCACTTTTT 0.958619 -157 AATGGAAATAGTCACTTTTTTCTACCCTAAC 58 236 0 GTCACTTTTT 0.729039 -65 ACCATTGCGGGGCGCTGTTTTTATTATTTCC 62 33 1 GGCGCTTTTT 0.896919 -268 CGCCCTTTGTGCCGTTATTTTATGCTGACAA 69 67 1 GCCGTTTTTT 0.857713 -234 TGCTGACAAAGGCACTTTTTTCTGTTTATCT 69 89 1 GGCACTTTTT 0.858401 -212 GCAAGTTATAGCCAATCTTTTTTTATTCTTT 80 82 1 GCCAATTTTT 0.807686 -83 ACATAAAATCGCCACGATTTTTGCAAGCAAC 81 189 0 GCCACGTTTT 0.852602 -176 CCACGATGGAGCCACTTTTTTAGGGAGGCTG 88 108 1 GCCACTTTTT 0.958619 -25 CATAACCGTAGCCGCATTTTTCATAGTGAGA 89 136 1 GCCGCATTTT 0.752708 -165 ****** **** Masking position 8 Map Score: 13.7026 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 312 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 GTGCGCTGAGAAAATACCCGTCGAACCTGATC 1 73 1 AAAATCCGTC 0.787098 -91 GGCGAGAATAAAAAAAACCAGCAGGTATAATC 3 29 1 AAAAACCAGC 0.819008 -181 GTATTGGTGTAAAATCACCCGCCAGCAGATTA 3 56 0 AAAATCCCGC 0.969817 -154 GGAGCACCTCAAAAACACCATCATACACTAAA 8 278 0 AAAAACCATC 0.624506 -23 ACTAACTCGGAATTTTCCCAGCAGTTATTGCT 16 102 0 AATTTCCAGC 0.435509 -65 TAAACCCCGTAAATTGTCCGGCATTTCGTGAG 22 27 1 AAATTCCGGC 0.826649 -191 TAATGCTGATAAATATTCCCGCTTGCAGGGGT 24 84 0 AAATACCCGC 0.849678 -166 TTTGCCGGAAAAATTCCCCTCTGCATGATGC 39 10 1 AAAATCCCTC 0.921933 -60 TCCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 42 44 0 AAAAACCCGC 0.922618 -135 TGTAACCCCCAAATAACCCCTCATTTCACCCA 42 83 1 AAATACCCTC 0.67506 -96 CCATCAAGGCAAAATATCCCGCCCCGTTAGAC 51 126 0 AAAATCCCGC 0.969817 -95 TCGTGCCATAAAATTGACCATCAAGGCAAAAT 51 143 0 AAATTCCATC 0.679986 -78 TGGCAGGGTGATAATGCCCGGCGTCACCGGGC 59 21 0 ATAATCCGGC 0.573074 -37 ATATTTACAGAATATTACCCGCCGTGGTTAGC 61 125 0 AATATCCCGC 0.810888 -85 CAGACCTTCTATATTTTCCCGCTTATCCGTGC 67 43 1 ATATTCCCGC 0.670271 -196 TAGAGAATGAAAAATGTCCAGCATAATCCCCT 69 16 1 AAAATCCAGC 0.924212 -285 GATCCTCCATAAAATGCCCCTCGTGACCTACA 73 138 0 AAAATCCCTC 0.921933 -163 AACAGGAAGAAAAATGCCCCGCTTACGCA 77 8 0 AAAATCCCGC 0.969817 -293 CAAGCACCTTAAAATCACCATCATACACTAAA 94 12 1 AAAATCCATC 0.817587 -280 ***** ***** Masking position 1 Map Score: 14.3746 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 436 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 ATCAGAAAAAGGGAACAGCG 10 136 1 GGGAACAGCG 0.731762 -10 TATTTGCATTTGCAATAGCGTAATGGCGCG 11 139 1 TGCAATAGCG 0.429205 -162 TTGATGGATTCGCATAAGCGCAATGTGATG 13 98 1 CGCATAAGCG 0.912994 -203 