AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_mjan_reg_300.orf -o064_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ07250 117 M_jannaschii_chromosome RMJ01820 25 M_jannaschii_chromosome RMJ10567 16 M_jannaschii_chromosome RMJ04312 88 M_jannaschii_chromosome Input sequences: #1 RMJ08451 53 M_jannaschii_chromosome #2 RMJ14035 95 M_jannaschii_chromosome #3 RMJ10166 154 M_jannaschii_chromosome #4 RMJ05879 24 M_jannaschii_chromosome #5 RMJ10649 118 M_jannaschii_chromosome #6 RMJ13451 62 M_jannaschii_chromosome #7 RMJ05793 41 M_jannaschii_chromosome #8 RMJ02853 151 M_jannaschii_chromosome #9 RMJ06762 126 M_jannaschii_chromosome #10 RMJ14744 37 M_jannaschii_chromosome #11 RMJ05778 300 M_jannaschii_chromosome #12 RMJ01263 194 M_jannaschii_chromosome #13 RMJ11621 200 M_jannaschii_chromosome #14 RMJ00313 27 M_jannaschii_chromosome #15 RMJ00018 300 M_jannaschii_chromosome #16 RMJ00407 205 M_jannaschii_chromosome #17 RMJ02054 97 M_jannaschii_chromosome #18 RMJ07240 80 M_jannaschii_chromosome #19 RMJ13697 22 M_jannaschii_chromosome #20 RMJ15370 178 M_jannaschii_chromosome #21 RMJ08703 34 M_jannaschii_chromosome Motif number 1 CTTCAAAGGATTTTTGTTATTTCTATTTAG 1 19 0 TTTTTGTTAT 0.84191 -35 GCATTCACATTTTTTATACTTTTTTAAATG 2 13 1 TTTTTATACT 0.815137 -83 ACCAAAAAGTTTTTTATGTTATTTTTAGAT 2 70 0 TTTTTATGTT 0.77659 -26 CATTAATAAATTTTTATTTTTTGAAAGACA 5 11 0 TTTTTATTTT 0.968741 -108 ATATTTATTTTAAAGACTTAA 6 2 1 TATTTATTTT 0.951821 -61 TTATACTTACTTTTTATTATATTTC 7 6 0 TTTTTATTAT 0.943008 -36 CCTATCCCTATTTTTATTATACTTACTTTT 7 22 0 TTTTTATTAT 0.943008 -20 CTACTTTCTTTTTTTATTTTTAAATATTAC 8 16 1 TTTTTATTTT 0.968741 -136 TATTTAAAAGTATTTATATATAAAGTATTT 8 79 1 TATTTATATA 0.705493 -73 ATATATAAAGTATTTATATATGGGGTTTTT 8 94 1 TATTTATATA 0.705493 -58 ATATATGGGGTTTTTATATAATATCTAAGT 8 109 1 TTTTTATATA 0.789847 -43 TATAATTAGTTATTTATATTTTTCGG 9 7 0 TATTTATATT 0.938235 -120 TGCAATTCACTATTTATAATTAGTTATTTA 9 21 0 TATTTATAAT 0.890237 -106 GTGTTTTATTTATTTGTTTTAACCGTAATA 9 80 0 TATTTGTTTT 0.864104 -47 TCCCCTTCACTTATTATTAT 10 1 0 TTATTATTAT 0.769558 -37 CCTCCTTTCTTTTTTATATTTAACAAAAAG 11 248 0 TTTTTATATT 0.959724 -53 AAAATCCTACTTTTAATTTTTGGTTGCATA 12 39 1 TTTTAATTTT 0.70951 -156 TTTGGTTGCATATTTGTTATTTTATAGGAG 12 57 1 TATTTGTTAT 0.772468 -138 TATAAGTTATTATTTATATTGCATTAGATT 12 155 1 TATTTATATT 0.938235 -40 TGCATTAGATTTATTATTTTTTGGTGATAA 12 174 1 TTATTATTTT 0.862157 -21 TCTTCTCACGTAATTATTATAT 14 