AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_bsub_reg_100.orf -o00300_bsub_100.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 Purged sequences: yacF 23 similar to transcriptional regulator (nitrogen regulation protein) Input sequences: #1 pabB 166 para-aminobenzoate synthase (subunit A) #2 lysS 91 lysyl-tRNA synthetase #3 ddlA 174 D-alanyl-D-alanine ligase A #4 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #5 patA 300 aminotransferase #6 ykuN 111 similar to flavodoxin #7 ykuQ 24 similar to tetrahydrodipicolinate succinylase #8 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #9 asd 125 aspartate-semialdehyde dehydrogenase #10 dapG 91 aspartokinase I (alpha and beta subunits) #11 dapA 30 dihydrodipicolinate synthase #12 pksF 300 pksF #13 ypjD 300 alternate gene name: jojD #14 lysA 105 diaminopimelate decarboxylase #15 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #16 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #17 yqiS 124 similar to phosphate butyryltransferase #18 bltD 168 spermine/spermidine acetyltransferase #19 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #20 ytjP 96 similar to Xaa-His dipeptidase #21 patB 80 aminotransferase #22 yutL 122 similar to diaminopimelate epimerase #23 hom 200 homoserine dehydrogenase Motif number 1 TCTATTTTCTTTTTTACTTGTTTTTAATTGTA 1 133 0 TTTTCTTGTT 0.643457 -34 GCTGGCAGTTTTTCTGCTTTTTTCATGAAACA 2 47 1 TTTTCTTTTT 0.930076 -45 TTTTACCGGCAGTGTCCTTCTTCA 4 3 0 AGTTCTTCTT 0.761596 -69 AATCGCTGGTTGTCTTCTTTTTTTCTGAAAAG 5 162 1 TGTTCTTTTT 0.959601 -139 ATATTTCGATTGTATGCGCCTTTTTTCTAAAC 5 202 0 TGTTCGCCTT 0.85687 -99 GCTGATCATTTGTCACCTTTTTAACTGATATA 5 231 0 TGTACTTTTT 0.760184 -70 ATTAGCTGGATGTATCCTTTTATTTACGCTAA 8 61 1 TGTTCTTTTA 0.945808 -115 TTTGACTATGATTTTACGTTTTATTTTACCAT 9 65 0 ATTTCGTTTT 0.815637 -61 GGCTCAAATCTGTGTCCGTCTAATTCAGGAAG 12 136 0 TGTTCGTCTA 0.907842 -165 GCACGTTTGCTGTTTTCTTTTTCATCCACTAT 13 214 0 TGTTCTTTTT 0.959601 -87 TCATTCCCTCTTTCTCCGCTTATGGATGAAAG 14 82 0 TTTTCGCTTA 0.837555 -24 AAGCCCCTCCTTTATGCTTTTAAAAATGAATG 16 50 0 TTTTCTTTTA 0.907176 -24 TTCGTGCAGATGTTTGCGTTTATTCTGCAAA 17 10 0 TGTTCGTTTA 0.953747 -115 ACTACATTCTCCTTTTTTCTTATCCCG 18 152 0 ATTTCTTTTT 0.78923 -17 CACCATTAATATTATTCGTTTTATTTGGTTTT 20 43 1 ATTTCGTTTT 0.815637 -54 CTCATGTATGTTTATTCTTCTAAGCTTCACTA 21 48 0 TTTTCTTCTA 0.823599 -33 ATAATTGTATTGTGTCCGCTTATAATAGCTTT 22 66 1 TGTTCGCTTA 