AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dgt 83 deoxyguanosine triphosphate triphosphohydrolase #2 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #3 tig 300 trigger factor; a molecular chaperone involved in cell division #4 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #5 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #6 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #7 hupB 208 DNA-binding protein HU-beta, NS1 (HU-1) #8 ybaU 191 putative protease maturation protein #9 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #10 trxB 300 thioredoxin reductase #11 motA 126 proton conductor component of motor; no effect on switching #12 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #13 ygjQ 76 orf, hypothetical protein #14 ygjR 60 orf, hypothetical protein #15 ygjT 283 putative transport protein #16 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #17 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #18 ftsY 149 cell division membrane protein #19 yihD 69 orf, hypothetical protein #20 yihE 77 orf, hypothetical protein #21 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #22 yjdA 300 putative vimentin #23 yjcZ 29 orf, hypothetical protein #24 proP 263 low-affinity transport system; proline permease II #25 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #26 HI0266 82 conserved hypothetical protein #27 HI0267 41 nitrate/nitrite sensor protein (narQ) #28 HI0269 125 RNA polymerase sigma-32 factor (rpoH) #29 HI0837 53 response regulator (cpxR) #30 HI0839 116 conserved hypothetical protein #31 HI0845 86 conserved hypothetical protein #32 HI0997 300 H. influenzae predicted coding region HI0997 #33 HI0998 180 ribosomal protein L34 (rpL34) #34 HI1002 130 thiophene and furan oxidation protein (thdF) #35 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #36 HI1157 71 ATP-binding protein protein (cydD) #37 HI1158 73 thioredoxin reductase (trxB) #38 HI1159 284 conserved hypothetical protein #39 HI1161 300 conserved hypothetical protein #40 HI1259 193 periplasmic serine protease Motif number 1 TCTTATAATCAATCACATTCCCTGTTACCAGAATCAT 3 193 0 AATCCCGTTA 0.483864 -108 TTAAAGGGGAGATAAAATCCCCCCTTTTTGGTTAACT 6 31 0 GACCCCCTTT 0.977264 -157 AGTATATGGGGATGTTTCCCCCACATTCAACGCCGAG 6 81 0 GACCCCCATT 0.786226 -107 CTTGTGGGCTGACAATTGCCCCCGTTTCTTGTCACAA 