ATGACAAATTCGACAAAGCGCACAATCCGT 13 244 0 CGACAAAGCG 0.753399 -57 AGGGAAGGTGCGAATAAGCGGGGAAATTCT 15 129 0 CGAATAAGCG 0.826121 -121 AGAAAATGCCCGACTAAGCGGGCATTCAGG 16 14 0 CGACTAAGCG 0.639517 -153 TTCGAGATGCGGCAAAAACGTGATGCACGA 18 191 0 GGCAAAAACG 0.760638 -110 AAAAAAACGGCGCATAAGCGCCGCTCATGG 28 20 0 CGCATAAGCG 0.912994 -166 TTTTTACCAGGGAAAAAGCGTATTTGTGAG 28 94 0 GGAAAAAGCG 0.880666 -92 ATGCCATGCCGGGATAAGCGCCAGAATGCT 32 184 0 GGGATAAGCG 0.832338 -74 GCATGAGATCTGCATAAGCGGAAAGCGCAG 32 210 1 TGCATAAGCG 0.682694 -48 TTTTGTGTAGGGCAAAAACGAATGACATTC 40 258 0 GGCAAAAACG 0.760638 -43 CGGGAAGCGTGGCAAAAACGGGCTTTTGCT 49 125 0 GGCAAAAACG 0.760638 -176 CCTGAAACAGGGCAACAGCGGAG 52 4 0 GGCAACAGCG 0.842673 -262 GGGACCTCTGCGAATCAGCGA 56 2 0 CGAATCAGCG 0.602606 -21 TCAAAGATAGCGAAAAAACGCCTGAATATT 58 85 0 CGAAAAAACG 0.607725 -216 TTAATGGAAAAGCGGGGGCAACTC 60 5 1 TGGAAAAGCG 0.65364 -128 AGATGGGGCACGGATAAGCGGGAAAATATA 67 52 0 CGGATAAGCG 0.846239 -187 ATTTCCCCTCCGGCAAAACGCCAATCCCCA 70 82 1 CGGCAAAACG 0.401216 -132 TGGACAAAGCGCACTTTGTCA 80 2 1 GGACAAAGCG 0.733715 -163 GCGGTAGCCAGGCAATAGCGCGCTAAACCC 82 58 0 GGCAATAGCG 0.773048 -47 CATCTGACAGCGCAATAGCGTTAAAGACAC 86 99 1 CGCAATAGCG 0.789962 -202 ********** Masking position 7 Map Score: 15.2686 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 973 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 ATCTAAGCGTGAAATACCGGATGGCGAGTTG 4 12 1 GAAATCCGGA 0.929568 -208 GATAATATTCGAAACGCTGGCGGGTTCGCAA 4 138 0 GAAACCTGGC 0.672467 -82 GAGAGGGCTGGAATTTCCGCCCCTGGTTCTT 14 15 0 GAATTCCGCC 0.920778 -155 CATTCCTCACGAAATGCCGGACAATTTACGG 22 33 0 GAAATCCGGA 0.929568 -185 TCTTTGTTGTGAATTACTGGCTTAGCTTTAT 24 127 0 GAATTCTGGC 0.767386 -123 GTTTGCCGTAGAATTACCGCCCTCATTAAGA 24 173 1 GAATTCCGCC 0.920778 -77 ACCAGCATGTGTAATCCCGGATTGGGACCCT 25 243 0 GTAATCCGGA 0.880431 -58 AGGAAACGCCGGACCGAATATGC 43 3 1 GAAACCCGGA 0.779885 -141 CCCTGCATAAGAAAAACCGGAGATACC 45 263 1 GAAAACCGGA 0.6961 -17 CGTGTGTGGTGAATTACCGCCTCTTGTCTCC 50 55 0 GAATTCCGCC 0.920778 -35 GCCAGATTCTGTAAAACCGGCATCAGCCCCT 53 27 0 GTAAACCGGC 0.787124 -274 TATATCACGGGAAATTCCGGCGATTTGCTCG 58 152 1 GAAATCCGGC 0.974481 -149 AGGGAATGAAGTATTGCTGCCGGATGGCGCT 72 71 0 GTATTCTGCC 0.564966 -102 AAGTCATTTTGTAATGCCGGATGCGGCGTAA 76 37 0 GTAATCCGGA 0.880431 -50 AGATCAATTTGAAATCCCGCCAAACAGGGTT 78 120 1 GAAATCCGCC 0.964215 -181 GAAAAAGGTAATTCCGCCATCGCGGAGT 