0.902032 -57 GCCTCCAACTTTTTTTCTTTTTCTTAGTATAA 22 97 0 TTTTCTTTTT 0.930076 -26 ATTTTGCGAATGTAAACGCTTAACGCATTGAT 23 57 0 TGTACGCTTA 0.551313 -144 *** * ****** Masking position 3 Map Score: 16.7652 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 868 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 CTCCCGGCGAACCGGGAGTTTTGGCTTTTT 1 9 0 ACGGGAGTTT 0.935633 -158 CTCCCGGTTCGCCGGGAGTTTTTTTATATTTC 1 23 1 GCGGGAGTTT 0.985311 -144 CTAGTTTTACGCTGGCAGTTTTTCTGCTTTTT 2 37 1 GCGGCAGTTT 0.917609 -55 AATGGCATTGAAAAGGAGATGTGACAT 3 6 0 AAAGGAGTGT 0.707281 -169 AGACAGCGAGGTGCTGTCTTTTTTTTA 6 6 1 GCAGGTGTGT 0.921379 -106 GCTGATTGGCGGAAGGAGTTTTACAG 9 110 1 GGAGGAGTTT 0.927772 -16 ACCAATATTTGCGAGGTGCTTCCTGAATTAGA 12 118 1 GCAGGTGTTC 0.802615 -183 AGTTAGTTGAGCTAGGAGCTGACTCTGTAGAC 12 176 1 GCAGGAGTGA 0.812165 -125 TCACGATGGTGCTAGAGGATTTATCGTTAAAA 12 221 1 GCAGAGGTTT 0.869918 -80 ATAGCTCAATGCGAGGGATTTTTAACGATAAA 12 240 0 GCAGGGATTT 0.853091 -61 CAATCTGGCTGAGGGCGGTTTTACAGGTATTA 13 48 0 GAGGCGGTTT 0.705133 -253 TAATGGAAGGAAAAGGGGTTTTGTGTGATGCT 13 167 0 AAAGGGGTTT 0.848941 -134 GTAAGAGGATGATAGGAGGTTTCGTTCA 13 283 1 GAAGGAGTTT 0.966118 -18 ATTGTGCCTAACCAGGGGCATTCCCTGCATCC 18 38 0 ACAGGGGATT 0.670734 -131 TTGCACTGACGCAAGGAGCTTTTATCGT 22 7 0 GCAGGAGTTT 0.991789 -116 TTGCGTCAGTGCAAGGAGCTTTTATGTATGAA 22 25 1 GCAGGAGTTT 0.991789 -98 ** ***** *** Masking position 5 Map Score: 14.229 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 328 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 3 TTTAATATAAAATAAAAAGGAATTACATAC 3 37 1 AATAAAAAGG 0.739431 -138 CCGTATATACAAAAGAAAGAGAGGGACCTT 4 50 1 AAAAGAAAGA 0.960684 -22 AGAACATGATACAATAAAGACAATCAAATC 5 136 1 ACAATAAAGA 0.682037 -165 TTTTTTTCTGAAAAGAAAGGTATGTTTAGA 5 179 1 AAAAGAAAGG 0.975133 -122 AGGTATGTTTAGAAAAAAGGCGCATACAAT 5 196 1 AGAAAAAAGG 0.931957 -105 ACAGATAAATAAAAAAAAGACAGCACCTCG 6 17 0 AAAAAAAAGA 0.938525 -95 ATTTTAGCGTAAATAAAAGGATACATCCAG 8 66 0 AAATAAAAGG 0.70686 -110 TTCAATGATAAAAAGAACGAATTAGAATGT 8 140 1 AAAAGAACGA 0.780916 -36 CGGAGTCGAAACAAGAAAGGTGGTAACAG 17 106 1 ACAAGAAAGG 0.937695 -19 TACCGGGATAAGAAAAAAGGAGAATGTAGT 18 149 1 AGAAAAAAGG 0.931957 -20 CGTGCGGGTGAGGAGAAAGAGCGCTTTGTC 19 130 0 AGGAGAAAGA 0.811879 -46 CTTTTATACTAAGAAAAAGAAAAAAAGTTG 22 94 1 AAGAAAAAGA 0.828273 -29 AAATAATTAGAAAATAAAGAATCTTGTCAT 23 27 1 AAAATAAAGA 0.84823 -174 GAGGACAATCAAAAGAAAGGTGGAGTTTTT 23 181 1 AAAAGAAAGG 0.975133 -20 ********** Masking position 6 Map Score: 12.1815 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 457 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 AGCATGCCCAAAAATAATTAGATCATTTTC 3 83 1 AAAATAATTA 0.925966 -92 AAAATAGGATAAACTCATTATATTTGTTAA 5 270 1 AAACTCATTA 0.933846 -31 GTTGACAATGAAAATCATTATCATTTAAAG 6 45 1 AAAATCATTA 0.978666 -67 TATGATATTGAAAATCATTATCAACTAATG 6 82 1 AAAATCATTA 0.978666 -30 CTGTATGCTTAAAATCATTACCACATCATT 8 101 1 AAAATCATTA 0.978666 -75 TATACCTATAAAAATCATTAAAATAATCCC 12 37 1 AAAATCATTA 0.978666 -264 AAATCTGACAAAAATAATTAGAAAATAAAG 23 16 1 AAAATAATTA 0.925966 -185 ********** Masking position 7 Map Score: 11.3358 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ACATGGCATATTTGATGCACGAAATATAAAAAAACT 1 39 0 TTATGGAAAA 0.973007 -128 CTGCGACGAATGTTATTCTTGGAAGAGAAATTCACT 1 75 1 TTATTGGAAA 0.95041 -92 TGTAAAGCAATGTTGTTAGTGAAAAAAGTGAATTTC 1 101 0 TTGTTGAAAA 0.955498 -66 AAAGATGAATTGTAGTGGGGGGAGTATCCATTGAAA 3 134 1 TTGTGGGAGA 0.916643 -41 TAAACATACCTTTCTTTTCAGAAAAAAAGAAGACAA 5 171 0 TTTTTGAAAA 0.804449 -130 CTGCCTATTCTTTTATTGCAGAAAAAATGCTGATAT 8 17 1 TTATTGAAAA 0.963056 -159 GACCGAATTTTTTAGTTTGGGAAAGATTTTCTGTAA 9 13 0 TTGTTGAAAA 0.955499 -113 TCTGTGTCCGTCTAATTCAGGAAGCACCTCGCAAAT 12 124 0 TTATTGAAGA 0.929458 -177 AGGGGTTTTGTGTGATGCTTGGAGAAATTAGATTAA 13 150 0 TTATGGGAGA 0.930397 -151 ATAAACGCTATCTAATGGAAGGAAAAGGGGTTTTGT 13 175 0 TTATGGGAAA 0.963608 -126 GCGTTTATATTATAGTGGATGAAAAAGAAAACAGCA 13 203 1 TTGTGGAAAA 0.96739 -98 TCATTGCTTTTTTTATTGTGGACAAAGCGCTCTTTC 19 110 1 TTATTGACAA 0.804557 -66 TGCAAGGAGCTTTTATGTATGAAAAACGGGGGATAA 22 34 1 TTATGGAAAA 0.973015 -89 * * *** **** * Masking position 16 Map Score: 12.384 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 173 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TTGTATCATTCCTCTATTTTCTTTTT 1 151 0 TATCACCCTA 0.979387 -16 TGTTATCACTCCATTACAGATATTGT 2 76 0 TATCACCTTA 0.973618 -16 GTTATCACCCCATTAGTTGATAATG 6 97 0 TATCACCTTA 0.973618 -15 CGTATCAAACCTCTCAACATTCTAA 8 161 0 TATCACCCTC 0.983916 -15 AGTAAGGCGCTATCAGCCTGCTCTCTTCTGTTA 10 43 1 TATCACTCTC 0.951748 -49 CGAAACCTCCTATCATCCTCTTACATGTTAGCT 13 274 0 TATCACTTTA 0.92363 -27 AGACATACATTATCATACTCTTCAGTCAGTTTC 14 18 0 TATCACTTTC 0.939661 -88 AATCTTGTCATATCAATGCGTTAAGCGTTTACA 23 46 1 TATCAGCTTA 0.842818 -155 ACAAACATTATATAAGCCCGCTCCTGTTTTGAC 23 107 0 TATAACCCTC 0.857065 -94 ***** ** *** Masking position 5 Map