3 0 TAATTATTAT 0.680399 -25 CTTTTCGGTTTTATTGTATTAAATATTTTA 15 144 1 TTATTGTATT 0.607518 -157 TAAAAAATTATTTTTATTTTGACGCCTATT 15 195 0 TTTTTATTTT 0.968741 -106 TAAAAATAATTTTTTATACTTTGATTTGTT 15 209 1 TTTTTATACT 0.815137 -92 AACTTCGCAGTTTTTATATTAAAAAGGTAT 16 85 0 TTTTTATATT 0.959724 -121 AACCATATGTTATTTATTTTATTATCCACA 16 153 1 TATTTATTTT 0.951821 -53 CAAAGTTATTATTTATAAAATCTTAAAAT 16 187 0 TATTTATAAA 0.561202 -19 GCTTCAAACTTTTTATTTTTTGTTGTAAA 17 10 1 TTTTTATTTT 0.968741 -88 TTGTTGTAAATATTTATAATTTATAGAACA 17 30 1 TATTTATAAT 0.890237 -68 CATCTGGTTGTTATTGTTATTATCTTTAAA 17 58 1 TTATTGTTAT 0.51803 -40 TTAAATTCTATTTTAATTTTAGTATTATTT 20 96 0 TTTTAATTTT 0.70951 -83 ********** Masking position 4 Map Score: 42.8929 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1086 Number in noncoding regions = 518 Number of orfs with sites within 600 bp upstream = 396 Fraction of orfs with sites within 600 bp upstream = 0.0636042 Motif number 2 GAAATAACAAAAATCCTTTGAAGTAAAAGGTGGTA 1 26 1 AAATTTAATA 0.966565 -28 ATAACATTTAAAAAAGTATAAAAAATGTGAATGCC 2 12 0 AAATATAAAA 0.677595 -84 GTATAAAGATAAATATCTAAAAATAACATAAAAAA 2 56 1 AAACTAAATA 0.515227 -40 CTAAAAATCTTTAAGTAGTAGTTCAAT 3 3 1 AAACTTAATA 0.797007 -152 CTTTAAAGTTAAAATTATTGAACTACTACTTAAAG 3 19 0 AAAATTAATA 0.590071 -136 AATTGAACATTAAGTATTAGAACAATAACTGTTTG 3 99 0 TAATTAAAAA 0.690488 -56 AAGAATAACTTAATGATTTGAATAAATTGAACATT 3 123 0 TAATTTAAAA 0.891789 -32 AGATAATTATTAAGTCTTTAAAATAAATAT 6 6 0 TAATTTAATA 0.93912 -57 TTAATAAATGTAATATTTAAAAATAAAAAAAGAAA 8 20 0 TAATTAAATA 0.806481 -132 CTTTATATATAAATACTTTTAAATATTACATAAAA 8 69 0 AAATTTAATA 0.966558 -83 CGTAATATCTAAACAATATTAATTTGAAGTAGAGT 9 52 0 AAATATAATT 0.563205 -75 TTAGCAATATAAAATTTTTCAAAATTTCCTGAAAT 11 136 1 AAATTTAAAT 0.834918 -165 ATTTGCTATTAAAGATTTATAAAATAGCCTCATCT 11 169 1 AAATTAAAAT 0.577896 -132 GTATCTGATATAAATATTTTACTTAAAAAAGATGA 11 198 0 TAATTTACTA 0.668611 -103 TAGTGCATTTTAACTCTTTTAAAAATCCTACTTTT 12 18 1 TAATTTAAAA 0.891792 -177 TTATAGGAGATAAAGCTATTAATTAAAAATGCAAT 12 78 1 TAATATAATA 0.677577 -117 TTTTACTAAAAAATAATTTTAAATTTATCTAAAAA 13 143 0 AAATTTAATT 0.904498 -58 TATTCCCACCAAACATTTTTACTAAAAAATAATTT 13 159 0 AAATTTACAA 0.668826 -42 ATAAAACCGAAAAGTATTTATAGTAGTTCTGAGTA 15 123 0 AAATTTTATA 0.709744 -178 TTTATTGTATTAAATATTTTAATTAATGTCTTGAA 15 153 1 TAATTTAATA 0.938855 -148 AAAGTATAAAAAATTATTTTTATTTTGACGCCTAT 15 196 0 AAATTTTATT 0.437505 -105 ATTCATTCATTAATTTTGTTAAATAACATAAACCA 