AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i100_Ion_Transporter_synecho_reg_300.orf -o100_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 RCY32683 300 Synechocystis #2 RCY15084 118 Synechocystis #3 RCY05328 25 Synechocystis #4 RCY34497 112 Synechocystis #5 RCY24958 106 Synechocystis Motif number 1 AAGAGTAATTCCACCGTTGTCGGCAAGGGGT 1 133 1 CCACGTTGTC 0.894685 -168 CCATTCAGGGCCGGGATGGGCCAACGGAGTT 1 218 0 CCGGATGGGC 0.989403 -83 CCCATCCCGGCCCTGAATGGCAGGGTTTTCC 1 229 1 CCCGAATGGC 0.995453 -72 CTTTGGGCTTCTGGCGATGGCATTACTCC 2 9 0 CTGCGATGGC 0.92267 -110 CAAAGATCCCCTATGATTGGCGAAGAAATTT 2 35 1 CTAGATTGGC 0.97274 -84 GTTTACAATGCCCTGATTGGCACGGTTTCGT 2 79 1 CCCGATTGGC 0.99716 -40 AGACCATTAACCGAGTATGGCAAAATGGGGC 4 37 1 CCGGTATGGC 0.981829 -76 AGCCGTTATCCCCGATTGTCCAATGTGGTG 4 93 0 CCCGATTGTC 0.987714 -20 *** ******* Masking position 9 Map Score: 11.4109 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 745 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 AAGGATTTAAGGATTTGCGGCCATAACTCTACTT 1 54 0 GGATTTGCAT 0.96966 -247 ATCTACCTAGGGACTACGGATAATTTCCCCCTCT 1 98 1 GGACTAGTAT 0.818693 -203 TGTCGGCAAGGGGTTTTGCTCTGTGTTGCCGTGG 1 150 1 GGGTTTCCGT 0.982118 -151 ATTAGAATCAGGATTAAACTCCGTTGGCCCATCC 1 202 1 GGATTACCGT 0.950233 -99 CTGAATGGCAGGGTTTTCCCGTGTCATACTTTTC 1 241 1 GGGTTTCGGT 0.965875 -60 GGGGATCTTTGGGCTTCTGGCGATGGCATTACTC 2 12 0 GGGCTTGCAT 0.990112 -107 CTCGGTTAATGGTCTTGGGGGGATGGCAGTGATG 4 18 0 GGTCTTGGAT 0.888682 -95 TGGCAAAATGGGGCTTAATTCGATCGATGTTAAT 4 54 1 GGGCTTTCAT 0.939361 -59 CCACCACATTGGACAATCGGGGATAACGGCT 4 92 1 GGACAAGGAT 0.716262 -21 ACGCTATTAGCGGTTAGCCTCAGTTTAAAGTCAA 5 53 1 CGGTTACCGT 0.829282 -54 ****** * * ** Masking position 14 Map Score: 3.62071 Number of sites scoring better than the average of aligned sites = 1501 Number in coding regions = 1339 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 ACTTTAATCAATACTACTGAT 1 2 1 CTTTAATCAA 0.853446 -299 ATCAATGTTTGTTAAATCGTAAAGTAGAGT 1 33 1 GTTAAATCGT 0.97736 -268 GCCGCAAATCCTTAAATCCTTAGAAAGCTT 1 67 1 CTTAAATCCT 0.967359 -234 GGCCAACGGAGTTTAATCCTGATTCTAATG 1 201 0 GTTTAATCCT 0.940772 -100 CAAAATGGGGCTTAATTCGATCGATGTTAA 4 57 1 CTTAATTCGA 0.958567 -56 TTCGATCGATGTTAATTCGACCACCACATT 4 72 1 GTTAATTCGA 0.958567 -41 ********** Masking position 5 Map Score: 3.34241 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 118 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 ATGTTTGTTAAATCGTAAAGTAGAGTTATG 1 37 1 AATCGTAAAG 0.813094 -264 TCCTGATTCTAATGACAAAGTACAGGCACA 1 185 0 AATGACAAAG 0.974501 -116 CCCGGCCCTGAATGGCAGGGTTTTCCCGTG 1 234 1 AATGGCAGGG 0.928321 -67 GGAGTAATGCCATCGCCAGAAGCCC 2 6 1 AATGCCATCG 0.861814 -113 CCATCGCCAGAAGCCCAAAGATCCCCTATG 2 20 1 AAGCCCAAAG 0.931593 -99 ATCCCCTATGATTGGCGAAGAAATTTTGAG 2 40 1 ATTGGCGAAG 0.868801 -79 AAATTTTGAGAATGCCAAAGTTTACAATGC 2 60 1 AATGCCAAAG 0.991236 -59 AAATCTTCAAGATCCCAAGGAAAGATTTTT 5 17 0 GATCCCAAGG 0.941635 -90 ATTAAATTGAGATGACGAAGATGGAGGTTT 5 85 0 GATGACGAAG 0.901294 -22 ********** Masking position 10 Map Score: 4.09833 Number of sites scoring better than the average of aligned sites = 1926 Number in coding regions = 1759 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 5 GTTGTCGGCAAGGGGTTTTGCTCTGTGTTG 1 148 1 AGGGGTTTTG 0.769827 -153 TCTGTGTTGCCGTGGCTGTGCCTGTACTTT 1 169 1 CGTGGCTGTG 0.932139 -132 CCCTGCCATTCAGGGCCGGGATGGGCCAAC 1 224 0 CAGGGCCGGG 0.909124 -77 CCCGGCCCTGAATGGCAGGGTTTTCCCGTG 1 234 1 AATGGCAGGG 0.933509 -67 CCGTGCCAATCAGGGCATTGTAAACTTTGG 2 74 0 CAGGGCATTG 0.967996 -45 CCCTGATTGGCACGGTTTCGTTCACGGTCT 2 89 1 CACGGTTTCG 0.813907 -30 CGGTTTCGTTCACGGTCTGGTTATCTGC 2 101 1 CACGGTCTGG 0.945351 -18 GTCTTGGGGGGATGGCAGTGATGTCAGAAA 4 11 0 GATGGCAGTG 0.892869 -102 ATACTCGGTTAATGGTCTTGGGGGGATGGC 4 25 0 AATGGTCTTG 0.899015 -88 ********** Masking position 5 Map Score: 4.18992 Number of sites scoring better than the average of aligned sites = 2817 Number in coding regions = 2625 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 6 TAACAAACATTGATAATCAGTAGTATTGAT 1 17 0 TGATAATCAG 0.990749 -284 TACTTTGTCATTAGAATCAGGATTAAACTC 1 193 1 TTAGAATCAG 0.940515 -108 TACTTTTCGGTAATAATCAGAAATTTAGGT 1 267 1 TAATAATCAG 0.964228 -34 AACGAAACCGTGCCAATCAGGGCATTGTAA 2 81 0 TGCCAATCAG 0.965869 -38 GCAGATAACCAGACCGTGAACG 2 107 0 AGATAACCAG 0.936156 -12 ********** Masking position 5 Map Score: 1.63642 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 51 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ********** No masking Map Score: -5.09159e-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: -5.09159e-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: -5.09159e-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