AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_bbur_reg_100.orf -o099_borburg_100.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 TAAATAAAAATATTTTAAAAAAAGGTCAAT 2 12 0 TATTTTAAAA 0.939088 -68 CATATTATAATAAATAAAAATATTTTAAAA 2 22 0 TAAATAAAAA 0.958674 -58 AATTACTGATAAATCTACAATTTCATATTA 2 45 0 AAATCTACAA 0.630204 -35 TTAAAATTAAAAACCAATTACTG 2 67 0 AAATTAAAAA 0.893009 -13 TTTATACCAAAAAATTAAAATATTTGCTAT 3 52 1 AAAATTAAAA 0.834697 -111 CTATTATTCCTCAATTATAACTTAATCAAT 3 78 1 TCAATTATAA 0.667951 -85 AATTATAACTTAATCAATAAAGTTAATTTG 3 90 1 TAATCAATAA 0.831561 -73 TTAAAATAAGTCAATTACAAATTAACTTTA 3 107 0 TCAATTACAA 0.761378 -56 ATAATAGCATTAATTTAAAATAAGTCAATT 3 121 0 TAATTTAAAA 0.962937 -42 TTAAATTAAAGAAAAAAAAACTTGAC 4 7 1 TAAAGAAAAA 0.74644 -83 TTTAAGGGATTCTTTTAAAAA 4 79 1 TCTTTTAAAA 0.82272 -11 ATTCACAACATATATAATAATAAAATTTCA 5 17 1 TATATAATAA 0.828256 -284 ATTGACAGCATATCTAACAAAGCTATTCTA 5 101 1 TATCTAACAA 0.641395 -200 CTAACAAAGCTATTCTAAAAACACTAATCA 5 114 1 TATTCTAAAA 0.87335 -187 CTAAAAACACTAATCAAAAACAATGTATTT 5 128 1 TAATCAAAAA 0.933761 -173 AAAAACAATGTATTTAATAAAAGATACATA 5 143 1 TATTTAATAA 0.860518 -158 TAATAAAAGATACATAAAAATCGAACCATC 5 157 1 TACATAAAAA 0.785465 -144 CTCTGTAGGCTATTTAACAAAAAAAGAATT 5 226 1 TATTTAACAA 0.912227 -75 TATTGGGATATAATTTAAAATCTAGGGATT 5 258 0 TAATTTAAAA 0.962937 -43 TAAGGCTTTAAAAATAAAAACT 5 289 1 AAAATAAAAA 0.85983 -12 ********** Masking position 7 Map Score: 22.1192 Number of sites scoring better than the average of aligned sites = 3080 Number in coding regions = 1829 Number in noncoding regions = 1251 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 AATTGACCTTTTTTTAAAATA 2 1 1 AATTGACCTT 0.961716 -79 ACCTCGCAAAACTTAACATATAAATCTAGTA 3 17 1 ACTTAACATT 0.905877 -146 GTCAATTACAAATTAACTTTATTGATTAAGT 3 97 0 AATTAACTTA 0.953513 -66 GTTAATTTGTAATTGACTTATTTTAAATTAA 3 111 1 AATTGACTTT 0.98242 -52 AGAAAAAAAAACTTGACTTAAGATCAAGTCA 4 20 1 ACTTGACTTA 0.988751 -70 AAATTGTATTACTTGACTTGATCTTAAGTCA 4 33 0 ACTTGACTTA 0.988748 -57 CAGATCAGGGAATTGACATTATACCTATTGC 5 63 1 AATTGACATA 0.985595 -238 TTGCAAGTTCAATTGACAGCATATCTAACAA 5 90 1 AATTGACAGA 0.948161 -211 ********* * Masking position 6 Map Score: 11.547 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 40 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 AATTGACCTTTTTTTAAAATATTTTTATTTATTA 2 10 1 TTTTAATTTT 0.861843 -70 TTTAATTTTTTGGTATAAATTACTACTAGATTTAT 3 36 0 TGTTAATCTA 0.956188 -127 TTTAAATTAATGCTATTATATACTTAAACAAAGGA 3 132 1 TGTTATTCTT 0.956203 -31 TTATTATATATGTTGTGAATGTCTTC 5 2 0 TGTTAAGCTT 0.985444 -299 GTCAATTCCCTGATCTGAAATGCTTCCCCAGTGTG 5 45 0 TGTTAATCTT 0.992832 -256 TTTATGTATCTTTTATTAAATACATTGTTTTTGAT 5 140 0 TTTTAATCAT 0.833146 -161 GTGCTGTTTATGGTTTGAAGTATTTTTTTGGTAGA 5 185 0 TGTTAATTTT 0.964631 -116 TTAAAATCTAGGGATTCAAATTCTTTTTTTGTTAA 5 239 0 GGATAATCTT 0.836104 -62 AGTTTTTATTTTTAAAGCCTTAATATTGGGA 5 280 0 TATTAAGCTT 0.897767 -21 ** * * ** * *** Masking position 8 Map Score: 5.50877 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 310 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TTAAAATTAAAAACCAATTACTGATAAATC 2 60 0 AAACCAATTA 0.897433 -20 GTAGTAATTTATACCAAAAAATTAAAATAT 3 45 1 ATACCAAAAA 0.973063 -118 TTGAGGAATAATAGCAAATATTTTAATTTT 3 62 0 ATAGCAAATA 0.932616 -101 TAAGTATATAATAGCATTAATTTAAAATAA 3 128 0 ATAGCATTAA 0.89613 -35 TTAAATTAAAGAAAAAAAAACTTGACT 4 8 1 AAAGAAAAAA 0.759941 -82 AAGTCAAGTAATACAATTTAACATTGGCAT 4 45 1 ATACAATTTA 0.666808 -45 ATCGAACCATCTACCAAAAAAATACTTCAA 5 176 1 CTACCAAAAA 0.905613 -125 AAAATACTTCAAACCATAAACAGCACAATA 5 194 1 AAACCATAAA 0.933495 -107 ********** Masking position 6 Map Score: 3.76969 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 332 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 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