8 97 1 GACCCCGTTT 0.936606 -95 TTAAATGATGAATAAACGCCCCTGTTAATGAATATCT 10 100 0 AACCCCGTTA 0.903808 -201 AGCGCCTAAAATCGACCTCCCCCCTTTCGTTAAGGAT 13 43 1 ATCCCCCTTT 0.903895 -34 TGCATCCTGCAATTCCCGCTCCCCTTTTGCGGCCGTC 24 185 1 AACTCCCTTT 0.916429 -79 AAATGAAATAAAAACAAACCGCACTTTTATAGCACTT 25 24 1 AACCGCCTTT 0.980762 -79 AAATTTTACCGCACTTTTCTAAATTTC 27 1 1 AACCGCCTTT 0.980762 -41 ATTTGCCGCAAATTATAACCGCACTTTTTCAGCAAGA 30 81 0 AACCGCCTTT 0.980762 -36 TTAGAGGGATAAGGCTTATCCCTGTTTCTACTAAAAA 34 97 0 AATCCCGTTT 0.790343 -34 AATTTTGCCAAAAAATGACCGCACTTTACGCTTC 35 8 0 AACCGCCTTT 0.980736 -265 ATCTTCTAACCAATTCCCCTCTTTTAACTCTTTT 36 8 1 AACCCCCTTT 0.990984 -64 GTGATTATAGAAAAAGTTCCCCTCTTTAAAAGAGTTA 36 35 0 AACCCCCTTT 0.990979 -37 AAACGTTTCTAAAATCTTCCGCACTTTGCTAAAATCA 38 25 1 AACCGCCTTT 0.980762 -260 TAAACAAGATAATTTGCTCTCCTCTTATTGAACATTT 40 112 1 AACTCCCTTA 0.731716 -82 ** **** **** Masking position 16 Map Score: 21.8435 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 94 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CTGCGGGCCGTTTTGTTTTGTCTGGATTTTGC 3 30 1 TTTTTTTTGC 0.866725 -271 AGGTGGTGGGCTTTTTTTTGTCATGAATTTTG 4 58 1 CTTTTTTTGC 0.970124 -188 TTTATCTCCCCTTTAATTTTTCCTCTATTCTC 6 52 1 CTTTATTTTC 0.749707 -136 GGCTTGCCAGCCTTTTTTTGTCTCGCTAAGTT 7 61 1 CCTTTTTTGC 0.784586 -148 TATGGGTCGCCTTTATTTTTTCCCCGTTGTAA 9 56 1 CTTTTTTTTC 0.975357 -67 AAGAATACTGTTTTTTTTCTTCCTCGAATGTT 10 11 1 TTTTTTTCTC 0.729344 -290 AATCGTCATACTCTTTTTTTACGTCTGTAAAT 10 234 1 CTCTTTTTTC 0.816157 -67 CGTACCGCTGCTTTTTTTTGCCCCAATCGCGC 11 50 1 CTTTTTTTGC 0.970124 -77 GAATAACCAACTTTATTTTTATGCGGTTTCAC 12 276 0 CTTTTTTTTT 0.648957 -25 TCTTCACTTGCTTTTTTTCTGCTCTGTTTGTT 16 238 1 CTTTTTTCTC 0.930821 -33 AAAAAGATTATTTTCTTTTTGCGTTTCCTTTC 22 44 0 TTTTTTTTTC 0.887976 -257 CGTTTCCCTTCTTTATTTTGGCTTTTGCCAAT 28 104 0 CTTTTTTTGC 0.970124 -22 TCTTTTTATTTTCACCACACTAC 29 2 1 CTTTTATTTC 0.848614 -52 AACCTAAATAATTTCTTTTTTCTTGCTGAAAA 30 61 1 ATTTTTTTTC 0.706682 -56 CCCCTGCCCACTTTCTTTTTCCCAAGCGGTCC 32 216 0 CTTTTTTTTC 0.975357 -85 CCCATGGCCATTTTTTTTCTACTGATAAAGAA 32 256 0 TTTTTTTCTC 0.729344 -45 CATTCCGTGCCTTTCTTTTTGCCTGTTCGTGA 34 11 0 CTTTTTTTTC 0.975357 -120 TTTTTGACCTTTTTATTGACTAGAAAATTG 40 9 1 CTTTTATTGC 0.821398 -185 **** ***** * Masking position 8 Map Score: 19.3382 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 69 