AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -x5 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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 map 300 methionine aminopeptidase #2 adk 180 adenylate kinase activity; pleiotropic effects on glycerol-3-phosphate acyltransferase activity #3 infA 284 protein chain initiation factor IF-1 #4 yojI 75 putative ATP-binding component of a transport system #5 ada 73 O6-methylguanine-DNA methyltransferase; transcription activator/repressor #6 yojL 111 orf, hypothetical protein #7 usg 65 putative PTS system enzyme II A component #8 pdxB 98 erythronate-4-phosphate dehyrogenase #9 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #10 rplQ 40 50S ribosomal subunit protein L17 #11 rpoA 25 RNA polymerase, alpha subunit #12 rpsD 33 30S ribosomal subunit protein S4 #13 rpsM 146 30S ribosomal subunit protein S13 #14 rpmJ 31 50S ribosomal subunit protein L36 #15 rpsH 33 30S ribosomal subunit protein S8, and regulator #16 rplN 164 50S ribosomal subunit protein L14 #17 rplC 32 50S ribosomal subunit protein L3 #18 rpsJ 237 30S ribosomal subunit protein S10 #19 fusA 27 GTP-binding protein chain elongation factor EF-G #20 rpsG 96 30S ribosomal subunit protein S7, initiates assembly #21 rpsL 125 30S ribosomal subunit protein S12 #22 tufB 114 protein chain elongation factor EF-Tu (duplicate of tufA) #23 secE 229 preprotein translocase #24 rplK 157 50S ribosomal subunit protein L11 #25 rplJ 300 50S ribosomal subunit protein L10 #26 rplL 66 50S ribosomal subunit protein L7/L12 #27 rpoB 300 RNA polymerase, beta subunit #28 rpoC 76 RNA polymerase, beta prime subunit #29 dnaB 82 replicative DNA helicase; part of primosome #30 ssb 253 ssDNA-binding protein #31 yjeB 204 orf, hypothetical protein #32 rpsF 300 30S ribosomal subunit protein S6 #33 rplI 41 50S ribosomal subunit protein L9 #34 HI0250 153 single-stranded DNA binding protein (ssb) #35 HI0349 84 adenylate kinase (adk) #36 HI0350 141 permease, putative #37 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #38 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #39 HI0517 172 ribosomal protein L11 (rpL11) #40 HI0546 28 primosomal replication protein N (priB) #41 HI0547 198 ribosomal protein S6 (rpS6) #42 HI0548 169 translation initiation factor 1 (infA) #43 HI0579 83 elongation factor G (fusA) #44 HI0580 156 ribosomal protein S7 (rpS7) #45 HI0581 181 ribosomal protein S12 (rps12) #46 HI0632 300 elongation factor Tu (tufB) #47 HI0640 271 ribosomal protein L10 (rpL10) #48 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #49 HI0716 237 preprotein translocase SecE subunit (secE) #50 HI0776 190 ribosomal protein S10 (rpS10) #51 HI0781 25 ribosomal protein S19 (rpS19) #52 HI0788 280 ribosomal protein L14 (rpL14) #53 HI0792 36 ribosomal protein S8 (rpS8) #54 HI0798.1 28 ribosomal protein L36 (rpL36) #55 HI0799 139 ribosomal protein S13 (rpS13) #56 HI0801 27 ribosomal protein S4 (rpS4) #57 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #58 HI0803 40 ribosomal protein L17 (rplQ) #59 HI0861 191 virulence-associated protein (vacB) #60 HI1573 300 pyruvate kinase, type II (pykA) #61 HI1574 33 replicative DNA helicase (dnaB) #62 HI1618 95 ABC transporter, ATP-binding protein #63 HI1624 89 H. influenzae predicted coding region HI1624 #64 HI1644 233 pseudouridylate synthase I (truA) #65 HI1722 135 methionine aminopeptidase (map) Motif number 1 GTGATACCATTGACGGCACTTACATATATAT 1 247 1 TACGGCACTT 0.945559 -54 ACCAACTCTGCGACCGCAATTATAACACTCT 3 34 0 CACCGCAATT 0.809966 -251 TCAGGCAAAATAACCGCACTTTTTTAGATAA 34 117 1 TACCGCACTT 0.995786 -37 TTTATAATTTTTACCGCACTT 35 1 0 TACCGCACTT 0.995786 -84 ATAAAAAATTTGACCGCACTATGCTTTATCA 35 27 1 TACCGCACTA 0.952872 -58 CAACTAAAATTAACCGCACTTT 36 130 1 TACCGCACTT 0.995786 -12 CGGAGAATTTTGACCGCACTTCGGCGATTTC 37 173 0 TACCGCACTT 0.995786 -69 CCGAAATTTTTAACCGCACTTTAAACCTTTA 37 201 1 TACCGCACTT 0.995786 -41 ACCGTTAAAATGACCGCACTCTGAACCTTAC 38 222 0 TACCGCACTC 0.967707 -79 GCTTGAAAAACAACCGCACTTTTTATATAAT 39 35 1 CACCGCACTT 0.988498 -138 ACCCCTATAATAACCGCACTTTTCTTATTAA 42 20 0 TACCGCACTT 0.995786 -150 AGATTAAAATTTACCGCACTTTTGTTTTTTT 45 21 0 TACCGCACTT 0.995786 -161 CTGGTGAAAACAACCGCACTTTTGCGATTAA 49 13 0 CACCGCACTT 0.988498 -225 CAGTTAAAATTTACCGCACTTTTGGAATTAT 52 103 0 TACCGCACTT 0.995786 -178 AATTTTTACCGCGCTTTTCATACTTT 59 6 1 TACCGCGCTT 0.965671 -186 AGTGTCAAACTCTCCGCACTTTTTAAAACTG 59 162 1 TTCCGCACTT 0.949948 -30 TGGGCTACCATAACCGCACTTTATTAAGCCA 64 202 1 TACCGCACTT 0.995786 -32 * ********* Masking position 10 Map Score: 56.4106 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 6 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 GCCCATCGTTTATCTCACCGCTCCCTTATACGT 3 113 1 TATACCGCTC 0.788229 -172 AGTGTTGCACAAACTGTCCGCTCAATGGACAGA 27 246 1 AATTCCGCTC 0.788229 -55 AATTTCAGGCAAAATAACCGCACTTTTTTAGAT 34 113 1 AATACCGCAC 