85 8 1 GTAATCCGCC 0.937628 -51 GGGGATTTCGGTAATGCTGCCAACTTACTGA 94 44 0 GTAATCTGCC 0.750665 -248 ***** ***** Masking position 3 Map Score: 13.6919 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 425 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ATACTCAGTCACACATGATGCAGGCAAGTCAAC 3 84 1 AACAGATGCG 0.642582 -126 CCATGCTTGAAGGACTGATGCAGTGGGATGACC 3 129 0 AGACGATGCG 0.803511 -81 TAAGCGTGAAATACCGGATGGCGAGTTGCCATC 4 15 1 AACCGATGGG 0.674965 -205 TGCGGTTTTCAGGCCCGATGGGGAACGACCATC 14 79 0 AGCCGATGGG 0.95959 -91 AAACCCATTAAAGCACGCTGCAGTGCGTGTCAT 27 16 0 AGCAGCTGCG 0.827505 -233 AAATTCCCCTCTGCATGATGCAGAGGGGGTGTG 39 21 1 CGCAGATGCG 0.80333 -49 GGTGGCGGGGAAGCACGTTGCTGACAAATTGCG 42 20 0 AGCAGTTGCG 0.637556 -159 TAGTGAAAGCATGCCGGATTGCGGCTAATGATG 47 37 1 AGCCGATTGG 0.674965 -39 ATGTCCGGATCGGCCAGATTCTGTAAAACCGGC 53 37 0 CGCCGATTCG 0.809196 -264 TCATCACCGTCAGCCAGATGGCGTGCAGCATGT 53 66 0 CGCCGATGGG 0.960979 -235 CCAGCCAGGCCAGCAGAATGCCGAACACCAGGT 53 123 0 CGCAAATGCG 0.475464 -178 CAACGGCAAGCAGCACGCTGGCGGCAGCCAGTG 62 226 0 CGCAGCTGGG 0.716468 -75 TGCTGGCGCGACGCTTGATGCCGTTCAGAAAAA 62 271 1 AGCTGATGCG 0.78639 -30 TGAAGTATTGCTGCCGGATGGCGCTGCACGCAG 72 63 0 CGCCGATGGG 0.960972 -110 TCATTTTGTAATGCCGGATGCGGCGTAAAACAC 76 32 0 AGCCGATGCG 0.979053 -55 AACTGAATGATGCCGGATGATGATG 84 3 1 CGAAGATGCG 0.638205 -63 GGGTTGCTATGCCTGATGCCGATTCGTAGGC 90 9 1 AGCCGATGCG 0.97902 -39 TGACCGACACATGCCAGAAGCAGAGGCTCCATC 94 129 1 AGCCGAAGCG 0.779687 -163 * *** ***** * Masking position 13 Map Score: 15.5927 Number of sites scoring better than the average of aligned sites = 1260 Number in coding regions = 1010 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 9 TGCGCTGAGAAAATACCCGTCGAACCTGATC 1 74 1 AAATACCCTC 0.394162 -90 TTAATTAACCAACTGCACTGCGTGTCTTTCA 11 187 1 AACTGCACGC 0.668625 -114 GAGAAAAAGAAAATGCCCGACTAAGCGGGCA 16 20 0 AAATGCCCAC 0.576278 -147 TGCATAAGCGGAAAGCGCAGCAATTTTTGTC 32 220 1 GAAAGCGCGC 0.811727 -38 ACAAATTGTCGAATGCACAGCAGATTAATCC 40 51 0 GAATGCACGC 0.798133 -250 CCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 42 44 0 AAAAACCCGC 0.719224 -135 TCGTCCGATTAAAAACCCTGCAGAAACGGAT 42 119 1 AAAAACCCGC 0.719224 -60 GATAAACAGCCCTGCGTTATATGAG 42 164 0 AACAGCCCGC 0.900967 -15 TCATTAACTCTACTGCCCCGCCGAGCATTTA 45 220 1 TACTGCCCGC 0.83842 -60 CGAGTTAACTGAAAGCACTGCTTAGGCAGTG 46 46 1 GAAAGCACGC 0.781195 -135 