AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_mixed15_synecho_reg_300.orf -o300_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 RCY43669 195 Synechocystis #2 RCY43837 121 Synechocystis #3 RCY26609 38 Synechocystis #4 RCY32578 235 Synechocystis Motif number 1 AATCATAGGAGTTTTGGCAAGGAGATT 1 8 0 GTTTTGGCAA 0.871444 -188 CCTACTGGGCGTTCTAACAGAGATGCTCTA 1 56 1 GTTCTAACAG 0.568858 -140 TAACAGAGATGCTCTACCCATTGTCCTGGG 1 70 1 GCTCTACCCA 0.942979 -126 TTACCATCTGGCTTTGTCAAGAACTGTAAC 1 119 0 GCTTTGTCAA 0.963196 -77 GTTAGTTAAACTTCTGCCAATTGTGCAAGT 2 35 0 CTTCTGCCAA 0.957887 -87 TTCAGTAGTGCCTTTAACAAATTCGCCCGT 2 63 0 CCTTTAACAA 0.895587 -59 CACTACTGAACCTTTGACAGTTCGCTCTTT 2 83 1 CCTTTGACAG 0.864483 -39 TTGACAGTTCGCTCTTTCAATGTTGGCAAA 2 96 1 GCTCTTTCAA 0.861159 -26 AAAACCTTTGCCAACATTGAAAGA 2 108 0 CCTTTGCCAA 0.982999 -14 GTTTCTTCCATCACCCCTAC 3 1 1 GTTTCTTCCA 0.675384 -38 CTTCGCTACCCTTTTCCCCAGCCTTCTCAA 4 72 1 CTTTTCCCCA 0.88523 -164 TTCACCGAATGTTTTGTCCAGACTGTGACT 4 119 1 GTTTTGTCCA 0.947809 -117 CTGTGACTGGGGTTTTCCAACCTAACTTCC 4 141 1 GGTTTTCCAA 0.803296 -95 ACCTAACTTCCCTTCACCCAATGGGTTAAA 4 160 1 CCTTCACCCA 0.888817 -76 ACTTCTCACACTTTAACCCATTGGGTGAAG 4 171 0 CTTTAACCCA 0.674919 -65 AATTATGGAACTTTTTTCAGACTTCTCACA 4 191 0 CTTTTTTCAG 0.755725 -45 ********** Masking position 3 Map Score: 12.6487 Number of sites scoring better than the average of aligned sites = 4446 Number in coding regions = 3949 Number in noncoding regions = 497 Number of orfs with sites within 600 bp upstream = 497 Fraction of orfs with sites within 600 bp upstream = 0.0798265 Motif number 2 TGTTAGAACGCCCAGTAGGTTGGTGTAATCGAG 1 42 0 CCCAGTTTGG 0.976553 -154 AGATGCTCTACCCATTGTCCTGGGGAGCAGAAT 1 76 1 CCCATTCTGG 0.996573 -120 TAAACTTCTGCCAATTGTGCAAGTTCCGCAAGC 2 26 0 CCAATTCAAG 0.939381 -96 CTAGAGCCCATTTTACAGGTAGGGGTGAT 3 20 0 CCCATTCAGG 0.997318 -19 AAGATTTACCCCCAGTTCTCTGCTGTAGTAGCC 4 11 0 CCCAGTCTGC 0.982655 -225 ATCTTCGCTACCCTTTTCCCCAGCCTTCTCAAT 4 70 1 CCCTTTCCAG 0.935686 -166 ATGATGAATCCCCATTGAGAAGGCTGGGGAAAA 4 83 0 CCCATTAAGG 0.983141 -153 ****** **** Masking position 6 Map Score: 6.33598 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 586 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 ATGGGTAGAGCATCTCTGTTAGAACGCCCA 1 61 0 CATCTCTGTT 0.95826 -135 ACTGGGGGTAAATCTTTAGTAATCTTTGTT 4 28 1 AATCTTTAGT 0.941689 -208 AATCTTTAGTAATCTTTGTTAAAAATTATG 4 38 1 AATCTTTGTT 0.954977 -198 AAAATTATGACATCTTCGCTACCCTTTTCC 4 59 1 CATCTTCGCT 0.950731 -177 AATGGGGATTCATCATTGGTTCACCGAATG 4 100 1 CATCATTGGT 0.977272 -136 ATAATTTAGCCATCGTTAGTCCCAATCCAC 4 215 1 CATCGTTAGT 0.95562 -21 ********** Masking position 3 Map Score: 2.13964 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 417 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 TATCTCGATTACACCAACCTACTGGGCGTT 1 39 1 ACACCAACCT 0.972954 -157 AAAACCTTTGCCAACATTGAAAGAGCG 2 105 0 TTGCCAACAT 0.905369 -17 TTCTTCCATCACCCCTACCTGTAAAATGGG 3 13 1 ACCCCTACCT 0.96033 -26 TATGACATCTTCGCTACCCTTTTCCCCAGC 4 64 1 TCGCTACCCT 0.927306 -172 GCTACCCTTTTCCCCAGCCTTCTCAATGGG 4 76 1 TCCCCAGCCT 0.98802 -160 TGACTGGGGTTTTCCAACCTAACTTCCCTT 4 144 1 TTTCCAACCT 0.957772 -92 ********** Masking position 10 Map Score: 1.66293 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 674 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 CTGTAACATTTCACCAAATTCTGCTCCCCA 1 96 0 TCACCAAATT 0.937926 -100 TGACCTACGGTTACCATCTGGCTTTGTCAA 1 129 0 TTACCATCTG 0.919246 -67 CATCATTGGTTCACCGAATGTTTTGTCCAG 4 110 1 TCACCGAATG 0.991868 -126 AAAACCCCAGTCACAGTCTGGACAAAACAT 4 127 0 TCACAGTCTG 0.946259 -109 TAACTTCCCTTCACCCAATGGGTTAAAGTG 4 163 1 TCACCCAATG 0.985136 -73 ********** Masking position 3 Map Score: 1.55944 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 164 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ********** No masking Map Score: 1.24588e-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: 1.24588e-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: 1.24588e-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