AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_mjan_reg_300.orf -o00030_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 Input sequences: #1 MJ0406 154 ribokinase (rbsK) #2 MJ0679 39 transketolase'' #3 MJ0680 23 pentose-5-phosphate-3-epimerase #4 MJ0681 156 transketolase' #5 MJ0682 26 conserved hypothetical protein #6 MJ0683 29 conserved hypothetical protein #7 MJ0684 68 aspartate aminotransferase (aspB2) #8 MJ1368 122 sulfate transport system permease protein (cysT) #9 MJ1603 300 ribose 5-phosphate isomerase #10 MJ1605 37 glucose-6-phosphate isomerase #11 MJ1606 167 glycogen synthase (glgA) Motif number 1 CTAAAAATCTTTAAGTAGTAGTTCAA 1 5 1 AAATTTAAGT 0.587174 -150 GAGTAACTTTAAAGTTAAAATTATTGAACTAC 1 28 0 AAATAAAATT 0.913375 -127 AAACAAAAATAATAAATTAATTATTT 2 5 1 AAATAATAAA 0.930307 -35 TAAATCACCAAAAAATAAAATT 3 1 0 AAATAAAATT 0.911448 -23 ACTTACACCTAAAAATAATAGATAGTAAATAG 4 18 0 AAATAATAGA 0.822263 -139 TAAAAAAAGCAAAAACAAAAAATCCATAATGA 4 84 0 AAACAAAAAA 0.841391 -73 TTAAGATTTAAAAAATAATATCATTACTCAAT 4 123 0 AAATAATATC 0.71539 -34 ATTATTTTTTAAATCTTAAAAAGGTGAAACT 4 136 1 AAATTAAAAA 0.830511 -21 TAAAAACACATTAATGGTGATGCAT 5 4 1 AAACATTAAT 0.860465 -23 ATAAGCAAAAACTTTATAAGGGGCTAAT 6 7 1 AAACTTTATA 0.80327 -23 TGCCACCACGAAAAGTATTATTAATTAATAAT 7 15 1 AAATATTATT 0.930247 -54 TTTTCATTAAAAATTTATTAAA 8 1 0 AAATATTAAA 0.924061 -122 TGTTTAACACAAATTTTATATAATTAGGTAAT 8 60 1 AAATTATATA 0.890357 -63 GATAAAACACAAAAATAATATTATTTTCTTTT 9 79 1 AAATAATATT 0.934053 -222 TTATAGATTTAAATATATAAATATAATGAAGA 9 111 0 AAATATAAAT 0.889544 -190 TTATATATTTAAATCTATAAATTACAAAAACT 9 123 1 AAATATAAAT 0.889553 -178 TAAATTACAAAAACTTTTTATAACATTCTTAA 9 140 1 AAATTTTATA 0.880989 -161 TCAAAATTCCAAACTCAATATATAGACTGTGA 9 182 0 AAACAATATA 0.897868 -119 TAACAACCACAAAGCCAGAAAAGAGGGATATA 9 279 1 AAACAGAAAA 0.709404 -22 ATTTCCCCCCAAATCTTTTATTACATAAAGTG 10 16 0 AAATTTTATT 0.871803 -22 TTAGATTTTTAAATATAGTATAAATCTTAGAA 11 22 1 AAATAGTATA 0.88 -146 TAAATCTTAGAAAGGTATAAAAACTATCTAAT 11 42 1 AAATATAAAA 0.897615 -126 TTTTAACAATAAATATTATATTATGATGTACA 11 114 0 AAATTATATT 0.881786 -54 ATTTATTGTTAAAATCTGAAATTGAAATTGCT 11 132 1 AAACTGAAAT 0.533313 -36 *** ******* Masking position 3 Map Score: 24.0221 Number of sites scoring better than the average of aligned sites = 3253 Number in coding regions = 2169 Number in noncoding regions = 1084 Number of orfs with sites within 600 bp upstream = 634 Fraction of orfs with sites within 600 bp upstream = 0.101831 Motif number 2 AACTTTAAAGTTAAAATTATTGAACTACTAC 1 25 0 TTAAATTATT 0.859784 -130 ATACTTAATGTTCAATTTATTCAAATCATTA 1 117 1 TTAATTTATT 0.823199 -38 TATTCAAATCATTAAGTTATTCTTAAAAATT 1 134 1 ATAAGTTATT 0.925443 -21 ACCCAAAATAATTAATTTATTATTTTTGTTT 2 11 0 ATAATTTATT 0.889558 -29 AAAATCCATAATGATGTTATGCTAAAATAAT 4 67 0 ATATGTTATG 0.774623 -90 TGCTTTTTTTATTAATTCATTGAGTAATGAT 4 105 1 ATAATTCATT 0.847401 -52 TCATTGAGTAATGATATTATTTTTTAAATCT 4 121 1 ATATATTATT 0.949885 -36 TATTTTCATTAAAAATTTATTAAA 8 4 0 AAAATTTATT 0.602124 -119 