AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_aful_mthe_100.orf -o216_aful_mthe_100.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 RAG49065 70 Archaeoglobus_fulgidus #2 RTH00518 35 M.thermo #3 RTH01836 222 M.thermo #4 RTH00222 184 M.thermo Motif number 1 TCACCGTGAACTCCATGTGAGAAGAAACCT 3 63 0 CTCCATGTGA 0.996223 -160 TCACATGGAGTTCACGGTGACATGAACATT 3 73 1 TTCACGGTGA 0.892604 -150 TCGCTGTGAACTCCATGTGAAATGTTCATG 3 93 0 CTCCATGTGA 0.996223 -130 TGGTGTTCATATCGCTGTGAACTCCATGTG 3 104 0 ATCGCTGTGA 0.937243 -119 GCGATATGAACACCATATGATGAACCTCAG 3 119 1 CACCATATGA 0.93135 -104 TGATGAACCTCAGAATGTGATATGCCGGTG 3 136 1 CAGAATGTGA 0.942236 -87 AGAATGTGATATGCCGGTGAAAGATATATA 3 147 1 ATGCCGGTGA 0.970606 -76 TGCCGCCCACCACCCTGTGACCTTTATATG 4 85 1 CACCCTGTGA 0.994418 -100 TTATCCATCACTGCAGGTGAAACC 4 171 1 CTGCAGGTGA 0.99116 -14 ********** Masking position 8 Map Score: 16.272 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 178 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 CCATTACCGGTAATATGATCTGATAGGTTT 3 39 1 TAATATGATC 0.831194 -184 TTTCTTCTCACATGGAGTTCACGGTGACAT 3 66 1 CATGGAGTTC 0.98228 -157 GAACATTTCACATGGAGTTCACAGCGATAT 3 96 1 CATGGAGTTC 0.98228 -127 AGGTTCATCATATGGTGTTCATATCGCTGT 3 116 0 TATGGTGTTC 0.984438 -107 CATATCTAGATAATGAATTCAATTTTCAAC 4 22 0 TAATGAATTC 0.798914 -163 TGAGGACCTATATTAAGATCCTCAATCATA 4 48 0 TATTAAGATC 0.893106 -137 CTTAATTATATAAGGTGATCCCAACAATAG 4 134 1 TAAGGTGATC 0.973897 -51 ********** Masking position 2 Map Score: 6.15564 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 337 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 TTTATTGAACCAGGCAGACTAAAATCG 1 3 0 CAGCGAAAAT 0.939332 -68 TTTAATACTTCCTGCTTAGTTATATCA 1 54 1 CCGCTATAAT 0.984357 -17 TCATTCTTTTTTTGATTTGAAGGGGC 2 2 1 CATCTTTTAT 0.921088 -34 CGGCATATCACATTCTGAGGTTCATCATATGGTGT 3 128 0 CATCGATTAT 0.979405 -95 ATCTTCAGTACATGAGTATATATATCTTTCACCGG 3 160 0 CAGATATAAT 0.894948 -63 TTAAGATCCTCAATCATATCTAGATAATGAATTCA 4 31 0 CATCTATAAT 0.983404 -154 CCGCCCACCACCCTGTGACCTTTATATGGCACAGC 4 87 1 CCTGGATTAT 0.866525 -98 GCCCATCCACCACTCTTAATTATATAAGGTGATCC 4 120 1 CATCTATAAT 0.983404 -65 GGTTTCACCTGCAGTGATGGATAATCATTAAC 4 163 0 CCGCGTTGAT 0.903482 -22 ** ** ** ** ** Masking position 14 Map Score: 4.12751 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 152 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CTGCTGGAGGCCCCTTCAAATCAA 2 22 0 TGGAGGCCCC 0.951801 -14 TCTTCTCACATGGAGTTCACGGTGACATGA 3 68 1 TGGAGTTCAC 0.985688 -155 ATGTGAAATGTTCATGTCACCGTGAACTCC 3 79 0 TTCATGTCAC 0.714664 -144 ACATTTCACATGGAGTTCACAGCGATATGA 3 98 1 TGGAGTTCAC 0.985688 -125 GTTCATCATATGGTGTTCATATCGCTGTGA 3 114 0 TGGTGTTCAT 0.900755 -109 ACATTTAATCTTCAGTACATGAGTATATAT 3 172 0 TTCAGTACAT 0.897914 -51 TCTTTTAACTTGGATTACATTTAATCTTCA 3 188 0 TGGATTACAT 0.911702 -35 TTGTTGAAAATTGAATTCATTATCTAGATA 4 20 1 TTGAATTCAT 0.813624 -165 CTAGATATGATTGAGGATCTTAATATAGGT 4 43 1 TTGAGGATCT 0.689135 -142 GGCAGATCCTTTGAGGACCTATATTAAGAT 4 59 0 TTGAGGACCT 0.962067 -126 ********** Masking position 1 Map Score: 7.80028 Number of sites scoring better than the average of aligned sites = 1194 Number in coding regions = 1131 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 GATCATATTACCGGTAATGGGAACAGGTGA 3 29 0 CCGGTAATGG 0.974576 -194 ATGTGATATGCCGGTGAAAGATATATATAC 3 150 1 CCGGTGAAAG 0.93616 -73 TAAAGGTCACAGGGTGGTGGGCGGCAGATC 4 81 0 AGGGTGGTGG 0.991778 -104 TATATAATTAAGAGTGGTGGATGGGCTGTG 4 116 0 AGAGTGGTGG 0.981658 -69 GGTTTCACCTGCAGTGATGGATAATCATTA 4 165 0 GCAGTGATGG 0.983644 -20 ********** Masking position 5 Map Score: 1.28774 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 406 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 ********** No masking Map Score: 4.00336e-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: 4.00336e-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: 4.00336e-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