AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_aful_mthe_300.orf -o254_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01518 160 M.thermo #2 RTH01238 192 M.thermo #3 RTH01260 198 M.thermo Motif number 1 AGCGGTACTTCATTTTCAATCACCATATTAA 1 43 1 CATTTCAATC 0.985469 -118 CCCTGGAGTCCCCTCCCCATCTATCTGTTAC 1 124 0 CCTCCCCATC 0.972007 -37 GATCCTTTCAATCGCAGAGACAG 2 3 1 TCTTTCAATC 0.985504 -190 CAGGACATTTCCATTTCAATCAGCACAGAAT 2 31 1 CCTTTCAATC 0.996003 -162 ATCTCCTGAACCTCTTCAATGAGGTACATTC 2 58 0 CCCTTCAATG 0.969914 -135 ATTGAAATTACCTCTCCCATCTCATCACCTG 3 85 0 CCCTCCCATC 0.987002 -114 ATGGGAGAGGTAATTTCAATCATAAACCAGA 3 96 1 TATTTCAATC 0.948839 -103 ** ******** Masking position 9 Map Score: 8.45598 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 383 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 AAACTGGCAGTAAATTATATATAATTTTTG 1 74 1 TAAATTATAT 0.965226 -87 GTATATGTGATAAGTTATAAGTTATCAGAT 3 23 0 TAAGTTATAA 0.98896 -176 TTATAACTTATAAAGTATATGTGATAAGTT 3 37 0 TAAAGTATAT 0.925949 -162 ATATACTTTATAAGTTATAAATTATAACTT 3 47 1 TAAGTTATAA 0.98896 -152 CTGCTGGATCTAAGTTATAATTTATAACTT 3 58 0 TAAGTTATAA 0.98896 -141 ********** Masking position 6 Map Score: 7.1268 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 3 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 3 ACTTCATTTTCAATCACCATATTAAAAACT 1 49 1 CAATCACCAT 0.954991 -112 CCCTGGAGTCCCCTCCCCATCTATCTGTTA 1 125 0 CCCTCCCCAT 0.976512 -36 CCCTTAAGGGTCATCATCTGAACATTACTA 2 89 1 TCATCATCTG 0.917287 -104 TATTTAAAAACCCTCACCTTAAAAACAATA 2 144 1 CCCTCACCTT 0.995308 -49 GCCATCACCTTGGTAAGAATA 2 182 0 CCATCACCTT 0.996107 -11 CTCTCCCATCTCATCACCTGCTGGATCTAA 3 75 0 TCATCACCTG 0.986242 -124 ********** Masking position 4 Map Score: 7.82086 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 368 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ACTACATATATGATCCGGAG 1 1 0 TGATCCGGAG 0.953273 -160 TCATTGAAGAGGTTCAGGAGATCCCTTAAG 2 67 1 GGTTCAGGAG 0.968446 -126 CCCCTAGTAATGTTCAGATGATGACCCTTA 2 93 0 TGTTCAGATG 0.943968 -100 TTTTAAATATTGCTCCGGTGGATCTTTAAA 2 123 0 TGCTCCGGTG 0.986387 -70 ATGTTATTGTTTTTAAGGTGAGGGTTTTTA 2 148 0 TTTTAAGGTG 0.906791 -45 TAGTTATTCTTACCAAGGTGATGGC 2 178 1 TACCAAGGTG 0.844381 -15 AGAACCCTCCTGTCAAGGAGGAAAGTGCTG 3 169 0 TGTCAAGGAG 0.970148 -30 ********** Masking position 7 Map Score: 3.09799 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 440 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 ATTGAAAATGAAGTACCGCTGCAAGGTATGT 1 32 0 AAGTACGCTG 0.988932 -129 CATAAACCAGAAGGGTGGCTGTGGAAAGACA 3 116 1 AAGGGTGCTG 0.993072 -83 CTGATAGATTAACGGCTGTTGTTGTCTTTCC 3 138 0 AACGGCGTTG 0.98171 -61 TCAAGGAGGAAAGTGCTGCTGATAGATTAAC 3 156 0 AAGTGCGCTG 0.997192 -43 ****** **** Masking position 2 Map Score: 1.58303 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 104 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TTACTGCCAGTTTTTAATATGGTGATTGAA 1 57 0 TTTTTAATAT 0.971199 -104 AGGTGAGGGTTTTTAAATATTGCTCCGGTG 2 133 0 TTTTAAATAT 0.932974 -60 AATGTTATTGTTTTTAAGGTGAGGGTTTTT 2 149 0 TTTTTAAGGT 0.945459 -44 TAATTTTTTTTAATCTGATAACTTAT 3 7 1 TTTTTAATCT 0.967235 -192 ********** Masking position 6 Map Score: 0.775143 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 20 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -1.75204e-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 8 ********** No masking Map Score: -1.75204e-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 9 ********** No masking Map Score: -1.75204e-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