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 3 AGATTTTATGAAAAACGGCCTGCGGGCCGTT 3 11 1 AAAAACGCCT 0.61097 -290 CATTCAGACGAAAATTGCCCGGGAATTGTGA 3 75 1 AAAATTGCCG 0.931153 -226 CTCTGCTACTTAAATTTCCCGCTTTATAAGC 10 140 0 TAAATTTCCG 0.559928 -161 TAAGCAGGTCAAATTCTCCCGTCATTATCAC 10 171 0 AAATTCTCCG 0.936038 -130 TTTAGCGCCTAAAATCGACCTCCCCCCTTTC 13 40 1 AAAATCGCCT 0.769854 -37 AAAATCACCTAAAATCGCCCGCTCGCGGCAT 16 50 0 AAAATCGCCG 0.956041 -221 TGTTTAAATACCTCCGAGGCAGAAAT 21 131 0 AAATACCCCG 0.725047 -16 AGAAAATTCTTCCTTAAAGCAAAT 22 287 0 AAATTCTCCT 0.692389 -14 AAATTTTACCGCACTTTTCTA 27 1 1 AAATTTTCCG 0.900999 -41 CTTTGAAAAATTTGCCGCAAATTATAA 30 100 0 AAAATTTCCG 0.936988 -17 AGTTTTTTTTAAAAATTTCCGTTTCTTATTT 33 88 1 AAAAATTCCG 0.874709 -93 AATTTTGCCAAAAAATGACCGCACTTTACGC 35 14 0 AAAAATGCCG 0.863945 -259 AAACACCACCAAATATTGCCGCTTTTGATTT 35 46 0 AAATATTCCG 0.810348 -227 TATAAATATAAAATTTTCCCGATTATAATCT 35 153 0 AAATTTTCCG 0.900999 -120 AAACGTTTCTAAAATCTTCCGCACTTTGCTA 38 25 1 AAAATCTCCG 0.959858 -260 GTAGTGCCAAAAAATCCGCCGATTCTTTATG 38 196 0 AAAATCCCCG 0.90174 -89 ******* *** Masking position 3 Map Score: 15.6731 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 436 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 TTAACCAAAAAGGGGGGATTTTATCTCCCCT 6 33 1 AGGGGGGATT 0.976373 -155 AGGAAAAATTAAAGGGGAGATAAAATCCCCC 6 45 0 AAAGGGGAGT 0.936784 -143 CGTTGTCCCCAGTGGGGATGTGACGAAGTTC 8 12 1 AGTGGGGATT 0.864738 -180 TTTAAGTAGCAGAGGTGATAATGACGGGAGA 10 157 1 AGAGGTGATA 0.706155 -144 CCTTAACGAAAGGGGGGAGGTCGATTTTAGG 13 47 0 AGGGGGGAGT 0.982787 -30 TGTTACCTGCAAAGGGGAGTAACTTCATTGC 15 79 1 AAAGGGGAGA 0.861011 -205 TTGCATTTTAAGAGGTGATTTTGATCACGGA 16 120 1 AGAGGTGATT 0.851821 -151 CCACAATAAAAGAGGCGATATCG 19 3 0 AGAGGCGATT 0.828525 -67 GACGGCCGCAAAAGGGGAGCGGGAATTGCAG 24 191 0 AAAGGGGAGG 0.736193 -73 AAGAGTTAAAAGAGGGGAATTGGTTAGAAGA 36 12 0 AGAGGGGAAT 0.934886 -60 ACTCTTTTAAAGAGGGGAACTTTTTCTATAA 36 37 1 AGAGGGGAAT 0.934886 -35 GCCCGAAGGGAAGGGGGATATAGGGATATGC 39 126 1 AAGGGGGATT 0.907025 -175 GCCGAAGGTGAGGGGGGATAAATGTTCAATT 39 225 0 AGGGGGGATA 0.945282 -76 CACCCATTTATGGGGGGAGCTGCCGAAGGTG 39 246 0 TGGGGGGAGT 0.839401 -55 ATGTTCAATAAGAGGAGAGCAAATTATCTTG 40 116 0 AGAGGAGAGA 0.653124 -78 ********* * Masking position 8 Map Score: 11.4166 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 82 