AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i289_moxr_protein_synecho_reg_300.orf -o289_synecho_300.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 RCY23271 201 Synechocystis #2 RCY11277 49 Synechocystis #3 RCY18066 196 Synechocystis Motif number 1 TTTCTCGGACTAGGTTAAAGACCAAGTTT 1 10 0 TAGGTTAAAG 0.781002 -192 TTAACCTAGTCCGAGAAAATCTTTGGAAAA 1 22 1 CCGAGAAAAT 0.894956 -180 CGAGAAAATCTTTGGAAAAGCGTCGTACCA 1 33 1 TTTGGAAAAG 0.938998 -169 AGCGTCGTACCATTGAAAAATCTATCGGAA 1 51 1 CATTGAAAAA 0.686174 -151 TCAAGAAGTTTTGTGAAAATTCTCCTTTGC 1 88 0 TTGTGAAAAT 0.847804 -114 ACTGACTGCCCAGGGAAAAATTCACTTTCA 1 125 0 CAGGGAAAAA 0.974767 -77 GGGTGTGATAGAGAGAAAAGGCGGTTGAGT 1 158 1 GAGAGAAAAG 0.944227 -44 ATTGAGTAAAGAAAGTTTTAC 3 2 1 TTGAGTAAAG 0.923313 -195 CAGAAACTTTGTGGGTAAAACTTTCTTTAC 3 16 0 GTGGGTAAAA 0.906219 -181 CCACAAAGTTTCTGGTAAATTGATTGCCAA 3 32 1 TCTGGTAAAT 0.746769 -165 GGATAAAAAGCAGGGAAAAGCTTTTGGCAA 3 55 0 CAGGGAAAAG 0.989983 -142 ********** Masking position 7 Map Score: 7.34723 Number of sites scoring better than the average of aligned sites = 4604 Number in coding regions = 3912 Number in noncoding regions = 692 Number of orfs with sites within 600 bp upstream = 662 Fraction of orfs with sites within 600 bp upstream = 0.106328 Motif number 2 TGGTCTTTAACCTAGTCCGAGAAAATCTTT 1 16 1 CCTAGTCCGA 0.985371 -186 TCTATCACACCCTAGACTGACTGCCCAGGG 1 140 0 CCTAGACTGA 0.990846 -62 CCCATGATATACTCAACCGCCTTTTCTCTC 1 168 0 ACTCAACCGC 0.945632 -34 CTGGTCGAGAACTAGACTGTCCCCAATCAT 2 24 1 ACTAGACTGT 0.935379 -26 TTTTACTGTACCTCACCCGATGTGCCCAAG 3 125 0 CCTCACCCGA 0.980941 -72 TCCAAATCCCCCTAGCCTGCGGCGCTATGC 3 170 1 CCTAGCCTGC 0.99213 -27 ********** Masking position 3 Map Score: 5.76789 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 286 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 ACTAGGTTAAAGACCAAGTTT 1 2 0 AGACCAAGTT 0.913388 -200 TCTTTAACCTAGTCCGAGAAAATCTTTGGA 1 19 1 AGTCCGAGAA 0.84471 -183 CAAAACTTCTTGACCGGGGTTGAAAGTGAA 1 105 1 TGACCGGGGT 0.985208 -97 CTAGACTGACTGCCCAGGGAAAAATTCACT 1 129 0 TGCCCAGGGA 0.979838 -73 CTGGGCAGTCAGTCTAGGGTGTGATAGAGA 1 142 1 AGTCTAGGGT 0.917476 -60 ACGTCTTATATGCCCATGATATACTCAACC 1 180 0 TGCCCATGAT 0.95552 -22 TCACCCGATGTGCCCAAGGTGACTGTGTAT 3 113 0 TGCCCAAGGT 0.993613 -84 ********** Masking position 4 Map Score: 5.01656 Number of sites scoring better than the average of aligned sites = 2173 Number in coding regions = 2023 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 ACGACGCTTTTCCAAAGATTTTCTCGGACT 1 29 0 TCCAAAGATT 0.863961 -173 TTTTCAATGGTACGACGCTTTTCCAAAGAT 1 40 0 TACGACGCTT 0.964587 -162 CAACCCCGGTCAAGAAGTTTTGTGAAAATT 1 97 0 CAAGAAGTTT 0.968189 -105 CATGGGCATATAAGACGTTT 1 192 1 TAAGACGTTT 0.941338 -10 AAGTTTTACCCACAAAGTTTCTGGTAAATT 3 23 1 CACAAAGTTT 0.968189 -174 AAATTGATTGCCAAAAGCTTTTCCCTGCTT 3 48 1 CCAAAAGCTT 0.945423 -149 ********** Masking position 5 Map Score: 2.09078 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 289 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CTTCTTGACCGGGGTTGAAAGTGAATTTTTCCC 1 110 1 GGGTGAAAGG 0.990812 -92 AGTCAGTCTAGGGTGTGATAGAGAGAAAAGGCG 1 148 1 GGGTGATAGG 0.997189 -54 GTTGGAATGATTGGGGACAGTCTAG 2 35 0 TGGTGATTGG 0.984205 -15 ACAGTCACCTTGGGCACATCGGGTGAGGTACAG 3 117 1 TGGACATCGG 0.961698 -80 AGGGGAAGCATAGCGCCGCAGGCTA 3 182 0 GGGGCATAGG 0.993029 -15 *** ****** * Masking position 8 Map Score: 1.45815 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 149 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GGAAAAGCGTCGTACCATTGAAAAATCTAT 1 46 1 CGTACCATTG 0.949525 -156 AATCTATCGGAATTCCTTTGCAAAGGAGAA 1 69 1 AATTCCTTTG 0.91744 -133 TTTGTGAAAATTCTCCTTTGCAAAGGAATT 1 79 0 TTCTCCTTTG 0.961595 -123 AATATCTGCTCCACTGGTCGAGAACT 2 7 1 TGCTCCACTG 0.963533 -43 ATCCCATTGGTTCACCATTGATGGATAAAA 3 77 0 TTCACCATTG 0.970241 -120 TGTATTTGCGAATCCCATTGGTTCACCATT 3 88 0 AATCCCATTG 0.924025 -109 ********** Masking position 9 Map Score: 0.671909 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 893 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 GAAAAATCTATCGGAATTCCTTTGCAAAGG 1 65 1 TCGGAATTCC 0.984097 -137 ACTGTGTATTTGCGAATCCCATTGGTTCAC 3 92 0 TGCGAATCCC 0.994098 -105 TAATTTGTTATCCAAATCCCCCTAGCCTGC 3 160 1 TCCAAATCCC 0.991288 -37 ********** Masking position 5 Map Score: 0.0372895 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ********** 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 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