0.993499 -41 ATTTTTTATAATTTTTACCGCACTT 35 3 0 ATTACCGCAC 0.986254 -82 AATTATAAAAAATTTGACCGCACTATGCTTTAT 35 23 1 AATACCGCAC 0.993499 -62 AATACAACTAAAATTAACCGCACTTT 36 126 1 AATACCGCAC 0.993499 -16 ATTTCGGAGAATTTTGACCGCACTTCGGCGATT 37 175 0 ATTACCGCAC 0.986254 -67 TTCTCCGAAATTTTTAACCGCACTTTAAACCTT 37 197 1 TTTACCGCAC 0.915437 -45 AATGACCGTTAAAATGACCGCACTCTGAACCTT 38 224 0 AATACCGCAC 0.993499 -77 AAGTGCTTGAAAAACAACCGCACTTTTTATATA 39 31 1 AACACCGCAC 0.972727 -142 AACAACCCCTATAATAACCGCACTTTTCTTATT 42 22 0 ATTACCGCAC 0.986254 -148 AACTAGATTAAAATTTACCGCACTTTTGTTTTT 45 23 0 AATACCGCAC 0.993499 -159 AAATCTGGTGAAAACAACCGCACTTTTGCGATT 49 15 0 AACACCGCAC 0.972727 -223 AATCCAGTTAAAATTTACCGCACTTTTGGAATT 52 105 0 AATACCGCAC 0.993499 -176 AATTTTTACCGCGCTTTTCATACT 59 2 1 ATTACCGCGC 0.906845 -190 TTACAGTGTCAAACTCTCCGCACTTTTTAAAAC 59 158 1 AATTCCGCAC 0.958433 -34 AACTTGGGCTACCATAACCGCACTTTATTAAGC 64 198 1 ACTACCGCAC 0.963282 -36 ** * ******* Masking position 10 Map Score: 42.4499 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 TATCTCGCCATTAACCGTTTCAGCCCCAGGTGC 2 77 1 TTACCGTTAG 0.849476 -104 TTGGTGCGGCTTAGCCGTGTGTTTTCGGAGTAA 3 153 1 TTACCGTTTT 0.964692 -132 GGCTCATTTCTGAGCCGTTTATTCGTATTGAGA 16 23 0 TGACCGTTTT 0.960627 -142 GGCTCAGAAATGAGCCGTTTATTTTTTCTACCC 16 40 1 TGACCGTTTT 0.960627 -125 TGAACCTCAGTTAGCCGAATTTGGCTACCTAAC 18 106 1 TTACCGATTG 0.786381 -132 TATCACCGATTTATCCGTGTCTTAGAGGGACAA 22 89 1 TTACCGTTTT 0.964692 -26 TGTGTCATAATTAACCGTTTGTGATCGCCGGTA 30 56 0 TTACCGTTTG 0.960627 -198 GCACTATGCTTTATCAGTATCTTAATCACGTTT 35 42 1 TTACAGTTTT 0.57537 -43 ATTGCTTAATTTAACCGTGTTTTTGATAGAAAG 38 97 1 TTACCGTTTT 0.964692 -204 GTGCCCATTATGAGCCGTTTGTGGCTCATATTT 39 68 1 TGACCGTTTG 0.956115 -105 TGCGAATTTCTCCGTATTTTAATCTTCAGG 44 137 0 TTCCCGTTTT 0.933482 -20 ACTATTAGAATTCGCCGTCTATTTCTATATAGA 45 101 1 TTCCCGTTTT 0.933482 -81 TTATTAAGCGTTTCTTACTTCATCTA 48 4 1 TTAGCGTTTT 0.797538 -51 CTTAAATAACTGAGCCGTTTTTGATTTCCAAAA 60 180 1 TGACCGTTTG 0.956115 -121 TCCAAAAGTTTTAAGCGTATAATGTGCACCGAT 60 206 1 TTAGCGTTAT 0.476758 -95 GCGTATAATGTGCACCGATTTTTTATCTGGCTA 60 220 1 TGCCCGATTT 0.654071 -81 TAACGCCATTTGCGCCGTTTCAGCTTTCAGCAG 62 66 0 TGCCCGTTAG 0.721322 -30 *** **** * ** Masking position 10 Map Score: 18.0011 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 90 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TACGTGTGTGTTGTTACACAAAGTGAGATTGT 1 31 1 TTGTTCAAAA 0.832473 -270 CGTTTATCGCTTTTTCAAAAAATTCGACACAT 2 