16 123 1 TAATGTAATA 0.694056 -83 TATTATTTATAAAATCTTAAAATTTATTGTGGATA 16 175 0 AAATTAAATT 0.716609 -31 TATAAATTATAAATATTTACAACAAAAAATAAAAA 17 20 0 AAATTAAAAA 0.80689 -78 TCACCATTATTAAGGTTTTAAAGATAATAACAATA 17 69 0 TAATTTAAAT 0.729755 -29 GACTATATATAAACTTTGTCAATTAAAAATCTATG 18 56 1 AAATGTAATA 0.80949 -25 GAGTCTTTTAAAACATTTTGAAATACTAAGGACCA 20 46 0 AAATTTAATA 0.966566 -133 GACTCTATAAAAAGAATTTAAAATAATACTAAAAT 20 76 1 AAATTTAATA 0.966565 -103 AACCTTTAGTAAAGCCTTTGAATAATTTTAATCAA 20 144 0 AAATTTAAAA 0.939157 -35 *** *** ** ** Masking position 3 Map Score: 30.8419 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 1086 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 3 AACAAAAATCCTTTGAAGTAAAAGGTGGTA 1 31 1 CTTTGAAGTA 0.811324 -23 TTTTTATACTTTTTTAAATGTTATATGTAG 2 23 1 TTTTTAAATG 0.694483 -73 TTTTATGTTATTTTTAGATATTTATCTTTA 2 59 0 TTTTTAGATA 0.88204 -37 AATTTTTAAGAATAACTTAATG 3 143 0 TTTTTAAGAA 0.722286 -12 AATATAATTTTTTGAGGGATGTCT 4 10 1 TTTTGAGGGA 0.630867 -15 AATTTTTATTTTTTGAAAGACA 5 3 0 TTTTGAAAGA 0.910118 -116 ATCCAAGAAGTTTTGAAAGACACTAATAAA 5 89 1 TTTTGAAAGA 0.910118 -30 ATATTTATTTTAAAGACTTAATAATT 6 7 1 ATTTTAAAGA 0.596171 -56 TCTTTTTTTATTTTTAAATATTACATTTAT 8 22 1 TTTTTAAATA 0.902289 -130 TATATAAATACTTTTAAATATTACATAAAA 8 69 0 CTTTTAAATA 0.882589 -83 ATATATGGGGTTTTTATATAATATCTAAGT 8 109 1 TTTTTATATA 0.652166 -43 TCTAAGTTAGTTGTTAAATAGGTGAAAATC 8 132 1 TTGTTAAATA 0.876389 -20 AACAATATTAATTTGAAGTAGAGTTTGCAA 9 46 0 ATTTGAAGTA 0.656181 -81 TTTCAGGAAATTTTGAAAAATTTTATATTG 11 140 0 TTTTGAAAAA 0.778257 -161 AGCCTCATCTTTTTTAAGTAAAATATTTAT 11 194 1 TTTTTAAGTA 0.944364 -107 TGGATGCTTTTTGTTAAATATAAAAAAGAA 11 242 1 TTGTTAAATA 0.876389 -59 CATTTTAACTCTTTTAAAAATCCTACTTTT 12 23 1 CTTTTAAAAA 0.484517 -172 TGCAATTGCATTTTTAATTAATAGCTTTAT 12 87 0 TTTTTAATTA 0.691337 -108 GGATAAAGCTTTTTTAGATAAATTTAAAAT 13 133 1 TTTTTAGATA 0.88204 -68 ATATGAGGATTTTTGAAGTA 13 191 1 TTTTGAAGTA 0.93798 -10 TTCATTAATTTTGTTAAATAACATAAACCA 16 128 1 TTGTTAAATA 0.876389 -78 ATTTTAAGATTTTATAAATAATAACTTTG 16 187 1 TTTATAAATA 0.618575 -19 TTTTAAAACATTTTGAAATACTAAGGACCA 20 46 0 TTTTGAAATA 0.959713 -133 ********** Masking position 2 Map Score: 21.7056 Number of sites scoring better than the average of aligned sites = 1158 Number in coding regions = 881 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 4 AAAAATTGTTTATATAGAGTAACTTTAAAG 3 46 0 TATATAGAGT 0.84899 -109 GTTTGAACCCTTTATATAGTAGATTAGCAA 3 74 