AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_mixed22_synecho_reg_100.orf -o308_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 RCY18056 198 Synechocystis #2 RCY08755 34 Synechocystis #3 RCY51306 167 Synechocystis #4 RCY51398 55 Synechocystis #5 RCY29713 300 Synechocystis Motif number 1 CTAAGGCGATCGCCTTACCCCAGACTAACT 1 22 1 CGCCTTACCC 0.994051 -177 TACCATCTACGGCCAAACCCAACGGCTTAA 3 81 1 GGCCAAACCC 0.960663 -87 TCAAACTTTGAGCATTACCC 4 46 1 AGCATTACCC 0.989858 -10 AAAAATGGAAAGTCATACCCGCCAGCAAAA 5 30 0 AGTCATACCC 0.980502 -271 AGACTTACCCCGCAATACCCTGTCTGAATG 5 158 0 CGCAATACCC 0.990592 -143 CGATGTTTGGAGACTTACCCCGCAATACCC 5 168 0 AGACTTACCC 0.985532 -133 CTACTCCATAAAAAATACCCAGGCGAAGCT 5 210 1 AAAAATACCC 0.847816 -91 ********** Masking position 7 Map Score: 10.004 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 289 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 TCTGGGGTAAGGCGATCGCCTTAGGTCAAAG 1 15 0 GGCGATCGCT 0.99844 -184 AATGCAAAATGGGGATCTTCTTCGATCATAC 1 159 0 GGGGATCTCT 0.98776 -40 TGTTGATAGAGGCGCTTTAGTTGCTTAATTT 3 119 0 GGCGCTTTGT 0.943945 -49 GCGTCTCCCCGGCGATCGCCTGCTAACG 3 150 1 GGCGATCGCT 0.99844 -18 AGGCGAAGCTGGCGATCGAGTGTAAAAGACT 5 230 1 GGCGATCGGT 0.99773 -71 ******** ** Masking position 6 Map Score: 7.17647 Number of sites scoring better than the average of aligned sites = 1539 Number in coding regions = 1394 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 AATTGGTAGATTATGGAGGCAAAAAACAGAA 3 32 0 TTATGGGGCA 0.963863 -136 GAGACGCTGTTGATAGAGGCGCTTTAGTTGC 3 126 0 TGATAGGGCG 0.959314 -42 CGTTAGCAGGCGATCGCCGGGG 3 156 0 GTTAGCGGCG 0.954267 -12 GCTCAAAGTTTGAAGGGGACAGAGAAACAGA 4 28 0 TGAAGGGACA 0.860861 -28 ATTGTAATTTTTTTGCTGGCGGGTATGACTT 5 20 1 TTTTGCGGCG 0.95064 -281 GTAGATCATTGCAAAGGGGCGTTGTAGGATG 5 75 1 GCAAAGGGCG 0.854171 -226 GGCAGGTGACGGTTGCTGACATTCCATCCTA 5 99 0 GGTTGCGACA 0.866724 -202 GGTAAAGTACCTATGGCGGCAGGTGACGGTT 5 116 0 CTATGGGGCA 0.956732 -185 AATACCCAGGCGAAGCTGGCGATCGAGTGTA 5 223 1 CGAAGCGGCG 0.979288 -78 GCAATAGGGGGGATACCGGCAAGATTTTCAG 5 278 1 GGATACGGCA 0.959102 -23 ****** **** Masking position 10 Map Score: 6.83147 Number of sites scoring better than the average of aligned sites = 2588 Number in coding regions = 2440 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 TCGCCTTAGGTCAAAGGCAA 1 1 0 TCAAAGGCAA 0.83806 -198 GATTTTTGCGTCAATGCCAGTCTTTTCCTG 1 78 1 TCAATGCCAG 0.940292 -121 GAATTGTTAGAAAACGCAAAATTGTCAGGA 1 103 0 AAAACGCAAA 0.908409 -96 AGTTCCTAATACAATGCAAAATGGGGATCT 1 172 0 ACAATGCAAA 0.974165 -27 TTGGCATTTAAAAATGGAAAGTCATACCCG 5 39 0 AAAATGGAAA 0.83909 -262 TTTCCATTTTTAAATGCCAAGTTTGAGTAG 5 49 1 TAAATGCCAA 0.958637 -252 TTTGAGTAGATCATTGCAAAGGGGCGTTGT 5 70 1 TCATTGCAAA 0.915543 -231 AAGACTCAACTCAACGCAGACCTGCAATAG 5 255 1 TCAACGCAGA 0.915308 -46 ********** Masking