Score: 7.92722 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 56 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 GATGCACGAAATATAAAAAAACTCCCGGCGA 1 31 0 ATATAAAAAA 0.556558 -136 TTTCCGGTGAAAATGATAAGATAGTAAAGAT 3 109 1 AAATGAAAGA 0.901027 -66 CACATATAAACAATAATAGAACATGATACAA 5 119 1 CAATAAAGAA 0.901087 -182 GTCAACAGATAAATAAAAAAAAGACAGCACC 6 20 0 AAATAAAAAA 0.823562 -92 ATTTTTTCTGCAATAAAAGAATAGGCAGCCC 8 14 0 CAATAAAGAA 0.901087 -162 ATTTTAGCGTAAATAAAAGGATACATCCAGC 8 65 0 AAATAAAGGA 0.823299 -111 GATGTGACTTCAATGATAAAAAGAACGAATT 8 132 1 CAATGAAAAA 0.946808 -44 GAACCAAGCCAAATGAAAAAATTGCCGCTCC 13 96 1 AAATGAAAAA 0.882224 -205 TGGTTAGGCACAATAAGAAAAGGTACTTAAT 18 56 1 CAATAAAAAA 0.917299 -113 AATTGATAAGCAATGAGAGTATTCCTCTCAT 19 83 1 CAATGAAGTA 0.697396 -93 ATAAAAAAAGCAATGAGAGGAATACTCTCAT 19 95 0 CAATGAAGGA 0.946717 -81 GCTTTGTCCACAATAAAAAAAGCAATGAGAG 19 107 0 CAATAAAAAA 0.917299 -69 CTAAGCTTCACTATGATAAGATAGAACTGCA 21 30 0 CTATGAAAGA 0.853304 -51 TAACGCATTGATATGACAAGATTCTTTATTT 23 38 0 ATATGAAAGA 0.709967 -163 TCCAAGAGGACAATCAAAAGAAAGGTGGAGT 23 176 1 CAATCAAAGA 0.781679 -25 ****** **** Masking position 6 Map Score: 12.4869 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 398 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 TGAAGAAAGAATCAGCTGACCTTCAAGAAG 5 24 1 ATCAGCTGAC 0.879635 -277 ACATCGGTGAATTAGCTGAGGTGCTTT 12 284 1 ATTAGCTGAG 0.936451 -17 CCTTTCATCCATAAGCGGAGAAAGAGGGAA 14 81 1 ATAAGCGGAG 0.987285 -25 TGAATATAGTATAAGCTGAGTTTTAGCAAT 18 112 1 ATAAGCTGAG 0.978771 -57 AAATTTTATTATAAGCGGTG 21 1 0 ATAAGCGGTG 0.950662 -80 AAAAGCTATTATAAGCGGACACAATACAAT 22 69 0 ATAAGCGGAC 0.976018 -54 ********** Masking position 4 Map Score: 4.49943 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 48 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TACTCACCTCTATTTGCTGCTCACTG 2 4 1 TCACCCATTG 0.961252 -88 CTTATCATTTTCACCGGAAAATGATCTAATTAT 3 96 0 TCACCGAATG 0.976554 -79 ACTTACCTGAATATGAAGAAAGAAT 5 3 1 TTACCGAATG 0.954955 -298 TTATCCTATTTTACCACTAGCTGATCATTTGTC 5 249 0 TTACCCACTG 0.913889 -52 CTTAAAATCATTACCACATCATTTGATGTGACT 8 108 1 TTACCCTATT 0.780833 -68 AATTCGGTCATCACCCGCATATTCTATGGTAAA 9 40 1 TCACCGAATT 0.891325 -86 TTTATTCACCTCATCATGATTCAATCAC 11 13 0 TCACCCTATG 0.972638 -18 GAAGTATTAATCACCAATATTTGCGAGGTGCTT 12 106 1 TCACCAATTG 0.793296 -195 TCTGTTACCCCCTCATGTATGTTTATT 21 64 0 TTACCCTATG 0.947625 -17 ***** * * *** Masking position 3 