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 ACGGCCCGCAGGCCGTTTTTCATAAAATCT 3 11 0 GGCCGTTTTT 0.859053 -290 TGCGCGCTGTCGCGTATTTTTTCACAATTC 3 97 0 CGCGTATTTT 0.721334 -204 CCAGGTGGTGGGCTTTTTTTTGTCATGAAT 4 56 1 GGCTTTTTTT 0.645327 -190 TCTACTGATGTGCCTTTTTTATTTGTATTC 8 52 1 TGCCTTTTTT 0.563982 -140 AAAAAGAGTATGACGATTTTGTTAACAATT 10 222 0 TGACGATTTT 0.386992 -79 AACGACGTACCGCTGCTTTTTTTTGCCCCA 11 45 1 CGCTGCTTTT 0.901229 -82 GACGTCCAGCCGCTGCTTTTTATGCATAGA 15 225 0 CGCTGCTTTT 0.901229 -59 TTCCGACGTTGGCCGTTTTTTTATGTGTAA 15 255 1 GGCCGTTTTT 0.859053 -29 TCTCTTCACTTGCTTTTTTTCTGCTCTGTT 16 236 1 TGCTTTTTTT 0.532009 -35 CGATATCGCCTCTTTTATTGTGGGAT 19 7 1 CGCCTCTTTT 0.779082 -63 TATCATTTCACGATGATTTTGGTGGCGCCG 20 22 0 CGATGATTTT 0.54022 -56 ACTGCTGATTTTAGACGACGAT 22 3 1 TGCTGATTTT 0.876973 -298 GCGGCCGTCGCGCTGATTTTTCTGGCGTTT 24 213 1 CGCTGATTTT 0.937871 -51 AAGTATCATTTGCCTATTTTTTACGATTAA 31 32 1 TGCCTATTTT 0.733692 -55 CCATTGATTCCGCTGATTTAGTGTTAAAAG 32 107 0 CGCTGATTTA 0.505951 -194 ATTTGACGAACGCGTATTTTATGACTAGAA 33 115 1 CGCGTATTTT 0.721334 -66 CACCAAATATTGCCGCTTTTGATTTAAATT 35 41 0 TGCCGCTTTT 0.830582 -232 AAAAAATAATGGCTGATTTTAGCAAAGTGC 38 45 0 GGCTGATTTT 0.919415 -240 GATAAAACATGGCTGATTTTCCTTTTATCG 38 82 1 GGCTGATTTT 0.919415 -203 ATAAAGAATCGGCGGATTTTTTGGCACTAC 38 197 1 GGCGGATTTT 0.852063 -88 ********** Masking position 7 Map Score: 17.868 Number of sites scoring better than the average of aligned sites = 1197 Number in coding regions = 1045 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 6 AACAATAAATTTTTACCTTTTGCAGAAACTTTAG 2 30 1 TTTTCCTTTA 0.825082 -100 GTCGCGTATTTTTTCACAATTCCCGGGCAATTTT 3 85 0 TTTTACATTC 0.770003 -216 GTACAGCAGGTTTTTTCAATTTTATCCAGGAGAC 4 218 1 TTTTTCATTA 0.845457 -28 ATAAGACAGATTTTATCAATTGAAAGTTCAATTA 28 19 0 TTTTTCATTA 0.845457 -107 ATTTGCCTATTTTTTACGATTAAAAAGGAAATAG 31 39 1 TTTTACATTA 0.895377 -48 TTTTTTAACTATGAAAATGAAGCTGC 32 3 1 TTTTACATGA 0.769984 -298 GAGGATGGAGTTTTCACTTTTTAAGATGCTAATT 35 109 1 TTTTACTTTA 0.882783 -164 AGATGCTAATTTTTTACGTTTAGATTATAATCGG 35 132 1 TTTTACTTTA 0.882782 -141 AAATATAAAATTTTCCCGATTATAATCTAAACGT 35 147 0 TTTTCCATTA 0.842823 -126 AAATTGTGCATTTTTTCAATTAACATTCTATAAC 35 190 0 TTTTTCATTC 0.681453 -83 AATTCCCCTCTTTTAACTCTTTTAAAGAGGGGAA 36 22 1 TTTTACCTTA 0.666704 -50 TTTAGAAACGTTTTACCATTTCTATTA 38 4 0 TTTTCCTTTA 0.825082 -281 