0 TTTATATAGT 0.853799 -81 ATAATTATCTTATATTAGATAAAGGATATT 6 31 1 TATATTAGAT 0.618705 -32 AAATATTACATTTATTAAGTTAAATATACA 8 37 1 TTTATTAAGT 0.895213 -115 AAAGTATTTATATATAAAGTATTTATATAT 8 85 1 TATATAAAGT 0.917605 -67 ATATGGGGTTTTTATATAATATCTAAGTTA 8 111 1 TTTATATAAT 0.821205 -41 TATATAAAGTCAGAATAGAA 11 1 1 TATATAAAGT 0.917605 -300 ATCCGTAGATTTTATAAGATTATAGGAAAA 11 34 0 TTTATAAGAT 0.849556 -267 TCAGAAACCATATATAAAATTTTCGGTTGA 11 102 0 TATATAAAAT 0.898356 -199 CTATTAAAGATTTATAAAATAGCCTCATCT 11 174 1 TTTATAAAAT 0.935208 -127 TTTGATTTGTTTTATTAGATTATGTTAGAT 15 228 1 TTTATTAGAT 0.726122 -73 GAATAAATGATTTATTGAATAATGATGCCT 16 43 1 TTTATTGAAT 0.773894 -163 AAAGTTATTATTTATAAAATCTTAAAATTT 16 185 0 TTTATAAAAT 0.935208 -21 TGACAAAGTTTATATATAGTCAGTGCTTAT 18 47 0 TATATATAGT 0.781439 -34 TTAAATTCTTTTTATAGAGTCTTTTAAAAC 20 67 0 TTTATAGAGT 0.901825 -112 TGTTGTGTAATTTATTAAATTCTATTTTAA 20 110 0 TTTATTAAAT 0.871465 -69 ********** Masking position 5 Map Score: 17.9233 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 403 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 5 AACATAAAAAACTTTTTGGTGAAATA 2 80 1 ACTTTTGGTG 0.931754 -16 TAGATAAAGGATATTGAGGTGGAGTAA 6 46 1 ATATTGGGTG 0.947643 -17 AAAGGAGAACATTTGGAGGTGTAAATT 9 110 1 ATTTGGGGTG 0.93047 -17 CATATATAAAATTTTCGGTTGAGTGAAAATG 11 93 0 ATTTTCGTTG 0.91579 -208 CCTACTTTTAATTTTTGGTTGCATATTTGTT 12 44 1 ATTTTTGTTG 0.967471 -151 TAGATTTATTATTTTTTGGTGATAAA 12 179 1 ATTTTTGGTG 0.983175 -16 AAGTTCTATAATATTGAGGTGAATCT 16 6 0 ATATTGGGTG 0.947643 -200 CAAACTTTTTATTTTTTGTTGTAAATATTTA 17 15 1 ATTTTTGTTG 0.967471 -83 CATAGATTTTTAATTGACAAAGTTTA 18 65 0 ATTTTTATTG 0.744622 -16 ****** **** Masking position 4 Map Score: 6.43172 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 77 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 AAAAGTTTTTTATGTTATTTTTAGATATTTA 2 65 0 TATTTATTTT 0.5745 -31 TAATACTTAATGTTCAATTTATTCAAATCAT 3 115 1 TGTCAATTTA 0.589092 -40 TCCCTATTTTTATTATACTTACTTTTTATTA 7 17 0 TATATACTTA 0.769058 -25 ACTTAATAAATGTAATATTTAAAAATAAAAA 8 26 0 TGTATATTTA 0.831623 -126 AAAATTTGTATATTTAACTTAATAAATGTAA 8 42 0 TATTAACTTA 0.735152 -110 ACAAATTTTATGTAATATTTAAAAGTATTTA 8 64 1 TGTATATTTA 0.831623 -88 TTTTATATAATATCTAAGTTAGTTGTTAAAT 8 120 1 TATTAAGTTA 0.509371 -32 TTCTCCTTTGTGTTTTATTTATTTGTTTTAA 9 88 0 TGTTTATTTA 0.921957 -39 CTGATATAAATATTTTACTTAAAAAAGATGA 11 198 0 TATTTACTTA 0.888074 -103 TTGTGGAGTCTATACTATTTATTGCAATTGC 12 108 0 