TAAATTTTTAATGAAAATATTATACTATCAA 8 16 1 ATAAAATATT 0.908015 -107 TTAAACAAAATTGATGACATTTGATAGTATA 8 36 0 TTATGACATT 0.659003 -87 TGGAGTTTCGATGATTATATTACAATTATTT 9 12 0 ATATTATATT 0.903017 -289 GAAAAAGAAAATAATATTATTTTTGTGTTTT 9 82 0 ATATATTATT 0.949885 -219 TTTCTTTTTCTTCATTATATTTATATATTTA 9 103 1 TTATTATATT 0.78875 -198 ACAAAAACTTTTTATAACATTCTTAATACAG 9 146 1 TTATAACATT 0.701414 -155 CACAGAGGATAAGATATTATTTAATGTAAAA 9 228 0 AAATATTATT 0.717142 -73 AAAAATCTAAATGATGATATT 11 1 0 ATATGATATT 0.910216 -167 ATTAGATAATATAAAAACATTGTGATATATG 11 85 1 ATAAAACATT 0.825962 -83 AACAATAAATATTATATTATGATGTACATAT 11 111 0 ATATATTATG 0.806533 -57 ** ******** Masking position 10 Map Score: 18.2878 Number of sites scoring better than the average of aligned sites = 1425 Number in coding regions = 1064 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 322 Fraction of orfs with sites within 600 bp upstream = 0.0517186 Motif number 3 ATTATTGAACTACTACTTAAAGATTTTTAG 1 9 0 TATATTAAAG 0.94637 -146 TTTGCTAATCTACTATATAAAGGGTTCAAACA 1 73 1 TATAATAAAG 0.98442 -82 GTTATTGTTCTAATACTTAATGTTCAATTTAT 1 105 1 TATATTAATG 0.87544 -50 AAATAATAGATAGTAAATAGAGGAAGT 4 6 0 TATAATAGAG 0.922808 -151 CTCAATGAATTAATAAAAAAAGCAAAAACAAA 4 97 0 TATAAAAAAG 0.981625 -60 GAAAATATTATACTATCAAATGTCATCAATTT 8 28 1 TATACAAATG 0.832483 -95 GTATTAAGAATGTTATAAAAAGTTTTTGTAAT 9 143 0 TGTAAAAAAG 0.909588 -158 AGATATTATTTAATGTAAAAAGATGCCTTTGG 9 216 0 TATGAAAAAG 0.909589 -85 CCAAATCTTTTATTACATAAAGTGGAAAG 10 8 0 TATAATAAAG 0.984478 -30 TTAAATTAGATAATATAAAAACATTGTGATAT 11 81 1 TATAAAAAAC 0.861855 -87 TAACAATAAATATTATATTATGATGTACATAT 11 111 0 TATAATTATG 0.762365 -57 ** ** ****** Masking position 4 Map Score: 9.19015 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 230 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 ACTTTAAAGTTAAAATTATTGAACTACTACT 1 24 0 TAAATTATTG 0.766132 -131 TTCAATTTATTCAAATCATTAAGTTATTCTT 1 127 1 TCAATCATTA 0.832466 -28 ACAAAAATAATAAATTAATTATTTTGGGTGA 2 13 1 TAATTAATTA 0.814839 -27 GATGTTATGCTAAAATAATTGTTAGTCATAT 4 55 0 TAAATAATTG 0.911963 -102 TATTTTAGCATAACATCATTATGGATTTTTT 4 69 1 TAAATCATTA 0.969024 -88 GCTTTTTTTATTAATTCATTGAGTAATGATA 4 106 1 TTATTCATTG 0.742034 -51 ATTTAAAAAATAATATCATTACTCAATGAAT 4 119 0 TAAATCATTA 0.958795 -38 GATAGTATAATATTTTCATTAAAAATTTATT 8 14 0 TATTTCATTA 0.814352 -109 AACACAAATTTTATATAATTAGGTAATTTAA 8 65 1 TTAATAATTA 0.854805 -58 TATAATTAGGTAATTTAATTACCTTAAAAAT 8 78 1 TAATTAATTA 0.650036 -45 GAAATAATTGTAATATAATCATCGAAACTCC 9 11 1 TAAATAATCA 0.669187 -290 AAAAAGAAAATAATATTATTTTTGTGTTTTA 9 81 0 TAAATTATTT 0.522603 -220 TTATTTTCTTTTTCTTCATTATATTTATATA 9 99 1 TTTTTCATTA 0.606454 -202 TTCATTATATTTATATATTTAAATCTATAAA 9 113 1 TTAATATTTA 0.474914 -188 AATATCATCATTTAGATTTTTAA 11 3 1 TATATCATTT 0.675745 -165 TTAGATAATATAAAAACATTGTGATATATGT 11 86 1 TAAAACATTG 0.604483 -82 TACATCATAATATAATATTTATTGTTAAAAT 11 116 1 TATATATTTA 0.456935 -52 *** ******* Masking position 9 Map Score: 11.3766 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 