ATCAGCCATGTTTTATCCTTGTGAAAAAAATAAT 38 65 0 TTTTTCTTGA 0.652998 -220 CTGATTTTCCTTTTATCGTTGAGATCAACGAACA 38 94 1 TTTTTCTTGA 0.652951 -191 TCGCTCTTTTTCACAATTTACTTTTCCAAGA 38 264 0 TTTTACATTC 0.770003 -21 TTTTTGACCTTTTTATTGACTAGAA 40 2 1 TTTTACTTTA 0.882783 -192 **** ** *** * Masking position 10 Map Score: 9.36697 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 78 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 GCGAAGCCAACAACCTGTGCTTGCGGGGTAAGAGTT 3 243 1 CAACCTTTGG 0.72715 -58 AAAAGCCCACCACCTGGCGGTGACGGGCCTTTGTGC 4 37 0 CACCTCTGGG 0.93196 -209 CCCCTTACAACACCCCTTAATAAGGGCAAGCCCGAT 7 102 0 CACCCTTAGG 0.907028 -107 AAGAAGGCGACACCATGCGACTATGGGTCGCCTTTA 9 35 1 CACCACCTGG 0.732424 -88 AAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGT 12 68 1 CCCCCCTGTG 0.90483 -233 GGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCC 12 248 0 CACCCTTGGC 0.943135 -53 AATCGACCTCCCCCCTTTCGTTAAGGATAACGACC 13 52 1 CCCCCTTTGG 0.974836 -25 CGTTGTTTTACACCCCCTGACGCATGTTTGCAGCCT 21 62 0 CACCCTCGTG 0.819241 -85 GGTTTGCTTACACCCTCCGGTTAAGGAATGTACAAT 24 128 0 CACCCCTTGG 0.980827 -136 AACAAAACACCACCAAATATTGCCGCTTTTGATTTA 35 45 0 CACCATTGGC 0.677255 -228 ATCTTGGCTCCACCCATTTATGGGGGGA 39 3 0 CACCCTTGGG 0.807423 -298 AACTTGCCTTCCCCTGCTTGTGGGGGAAGGTGCCCG 39 95 1 CCCCTTTGGG 0.82866 -206 ATCCCTATATCCCCCTTCCCTTCGGGCACCTTCCCC 39 117 0 CCCCCCTTGG 0.976653 -184 GAACATTTATCCCCCCTCACCTTCGGCAGCTCCCCC 39 229 1 CCCCCCCTGG 0.946681 -72 ATCTTGGCTCCACCCATTTATGGGGGGAGCTGCCGA 39 251 0 CACCCTTGGG 0.807423 -50 ***** * ** ** Masking position 4 Map Score: 14.0487 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 204 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ACTCATAAAAGTGATGCCGCTATAATGCCG 3 140 1 GTGATGCCGC 0.979287 -161 AATTTAGCGCGTTATGCTGCGTAAA 4 6 0 GTTATGCTGC 0.792751 -240 TTGAAATATGGTGATGCCGTACCCATAACA 4 149 1 GTGATGCCGT 0.805604 -97 TAGCGGCACAGTTGCGCCTCTGGCA 5 6 0 GTTGCGCCTC 0.892534 -120 CGCTTACAGCGTTGTGCCGCCCTGGATAAG 5 38 0 GTTGTGCCGC 0.985864 -88 TTCTTTGTTCTTTGTGCCGCACACGACGAC 5 93 0 TTTGTGCCGC 0.859154 -33 CTGCTGGAATGTTGCGCCTCACCGTATCAG 11 11 0 GTTGCGCCTC 0.892534 -116 ACCGCACCCCGTGATGTCGCCGGGAAGCCC 12 248 0 GTGATGTCGC 0.805571 -53 GGCATAGCGGGATATGCCGCGAGCGGGCGA 16 37 1 GATATGCCGC 0.860337 -234 GATGATTTTGGTGGCGCCGCTTACAAGCTT 20 11 0 GTGGCGCCGC 0.94409 -67 ********** Masking position 6 Map