Map Score: 2.27999 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 119 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TTCCATTAGATAGCGTTTATATTATAGTGG 13 191 1 TAGCGTTTAT 0.95679 -110 GTGCAGATGTTTGCGTTTATTCTGCAAA 17 9 0 TTGCGTTTAT 0.922286 -116 ATTCCTCTCATTGCTTTTTTTATTGTGGAC 19 103 1 TTGCTTTTTT 0.779327 -73 CTGACGCAAGGAGCTTTTATCGT 22 4 0 GAGCTTTTAT 0.95679 -119 TCAGTGCAAGGAGCTTTTATGTATGAAAAA 22 30 1 GAGCTTTTAT 0.95679 -93 CCGCTTATAATAGCTTTTATACTAAGAAAA 22 81 1 TAGCTTTTAT 0.963911 -42 ********** Masking position 6 Map Score: 2.37154 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 51 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TGGAAGAGAAATTCACTTTTTTCACTAACA 1 94 1 ATTCACTTTT 0.694137 -73 GGCAGTTTTTCTGCTTTTTTCATGAAACAA 2 50 1 CTGCTTTTTT 0.769306 -42 CTCCTTTTCAATGCCATTTTAATATAAAAT 3 20 1 ATGCCATTTT 0.609015 -155 TTTGTATGTAATTCCTTTTTATTTTATATT 3 40 0 ATTCCTTTTT 0.808309 -135 GGAAAAAACACTGCCCTTTTACCGGCAGTG 4 21 0 CTGCCCTTTT 0.922008 -51 AGGTCAGCTGATTCTTTCTTCATATTCAGG 5 16 0 ATTCTTTCTT 0.752389 -285 GATACGGAGGATGCTCTTCTTGAAGGTCAG 5 39 0 ATGCTCTTCT 0.718488 -262 CGCTGGTTGTCTTCTTTTTTTCTGAAAAGA 5 165 1 CTTCTTTTTT 0.732897 -136 TCTTTAGAAAATTCTCTCTT 10 1 0 ATTCTCTCTT 0.913578 -91 CGCTATCAGCCTGCTCTCTTCTGTTACGTC 10 50 1 CTGCTCTCTT 0.894945 -42 TACTTCAAAGATTCTCTGTTTATCCATAAT 12 82 0 ATTCTCTGTT 0.750143 -219 CTTTTGCTTTATGCCCTTTTCCACATCAGC 13 16 0 ATGCCCTTTT 0.94689 -285 TGTCATTCCCTCTTTCTCCGCTTA 14 92 0 ATTCCCTCTT 0.915052 -14 ACTACATTCTCCTTTTTTCTTATCC 18 154 0 ATTCTCCTTT 0.677422 -15 ********** Masking position 2 Map Score: 7.53217 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 446 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 12 ATACCTTTCTTTTCAGAAAAAAAGAAGACA 5 172 0 TTTCAGAAAA 0.920011 -129 TATTCTTTTATTGCAGAAAAAATGCTGATA 8 22 1 TTGCAGAAAA 0.962961 -154 ATTTACAGAAAATCTTTCCCAA 9 3 1 TTACAGAAAA 0.867472 -123 ATAGGTATATTTTCATAATATTCAAACTTT 12 16 0 TTTCATAATA 0.795711 -285 TTTGCAGAATAAACGCAAACA 17 2 1 TTGCAGAATA 0.962974 -123 GGCATGGAACTTGCATAATAAAAGGCGGAG 17 81 1 TTGCATAATA 0.897826 -44 ********** Masking position 5 Map Score: 1.59921 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 152 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 13 AACATTCGTCGCAGACATGGCATATTTGATGC 1 57 0 GCAGACTGGA 0.945749 -110 TTTTGGGCATGCTGATGTTGAATGCATTTGTA 3 64 0 GCTGATTTGA 0.966272 -111 GAAAGAATCAGCTGACCTTCAAGAAGAGCATC 5 28 1 