AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_pyro_reg_100.orf -o101_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH00338 102 Pyrococcus_OT3 #2 RPH00337 40 Pyrococcus_OT3 #3 RPH00336 19 Pyrococcus_OT3 #4 RPH01136 73 Pyrococcus_OT3 #5 RPH01137 59 Pyrococcus_OT3 #6 RPH01139 48 Pyrococcus_OT3 #7 RPH01525 213 Pyrococcus_OT3 Motif number 1 TATTTAAGACAAAAATCCTATATATACCTT 1 35 1 AAAAATCCTA 0.936747 -68 AAACCCCAATAAAAGAGCAAATTTATGCCT 2 18 0 AAAAGAGCAA 0.911882 -23 AACAATTTTTAAAAGTTTTAGTTTTCAACT 4 17 0 AAAAGTTTTA 0.913878 -57 AAAACTTTTAAAAATTGTTAAAAGCTGTAA 4 28 1 AAAATTGTTA 0.820087 -46 CAATTTCAGAAAAAGTGTTACAGCTTTTAA 4 45 0 AAAAGTGTTA 0.978943 -29 TTTTTAAAATAAAAGGTTAAAAA 5 4 0 AAAAGGTTAA 0.775533 -56 TTTTATTTTAAAAACTCCTAAAAGCCCTTT 5 20 1 AAAACTCCTA 0.925639 -40 TGAAAAATAGAAAAGGGCTTTTAGGAGTTT 5 31 0 AAAAGGGCTT 0.901782 -29 TTAATGGATAAAAAGTCCAAGTAA 7 5 0 AAAAGTCCAA 0.977991 -209 TATTTGGACGAATAATCCAAGGAGGTTCTA 7 57 1 AATAATCCAA 0.731978 -157 TATAGCTAGGAATAGGGGTACAATTAACCT 7 95 0 AATAGGGGTA 0.823468 -119 TCCTAGCTATAATAGTGCTAGTTAGTGGGT 7 114 1 AATAGTGCTA 0.978261 -100 ********** Masking position 4 Map Score: 10.0262 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 541 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 CTCAAATTTGTCTAGGTTGCAATCATTTTTGC 1 69 1 TCAGGTTGAA 0.90473 -34 TGCTCTTTTATTGGGGTTTAAA 2 29 1 TTGGGTTTAA 0.897348 -12 TTTTAAAAGTTTTAGTTTTCAACTTTAGGT 4 9 0 TTAGTTTTAA 0.978287 -65 ACAGCTTTTAACAATTTTTAAAAGTTTTAGTT 4 24 0 ACATTTTTAA 0.877316 -50 TTTTTAACCTTTTATTTTAAAAACTCCTAAAA 5 11 1 TTATTTTAAA 0.952676 -49 AAAGCCCTTTTCTATTTTTCAAAGATCGTC 5 40 1 TCATTTTTAA 0.978426 -20 GGATTAACACTTGATTTTTAAAT 6 2 0 TTATTTTTAA 0.981997 -47 TTTTTATCCATTAATTTTTTAAACAACGATCC 7 21 1 TTATTTTTAA 0.981997 -193 AATTAACCTCTTCATGTTAGAACCTCCTTGGA 7 72 0 TTATGTTAAA 0.943198 -142 ** ****** ** Masking position 7 Map Score: 9.77895 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 75 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 ATGGAAATAAGGAGGTGGAAGAG 1 3 0 GGGGTGGAAG 0.995933 -100 TCATTTTTGCAGGGGTGGTGGG 1 91 1 AGGGTGGTGG 0.99383 -12 TGGTGGTAGTGGTGGGGGTAGTAGAAGATCC 7 149 0 GGGGGGGTAG 0.998851 -65 GTGTTTGGGGAGTGGTGGTAGTGGTGGGGGT 7 161 0 AGGGTGGTAG 0.997211 -53 TCTTAGTTATGGTATGGGTAGATTGTGTTTG 7 185 0 GGATGGGTAG 0.969637 -29 ** ******** Masking position 7 Map Score: 7.35994 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 50 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TTATTTCCATATATTTAAGACAAAAATCCT 1 24 1 ATATTTAAGA 0.955054 -79 GGATCAAGGTATATATAGGATTTTTGTCTT 1 40 0 ATATATAGGA 0.964477 -63 ATTCGTCCAAATAATTAGGATCGTTGTTTA 7 40 0 ATAATTAGGA 0.97954 -174 TAGCACTATTATAGCTAGGAATAGGGGTAC 7 104 0 ATAGCTAGGA 0.984189 -110 TACCCATACCATAACTAAGACTAAGGAG 7 196 1 ATAACTAAGA 0.970474 -18 ********** Masking position 6 Map Score: 4.64124 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 68 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 TGGATAAAAAGTCCAAGTAA 7 1 0 GTCCAAGTAA 0.993006 -213 TGGATTATTCGTCCAAATAATTAGGATCGT 7 46 0 GTCCAAATAA 0.990015 -168 AGGAATAGGGGTACAATTAACCTCTTCATG 7 88 0 GTACAATTAA 0.973113 -126 ********** Masking position 5 Map Score: 0.947811 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CTCTTCCACCTCCTTATTTCCATATAT 1 8 1 ACCTCCTTAT 0.981651 -95 CCCACCACCCCTGCAAAAATGAT 1 90 0 ACCACCCCTG 0.96034 -13 CTCGCAACCTCCCGAGATTTATTAAG 6 33 0 ACCTCCCGAG 0.99094 -16 TCATGTTAGAACCTCCTTGGATTATTCGTC 7 63 0 ACCTCCTTGG 0.986053 -151 GGTACAATTAACCTCTTCATGTTAGAACCT 7 79 0 ACCTCTTCAT 0.940682 -135 ********** Masking position 1 Map Score: 1.54816 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 169 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TATATAGGATTTTTGTCTTAAATATATGGAA 1 28 0 TTTTTCTTAA 0.868312 -75 AAAATCCTATATATACCTTGATCCTCAAATT 1 46 1 ATATCCTTGA 0.94176 -57 AAGAGCAAATTTATGCCTTAAAAAC 2 5 0 TTATCCTTAA 0.912461 -36 AAATCAAGTGTTAATCCTTAATAAATCTCGG 6 17 1 TTAACCTTAA 0.786989 -32 CTTGGACTTTTTATCCATTAATTTTTTAAAC 7 14 1 TTATCATTAA 0.953601 -200 **** ****** Masking position 8 Map Score: 1.01619 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 142 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CTCTTCCACCTCCTTATTTCCATATATTT 1 10 1 CTCCTTATTT 0.900979 -93 ATATACCTTGATCCTCAAATTTGTCTAGGT 1 56 1 ATCCTCAAAT 0.810092 -47 CTCGCAACCTCCCGAGATTTATTAAGGA 6 31 0 CTCCCGAGAT 0.968469 -18 ATGTTAGAACCTCCTTGGATTATTCGTCCA 7 61 0 CTCCTTGGAT 0.934635 -153 ACTACCACCACTCCCCAAACACAATCTACC 7 170 1 CTCCCCAAAC 0.979574 -44 CAAACACAATCTACCCATACCATAACTAAG 7 185 1 CTACCCATAC 0.861512 -29 CTCCTTAGTCTTAGTTATGG 7 204 0 CTCCTTAGTC 0.961175 -10 ********** Masking position 2 Map Score: 1.11182 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 758 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 ********** No masking Map Score: -3.81261e-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 10 ********** No masking Map Score: -3.81261e-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 11 ********** No masking Map Score: -3.81261e-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