Score: 7.49641 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 793 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 GGGAATTGTGAAAAAATACGCGACAGCGCGCAATA 3 95 1 AAAAAAGACA 0.719468 -206 GAAAGCATTCAAATAGGACGCGGCATTATAGCGGC 3 155 0 AAATAAGGCA 0.795798 -146 TGTTACCTCAAAAAATCACAGTGCTCGGTCAACTC 3 274 0 AAAAAATGCT 0.579575 -27 AGAATAGAGGAAAAATTAAAGGGGAGATAAAATCC 6 48 0 AAAAAAGGGA 0.781007 -140 AAAATGCACTAATAAAAACAGGGCTGGCAGGCTAA 7 22 1 AATAAAGGCT 0.759494 -187 TTAGCGAGACAAAAAAAGGCTGGCAAGCCCGAATT 7 55 0 AAAAAGGGCA 0.860203 -154 AAGCCCCGGTAAAAAATAATTAGCATTAGAATAGT 12 219 0 AAAAAAAGCA 0.913153 -82 GCCTGCGTTCAAAAATAAAATGGCATAGCGGGATA 16 16 1 AAAAAAGGCA 0.979806 -255 AACAGAACTCAAAAACAATCTGGCTAAATAAAATA 22 247 1 AAAAAAGGCT 0.9544 -54 TGTTAAAAATAAAAAAAATTTGGCTTATGATACCC 30 13 1 AAAAAAGGCT 0.9544 -104 TTTTACGATTAAAAAGGAAATAGCAATGAAATAAA 31 50 1 AAAAAAAGCA 0.913153 -37 GCAATGAAATAAAAAGGAAATAGCA 31 72 1 AAAAAAAGCA 0.913153 -15 CCGCTTGGGAAAAAGAAAGTGGGCAGGGGGTAGGG 32 219 1 AAAAGAGGCA 0.85242 -82 CAACTAAAAACGATACAGCAATCAAACCTA 35 253 0 AAAAAAAGCA 0.913153 -20 TATCCTTGTGAAAAAAATAATGGCTGATTTTAGCA 38 51 0 AAAAATGGCT 0.641685 -234 AATCCTTAGGAAAAACCACTTGTCATCAATTTTTA 38 151 1 AAAAAAGTCA 0.719468 -134 TAAAACCTCTAATAAGCAGAAGGCAAGTTATCATT 39 58 0 AATAAAGGCA 0.87982 -243 ***** * **** Masking position 2 Map Score: 12.3568 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 264 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 TATGAAAAACGGCCTGCGGGCCGTTTTGTTT 3 17 1 GGCCTGCGGC 0.955562 -284 CAACAACCTGTGCTTGCGGGGTAAGAGTTGA 3 250 1 TGCTTGCGGG 0.904746 -51 ATAAAAACAGGGCTGGCAGGCTAATTCGGGC 7 33 1 GGCTGGCGGC 0.982693 -176 GGCTAATTCGGGCTTGCCAGCCTTTTTTTGT 7 51 1 GGCTTGCAGC 0.830962 -158 TGTTGTAAGGGGATGGCTGGCCTGATATAAC 7 126 1 GGATGGCGGC 0.789603 -83 GACTTTCTGCGTCTTGTGGGCTGACAATTGC 8 85 1 GTCTTGTGGC 0.667986 -107 TTTTTACCGGGGCTTCCCGGCGACATCACGG 12 239 1 GGCTTCCGGC 0.930421 -62 AGTGAGACCTTGCCGGAAGGCGAGGTCTATG 15 200 1 TGCCGGAGGC 0.871504 -84 AAAAAGCAGCGGCTGGACGTCTTCCGACGTT 15 234 1 GGCTGGAGTC 0.668377 -50 GATGGCCTTGTTCTTGAAGGCTATTTAGAAT 16 206 1 TTCTTGAGGC 0.795617 -65 AGATAACACATACTTGCAGGCGGTGATGTGA 18 31 1 TACTTGCGGC 0.878539 -119 TCCTCGCTGTTGCTTCATGGCACAGCGTTAA 18 117 0 TGCTTCAGGC 0.836304 -33 CCAAGACGTTACTTGACGGCCCCGGTCGC 23 10 1 TACTTGAGGC 0.795634 -20 CAGTTTTTCTTGCTGGAGTGCAAA 26 69 1 