AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_bsub_reg_300.orf -o00400_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 Input sequences: #1 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 pabB 166 para-aminobenzoate synthase (subunit A) #11 aroI 275 shikimate kinase #12 ykrV 94 similar to aspartate aminotransferase #13 aspB 22 aspartate aminotransferase #14 ypmA 142 ypmA #15 dinG 125 ATP-dependent helicase #16 panB 245 ketopantoate hydroxymethyltransferase #17 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #18 ypjD 300 alternate gene name: jojD #19 tyrA 48 prephenate dehydrogenase #20 trpE 215 anthranilate synthase #21 aroB 61 3-dehydroquinate synthase #22 aroF 69 chorismate synthase #23 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #24 ndk 115 nucleoside diphosphate kinase #25 gerCA 162 heptaprenyl diphosphate synthase component I #26 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #27 mtrA 187 GTP cyclohydrolase I #28 hbs 300 non-specific DNA-binding protein HBsu #29 aroC 111 3-dehydroquinate dehydratase #30 sigX 203 RNA polymerase ECF-type sigma factor (sigma-X) #31 resD 80 two-component response regulator #32 resC 135 essential protein similar to cytochrome c biogenesis protein #33 resA 131 essential protein similar to cytochrome c biogenesis protein #34 ypuL 91 similar to hypothetical proteins #35 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #36 ypuI 54 similar to hypothetical proteins from B. subtilis #37 ypuG 280 similar to hypothetical proteins #38 yqhS 86 similar to 3-dehydroquinate dehydratase #39 yqhR 226 yqhR #40 yqeG 300 similar to hypothetical proteins #41 pheB 60 chorismate mutase #42 obg 33 GTPase activity #43 spo0B 300 sporulation initiation phosphoprotein #44 pheS 300 phenylalanyl-tRNA synthetase (alpha subunit) #45 tyrS 300 tyrosyl-tRNA synthetase #46 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #47 ytxJ 23 alternate gene name: csb40; similar to general stress protein #48 ytxH 27 alternate gene name: csb40; similar to general stress protein #49 ytxG 161 alternate gene name: csb40; similar to general stress protein #50 murC 249 UDP-N-acetyl muramate-alanine ligase #51 ytpS 159 ytpS #52 ytpP 234 similar to thioredoxin H1 #53 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #54 eno 29 enolase #55 tpi 30 triose phosphate isomerase #56 pgk 300 phosphoglycerate kinase #57 ywfB 151 alternate gene name: ipa-80d #58 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #59 rocB 73 alternate gene name: ipa-77d #60 rocA 226 pyrroline-5 carboxylate dehydrogenase #61 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #62 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #63 ywaE 150 alternate gene name: ipa-10r; similar to transcriptional regulator (MarR family) #64 