AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_bbur_reg_300.orf -o099_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00685 25 3615 #2 RBB00684 79 3615 #3 RBB00526 162 3615 #4 RBB00776 89 3615 #5 RBB00523 300 3615 Motif number 1 AATTGACCTTTTTTTAAAATATTTTTATTTATTA 2 11 1 TTTTTAATAT 0.96862 -69 GAAATTGTAGATTTATCAGTAATTGGTTTTTAAT 2 51 1 ATTTATATAT 0.840779 -29 TACTACTAGATTTATATGTTAAGTTTTGCGAGGT 3 17 0 TTTATAGTAT 0.782818 -146 ATATTTTAATTTTTTGGTATAAATTACTACTAGA 3 41 0 TTTTTGTTAT 0.825072 -122 ACAAATTAACTTTATTGATTAAGTTATAATTGAG 3 87 0 TTTATTATAT 0.938301 -76 TAATTGACTTATTTTAAATTAATGCTATTATATA 3 120 1 ATTTTAATAG 0.797176 -43 GCAAACTCCTTTGTTTAAGTATATAATAGCATTA 3 139 0 TTGTTTATAT 0.886707 -24 AGTCAAGTTTTTTTTTCTTTAATTTAA 4 4 0 TTTTTTTTAT 0.964885 -86 CAGTGTGAAATTTTATTATTATATATGTTGTGAA 5 18 0 TTTTATATAT 0.937337 -283 TTGATTAGTGTTTTTAGAATAGCTTTGTTAGATA 5 111 0 TTTTTAATAT 0.968621 -190 TAAATACATTGTTTTTGATTAGTGTTTTTAGAAT 5 125 0 GTTTTTATAG 0.790429 -176 TTATGTATCTTTTATTAAATACATTGTTTTTGAT 5 140 0 TTTATTATAT 0.938299 -161 AGATGGTTCGATTTTTATGTATCTTTTATTAAAT 5 154 0 ATTTTTTTAT 0.905865 -147 GTTTGAAGTATTTTTTTGGTAGATGGTTCGATTT 5 174 0 TTTTTTGTAT 0.970751 -127 ATTCAAATTCTTTTTTTGTTAAATAGCCTACAGA 5 227 0 TTTTTTGTAT 0.969813 -74 GAATCCCTAGATTTTAAATTATATCCCAATATTA 5 257 1 ATTTTAATAT 0.914983 -44 AGTTTTTATTTTTAAAGCCTTAATATT 5 284 0 TTTTATTTAG 0.695401 -17 ****** * ** * Masking position 10 Map Score: 21.2435 Number of sites scoring better than the average of aligned sites = 1533 Number in coding regions = 979 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 AATTGACCTTTTTTTAAAATAT 2 1 1 AATTGACTTT 0.989199 -79 ACCTCGCAAAACTTAACATATAAATCTAGTAG 3 17 1 ACTTAACTTA 0.816114 -146 TATACCAAAAAATTAAAATATTTGCTATTATT 3 54 1 AATTAAATTT 0.746413 -109 GTCAATTACAAATTAACTTTATTGATTAAGTT 3 96 0 AATTAACTAT 0.973678 -67 GTTAATTTGTAATTGACTTATTTTAAATTAAT 3 111 1 AATTGACTTT 0.989174 -52 AGAAAAAAAAACTTGACTTAAGATCAAGTCAA 4 20 1 ACTTGACTAG 0.96113 -70 AAATTGTATTACTTGACTTGATCTTAAGTCAA 4 32 0 ACTTGACTAT 0.989373 -58 CAGATCAGGGAATTGACATTATACCTATTGCA 5 63 1 AATTGACTAT 0.991218 -238 TTGCAAGTTCAATTGACAGCATATCTAACAAA 5 90 1 AATTGACGAT 0.963464 -211 ******* * ** Masking position 6 Map Score: 12.4829 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 41 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 ATATTATAATAAATAAAAATATTTTAAAAA 2 21 0 AAATAAAAAT 0.974233 -59 TTAAAATTAAAAACCAATTACTGA 2 66 0 AATTAAAAAC 0.970825 -14 TTATACCAAAAAATTAAAATATTTGCTATT 3 53 1 AAATTAAAAT 0.92328 -110 AAAATAAGTCAATTACAAATTAACTTTATT 3 105 0 AATTACAAAT 0.837418 -58 TAATAGCATTAATTTAAAATAAGTCAATTA 3 120 0 AATTTAAAAT 0.907389 -43 TAAATTAAAGAAAAAAAAACTTGACTTAAG 4 12 1 AAAAAAAAAC 0.952373 -78 TAAAAACACTAATCAAAAACAATGTATTTA 5 129 1 AATCAAAAAC 0.886049 -172 CAATGTATTTAATAAAAGATACATAAAAAT 5 148 1 AATAAAAGAT 0.744108 -153 AATAAAAGATACATAAAAATCGAACCATCT 5 158 1 ACATAAAAAT 0.856462 -143 ACCATCTACCAAAAAAATACTTCAAACCAT 5 181 1 AAAAAAATAC 0.698442 -120 CTATTTAACAAAAAAAGAATTTGAATCCCT 5 235 1 AAAAAAGAAT 0.755805 -66 ATTGGGATATAATTTAAAATCTAGGGATTC 5 257 0 AATTTAAAAT 0.907389 -44 AAGGCTTTAAAAATAAAAACT 5 290 1 AAATAAAAAC 0.974718 -11 ********** Masking position 9 Map Score: 15.5567 Number of sites scoring better than the average of aligned sites = 1725 Number in coding regions = 1147 Number in noncoding regions = 578 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 TAAAAATATTTTAAAAAAAGGTCAATT 2 8 0 TTAAAAAAAG 0.965232 -72 ATTATAATAAATAAAAATATTTTAAAAAAA 2 19 0 ATAAAAATAT 0.628239 -61 AGTAATTTATACCAAAAAATTAAAATATTT 3 47 1 ACCAAAAAAT 0.761006 -116 TAGCATTAATTTAAAATAAGTCAATTACAA 3 117 0 TTAAAATAAG 0.779124 -46 TATTATATACTTAAACAAAGGAGTTTGC 3 145 1 TTAAACAAAG 0.905852 -18 TTTTTAAAAGAATCCCTTAAAGC 4 77 0 TTAAAAGAAT 0.765614 -13 AACATATATAATAATAAAATTTCACACTGG 5 23 1 ATAATAAAAT 0.765288 -278 TGACAGCATATCTAACAAAGCTATTCTAAA 5 103 1 TCTAACAAAG 0.586122 -198 AACAATGTATTTAATAAAAGATACATAAAA 5 146 1 TTAATAAAAG 0.861489 -155 AATAAAAGATACATAAAAATCGAACCATCT 5 158 1 ACATAAAAAT 0.661983 -143 GAACCATCTACCAAAAAAATACTTCAAACC 5 179 1 CCAAAAAAAT 0.860772 -122 AGGCTATTTAACAAAAAAAGAATTTGAATC 5 232 1 ACAAAAAAAG 0.964366 -69 ********** Masking position 9 Map Score: 5.31792 Number of sites scoring better than the average of aligned sites = 2611 Number in coding regions = 1784 Number in noncoding regions = 827 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 ********** No masking Map Score: -9.63906e-13 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 6 ********** No masking Map Score: -9.63906e-13 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 7 ********** No masking Map Score: -9.63906e-13 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