TGCTGGATGC 0.606052 -14 TGCCTTCCCCTGCTTGTGGGGGAAGGTGCCC 39 99 1 TGCTTGTGGG 0.651608 -202 ******* *** Masking position 3 Map Score: 6.13994 Number of sites scoring better than the average of aligned sites = 2000 Number in coding regions = 1917 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 AATACGCTTCCCCGTAAGCGCATGGTAAACT 1 45 0 CCCGTAGCGC 0.969197 -39 TGAAAAAATACGCGACAGCGCGCAATAACCG 3 103 1 CGCGAAGCGC 0.933901 -198 CAACTCTTACCCCGCAAGCACAGGTTGTTGG 3 249 0 CCCGCAGCAC 0.843776 -52 CGCACAAAGGCCCGTCACCGCCAGGTGGTGG 4 36 1 CCCGTACCGC 0.955705 -210 CGTATCGATGCGCGCAAAGGCCTATTGTGAC 8 127 0 CGCGCAAGGC 0.961413 -65 GCCCCAATCGCGCGTTAACGCCTGACGACTG 11 69 1 CGCGTAACGC 0.979349 -58 TTCATGGCACAGCGTTAACGCTATGTACATA 18 104 0 AGCGTAACGC 0.903275 -46 CAGAAAAATCAGCGCGACGGCCGCAAAAGGG 24 206 0 AGCGCACGGC 0.767516 -58 TTGGCCCATTTCCGCAAACGCCAGAAAAATC 24 227 0 TCCGCAACGC 0.875669 -37 TCAATTTTTACGCGCCAACGCATAAAGAATC 38 176 1 CGCGCAACGC 0.989382 -109 ***** ***** Masking position 7 Map Score: 6.51902 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 907 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 AGCAATTTTGCGTTATCTGTTAATCGAGACTG 2 102 1 CGTTATTTTA 0.805291 -28 TATGGGTCGCCTTTATTTTTTCCCCGTTGTAA 9 56 1 CTTTATTTTC 0.869279 -67 AGCCCCCCTCCGTTGTATGTGCGTGTAGTGAC 12 75 1 CGTTGTTTGC 0.79816 -226 TGATGTCAGGCGTTATCTTTTCTTTCTTTAGC 13 14 1 CGTTATTTTC 0.964088 -63 AAAGAGACCCCGTTGTCTCTTCCCGGTATTTC 17 57 1 CGTTGTTTTC 0.911531 -188 ACATTTTGTGCGTAATTTATTCACAAGCTTGC 17 100 1 CGTAATTTTC 0.957612 -145 CTTCGTCATTCGTAATGTTTTCCGGATGATGG 20 55 1 CGTAATTTTC 0.957612 -23 CGTCTGATGACGTAATTTCTGCCTCGGAGGTA 21 117 1 CGTAATTTGC 0.896593 -30 TATCAGAAGACGTTATTTATTCTGATAAAAAA 22 166 1 CGTTATTTTC 0.964088 -135 TAATACAACCCTTAATTTTTTAGAGGGAAAAC 25 78 1 CTTAATTTTA 0.462977 -25 ATTATTTGATCTTAATATATTCTGCATTTTGT 34 53 1 CTTAATTTTC 0.848393 -78 ****** * *** Masking position 6 Map Score: 6.87278 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 68 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TAAAGTTTCTGCAAAAGGTAAAAATTTATT 2 33 0 GCAAAAGGTA 0.656201 -97 GGCAAAAAGCGCAAAATCCAGACAAAACAA 3 42 0 GCAAAATCCA 0.935687 -259 ACGGTTCCATGCAAAATTCATGACAAAAAA 4 71 0 GCAAAATTCA 0.736002 -175 ACACGACGACGCAAATGCCATTCTCAGGCG 5 73 0 GCAAATGCCA 0.786254 -53 TGACCTCGCGCAAAATGCACTAATAAAAA 7 10 1 GCAAAATGCA 0.96603 -199 AGCGGGAATTGCAGGATGCAATCTCTGTAA 