tyrZ 248 tyrosyl-tRNA synthetase Motif number 1 TCTAAAAATGAAAAAAATCGGCTTCTGCAAGA 1 130 0 AAAAAAACGC 0.849326 -171 CTTTCTTTCTAAAAAAACTGCCGGCTGACGCT 6 15 1 AAAAAAATCC 0.871913 -180 TCATTTACATAAAAAAACTGCCAGCGTCAGCC 6 37 0 AAAAAAATCC 0.871913 -158 ACGAAATATAAAAAAACTCCCGGCGAACCGGG 10 25 0 AAAAAACCCG 0.945151 -142 AAGAAAAGCCCCCTTTATCGGG 15 1 1 AAGAAAACCC 0.921802 -125 AAAATCTTAAAAGAAAACCCCCGATAAAGGGG 15 20 0 AAGAAAACCC 0.921802 -106 TCTGCAAGCCAAAAAACCTTCCGTTACAACGA 16 180 0 AAAAAACTCC 0.88087 -66 TTGTTTCAATAAAAAAATCAGCTTTTCAGCTG 23 152 0 AAAAAAACGC 0.849326 -85 ACGGCTTTTTAAGAAAAACTGCACTCTGAGGA 28 159 0 AAGAAAACGC 0.653489 -142 CTTGTTCCATAAGAAACACCCGCTGACTGAGC 30 37 1 AAGAAACCCG 0.852185 -167 TTGGCTATTAAAAAAACACCCGCTCAGTCAGC 30 58 0 AAAAAACCCG 0.945151 -146 AGGCCGCATAAAGAAAATTTCCGCTCAGCTCT 32 35 0 AAGAAAATCC 0.694886 -101 TGCCAAATCTAAAAAAAACGCCGTTT 34 5 0 AAAAAAACCC 0.972401 -87 AGCAAACATAAAAAAACTCTCCCTGAAAAAGG 35 22 0 AAAAAACCCC 0.974537 -101 GATAAAAGGAAAAAAGAACGCCCGGCCTCTAG 37 53 1 AAAAAGACCC 0.962979 -228 ATAAGCCACCAAAAAGCTCTCGTCCAATACTA 37 202 0 AAAAAGCCCG 0.927123 -79 AATGTCAATAAAAAAGCTCACACTTTTTGGCA 39 172 0 AAAAAGCCCA 0.804048 -55 AAAACTGAGCAAAAAAATTTCGACAAAAATTG 40 210 0 AAAAAAATCG 0.753992 -91 CGCATATTGCAAAAAAAACTCCAGTCATCATC 43 11 0 AAAAAAACCC 0.972401 -290 TTTGGAAAATAAAAAAAACCCGTCCCTTGTAC 44 240 0 AAAAAAACCG 0.940702 -61 TAATTAAAATAAAAAACGCCCCTTCGTTTACA 45 261 0 AAAAAACCCC 0.974537 -40 AAAAAAGCGTCCAGATATCATCT 46 2 1 AAAAAGCTCA 0.4422 -234 GTTTTTTACAAAAAAAAGCGCCAGATGATATC 46 24 0 AAAAAAACCC 0.972401 -212 AATAAAAATCCCTCCTTATGTATAT 52 4 1 AAAAATCCCC 0.711696 -231 CCCTGTGCCGAAAAAGACTGCGATCTGCCCTA 56 201 1 AAAAAGATCG 0.693508 -100 AAAAAGCTCTCCGGGAGGCCGG 58 1 1 AAAAAGCCCC 0.965818 -209 TAACACGTAAAAAAAGCTCTCCGGCCTCCCGG 58 21 0 AAAAAGCCCC 0.965818 -189 AATTTTTAAGAAAAAGAACTGGTAATTCGCGA 62 208 1 AAAAAGACGG 0.652018 -93 TCGGTTGAATAAAAAAAGCCCAAACAACGCCA 63 45 0 AAAAAAACCA 0.836515 -106 TACAAACACAAAAAAGAGCCCATCCCAATAAG 64 213 0 AAAAAGACCA 0.790687 -36 ******* * ** Masking position 5 Map Score: 40.9387 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 479 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 2 GAATAGTTTCTCTACTTTACTTTTTACAAACATTC 6 153 0 TTTTCTTTTT 0.769221 -42 GTATCATTCCTCTATTTTCTTTTTTACTTGTTTTT 10 140 0 TTTTTTTTTT 0.672993 -27 CACCCCAAATTTTTCTTTACTTTTTTCATTTAACC 12 19 1 TTTTCTTTTT 0.769221 -76 TAAGCACGTTTGCTGTTTTCTTTTTCATCCACTAT 18 214 0 TTTTCTTTTT 0.769221 -87 GGAGGATACAGCCAATTCTTTTTTTTATGCTATAA 25 54 1 GTTCTTTTTT 0.720952 -109 CGAATATTCCTTTTTTTCCTTTTTTCATCC 28 6 0 TTTCTTTTTT 0.920452 -295 TTTCTCTTACTTGCTCTCATTTTTTTCTGAGACAG 28 200 1 TCTCTTTTTT 0.936025 -101 TTGAAACCCCTCCGTTCACTTTTTTGTCGTATGA 30 180 0 CTTCCTTTTT 0.890345 -24 CGGTTTGGCCTGCCCTTTTTATCTTTATTC 32 116 0 TTGCCTTTTT 0.877955 -20 GTTCATTTCACATTTCTTACTTTTTGAAGGTTATG 