TATCTATTTA 0.845384 -87 ATATAATAATTACGTGAGAAGA 14 2 1 TATATAATTA 0.596432 -26 TTGTATTAAATATTTTAATTAATGTCTTGAA 15 157 1 TATTTAATTA 0.779175 -144 ACATATGGTTTATGTTATTTAACAAAATTAA 16 132 0 TATTTATTTA 0.939461 -74 ACATAAACCATATGTTATTTATTTTATTATC 16 148 1 TATTTATTTA 0.939461 -58 AGTCAGTGCTTATATTATTTACTGTATAAGA 18 29 0 TATTTATTTA 0.938537 -52 CAATGAATGTTGTGTAATTTATTAAATTCTA 20 116 0 TGTTAATTTA 0.805275 -63 *** ******* Masking position 7 Map Score: 14.619 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 234 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 7 CAATACCACCTTTTACTTCAA 1 43 0 AATACCACCT 0.86471 -11 TATTTCACCAAAAAGTTTTT 2 86 0 TATTTCACCA 0.807151 -10 AATATCACTATTTATTAGTG 5 109 0 AATATCACTA 0.63462 -10 GATTTTCACCTATTTAACAAC 8 141 0 ATTTTCACCT 0.752493 -11 TAGACTCCACAATACCACCATATATGCATA 12 127 1 AATACCACCA 0.924944 -68 TTTATCACCAAAAAATAATA 12 185 0 TTTATCACCA 0.892529 -10 AAATCCTCATATTCCCACCAAACATTTTTA 13 173 0 ATTCCCACCA 0.906528 -28 GAGTGAGAGTAATCTCACAATATCTAACAT 15 249 0 AATCTCACAA 0.652988 -52 AATAATCACCAGTAAAATTCT 15 290 0 ATAATCACCA 0.782023 -11 AATCTCACCATTATTAAGGT 17 88 0 AATCTCACCA 0.95981 -10 TTTCTCACCTTGATTTTTTC 18 1 1 TTTCTCACCT 0.823528 -80 TTAAATCACCTATATGAATAA 21 24 0 TAAATCACCT 0.570552 -11 ********** Masking position 7 Map Score: 5.63904 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 236 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 8 AATTTTTGCTAATCTACTATATAAAGGGTT 3 69 1 AATCTACTAT 0.717146 -86 ACTAACGAACGTCTTCCTTTGGAAGGCGTT 5 49 0 GTCTTCCTTT 0.540314 -70 ATTTTCTACTTTCTTTTTTTAT 8 3 1 TTTCTACTTT 0.647186 -149 GATTTTCACCTATTTAACAACTA 8 139 0 TTTCACCTAT 0.636191 -13 ACCTCCAAATGTTCTCCTTTGTGTTTTATT 9 100 0 GTTCTCCTTT 0.917536 -27 GAATAGAATTATTTTCCTATAATCTTATAA 11 23 1 ATTTTCCTAT 0.730985 -278 TTGAGACTTTATTCTACTATTTAATTCTCA 11 65 1 ATTCTACTAT 0.858455 -236 CTACTATTTAATTCTCATTTTCACTCAACC 11 78 1 ATTCTCATTT 0.673554 -223 GTCCATAGTCATCCTCCTTTCTTTTTTATA 11 260 0 ATCCTCCTTT 0.941718 -41 TCTTTTAAAAATCCTACTTTTAATTTTTGG 12 32 1 ATCCTACTTT 0.807274 -163 TTAATAGCTTTATCTCCTATAAAATAACAA 12 70 0 TATCTCCTAT 0.795736 -125 CATAGGAGGAGACCTCCTATTGGGATACCT 13 61 0 GACCTCCTAT 0.847829 -140 TACTTCAAAAATCCTCATATTCCCACCAAA 13 181 0 ATCCTCATAT 0.711939 -20 TTAAATCACCTATATGAATAAGT 21 22 0 AATCACCTAT 0.647303 -13 ********** Masking position 8 Map Score: 5.44777 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 681 