782 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 5 CTAAAAATCTTTAAGTAGTAGTTCA 1 6 1 AATCTTTAAG 0.874676 -149 TTGCTAATCTACTATATAAAGGGTTCAAAC 1 74 1 ACTATATAAA 0.73399 -81 AATTTTTAAGAATAACTTAA 1 145 0 AATTTTTAAG 0.952691 -10 AATTGTTAGTCATATTTAAAACTTACACCT 4 40 0 CATATTTAAA 0.828702 -117 TAATGATATTATTTTTTAAATCTTAAAAAG 4 129 1 ATTTTTTAAA 0.699843 -28 AGTTTCACCTTTTTAAGATTTAAAAAA 4 140 0 CCTTTTTAAG 0.943372 -17 ATAAGCAAAAACTTTATAAGGGGCTAATA 6 11 1 ACTTTATAAG 0.912618 -19 GACATCACCATTTATAAACACTAAAAGG 7 51 0 CATTTATAAA 0.895762 -18 TTTAATAAATTTTTAATGAAAATATTA 8 8 1 AATTTTTAAT 0.723156 -115 CAATCTTAATCATTTTTAAGGTAATTAAAT 8 90 0 CATTTTTAAG 0.948215 -33 TATAGATTTAAATATATAAATATAATGAAG 9 112 0 AATATATAAA 0.751966 -189 TATATATTTAAATCTATAAATTACAAAAAC 9 124 1 AATCTATAAA 0.766103 -177 AATTACAAAAACTTTTTATAACATTCTTAA 9 142 1 ACTTTTTATA 0.579781 -159 TCATCATTTAGATTTTTAAATATAGTATAA 11 15 1 GATTTTTAAA 0.775568 -153 AGTTTTTATACCTTTCTAAGATTTATACTA 11 37 0 CCTTTCTAAG 0.776505 -131 ********** Masking position 8 Map Score: 11.0715 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 718 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 ACTTCCTCTATTTACTATCTA 4 1 1 ACTTCCTTAT 0.922519 -156 AATTAATAATAATTCCTTTTAGTGTTTATAA 7 37 1 AATTCCTTTA 0.937455 -32 CTCCAACCATAATCCCTATAATTAAAATCAG 9 38 1 AATCCCTTAA 0.956924 -263 TAGACTGTGAAAGTCCTGTATTAAGAATGTT 9 161 0 AAGTCCTTAT 0.96428 -140 TCCTCTGTGAAAGTCCTGTAATATTTCAATA 9 250 1 AAGTCCTTAA 0.980533 -51 CTGAAATTGAAATTGCTTTAAAGGGGTAATT 11 147 1 AATTGCTTAA 0.933023 -21 ******* *** Masking position 7 Map Score: 1.21308 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 138 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ACAAAAAATCCATAATGATGTTATGCTAAA 4 72 0 CATAATGATG 0.864543 -85 AAAACACATTAATGGTGATGCATA 5 13 1 AATGGTGATG 0.981381 -14 AGTGTTTATAAATGGTGATGTC 7 57 1 AATGGTGATG 0.981381 -12 TGTGTTAAACAAAATTGATGACATTTGATA 8 41 0 AAAATTGATG 0.758802 -82 TTGAGTTTGGAATTTTGATGCCAAAGGCAT 9 196 1 AATTTTGATG 0.93806 -105 TAAAAATCTAAATGATGATATT 11 3 0 AATGATGATA 0.863366 -165 ATAAATATTATATTATGATGTACATATATC 11 108 0 TATTATGATG 0.839636 -60 ********** Masking position 8 Map Score: 2.68643 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 219 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 TATTATTTTTAGGTGTAAGTTTTAAATATG 4 30 1 AGGTGTAAGT 0.956934 -127 AATCTTAAAAAGGTGAAACT 4 147 1 AGGTGAAACT 0.954178 -10 AATATATAGACTGTGAAAGTCCTGTATTAA 9 168 0 CTGTGAAAGT 0.98251 -133 ATCTTATCCTCTGTGAAAGTCCTGTAATAT 9 244 1 CTGTGAAAGT 0.98251 -57 ********** Masking position 4 Map Score: 0.750345 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 9 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 ********** No masking Map Score: 2.16248e-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 10 ********** No masking Map Score: 2.16248e-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 11 ********** No masking Map Score: 2.16248e-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