33 61 0 CCTTCTTTTT 0.646149 -71 CGTTTACTCTCCCTTTTTCAGGGAGAGT 35 4 1 TCTCCTTTTT 0.959508 -119 AAGTTTAATGAATCGCGCTTTTTCATCATCATA 36 9 1 TCGCCTTTTT 0.900951 -46 GCACTAGAGGCCGGGCGTTCTTTTTTCCTTTTATC 37 53 0 CCGTCTTTTT 0.412095 -228 CTTTTTTATTGACATTTCATTTTTTGGGCACACTT 39 188 1 GTTCTTTTTT 0.720952 -39 AACCCGCACCCTTCCCTTTTTCTTTCTTTCA 40 280 0 CTTCCTTTTT 0.890345 -21 CCCAGAAATATCATGTTCCTTTTTTCTGGCTTTGG 43 176 0 TTTCTTTTTT 0.920452 -125 AAGATAAAGCTCCTTTTTTAATTAAAATA 45 282 0 TCTCTTTTTT 0.936025 -19 CCAGATATCATCTGGCGCTTTTTTTTGTAAAAAAC 46 21 1 TCGCTTTTTT 0.848859 -215 TCCTTTCCCTGCACATTCATTTTTTATTTTGTAGT 46 203 0 GTTCTTTTTT 0.720952 -33 CGGCTTTTCACATGATTCGTTTTTTTTGGCGGATT 51 20 0 CTTCTTTTTT 0.833703 -140 TCTGTGTCACTCCCTTTTTTTGATGGTTG 53 5 1 TCTCCTTTTT 0.959508 -143 TAGCGGAAGTTTCTCCTCGTTTTTTCTTAGCATTC 53 65 1 TCTCTTTTTT 0.936025 -83 GGGGACGGACTCCCTTTCCCTTTTTCCATGAAGAC 56 65 1 TTTCCTTTTT 0.949342 -236 CAAAATAATTTTGCATTTGTTTTTTGCGTAAAGAG 60 26 1 TTTTTTTTTT 0.672993 -201 AACGCAAATTTATTTTGCGTTTTTTGCTCTTTACG 60 52 0 TTGCTTTTTT 0.816234 -175 AACAGGTGATCACCTTTCTCTTTTTCCGATCTTGA 60 86 0 CTTCCTTTTT 0.890345 -141 TGAGATGTTTTCAGTCTCTTTTTTTGTGGATTCAA 61 34 1 TCTCTTTTTT 0.936025 -143 CTTTTTCACCTCATTGTTTTTTTGGCCGG 61 158 0 TCTCTTGTTT 0.633001 -19 ATCTTCGACTTTTTTTGCCCTTTTTTAAAATAGGA 62 21 1 TTGCCTTTTT 0.877955 -280 AAATGGACGATTTCCCTCTCTTTTTCTAGTAACAT 62 80 0 TCTCCTTTTT 0.959508 -221 CCAGTAGCGGTTTGTCTCCCTGTTTCAGAGAGCCG 64 25 1 TCTCCTGTTT 0.736388 -224 TTTTCCTCCTTTTTTACAAACACAA 64 234 0 TCTCTTTTTT 0.936025 -15 * *** ****** Masking position 11 Map Score: 36.9094 Number of sites scoring better than the average of aligned sites = 931 Number in coding regions = 686 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 3 TTCTCAAATTAAAAACCCGCTAAAGAGC 8 8 0 AAAAACCCCT 0.717106 -39 ATCATACAGAAAAAGACCCTTCCATCGAAGA 11 33 1 AAAAGACCTT 0.847152 -243 ACTTCGACGCAAAAAAGCGTTAAAACCTTCC 11 88 0 AAAAAAGCTT 0.447727 -188 CCCACACCGCAAAAGCCGCTTTATGCGGCTT 14 11 0 AAAAGCCGTT 0.897839 -132 TGTTTTATTTAAAAGCGGATTTCCCGCTCTG 14 52 1 AAAAGCGGTT 0.781781 -91 AAGAAAAGCCCCCTTTATCGGGGG 15 4 1 AAAAGCCCCT 0.875967 -122 AATGGAGCGGCAAAACCGTTTTACTCTCAAA 15 49 0 CAAAACCGTT 0.356977 -77 TGTGTTGGTACAAGCCCGTTGATTTTGGTA 16 10 1 ACAAGCCCTT 0.776655 -236 AAGCATCACACAAAACCCCTTTTCCTTCCAT 18 166 1 CAAAACCCTT 0.706752 -135 TTCTTCACAGAAAAGCCCCTTTCTAAGGGGC 27 56 1 AAAAGCCCTT 0.974462 -132 TTGAAATATGAAAAGCCCCTTAGAAAGGGGC 27 70 0 AAAAGCCCTT 0.974462 -118 GTTTTTCTTAAAAAGCCGTTTAATTGTCTTT 28 172 1 AAAAGCCGTT 0.89753 -129 AAAGAGCCCTTTAAGGCTCTTT 29 2 1 AAGAGCCCTT 0.776608 -110 TAGCAACTAAAAAAGAGCCTTAAAGGGCTCT 29 13 0 AAAAGAGCTT 0.693124 -99 GGATCACGGTAAAAACGCTTTCTAAATTTCA 33 30 1 AAAAACGCTT 0.84808 -102 ATGATGATGAAAAAGCGCGATTCATTAAACT 36 12 0 AAAAGCGCAT 0.51341 -43 ATGGTACACTAAAAGCACATTAAAGGAGGAA 37 16 0 AAAAGCACTT 0.668585 -265 TTAAAATAAAAAACGCCCCTTCGTTTACACG 45 259 0 AAACGCCCTT 0.77656 -42 TTTTTTTTGTAAAAAACCCTTGAACATTGCC 46 39 1 AAAAAACCTT 0.665487 -197 TCCTATAATTAAAAACCCTTTTTAAAGGGTT 57 26 1 AAAAACCCTT 0.931968 -126 ATACAAACAAAAAAACCCTTTAAAAAGGGTT 57 39 0 AAAAACCCTT 0.931968 -113 CCTCTGCAGAAAAAGCGCTTTTTCATAATTC 62 238 0 AAAAGCGCTT 0.939587 -63 ******** ** Masking position 11 Map Score: 21.6741 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 507 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 GGATGATTGTAAAAGCCGCAGCTGAGCCAA 6 69 0 AAAAGCCGCA 0.734616 -126 TCTCAAATTAAAAACCCGCTAAAGAGC 8 8 0 AAAACCCGCT 0.614228 -39 CCCACACCGCAAAAGCCGCTTTATGCGGCT 14 12 0 AAAAGCCGCT 0.960533 -131 AAGAAAAGCCCCCTTTATCGGGG 15 4 1 AAAAGCCCCC 0.916811 -122 CTGCAAGCCAAAAAACCTTCCGTTACAACG 16 181 0 AAAAACCTTC 0.449443 -65 TTCTTCACAGAAAAGCCCCTTTCTAAGGGG 27 56 1 AAAAGCCCCT 0.956828 -132 TTGAAATATGAAAAGCCCCTTAGAAAGGGG 27 71 0 AAAAGCCCCT 0.956828 -117 GTTTTTCTTAAAAAGCCGTTTAATTGTCTT 28 172 1 AAAAGCCGTT 0.928923 -129 GGATCACGGTAAAAACGCTTTCTAAATTTC 33 30 1 AAAAACGCTT 0.558871 -102 AATCTAAAAAAAACGCCGTTT 34 2 0 AAACGCCGTT 0.860763 -90 AAGCGGGAGAAAAAGCCTTTGCTTCTGGTT 37 102 0 AAAAGCCTTT 0.838999 -179 CGCTCCGAGCAAACACCTCTTGTGTTTTGA 37 135 1 AAACACCTCT 0.591624 -146 ATTGTACAGGAAACACCGCTAAACCTCTAG 39 62 1 AAACACCGCT 0.783471 -165 TCCAGGGAGAAAATGCCGCTGACTGAGAGC 44 44 1 AAATGCCGCT 0.599381 -257 CTTTGTTTGCAAAAGCGGTTCATGAGTGTA 45 112 0 AAAAGCGGTT 0.815809 -189 TTAAAATAAAAAACGCCCCTTCGTTTACAC 45 260 0 AAACGCCCCT 0.913069 -41 AAAAAAGCGTCCAGATATCATC 46 3 1 AAAAGCGTCC 0.621809 -233 TTTTACAAAAAAAAGCGCCAGATGATATCT 46 23 0 AAAAGCGCCA 0.461009 -213 TTTTTTTGTAAAAAACCCTTGAACATTGCC 46 40 1 AAAAACCCTT 0.788752 -196 TTTATCACTTAAAAGCGTTTGGGTAATAAA 46 102 1 AAAAGCGTTT 0.626273 -134 GCGGCGGCTGAAAAGCCTCCCTTAGCGGCG 50 166 0 AAAAGCCTCC 0.828932 -84 GAATCATGTGAAAAGCCGCTAAGCCCTTGT 51 37 1 AAAAGCCGCT 0.960533 -123 GTGGTATACTAAAAACCGTCCCAGAAAACT 51 118 1 AAAAACCGTC 0.670932 -42 AAGCTGCTTAAAACGCGGTCGTTTCTCTAT 56 123 0 AAACGCGGTC 0.510998 -178 TCCTATAATTAAAAACCCTTTTTAAAGGGT 57 26 1 AAAAACCCTT 0.788752 -126 ATACAAACAAAAAAACCCTTTAAAAAGGGT 57 40 0 AAAAACCCTT 0.788752 -112 TCTTTCTCAAACACCTCTTCCATAATCT 58 192 0 AAACACCTCT 0.591624 -18 CCTCTGCAGAAAAAGCGCTTTTTCATAATT 62 239 0 AAAAGCGCTT 0.80134 -62 ********** Masking position 3 Map Score: 26.5032 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 963 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 5 GGATTCGAACCCGTGTTACCGCCGTGAAAGGG 1 69 0 CGTGTTCCGC 0.813138 -232 ATATAGATACCGGCTTTACCGGTCAAGCTTAT 11 189 0 CGCTTTCCGG 0.986554 -87 CCGCATAAAGCGGCTTTTGCGGTGTGGGAGTA 14 14 1 CGCTTTGCGG 0.877499 -129 TATTTAAAAGCGGATTTCCCGCTCTGTGATAC 14 57 1 CGATTTCCGC 0.860978 -86 GAGAGTAAAACGGTTTTGCCGCTCCATTTCCG 15 52 1 CGTTTTCCGC 0.967565 -74 TGGCTGAGGGCGGTTTTACAGGTATTACACTT 18 43 