141 1 TTTTTAAAAA 0.535224 -40 TTTTCCAGGTTTGTTGGAGAAAGAAA 12 18 1 TTGTTGAAAA 0.831628 -16 TCTGATGCAGTTGTTCAAAAAAACACCATGAT 32 80 1 TTGTTAAAAA 0.893756 -221 TAACCGCACTTTTTTAGATAAAAAATGAGGTT 34 127 1 TTTTTGAAAA 0.727725 -27 AATCCCCTAATTTTTACAAAAATCCTTTAATT 36 76 1 TTTTTCAAAA 0.620485 -66 GTTTGAGTTCTTTTTGAACAAAAAAGAAGGTC 41 51 0 TTTTTAAAAA 0.851743 -148 AAAAATAATATTGTTCATGAAAAACTCAATTT 42 86 0 TTGTTATAAA 0.80884 -84 GCACTTTTGTTTTTTTATAAAAAACT 45 5 0 TTTTTATAAA 0.612844 -177 GAATAGAATGTTGTTCAAAAAATCTACTTCTA 45 130 0 TTGTTAAAAA 0.893756 -52 GTAAAGAATATTGTTGAAAAAAGAGCCAAATT 47 12 0 TTGTTAAAAA 0.893756 -260 GCAACCGAAATTGTTGATAAAAAGAAAAATAC 49 156 1 TTGTTATAAA 0.807959 -82 TACTCCTTGTTTGTTTAAGAAAATCTAGGCGT 63 62 0 TTGTTAAAAA 0.936961 -28 CTATCGCTTATTTTTGAATAAATTTTGGAGTG 64 141 1 TTTTTAAAAA 0.851743 -93 TTATCTCACTTTTTTGAAAAAACTTTACGAGA 65 112 0 TTTTTAAAAA 0.535224 -24 ***** ** *** Masking position 10 Map Score: 13.7615 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 55 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 CGACCGCAATTATAACACTCTGGGGAGAAATGTGCCGAA 3 16 0 TACCCGGAGA 0.777169 -269 TAAAACGTTTGGCCTTACTTAACGGAGAACCA 20 4 0 GTTCTGGAGA 0.720943 -93 TAAACAGAAGGAAAAAACAGGGAGGAGAAAAGAAG 22 7 0 GAACGGGAGA 0.972706 -108 TAATTAAGACGCTCTCTCCGTTTGGAGGAGTGAAGTGAG 25 231 1 GTCCGGGAGA 0.952008 -70 AGATTTTCTCTGGCAAACATCCAGGAGCAAAGCTA 25 276 1 TAACTGGAGA 0.833752 -25 AGCGGATTGTGCTAACTCCGACGGGAGCAAATCC 28 53 1 GACCGGGAGA 0.985461 -24 AGCAGACCCTGACGATACGTTCTGGAGGACAC 29 4 0 GATCTGGAGA 0.898246 -79 CCGGGATTCGGCTGACCCAGACAGGAGGCTGAATAATCC 32 257 1 GACCGGGAGC 0.908152 -44 ACAGGAGGCTGAATAATCCGTAAGGAGCAATTCG 32 277 1 GAACGGGAGA 0.972706 -24 ACTTTAAACCTTTAACTCCGACAGGAGAACATTT 37 218 1 TACCGGGAGA 0.960006 -24 GTCAAAGGCTGATTAACCCGTAAGGAGCAGTA 41 177 1 GAACGGGAGA 0.972706 -22 TTAGACGTTTGGCCTTACTTAACGGAGAACCA 44 4 0 GTTCTGGAGA 0.720943 -153 AAGGGTGTTTTTTTAATCTTAACGGAGCACTAAT 52 257 1 TAACTGGAGA 0.833752 -24 GTGCGGAGAGTTTGACACTGTAAGGAGGATAATGCAAGA 59 142 0 TACCGGGAGA 0.960006 -50 * ** * * **** * Masking position 16 Map Score: 14.2458 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 53 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AGTATGCCTGGCCGCGAGATTATGGCACACTTGT 8 40 1 GCGCAATTTG 0.832991 -59 CCATATCGAGGGCGCGGCATTATAACACCGCTTC 16 81 0 GCGCGATTTA 0.970855 -84 ACTACGACAAGCCCGCGCATTATACATACTTAAC 18 55 0 GCCGGATTTA 0.773925 -183 ACAATATGAGGACGCCGAATTTTAGGGCGATGCC 21 46 0 GCGCGATTTA 