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 TAAATATCTAAAAATAACATAAAAAACTTT 2 65 1 AAAATAACAT 0.733681 -31 TTGTTTATATAGAGTAACTTTAAAGTTAAA 3 41 0 AGAGTAACTT 0.639772 -114 AAGTATTAGAACAATAACTGTTTGAACCCT 3 93 0 ACAATAACTG 0.859121 -62 AATTTTTAAGAATAACTTAATGATTTGA 3 137 0 AGAATAACTT 0.911859 -18 TGCAATATAAATAATAACTTATATGCATAT 12 148 0 ATAATAACTT 0.905507 -47 ATTGCAAGCAACAATAACATACTCAGAACT 15 104 1 ACAATAACAT 0.955037 -197 GAGTAATCTCACAATATCTAACATAATCTA 15 243 0 ACAATATCTA 0.619136 -58 TTTATTGTGGATAATAAAATAAATAACATA 16 158 0 ATAATAAAAT 0.491665 -48 TTTATTATCCACAATAAATTTTAAGATTTT 16 170 1 ACAATAAATT 0.802482 -36 GATTTTATAAATAATAACTTTG 16 194 1 ATAATAACTT 0.905507 -12 AAAGATAATAACAATAACAACCAGATGTTC 17 55 0 ACAATAACAA 0.84052 -43 ACAATATCATTACTTATTCA 21 1 1 ACAATATCAT 0.826329 -34 ********** Masking position 6 Map Score: 5.42336 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 297 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GTTAAAATTATTGAACTACTACTTAAAGAT 3 17 0 TTGAACTACT 0.893652 -138 TTTTTATTTTTTGAAAGACA 5 1 0 TTGAAAGACA 0.94236 -118 TAATGAACTTTTGAACGCCTTCCAAAGGAA 5 36 1 TTGAACGCCT 0.972375 -83 CCAAGAAGTTTTGAAAGACACTAATAAATA 5 91 1 TTGAAAGACA 0.94236 -28 ATATTTATTTTAAAGACTTAATAATTAT 6 9 1 TTTAAAGACT 0.85245 -54 GCTCTCACGGTGAAAGCCTATG 19 4 0 GTGAAAGCCT 0.908847 -19 TGAATTTTGAACGCTTTCATAAAGGG 20 7 1 TTGAACGCTT 0.775319 -172 TTAAAACATTTTGAAATACTAAGGACCAAT 20 44 0 TTGAAATACT 0.910615 -135 TCAAAATGTTTTAAAAGACTCTATAAAAAG 20 60 1 TTAAAAGACT 0.85245 -119 ********** Masking position 5 Map Score: 4.51024 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 55 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 AAATTTTATATATGGTTTCTGATATCTTAGC 11 110 1 TATGGTTTTG 0.970421 -191 ATCCATATTATATGGTATCTGATATAAATAT 11 216 0 TATGGTATTG 0.890035 -85 GGTCTCCTCCTATGGTTGGAGAAAGACCACA 13 77 1 TATGGTTGAG 0.92715 -124 GACCACATATTATGTTTGTTGGAGTTTGGGA 13 101 1 TATGTTTGTG 0.945745 -100 TTTTAGTAAAAATGTTTGGTGGGAATATGAG 13 167 1 AATGTTTGTG 0.811336 -34 ATAAATAACATATGGTTTATGTTATTTAACA 16 139 0 TATGGTTTTG 0.970421 -67 ******** ** Masking position 6 Map Score: 0.949918 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 44 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ********** No masking Map Score: 2.88013e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: 2.88013e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 2.88013e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0