0 CGTTTTCAGG 0.960929 -258 ATAAAAAAATCAGCTTTTCAGCTGATTTTAGA 23 144 0 CGCTTTCAGC 0.971877 -93 CGTTTACTCTCCCTTTTTCAGGGAGAGTTTTT 35 11 1 CCTTTTCAGG 0.689338 -112 ATTTCATATCCTGTTTTGAAGGAGTTTGTACA 37 171 0 CGTTTTAAGG 0.618313 -110 ATAGGGTAGCCAGTTTTTCCGGCAATGAGAGT 37 237 1 CGTTTTCCGG 0.97529 -44 TTCTGATCAACTGCTTTCCAGGGAGAAAATGC 44 28 1 CGCTTTCAGG 0.978598 -273 AACAGCTATGCCGCTTTACAGCAGCTGTGCAT 50 61 1 CGCTTTCAGC 0.971877 -189 CCGCTAAGGGAGGCTTTTCAGCCGCCGCGGTC 50 168 1 AGCTTTCAGC 0.677799 -82 GCGTTTTAAGCAGCTTTGCCGGCGCTTTCGCC 56 137 1 CGCTTTCCGG 0.986555 -164 * ***** **** Masking position 6 Map Score: 15.8209 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 265 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CCTCTATCACCACTTTTGAATAGTTTCTCTACTTTACTT 6 166 0 TTTTGTTTTC 0.64667 -29 ATGTATATAATCTATCAATTTCAAAATTTTTTGTCAA 9 3 0 TTTTTTTTTC 0.925661 -73 AAGCTTATAGTGCGCTTTGTTGTAGCCATTTTTGCCTGAATGACA 11 152 0 TCTTTTTTGC 0.810822 -124 CTTTTTAACACCCCAAATTTTTCTTTACTTTTTTCATTTAACCAT 12 11 1 CCTTTTTTTC 0.613207 -84 GATTCTTCACTTTCTAAAGTTCGGCGAGTTTCATCCCTCTGTCCC 16 131 0 TTTTTTTCTC 0.686587 -115 TTCTTTTGGGTTTATTTGTTATATAGTATTTTATCCTCTCATGCC 20 145 1 TTTATTTTTC 0.401556 -71 CCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTC 21 19 0 TTTTTTTTTC 0.925661 -43 CACATTTATTTCTTAATCTATGTATGAGTTTTATCTTTTCATTCG 25 104 0 TTATTTTTTC 0.638749 -59 ACCGAACGAATATTCCTTTTTTTCCTTTTTTCATCC 28 2 0 TTTTTTTCTC 0.686587 -299 TAATTGTCTTTCTCTTACTTGCTCTCATTTTTTTCTGAGACAGGT 28 192 1 TTTGTTTTTC 0.498622 -109 TCCCCCTGCTTTCCTTCTGTTACTTTCATTTTATCAAATCGTGAG 31 42 0 TCTTTTTTTC 0.915154 -39 CGCTCAGCTCTGCCATGACATCACTCCCTTTTCGC 32 1 0 TCATTTTTGC 0.378346 -135 GTCTTTCACCTCAAGTATTATCTTACTTTTTTCAACCTTAACA 34 59 0 CTTTTTTTTC 0.64667 -33 CTCACGTCCTTGTGGTGGTTTGTACAAGTTTATGCGCATGTCCAT 35 83 0 TTTTTTTAGC 0.512198 -40 ACAATCTCTCCTTTTCGCGAGGGTTTCTCATGTAAAAAA 38 58 0 TTTTGTTTTC 0.64667 -29 ACATGCATTATACCCGTTATTTTCAAATTTTACTCGCAGCTGCCA 39 132 1 TCTTTTTATC 0.695948 -95 GCACATACTCTGCATTTCATTCTAGGTGTTTACTCCGCATATTGC 43 33 0 TCTTTTTATC 0.695948 -268 GGGGAACATATCCAGTGGGTTTGAGATGTTTATTCTCATTCTTGG 43 90 0 TCTTTTTATC 0.695948 -211 TATTCCTCCTCTTAGTATTTTTTTCTC 48 1 0 TCTTTTTTTC 0.915154 -27 CTTAGCGGCTTTTCACATGATTCGTTTTTTTTGGCGGATTTATGG 51 15 0 TTATTTTTGC 0.412666 -145 CCTCCAGTTGTTTATGTTCTTACATGTTTTTTATCGATACTCGTC 52 192 0 TTTTTTTTTC 0.925661 -43 CAACCAATCTTTTAAAATTTTAAGTAAATTTTATCCAGTGGAAAT 57 111 0 TTTTTTTTTC 0.92566 -41 CATAAAGTTGTATTATAGTTTAGCATTGTTTTTTCTCTATTTACA 58 141 0 TTTTTTTTTC 0.925661 -69 TAGACAAATTTCTGTTCGATTCAACAAGTTTTTTCAGCAAAAGAC 60 120 1 TTTTTTTTTC 0.925661 -107 TAGTAACATCTGCCTGACATTTTATATCTTTTATCCTATTTTAAA 62 44 0 TCTTTTTTTC 0.915154 -257 TGCACCCCCGTTTTCGGGTTTTTGTTTATTTTGGCGTTGTTTGGG 63 14 1 TTTTTTTTGC 0.831876 -137 * * ** **** ** Masking position 20 Map Score: 20.9977 