24 175 0 GCAGGATGCA 0.739476 -89 GCCCATTTCCGCAAACGCCAGAAAAATCAG 24 225 0 GCAAACGCCA 0.755607 -39 ACATTGATTGGCAAAAGCCAAAATAAAGAA 28 98 1 GCAAAAGCCA 0.93681 -28 TCTAACTTTAGCAAAGTGCATATATTTTTT 33 45 1 GCAAAGTGCA 0.855714 -136 CTCTATCTCTACAAAATGCAGAATATATTA 34 65 0 ACAAAATGCA 0.651942 -66 TTTATAATCAGTAAAATGCAACTTATTGCA 37 19 1 GTAAAATGCA 0.651942 -55 CACTACTTGAGCAAGTTGCAGAACAATATC 38 221 1 GCAAGTTGCA 0.690326 -64 CCTCTAATAAGCAGAAGGCAAGTTATCATT 39 58 0 GCAGAAGGCA 0.901527 -243 ********** Masking position 3 Map Score: 4.90475 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 416 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 14 TCAGGCTATAAAACGAATCTGAAGAACACAGCA 2 73 1 AAACGAATGA 0.713513 -57 GGGCAACCCGAAAGGAATACGCAGACGTATTCC 15 155 1 AAAGGAATGA 0.950578 -129 TTACAACAAAAAAGGAATACGTCTGCGTATTCC 15 168 0 AAAGGAATGC 0.817978 -116 TTTTCATTTGAAAGGAAACGCAAAAAGAAAATA 22 35 1 AAAGGAAACA 0.92867 -266 ATAATTGGTAAAAGGAATCTCCA 29 41 1 AAAGGAATCA 0.92867 -13 TTACGATTAAAAAGGAAATAGCAATGAAATAAA 31 52 1 AAAGGAAAGA 0.950578 -35 AATGAAATAAAAAGGAAATAGCA 31 74 1 AAAGGAAAGA 0.950578 -13 TGTTTTGTTGATAGGAATTGCTATTAGCTGGCT 35 72 1 ATAGGAATCA 0.646884 -201 CTCAACGATAAAAGGAAAATCAGCCATGTTTTA 38 84 0 AAAGGAAACG 0.75259 -201 ATCTTGTTTAAAAGGAAATCGGAGCAGTACAAA 40 89 0 AAAGGAAAGA 0.950578 -105 ******** * * Masking position 7 Map Score: 3.34688 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 33 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 AACCTGTGCTTGCGGGGTAAGAGTTGACCG 3 254 1 TGCGGGGTAA 0.913249 -47 CGGCGTTGAATGTGGGGGAAACATCCCCAT 6 83 1 TGTGGGGGAA 0.911975 -105 GCAATGTTACAACGGGGAAAAAATAAAGGC 9 64 0 AACGGGGAAA 0.648338 -59 CATCACGGGGTGCGGTGAAACCGCATAAAA 12 262 1 TGCGGTGAAA 0.935696 -39 CGGAACCCATTGCAGGGAAAGAGTATAACA 17 19 0 TGCAGGGAAA 0.935696 -226 TGGGTTCCGTAGCAGGGAAAGAGACCCCGT 17 40 1 AGCAGGGAAA 0.852853 -205 GGGCCAACTCTGCGAGGAAAGCT 24 251 1 TGCGAGGAAA 0.822336 -13 TTTAGAAAAGTGCGGTAAAATTT 27 4 0 TGCGGTAAAA 0.534132 -38 CTTATTGTAGTGTGGTGAAAATAAAAAGA 29 10 0 TGTGGTGAAA 0.782816 -44 TTCCCCCACAAGCAGGGGAAGGCAAGTTTT 39 93 0 AGCAGGGGAA 0.804944 -208 TTCCCCTGCTTGTGGGGGAAGGTGCCCGAA 39 103 1 TGTGGGGGAA 0.911975 -198 ********** Masking position 9 Map Score: 4.65283 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 380 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281