0.970855 -80 AAAAACAAAAGGCGCGAAATTGTATTCCAATCTC 24 55 0 GCGCAATTTA 0.921855 -103 CGGACGTCCTGTCGCAGTATATTAAGTCGTCGAT 27 129 0 GCGCGATATA 0.852535 -172 GTTAAAACCCGGCAGCGGATTGTGCTAACTCCGA 28 40 1 GCAGGATTTG 0.494074 -37 GCTGAAAAATGACGCGTTATAGTACTTGTATGCC 32 197 0 GCGCTATATA 0.335589 -104 GGTTAAAAATTTCGGAGAATTTTGACCGCACTTC 37 182 0 TCGGGATTTG 0.727516 -60 CTAATTTTAAGGCGGTAAATTTTAAATGAATGCA 38 24 0 GCGGAATTTA 0.930736 -277 AAAACAAAAGTGCGGTAAATTTTAATCTAGTTTT 45 24 1 TCGGAATTTA 0.691006 -158 TATAGAAATAGACGGCGAATTCTAATAGTTTTAC 45 96 0 GCGGGATTTA 0.974322 -86 GACTAACACAGGCGCAGGATTATAGAGAAAAGCT 47 52 0 GCGCGATTTA 0.970855 -220 ATTCCAAAAGTGCGGTAAATTTTAACTGGATTAT 52 106 1 TCGGAATTTA 0.691006 -175 ATGGCAGATAGGCGGCGGATTTTATCAAAAGAAA 52 190 0 GCGGGATTTA 0.974322 -91 * *** * *** ** Masking position 9 Map Score: 12.1494 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 174 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 7 GCAGATGATGAAAAGAAAAATGCCGGATGA 2 34 0 AAAAGAAAAA 0.855554 -147 ACATCTGATGGCAAGAAAATAGCGGTATTG 9 219 1 GCAAGAAAAT 0.675438 -33 ACCCAACTTTGCAAGAAAAATATGCGAAAA 13 13 0 GCAAGAAAAA 0.917287 -134 GCAATAAACAGAAGGAAAAAACAGGGAGGA 22 20 0 GAAGGAAAAA 0.852865 -95 TCAGTTCGGGGAAGGAAAAAAGCGAGGATT 31 105 0 GAAGGAAAAA 0.852865 -100 TTCTTCCTAAAAAAGAAAAACAAATATTAG 36 17 0 AAAAGAAAAA 0.855554 -125 CAAAGGCAAGGAACGAAAAATTCAATGTGG 41 127 0 GAACGAAAAA 0.759017 -72 AGCTTTCTACGAAAGAAAAAATAATATTGT 42 104 0 GAAAGAAAAA 0.943583 -66 GCGCCCAGAAGCAAGAAAAATTCTTATTCT 47 179 0 GCAAGAAAAA 0.917287 -93 AGGCAAGGCGAAAAGAAAATGCTACAATCG 49 71 1 AAAAGAAAAT 0.526395 -167 ATTGTTGATAAAAAGAAAAATACGCAAGAA 49 165 1 AAAAGAAAAA 0.855554 -73 AAAATTTATCGAATGAAAAATAAACTGCAG 52 52 0 GAATGAAAAA 0.680012 -229 GGATTTTATCAAAAGAAAAAGAGAAAGGCA 52 178 0 AAAAGAAAAA 0.855554 -103 CTGGTTCTTGGCAAGAAAAATGTTAA 55 7 0 GCAAGAAAAA 0.917287 -133 ********** Masking position 6 Map Score: 13.416 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 77 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TTTTACTGAGAAGGATAAGGTC 10 29 1 AAGGATAAGG 0.97617 -12 ACACCGCTTCAAGGATATGGGTAGAAAAAA 16 61 0 AAGGATATGG 0.838838 -104 ACGACTTTGAGAGGATAAGGTA 33 30 1 GAGGATAAGG 0.962486 -12 CAGTTTATATAAGGGTAAGGCTTCATCAAC 43 39 0 AAGGGTAAGG 0.946277 -45 ATTAGCTTGGAAGGCTAAGGTAATAGCCAT 46 67 0 AAGGCTAAGG 0.905402 -234 CACCCTTGGTAAGGGTGAGGTCGGCGGTTC 46 157 1 AAGGGTGAGG 0.916888 -144 TGATTGATATAAGGATGAGGAATTATAAGA 46 208 0 AAGGATGAGG 0.962486 -93 