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 235 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 AATGTCCTCCTCACAATGAGCAG 4 91 0 TTCCTCCTCA 0.956766 -13 TCCTTACCTCCTCCCACAGTAAGC 5 84 0 TACCTCCTCC 0.955938 -14 TTTTTCATCCTCCAGTTTGAACA 14 130 0 TTCATCCTCC 0.951742 -13 GTTTTCTCCTCCTCATGTTTAGAGG 16 231 0 TTCCTCCTCA 0.956766 -15 CGAAACCTCCTATCATCCTCTTACATGTTAG 18 276 0 TTCATCCTCT 0.659101 -25 GAATTGGCTGTATCCTCCCGCTGTTTGCGAG 25 41 0 TTCCTCCCGC 0.849482 -122 GTTCTATGTCCTCCACCAATGAATACA 27 171 0 TTCCTCCACC 0.844434 -17 GCCTTTCACCTCCTCCCAAAAGGATA 28 285 0 TACCTCCTCC 0.955938 -16 GTTTTCCCCCTGCTTTCCTTCTG 31 68 0 TTCCCCCTGC 0.767026 -13 TTGCATCCCCCCTTTAAAATA 41 50 0 TGCATCCCCC 0.776948 -11 TTTGCATCCTCCTTTTATGTAA 44 289 0 TGCATCCTCC 0.883303 -12 CATCTGTAAATTTCACCCTCATGTACACGAT 52 37 1 TTCACCCTCA 0.714294 -198 TTTTTACGTGTTACATCCTCATGTATTTTTA 58 40 1 TACATCCTCA 0.811723 -170 AAATTGTCCTCCTGATCAAAAAGTT 59 59 0 TTCCTCCTGA 0.85275 -15 CAAACGTGAATTACCTCCCCAAGCTTTCTTT 64 86 1 TACCTCCCCA 0.825009 -163 * ********* Masking position 1 Map Score: 10.4184 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 199 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 AGTTTCATCCCTCTGTCCCAGTCCTTTTTT 16 120 0 CTCTGTCCCA 0.864285 -126 TGTATTTAATCGCTGTCCCAATCTTCGGCG 32 73 1 CGCTGTCCCA 0.980035 -63 GCGCAGTGTACGCGGTCCCGGCGACAACTC 44 109 0 CGCGGTCCCG 0.981954 -192 GAGTTGTGGCCGCGGTACCACCCTTATTTC 44 203 0 CGCGGTACCA 0.988652 -98 GATTGATTATCGCGGTACCACCCTACTAAT 45 222 0 CGCGGTACCA 0.988652 -79 TTTCAGCCGCCGCGGTCGCAAATTGAAATG 50 183 1 CGCGGTCGCA 0.971604 -67 GCTCAATGCACGCGGTACCACCCTGGTTGA 64 176 0 CGCGGTACCA 0.988652 -73 ********** Masking position 6 Map Score: 8.60344 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 GAAAAGGGGCTGAAAGCAGGT 8 36 1 TGAAAGCAGG 0.654202 -11 TACTAGTATCACAGAGCGGGAAATCCGCTT 14 64 0 ACAGAGCGGG 0.810169 -79 AAAATAAGCAACAGAGCCGGCAACATATAA 23 19 1 ACAGAGCCGG 0.967076 -218 TTGGCTGAAAAGAGAGCCTGGTGCCAGGCT 41 17 1 AGAGAGCCTG 0.949187 -44 CCTTTAAAATAGAGAGCCTGGCACCAGGCT 41 31 0 AGAGAGCCTG 0.949187 -30 GCTTTTGCAAACAAAGCCGGCCAGGCTTTC 45 126 1 ACAAAGCCGG 0.926118 -175 CTTTCACTACTGAAAGCCTGGCCGGCTTTG 45 137 0 TGAAAGCCTG 0.844842 -164 GAGCGTTTTCTGAAAGCCGGTCTTCATGGA 56 89 0 TGAAAGCCGG 0.950734 -212 TCCCTGTTTCAGAGAGCCGGCGGTAGGTGC 64 41 1 AGAGAGCCGG 0.98512 -208 CGGCGGTAGGTGCGAGCCGGCGCACAGGCA 64 58 1 TGCGAGCCGG 0.904128 -191 ********** Masking position 5 Map Score: 7.91609 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 137 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 AATGTCCTCCTCACAATGAGCAGG 4 90 0 TCCTCCTCAC 0.687687 -14 CTTGAACTCCCCCTAATTCGTC 13 6 0 TCCCCCTAAT 0.909493 -17 GTTTTCTCCTCCTCATGTTTAGAGGA 16 230 0 TCCTCCTCAT 0.945542 -16 AAACCTCCTATCATCCTCTTACATGTTAGC 18 275 0 TCATCCTCTT 0.764587 -26 AAATATCACCCTTGTCCCCAAATTC 25 148 0 TCACCCTTGT 0.580891 -15 