ATGAAAACAAAAAAGCACTGCCTAAGCAGTG 46 61 0 AAAAGCACGC 0.812978 -120 CCAGGGAAGTTAAAGCGCGTCACCAGCCAGG 53 147 0 TAAAGCGCTC 0.382746 -154 GGCAGGGTGATAATGCCCGGCGTCACCGGGC 59 21 0 TAATGCCCGC 0.925259 -37 CCGCCCACCCGACTGCCCATCTATTGATCCA 71 12 1 GACTGCCCTC 0.654915 -99 ATCCTCCATAAAATGCCCCTCGTGACCTACA 73 138 0 AAATGCCCTC 0.846457 -163 ACAGGAAGAAAAATGCCCCGCTTACGCA 77 8 0 AAATGCCCGC 0.960058 -293 TGCTGCAACGTAATGCGCTGCGTGCACCAGA 78 92 1 TAATGCGCGC 0.749624 -209 TGAAAGGGGCGAAAGCCCCTCTGATTATCGG 82 29 1 GAAAGCCCTC 0.803485 -76 TGTGTTAACGCCCGGCTTGCCGGGCT 92 6 1 TAACGCCCGC 0.699819 -33 ATTCCAGCTAAAAGCCCGGCAAGCCGGGCG 92 19 0 AAAAGCCCGC 0.955957 -20 ******** ** Masking position 2 Map Score: 11.5395 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 753 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 GTCGAACCTGATCCGGATAACGCCGGCGAAG 1 92 1 ATCCGATAAC 0.657903 -72 GTTCTCGGTGATGCTGCCAACTTACTGATTT 8 250 1 ATGCGCCAAC 0.958664 -51 AACACGACGCATCCCGCTACCGCGAAAACCT 11 225 0 ATCCGCTACC 0.831515 -76 GTAGCAGTTAACGCTGCTACCCTCTTTTTTC 14 137 1 ACGCGCTACC 0.548169 -33 CATTAAGGTAATGCTGATAAATATTCCCGCT 24 93 0 ATGCGATAAA 0.463525 -157 ACGGATAATCATGCCGATAACTCATATAACG 42 144 1 ATGCGATAAC 0.683341 -35 CACTCTTTTGATCCTGCTACAGGTTTTACCC 49 156 1 ATCCGCTACA 0.663979 -145 GGGCATTATCACCCTGCCAAAAAAAGGAATA 59 34 1 ACCCGCCAAA 0.644501 -24 TTTTGACTTTATGCGGCTAAAAAGTAAAACA 61 81 1 ATGCGCTAAA 0.822735 -129 CCGTTATTTTATGCTGACAAAGGCACTTTTT 69 78 1 ATGCGACAAA 0.633518 -223 TTAGCAGAGTATGCTGCTAAAGCACGGGTAG 70 172 1 ATGCGCTAAA 0.822735 -42 GAAAACGTCAATACAGCCAACCGGGATTTAC 73 90 0 ATACGCCAAC 0.669555 -211 TTAATCAAACATCCTGCCAACTCCATGTGAC 77 46 1 ATCCGCCAAC 0.95385 -255 TCAATTTGAAATCCCGCCAAACAGGGTTATC 78 123 1 ATCCGCCAAA 0.892188 -178 GAAGTGTCTTATCCGGCCAACAAAATAACCT 84 41 1 ATCCGCCAAC 0.95385 -25 GATGCAGCCTCCCTAAAAAAGT 88 121 0 ATGCGCCTCC 0.610775 -12 CGAGCGCCTTATCCGGCCTACGAATCGGCAT 90 26 0 ATCCGCCTAC 0.745372 -22 GATTTCGGTAATGCTGCCAACTTACTGATTT 94 41 0 ATGCGCCAAC 0.958664 -251 **** ****** Masking position 1 Map Score: 10.582 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 652 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 TTTCTCTTTTGGGGCACGGATTTCCGTGC 5 10 1 TGGGGCACGG 0.920721 -41 ATTGCAACTGTCGGGCATGGTCGTCATCAA 11 254 0 TCGGGCATGG 0.925449 -47 TGGCCGTGTCTGCGGCATGGGATAACAATG 21 121 0 TGCGGCATGG 0.964591 -53 GAGATATTTTTACGGCACGGCGGCTGAACA 