AAATTTTTGAGAGGATGAGGATATTTTTAT 52 75 1 GAGGATGAGG 0.941416 -206 TTTAAAGTAAAAGGATAAGCA 54 18 1 AAGGATAAGC 0.84138 -11 TTTTTCTGAGAAGGATAAGATC 58 29 1 AAGGATAAGA 0.781608 -12 ACACTGTAAGGAGGATAATGCAAGACGGGG 59 137 0 GAGGATAATG 0.669047 -55 ********** Masking position 2 Map Score: 8.8611 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 22 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 CGTGATGGTGACCGGGCAGCCTAAAGGCTA 5 33 1 ACCGGGCAGC 0.977022 -41 GCTATCCTTAACCAGGGAGCTGATT 5 59 1 ACCAGGGAGC 0.96511 -15 CCAATGTTACAGCAGAGAGCATGAAGAAGA 7 13 0 AGCAGAGAGC 0.587696 -53 CTGTAACATTGGCAGGGAGCTTTGCTATTT 7 31 1 GGCAGGGAGC 0.809644 -35 AATGCTCCCAATCGGGGAGCTACGTAAGAA 18 139 1 ATCGGGGAGC 0.936811 -99 AGAAGGAAAAAACAGGGAGGAGAAAAGAAG 22 11 0 AACAGGGAGG 0.608269 -104 TTTTTTATATCACGGGGAGCCTCTCAGAGG 24 110 1 CACGGGGAGC 0.837083 -48 CCGGGTTTTAACCCGACAGCAGTGACCTGT 28 22 0 ACCCGACAGC 0.686621 -55 TCGGGTTAAAACCCGGCAGCGGATTGTGCT 28 36 1 ACCCGGCAGC 0.949659 -41 CACACTGTTCGCCCGGCAGGCAAAATATCT 31 27 0 GCCCGGCAGG 0.650813 -178 TCAGCCGAATCCCGGGGAGGCAAGGAACGT 32 242 0 CCCGGGGAGG 0.881496 -59 CCACCCGTTTACGGGGGAGCTGGCGCGAAG 37 47 1 ACGGGGGAGC 0.871673 -195 ACTAAAAATTATCGGGGAGCTATTTAATAG 39 124 1 ATCGGGGAGC 0.936811 -49 CAGCGTCTGGAGCGGGCAGCGGGAATCGAA 46 105 0 AGCGGGCAGC 0.949659 -196 ********** Masking position 8 Map Score: 8.95953 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 421 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 ATCAGGTCGTTAAAAATCCCCATATCGAGGGC 16 102 0 TAAAATCCCA 0.474568 -63 AACACGTAATAAAACGTCCTCACACAATATGA 21 71 0 AAAAGTCTCA 0.904695 -55 AATGCGCACTAAAAGGGCATCATTTGATGCCC 23 31 1 AAAAGGCTCA 0.9384 -199 AAAGCGTGCAAAAAGGGCATCAAATGATGCCC 23 45 0 AAAAGGCTCA 0.9384 -185 GCTGGTGACTAAAAAGTCACCAGCCATCAGCC 27 24 0 AAAAGTCCCA 0.915262 -277 ACTGCATCAGAAATGGTCACCATCAACTTCTT 32 59 0 AAATGTCCCA 0.464533 -242 GCAGTTGTTCAAAAAAACACCATGATGAAGTG 32 86 1 AAAAAACCCA 0.730497 -215 AAAAAAACCTCATTTTTTATCT 34 142 0 AAAAAACTCA 0.704334 -12 AAAAAATCTCCATTAATACAAA 35 73 0 AAAAATCCCA 0.856859 -12 TTTTTTGTTCAAAAAGAACTCAAACTGGTTGC 41 58 1 AAAAGAATCA 0.380621 -141 TTTTTGAATTTAAAGGGCTTCATCGTTGATGA 43 15 1 TAAAGGCTCA 0.696832 -69 TAAAAAAGCTCCAGTTTAAATGT 45 169 0 AAAAAGCCCA 0.905718 -13 AATATTGTTGAAAAAAGAGCCAAATTC 47 6 0 AAAAAGACCA 0.578666 -266 TTGCCTATTGAAAATAGCATCAACATAGAAAA 49 45 0 AAAAAGCTCA 0.894099 -193 ATTTCCATTTAAAACGGATTCAATTCTATGGC 49 126 1 AAAAGGATCA 0.685331 -112 TGGAATTATAAAAATATCCTCATCCTCTCAAA 52 