GTTTTCCCCCTGCTTTCCTTCTGT 31 67 0 TCCCCCTGCT 0.74235 -14 TGCCCCCTTCCCCCTATTGCAGATCCAT 33 114 0 TCCCCCTATT 0.896632 -18 TTTGCATCCTCCTTTTATGTAAACAA 44 285 0 TCCTCCTTTT 0.846307 -16 TATTCCTCCTCTTAGTATTTTTT 48 15 0 TCCTCCTCTT 0.937452 -13 TCTGTAAATTTCACCCTCATGTACACGATG 52 39 1 TCACCCTCAT 0.885292 -196 AAATTGTCCTCCTGATCAAAAAGTTG 59 58 0 TCCTCCTGAT 0.84098 -16 ATGTAGTCCCCCTCGTGTTATGAAAT 60 211 0 TCCCCCTCGT 0.945677 -16 TTCATTGGATTCACCCTTATCATCATGCAA 61 84 0 TCACCCTTAT 0.739279 -93 ATGGACGATTTCCCTCTCTTTTTCTAGTAA 62 83 0 TCCCTCTCTT 0.619042 -218 GACATTTCCCCCTAATTGATTGTTGA 62 285 0 TCCCCCTAAT 0.909493 -16 TTTTCCTCCTTTTTTACAAACAC 64 236 0 TCCTCCTTTT 0.846307 -13 ********** Masking position 7 Map Score: 10.7161 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 140 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 11 ACGACAATCAAAGGCAAGTGGAATGGAAACA 3 24 1 AAGGCAAGGG 0.778232 -65 AAGAAAGAAAAAGGGAAGGGTGCGGGTT 40 283 1 AAGGGAAGGT 0.946226 -18 TCCCTTGTACAAGGGACGAGTTGTGGCCGCG 44 219 0 AAGGGACGGT 0.981999 -82 TCCCTTGTACAAGGGACGGGTTTTTTTTATT 44 234 1 AAGGGACGGT 0.982 -67 CGTTTACACGAAGGGACGATTGATTATCGCG 45 238 0 AAGGGACGTT 0.940037 -63 CGTGTAAACGAAGGGGCGTTTTTTATTTTAA 45 259 1 AAGGGGCGTT 0.712092 -42 ATACGCCGCTAAGGGAGGCTTTTCAGCCGCC 50 163 1 AAGGGAGGTT 0.694972 -87 GTATGATCCAAATGGACGAGTATCGATAAAA 52 178 1 AATGGACGGT 0.915692 -57 GAAAGCGGACAAGGGAAGGGGACGGACTCCC 56 48 1 AAGGGAAGGG 0.947175 -253 TTCATGGAAAAAGGGAAAGGGAGTCCGTCCC 56 66 0 AAGGGAAAGG 0.541497 -235 ACAAGGTTCAAATGGACGATTTCCCTCTCTT 62 93 0 AATGGACGTT 0.757387 -208 GACGTGGCTCAATGCACGCGGTACCACCCTG 64 181 0 AATGCACGGG 0.684149 -68 CCATCCCAATAAGGGACGTGGCTCAATGCAC 64 195 0 AAGGGACGGG 0.98233 -54 ******** ** Masking position 2 Map Score: 10.4832 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 88 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 TATGATAAATAGGAAGGGAGGAATGGCG 11 9 0 AGGAAGGGAG 0.830253 -267 CGTTTTGTACGGAAATGGAGCGGCAAAACC 15 63 0 GGAAATGGAG 0.801638 -63 TCTAATGGAAGGAAAAGGGGTTTTGTGTGA 18 171 0 GGAAAAGGGG 0.769235 -130 TAGATCGTTGGGAAAGGCAGAGGTCTGATG 23 118 0 GGAAAGGCAG 0.870483 -119 GCGAAAAGGGAGTGATGTCATG 32 3 1 GAAAAGGGAG 0.7847 -133 CTGCAATAGGGGGAAGGGGGCA 33 120 1 GGGAAGGGGG 0.980844 -12 GAAAGAAAAAGGGAAGGGTGCGGGTT 40 285 1 GGGAAGGGTG 0.95785 -16 GAATGTGCAGGGAAAGGATGAAAAAA 46 220 1 GGAAAGGATG 0.745375 -16 GCAGGGAAGGAAGAGCTTGAGTC 47 4 1 GGGAAGGAAG 0.914755 -20 AAGCGGACAAGGGAAGGGGACGGACTCCCT 56 50 1 GGGAAGGGGA 0.801366 -251 ATGGAAAAAGGGAAAGGGAGTCCGTCCCCT 56 64 0 GGAAAGGGAG 0.978839 -237 ********** Masking position 5 Map Score: 5.95498 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 74 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 TCCTCTCATCTCCCACCTGTTATATTCGTTG 1 280 0 TCCACCTGTT 0.827543 -21 CTATTCTCACCTTCTAAAAAAATCT 12 80 0 TCCACCTTCT 0.738168 -15 TGCTCTCACTCCTTATGGCAAGGAGA 