GCTGACTTCA 0.903062 -273 ATCCTCCGTATCTGATTTGGCACGAAGACCTT 5 57 1 TCTGATTGGA 0.846579 -244 GATACATCCAGCTAATCTTGAAAGATATCAGC 8 45 0 GCTAATTTGA 0.849427 -131 TGAGCTAGGAGCTGACTCTGTAGACAGAGCTG 12 183 1 GCTGACCTGA 0.929333 -118 GAGGGGCTGATGTGGAAAAGGGCATAA 13 6 1 GCTGATTGGA 0.982544 -295 ATCTGAATTAGCTAACATGTAAGAGGATGATA 13 265 1 GCTAACTGTA 0.708599 -36 ACCCTTAAGAGCTGGCATGGAACTTGCATAAT 17 68 1 GCTGGCTGGA 0.962739 -57 ****** *** * Masking position 12 Map Score: 1.68102 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 315 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 GCGTAAAACTAGCAGTGAGCAGCAAATAGA 2 19 0 AGCAGTGAGC 0.944726 -73 AAAGACGAATAGAAGAGAGTAAGGCGCTAT 10 26 1 AGAAGAGAGT 0.907798 -66 CGGACGTAACAGAAGAGAGCAGGCTGATAG 10 52 0 AGAAGAGAGC 0.980909 -40 TAATCCCTTGAGGAGAGAGCGCATTATGGA 12 60 1 AGGAGAGAGC 0.987574 -241 TTGTCAAAACAGGAGCGGGCTTATATAATG 23 105 1 AGGAGCGGGC 0.954548 -96 ********** Masking position 4 Map Score: 0.205499 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 43 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 CATTTTCACCGGAAAATGATCTAATTATTT 3 94 0 GGAAAATGAT 0.652356 -81 CATTTTCCGGTGAAAATGATAAGATAGTAA 3 106 1 TGAAAATGAT 0.92787 -69 GATAAGATAGTAAAGATGAATTGTAGTGGG 3 123 1 TAAAGATGAA 0.425425 -52 ACTTACCTGAATATGAAGAAAGAATCA 5 8 1 TGAATATGAA 0.917383 -293 ATAGCCATAATCAAAATGAAGGTCTTCGTG 5 77 0 TCAAAATGAA 0.781453 -224 ATTTATCTGTTGACAATGAAAATCATTATC 6 37 1 TGACAATGAA 0.901566 -75 TCACTTTAAATGATAATGATTTTCATTGTC 6 48 0 TGATAATGAT 0.830571 -64 CCCCATTAGTTGATAATGATTTTCAATATC 6 85 0 TGATAATGAT 0.830571 -27 TATTTACGCTAAAATATGAACTGTATGCTT 8 81 1 AAAATATGAA 0.43795 -95 TGAATTGATTTGACTATGATTTTACGTTTT 9 75 0 TGACTATGAT 0.767591 -51 TTATAGTGGATGAAAAAGAAAACAGCAAAC 13 212 1 TGAAAAAGAA 0.738143 -89 ATGTATGTCTTAATTATGAAGGGACAGTCC 14 41 1 TAATTATGAA 0.478349 -65 TTTATGCTTTTAAAAATGAATGGCTTTGCC 16 42 0 TAAAAATGAA 0.811784 -32 TTAACTTTATAGAAAATGAA 18 1 0 AGAAAATGAA 0.86568 -168 TAGCCCTCCAAGAAAATGATTTCTTGACAG 19 23 0 AGAAAATGAT 0.80641 -153 TCATCATAAATGATTATGAACAACGAGATA 19 51 0 TGATTATGAA 0.808852 -125 CTTCTAAGCTTCACTATGATAAGATAGAAC 21 34 0 TCACTATGAT 0.372395 -47 TTTTATACTAAGAAAAAGAAAAAAAGTTGG 22 95 1 AGAAAAAGAA 0.477206 -28 ********** Masking position 6 Map Score: 10.1757 Number of sites scoring better than the average of aligned sites = 1490 Number in coding regions = 1271 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117