31 199 1 TACGGCACGG 0.767686 -46 TGGCGCTTATCCCGGCATGGCATGAGATCT 32 191 1 CCCGGCATGG 0.977494 -67 TGGAGCGTTACCGGGCATGGAAGAACGAAT 45 157 1 CCGGGCATGG 0.950289 -123 TTAGCCGCAATCCGGCATGCTTTCACTATG 47 35 0 TCCGGCATGC 0.925486 -41 GTAATATTTGAGCGGCACGCGCTGCCGCTC 57 23 1 AGCGGCACGC 0.706869 -74 AAATGGGAGATGGGGCACGGATAAGCGGGA 67 59 0 TGGGGCACGG 0.920721 -180 AATTCATTCACGCGGCATGGAGAGAAATCA 75 40 0 CGCGGCATGG 0.977578 -38 AAACACCGTACCCGGCCTGGAGTTTTA 76 8 0 CCCGGCCTGG 0.867851 -79 TTTGCGTCTGCGCGGCAAGCTGTACTTGCT 78 63 1 CGCGGCAAGC 0.862674 -238 CAGCTAAAAGCCCGGCAAGCCGGGCGTTAA 92 15 0 CCCGGCAAGC 0.862672 -24 ********** Masking position 6 Map Score: 9.0741 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 481 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 CGTTCAACACAACATAAATAATTGAAG 6 5 1 CAACCACAAA 0.888847 -35 TGTACCGTCCATAATCAGCAAAATTGCTGCTTG 10 27 1 ATAACGCAAA 0.674585 -119 CTAACAGGCACAACACTGCACAATAAAGTTGCA 15 157 1 CAACCGCAAA 0.957592 -93 GTGATAAAGCCAAATCGACACAAGAGAAGTGAA 20 47 0 CAAACACAAA 0.739031 -254 AAACGAGAGACTACTCCGCAGAAAATAAACTGT 28 162 0 CTACCGCAAA 0.957592 -24 CAAAACTGCACTACGCTGCACAAATGTTGATCA 32 125 1 CTACCGCAAA 0.957592 -133 AACAATGGCTCTACACTGCAAACAGACATAACA 41 50 1 CTACCGCAAC 0.767111 -38 GTCCGATTAAAAACCCTGCAGAAACGGATAATC 42 121 1 AAACCGCAAA 0.854093 -58 ATCTCAAGCACTACCCTGCATAAGAAAAACCGG 45 250 1 CTACCGCAAA 0.957592 -30 AATGAGAGAGCAAACCAGCAGAAATATCTCTGG 49 47 1 CAAACGCAAA 0.888847 -254 GAGCGACCAAATAAACCGCATAATTAATAAGCC 49 242 0 ATAACGCAAA 0.674585 -59 ACACAACACAATACACAACATAAAAAAGCCATT 52 225 1 ATACCACAAA 0.674585 -41 CACATAAAAACAAAGCAACACAACATCACGAAT 69 264 1 CAAACACAAA 0.739031 -37 TTGCTCATCACAACACAACATAAGAGAGTCGGG 80 140 1 CAACCACAAA 0.888847 -25 **** * *** ** Masking position 10 Map Score: 8.63295 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 86 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GCCGTTCTCAACGGGGTGCCACGCGTACGCGTG 1 43 1 ACGGGGTCAG 0.940072 -121 CGAAACGCTGGCGGGTTCGCAAGCGGTACGCAA 4 127 0 GCGGGTTCAG 0.966681 -93 AACACTCACAACGGGTATCCATGCGTTCTTAAC 15 205 1 ACGGGTACAG 0.961606 -45 GCCCGACTAAGCGGGCATTCAGGGAA 16 4 0 GCGGGCACAG 0.871444 -163 TAGAGAAATCACGGGTACGAATGTTGAACAGAT 27 102 1 ACGGGTAAAG 0.846835 -147 GATACCGAAAACGGGTTTGAACGTGCGAAGCCC 30 105 1 ACGGGTTAAG 0.846835 -196 GCCCGCACTCGCGGGTTTTCATTTAACGTGACA 32 23 1 GCGGGTTCAT 0.675507 -235 CCCGCCGGTGGCGGGGAAGCACGTTGCTGACAA 42 26 0 GCGGGGACAG 0.947839 -153 CCCTGCAGAAACGGATAATCATGCCGATAACTC 42 134 1 ACGGATACAG 0.642484 -45 ACTGTTACATACGGGTTACAACGTTAAAACGGT 45 69 0 ACGGGTTAAG 0.846835 -211 TTTTATGCTCGCGGGGTAACATGACATGCTCGA 67 175 0 GCGGGGTCAG 0.947839 -64 CTGCTAAAGCACGGGTAGTCATGCATAAAACGA 70 185 1 ACGGGTACAG 0.961606 -29 ******* ** * Masking position 11 Map Score: 7.69138 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 131 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 GGTGTTGCATTGACAGATTGAATCTACAGCA 8 72 0 TGACAGATGA 0.630509 -229 TTGCCTATTATGTCAGAAAAACGCCACAGAC 19 41 1 TGTCAGAAAA 0.88455 -163 ATAGTACCTTTGACAGAATAATTATGCAATA 22 154 0 TGACAGATAA 0.771702 -64 TTTAGTTTATTTTCAGAAAAAGATACACAAA 23 187 1 TTTCAGAAAA 0.492229 -114 AAATAAGGTGTGACAGAAAAAAAAACGGCGC 28 37 0 TGACAGAAAA 0.94302 -149 AAAGCCAATTTGTCAGACAAATTGTCGAATG 40 67 0 TGTCAGAAAA 0.88455 -234 GGGGCCAAAATGACAAATAAAATAGCCTGGT 54 64 0 TGACAAAAAA 0.521549 -237 GATAGTAAGGTGTCAGAAAGATGACAAGGCG 67 109 0 TGTCAGAAGA 0.794569 -130 CATGCTCGAATTACAGAAAAATAACTTTTTT 67 153 0 TTACAGAAAA 0.676792 -86 CTGAATTTATTGATAGATAAACAGAAAAAAG 69 103 0 TGATAGAAAA 0.521549 -198 TTTCATTCTGTGACAGAGAAAAAGTAGCCGA 77 89 0 TGACAGAAAA 0.94302 -212 AACGAAGAGATGACAGAAAAATTTTCATTCT 77 111 0 TGACAGAAAA 0.94302 -190 GACAGTTTTATGACAGAGAGATAAAGTCTTC 77 190 0 TGACAGAAGA 0.893104 -111 ******* *** Masking position 5 Map Score: 6.36014 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 130 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 CCTGAAAACCGCAATACGCTGGGTAACAATC 14 99 1 GCAATACCTG 0.947752 -71 TCCCTAACAGGCACAACACTGCACAATAAAG 15 154 1 GCACAACCTG 0.91994 -96 CCATTCTGGGGCACCAATCTGGTGCGCTAAA 18 133 0 GCACCAACTG 0.899897 -168 CCCTGAAGATGCACCATTCTGGGGCACCAAT 18 146 0 GCACCATCTG 0.836013 -155 GATTTATAGGGCAATACCCTGAAGATGCACC 18 162 0 GCAATACCTG 0.947752 -139 CACCAAAACTGCACTACGCTGCACAAATGTT 32 122 1 GCACTACCTG 0.982253 -136 ACAAACAATGGCTCTACACTGCAAACAGACA 41 47 1 GCTCTACCTG 0.886207 -41 TTTATCTCAAGCACTACCCTGCATAAGAAAA 45 247 1 GCACTACCTG 0.982253 -33 ATTTCGCGTCGCAATAAGCTGAGTGTAGACA 62 64 0 GCAATAACTG 0.781274 -237 GCAACGGCAAGCAGCACGCTGGCGGCAGCCA 62 229 0 GCAGCACCTG 0.897715 -72 ******* *** Masking position 6 Map Score: 5.56822 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 84 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925