20 200 0 TCCTCCTTAT 0.86689 -16 TGCCATGACATCACTCCCTTTTCGC 32 5 0 TCCTCCCTTT 0.91642 -131 CATCTCACCATTTTCAAGTATCA 37 268 0 TCCACCATTT 0.784982 -13 ACAATCTCTCCTTTTCGCGAGGGTT 38 72 0 TCCTCCTTTT 0.971993 -15 ATAAAAAAGCTCACACTTTTTGGCAGCTGCG 39 166 0 TCCACTTTTT 0.502831 -61 AGCAGTGAGATCACTGCTTTTTA 49 3 0 TCCTGCTTTT 0.852123 -159 AGCAGTGATCTCACTGCTTTTTATTTATCTG 49 16 1 TCCTGCTTTT 0.852123 -146 AATAAAAATCCCTCCTTATGTATATCCAT 52 9 1 TCCTCCTTAT 0.86689 -226 TTCATATCCCTCCAGTTGTTTATGTTC 52 218 0 TCCTCCAGTT 0.655521 -17 TCTGTGTCACTCCCTTTTTTTGATGGT 53 7 1 TCCTCCCTTT 0.91642 -141 TTGATTCACACCTTTGCAATGTCAAG 53 132 0 TCCACCTTTG 0.708048 -16 GAGTTTTGTCTCTCCTTTTGATTTTCAAA 54 11 0 TCCTCCTTTT 0.971993 -19 TTTTCCTCCTTTTTTACAAACAC 64 236 0 TTCTCCTTTT 0.662587 -13 ** ******** Masking position 1 Map Score: 10.5192 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 171 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 14 ATTTTTTTCATTTTTAGACAACATTCCGGAA 1 144 1 TTTTTGACAA 0.926932 -157 ATTGTTACCTTCTTTTGACAAAATCCTATCT 1 227 1 TCTTTGACAA 0.866199 -74 AATTTCAAAATTTTTTGTCAA 9 1 0 TTTTTGTCAA 0.577347 -75 ATTCTTCACTTTGTTGGACAAACATTCCTCA 28 134 1 TTGTTGACAA 0.800918 -167 TTAAACGGCTTTTTAAGAAAAACTGCACTCT 28 164 0 TTTTAGAAAA 0.583526 -137 CGTACAACTTTTTTTTGAAAATTTCTATTAT 29 49 0 TTTTTGAAAA 0.871128 -63 ATTACATCACTCTTTAGACAAATTATAAACA 40 132 0 TCTTTGACAA 0.866199 -169 AAGTTCGATTTTTTTCGACAATCATTTTGAA 40 253 1 TTTTTGACAA 0.926932 -48 AGAGAAGGCTTTGTTAGAAAAACAATTGTTT 43 213 0 TTGTTGAAAA 0.682244 -88 CCGTCATATGTCTTTGGAAAATAAAAAAAAC 44 253 0 TCTTTGAAAA 0.776737 -48 TTATATCACGTTTTTTGACGAATGCTAAGAA 53 88 0 TTTTTGACGA 0.669097 -60 ACTGTCAATGTTTTTTGAAAATATTGATAAT 57 77 0 TTTTTGAAAA 0.871128 -75 ATAGATTAATTTTTAAGAAAAAGAACTGGTA 62 201 1 TTTTAGAAAA 0.583526 -100 ***** ***** Masking position 11 Map Score: 5.58371 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 143 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 15 CCTTCTAAAAAAATCTTGAAATGATAGTCCA 12 65 0 AAATCTTGAA 0.873176 -30 TTTACTCTCAAAATCTTAAAAGAAAACCCCC 15 30 0 AAATCTTAAA 0.514726 -96 ATTTCCGTACAAAACGTGTTACACTTTTGTC 15 77 1 AAAACGTGTA 0.635737 -49 CTGCACACCGAAATCGTAACATCTTTCTGAT 24 56 0 AAATCGTAAA 0.81068 -60 TCATTTTATCAAATCGTGAGAAAGTTTGAGA 31 31 0 AAATCGTGAA 0.965272 -50 TGATACTTGAAAATGGTGAGATG 37 268 1 AAATGGTGAA 0.764479 -13 GTGCATAGACAAATCTTGATATCTGGGTTTA 50 87 1 AAATCTTGAA 0.873176 -163 CATTCGTCAAAAAACGTGATATAATGTCATG 53 95 1 AAAACGTGAA 0.917158 -53 TACAGCACGAAAAACGTGAAACCGTCTGTTC 56 248 0 AAAACGTGAA 0.917158 -53 GAGAGAAATAAAATCGTGCGATTCTTTAGCG 59 14 1 AAATCGTGCA 0.922788 -60 CAAAAAGTTGAAATCGTGCGATCCGCTAAAG 59 37 0 AAATCGTGCA 0.922788 -37 ********* * Masking position 3 Map Score: 3.21674 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 78 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049