AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i234_sensory_cassete_synecho_reg_100.orf -o234_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY53594 127 Synechocystis #2 RCY01388 237 Synechocystis #3 RCY37634 300 Synechocystis Motif number 1 TCTGCCCCATCCCCATTGATACCA 1 5 1 CCCCATCCCC 0.968596 -123 CGTGGCAAAAAGCCATTTCCCTAAGCATAT 1 60 0 AGCCATTTCC 0.808506 -68 CTGAGGAAGAAGCCATGGCAACAGCCAATG 2 65 0 AGCCATGGCA 0.657535 -173 TTGAGACCTTCCCCTTGGCTTAACCCAGGT 2 138 1 CCCCTTGGCT 0.962087 -100 CATCCTAAGGCCCCATTGCGGCTTTCAACC 2 165 0 CCCCATTGCG 0.884181 -73 GAACACGGTGACTCATGGCAAACTAGGCGA 2 213 0 ACTCATGGCA 0.756943 -25 CCCCGCTGGAACCTATTGCCTAGCATTGCA 3 63 0 ACCTATTGCC 0.904046 -238 ACCAAAAACTCGCCTTGGCCCCGCTGGAAC 3 81 0 CGCCTTGGCC 0.958654 -220 CTTTAAATCTCCCAATGCCCCGACCCGGGT 3 139 1 CCCAATGCCC 0.952833 -162 AAAACAATCACCCCATTCTATTACGGCTTT 3 178 1 CCCCATTCTA 0.855932 -123 CCCCCTGGCCCCCATTTGTCTGTAGCACAC 3 212 0 CCCATTTGTC 0.732059 -89 ATGGCTTACTCCCCCTGGCCCCCATTTGTC 3 222 0 CCCCCTGGCC 0.989264 -79 AGGGGGAGTAAGCCATTGCTTTTCCTGAAT 3 236 1 AGCCATTGCT 0.56675 -65 CTGAATGATCCCCCATTGTGGGCACTCCTT 3 260 1 CCCCATTGTG 0.947573 -41 ********** Masking position 6 Map Score: 17.4766 Number of sites scoring better than the average of aligned sites = 7491 Number in coding regions = 6794 Number in noncoding regions = 697 Number of orfs with sites within 600 bp upstream = 642 Fraction of orfs with sites within 600 bp upstream = 0.103116 Motif number 2 TGTAATTACCTGGGTGATATTTTC 2 3 0 TGGGGATTTT 0.994702 -235 TTCTTCCTCAGGGGAAATTTTTTCTGGGCCAT 2 84 1 GGGGAATTTT 0.932385 -154 AAATTTTTTCTGGGCCATGTTTTTGAAAGGTT 2 98 1 TGGGCATTTT 0.97304 -140 CTCCATAACCTGGCAGATCCTAGGATCTTTAA 3 113 1 TGGCGATCTA 0.937987 -188 GTCGGGGCATTGGGAGATTTAAAGATCCTAGG 3 131 0 TGGGGATTAA 0.977191 -170 GTAATAGAATGGGGTGATTGTTTTGCTCAATT 3 170 0 GGGGGATGTT 0.97492 -131 GTGCCCACAATGGGGGATCATTCAGGAAAAGC 3 253 0 TGGGGATATT 0.978866 -48 GGATTGAGGTTGGCGGATCTAAGGAGTGCCCA 3 278 0 TGGCGATTAA 0.938109 -23 **** *** *** Masking position 7 Map Score: 7.18617 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 386 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 ATTTCCCTAAGCATATAGCCAAATTGGGGGT 1 45 0 GCATTAGCCA 0.960363 -83 AAGTTTCGTGGCAAAAAGCCATTTCCCTAAG 1 65 0 GCAAAAGCCA 0.991321 -63 AAGAAGCCATGGCAACAGCCAATGAATTTGA 2 58 0 GGCACAGCCA 0.987896 -180 TTTCCCCTGAGGAAGAAGCCATGGCAACAGC 2 70 0 GGAAAAGCCA 0.995445 -168 CCTTCCCCTTGGCTTAACCCAGGTTGAAAGC 2 144 1 GGCTAACCCA 0.966652 -94 GGGGCCAGGGGGAGTAAGCCATTGCTTTTCC 3 230 1 GGAGAAGCCA 0.992255 -71 **** ****** Masking position 7 Map Score: 6.78999 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 255 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 ATTACCTGTAATTACCTGGGTGATATTTTC 2 11 0 ATTACCTGGG 0.991065 -227 CAGGGGAAATTTTTTCTGGGCCATGTTTTT 2 92 1 TTTTTCTGGG 0.902509 -146 ATTGCGGCTTTCAACCTGGGTTAAGCCAAG 2 151 0 TCAACCTGGG 0.980379 -87 TGGTCACTCCATAACCTGGCAGATCCTAGG 3 107 1 ATAACCTGGC 0.956495 -194 TTTTGCTCAATTTACCCGGGTCGGGGCATT 3 152 0 TTTACCCGGG 0.986226 -149 ********** Masking position 6 Map Score: 2.56318 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 618 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 TGATACCAACGATACCAAACCCCCAATTTGGCTATA 1 27 1 GTCAAACCAA 0.925089 -101 ATGGCTTTTTGCCACGAAACTTCACTAATCGTTATA 1 74 1 GCCAAACTCT 0.994442 -54 GATCCACAACCCTCCTTTGATTAACT 1 112 0 GTCCAACCCT 0.975409 -16 CAAGGGGAAGGTCTCAAAACGTTGCAACCTTTCAAA 2 119 0 GCCAAACTCA 0.992776 -119 CAACTCCTGACACCAAAAATTTAAGCGGACTCTC 3 9 1 GCCAAAATAA 0.829423 -292 AATTTAAGCGGACTCTCAACTTACCTATTCAGGTCT 3 28 1 GCCCAACTCT 0.991763 -273 GTTATGGAGTGACCAAAAACTCGCCTTGGCCCCGCT 3 86 0 GCAAAACCCT 0.96555 -215 * * * **** * ** Masking position 8 Map Score: 2.4123 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 262 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ********** No masking Map Score: 1.58694e-12 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: 1.58694e-12 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: 1.58694e-12 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