80 0 AAAAATCTCA 0.84028 -201 AAATATCTATAAAAAGTCATCACTGTTATAGT 59 39 1 AAAAGTCTCA 0.904695 -153 **** *** *** Masking position 3 Map Score: 11.0962 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 350 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 TGCGAAAATCCCCTTAAAATGTGTCGAAT 2 162 0 TCCCTTAAAA 0.86109 -19 ACTGAGTTTGTACGCTGAAAACAATGAAAAA 6 47 0 TAGCTGAAAA 0.934603 -65 TCCATTTGAGTATCCTGAAAACGGGCTTTTC 13 89 1 TACCTGAAAA 0.915264 -58 ATGTACGTTCCATGCTGAAAAGCCCGTTTTC 13 105 0 CAGCTGAAAA 0.80576 -42 GTCACTGCTGTCGGGTTAAAACCCGGCAGCG 28 26 1 TCGGTTAAAA 0.595713 -51 GTTCGTGTCTCCTGAAAAAAATCGTTCT 30 236 0 TCCCTGAAAA 0.929215 -18 GTGTTAAAGGTCGGCTGAAAAATGACGCGTT 32 213 0 TCGCTGAAAA 0.94556 -88 TTAAAATTTACCGCCTTAAAATTAGCAAAGA 38 33 1 CCCCTTAAAA 0.64277 -268 TTTAGGCGGAAAAGTTAAGAAAA 42 157 0 TAGCGGAAAA 0.675822 -13 ACATAGAAAATCTGGTGAAAACAACCGCACT 49 24 0 TCGGTGAAAA 0.757305 -214 TCTGTTTGAGTATCCTGAAAACGGGCTTTTC 55 78 1 TACCTGAAAA 0.915264 -62 TAGTTAAGCTTAAAACCAAAGAGAG 57 5 1 TAGCTTAAAA 0.870943 -27 AATTTTAAAATATCCTTAAAATATACAGTGA 59 97 1 TACCTTAAAA 0.83608 -95 GTGCACATTATACGCTTAAAACTTTTGGAAA 60 204 0 TAGCTTAAAA 0.870943 -97 ** ******** Masking position 8 Map Score: 8.3081 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 165 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 GAACGGTCGCAAGAGTACACCAAAAAACTGAGTTTG 6 68 0 AATCACAAAA 0.851626 -44 CATACTTGCGAAGATTTCAGGTATAAGGATACGTA 8 10 0 AATCAGATAA 0.895552 -89 AGCTCAACCCAACTTTGCAAGAAAAATATGCGAAAA 13 13 0 AATCAAAAAA 0.677868 -134 ATATCTGTGCAAATATCCAGTTAAAATATATAGATC 34 69 1 AATCAGAAAA 0.963908 -85 GATCTTTTAAAAAATTTCAGGCAAAATAACCGCACT 34 101 1 AATCAGAAAA 0.963908 -53 TGGTGCAATGAATCTTGCACTAAAAATTATCGGGGA 39 106 1 AATCACAAAA 0.851626 -67 ATTTAAACCATAAACTCCAGTCAAAAGCGCTTTGCG 44 55 1 TATCAGAAAA 0.845074 -102 CTCATTGAGAAAATTTGCAGCGCAAAGCGCTTTTGA 44 75 0 AATCAGCAAA 0.820941 -82 TAAAAAAGCTCCAGTTTAAATGTTATTCAA 45 162 0 AATCAGTAAA 0.755702 -20 GAATGAAAAATAAACTGCAGAAAAAATGAAATGCTC 52 36 0 TATCAGAAAA 0.845074 -245 CTATTTACTAAATAATCCAGTTAAAATTTACCGCAC 52 115 0 AATCAGAAAA 0.963908 -166 AATATCCTTAAAATATACAGTGATAATTTTATCCCC 59 105 1 AATCAGATAA 0.895552 -87 ATAGTTTCTAAAAATTGCAGTAATAAATGTGAATTT 64 109 0 AATCAGATAA 0.895552 -125 ** * *** **** Masking position 9 Map Score: 7.748 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 32 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 TCGCTTCCGTCCAGTCTGTGTATACGAAAT 1 62 1 CCAGTCTGTG 0.787995 -239 GAGGCAATCGCCTGTTGGTGGTATCGTTTA 2 117 1 CCTGTTGGTG 0.842182 -64 GTTTGTGTTACCTGTATGAGACGAGAGTTA 8 79 0 CCTGTATGAG 0.861863 -20 CTCAACAGAGCCTGTCTCAGCAATGATTAT 23 114 0 CCTGTCTCAG 0.91976 -116 GAACGGACGTCCTGTCGCAGTATATTAAGT 27 136 0 CCTGTCGCAG 0.914674 -165 ACAGCAGTGACCTGTTTGAGCGAGAA 28 7 0 CCTGTTTGAG 0.953547 -70 GGATTTGCTCCCGTCGGAGTTAGCACAAT 28 58 0 CCCGTCGGAG 0.913121 -19 TATTCAGCCTCCTGTCTGGGTCAGCCGAAT 32 262 0 CCTGTCTGGG 0.918291 -39 AAATGTTCTCCTGTCGGAGTTAAAGGTTT 37 223 0 CCTGTCGGAG 0.978253 -19 CGCTCCGCAACCAGTTTGAGTTCTTTTTGA 41 66 0 CCAGTTTGAG 0.850883 -133 TCCTTGATATTCTGTTTGAGTATCCTGAAA 55 68 1 TCTGTTTGAG 0.617944 -72 ********** Masking position 5 Map Score: 6.871 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 94 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 ACGGCTCATTTCTGAGCCGTTTATTCGTATT 16 27 0 TTGAGCCGTT 0.986656 -138 ACGGCTCAGAAATGAGCCGTTTATTTTTTCT 16 38 1 ATGAGCCGTT 0.964371 -127 GGGGAGCCTCTCAGAGGCGTTATTACCCAAC 24 123 1 TAGAGGCGTT 0.884101 -35 CCGTGCCCATTATGAGCCGTTTGTGGCTCAT 39 66 1 TTGAGCCGTT 0.986656 -107 AACGGGCGGATTATAGCCGTTTTTAGCTTTC 42 127 0 TATAGCCGTT 0.837314 -43 GCTCTCAATATGAGAGCCGTTTAATGTAATC 50 59 1 TAGAGCCGTT 0.978764 -132 AGCTTAAATAACTGAGCCGTTTTTGATTTCC 60 178 1 ATGAGCCGTT 0.964372 -123 TTTAACGCCATTTGCGCCGTTTCAGCTTTCA 62 70 0 TTGCGCCGTT 0.951547 -26 * ********* Masking position 10 Map Score: 6.32994 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 TAATCTCGCGGCCAGGCATACTTGCGAAGAT 8 31 0 GCCAGGCTAC 0.940503 -68 TCTCCGTTAAGTAAGGCCAAACGTTTTAACT 20 15 1 GTAAGGCAAA 0.853671 -82 CCCCGCGATCGCGAGGCAAACCAAATCGAAA 23 172 0 GCGAGGCAAC 0.946944 -58 CGTTTTACGGGCAAGGCCATAAAAACAAAAG 24 78 0 GCAAGGCATA 0.737702 -80 CAAAATATCTGCCAGGCGTACCAGAA 31 6 0 GCCAGGCTAC 0.940503 -199 TATTTTGCCTGCCGGGCGAACAGTGTGATAC 31 30 1 GCCGGGCAAC 0.843404 -175 CTTGAGTTTAGCGAGGCATACAAGTACTATA 32 183 1 GCGAGGCTAC 0.892036 -118 TCCTTTAATTGAAAGGCGAAATTTCTAAAAT 36 98 1 GAAAGGCAAA 0.697792 -44 TCTCCGTTAAGTAAGGCCAAACGTCTAAATT 44 15 1 GTAAGGCAAA 0.853671 -142 TACGATGCCCGCAAGTCCTAAATTCGTCTGT 46 34 0 GCAAGTCTAA 0.607535 -267 TTTTCAATAGGCAAGGCGAAAAGAAAATGCT 49 63 1 GCAAGGCAAA 0.963542 -175 GATCGTGAAGGCAAGTCTAAAGGTTTAAATA 49 197 1 GCAAGTCAAA 0.769789 -41 ATGACGATATGTCAGGCTAACAATGTTTCCG 50 105 1 GTCAGGCAAC 0.882708 -86 ******* *** Masking position 7 Map Score: 6.50427 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 393 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