position 3 Map Score: 3.72619 Number of sites scoring better than the average of aligned sites = 1143 Number in coding regions = 1029 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 AGACTAACTGGCCAGGTGTTGTCAATCAGA 1 43 1 GCCAGGTGTT 0.924152 -156 TTGCGTCAATGCCAGTCTTTTCCTGACAAT 1 83 1 GCCAGTCTTT 0.978666 -116 GTCTTTTCCTGACAATTTTGCGTTTTCTAA 1 97 1 GACAATTTTG 0.917993 -102 TTTCGGTTAAGCCAATCTTTTGAGATTGTT 2 12 1 GCCAATCTTT 0.966578 -23 AGATGGTATCGATAGGCTTTAGTCCTAATT 3 59 0 GATAGGCTTT 0.856121 -109 TGCTTAATTTGACTGGTTTTAAGCCGTTGG 3 99 0 GACTGGTTTT 0.838264 -69 ATTTTTAAATGCCAAGTTTGAGTAGATCAT 5 54 1 GCCAAGTTTG 0.965925 -247 GACTGAAAATCTTGCCGGTATCCC 5 287 0 GAAAATCTTG 0.698573 -14 ********** Masking position 9 Map Score: 3.43163 Number of sites scoring better than the average of aligned sites = 1130 Number in coding regions = 987 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 TTGCCTTTGACCTAAGGCGATCGCCTTAC 1 10 1 ACCTAAGGCG 0.984828 -189 TATCGATACCATCTACGGCCAAACCCAACG 3 75 1 ATCTACGGCC 0.965607 -93 TACGGCCAAACCCAACGGCTTAAAACCAGT 3 88 1 CCCAACGGCT 0.914804 -80 CAAATTAAGCAACTAAAGCGCCTCTATCAA 3 118 1 AACTAAAGCG 0.817033 -50 AAGCGCCTCTATCAACAGCGTCTCCCCGGC 3 133 1 ATCAACAGCG 0.947092 -35 TCAACAGCGTCTCCCCGGCGATCGCCTGCT 3 144 1 CTCCCCGGCG 0.919311 -24 GAGGTAAAGTACCTATGGCGGCAGGTGACG 5 119 0 ACCTATGGCG 0.972891 -182 ********** Masking position 3 Map Score: 1.83015 Number of sites scoring better than the average of aligned sites = 1320 Number in coding regions = 1206 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 CTTTTCCTGACAATTTTGCGTTTTCTAACA 1 99 1 CAATTTTGCG 0.93412 -100 AAGAAGATCCCCATTTTGCATTGTATTAGG 1 168 1 CCATTTTGCA 0.989695 -31 TCCTACAACGCCCCTTTGCAATGATCTACT 5 74 0 CCCCTTTGCA 0.988653 -227 CCGGTATCCCCCCTATTGCAGGTCTGCGTT 5 267 0 CCCTATTGCA 0.983248 -34 ********** Masking position 6 Map Score: 1.31574 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 108 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AAACCCAACGGCTTAAAACCAGTCAAATTA 3 95 1 GCTTAAAACC 0.905641 -73 AATTCAGCAAATTAAAATCTGTTTCTCTG 4 10 1 AATTAAAATC 0.913638 -46 CCAGCAAAAAAATTACAATCGTTTATTT 5 9 0 AATTACAATC 0.942888 -292 GGTGACGGTTGCTGACATTCCATCCTACAA 5 96 0 GCTGACATTC 0.948454 -205 TACCTCGGGGACTTACATTCAGACAGGGTA 5 143 1 ACTTACATTC 0.963992 -158 GACTGAAAATCTTGCCGGTAT 5 290 0 ACTGAAAATC 0.963418 -11 ********** Masking position 5 Map Score: 2.39097 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 97 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 ********** No masking Map Score: -1.43997e-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 10 ********** No masking Map Score: -1.43997e-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 11 ********** No masking Map Score: -1.43997e-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