AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_synecho_reg_300.orf -o020_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 RCY26206 300 Synechocystis #2 RCY07849 300 Synechocystis #3 RCY27056 300 Synechocystis #4 RCY16813 175 Synechocystis #5 RCY36770 293 Synechocystis #6 RCY48012 163 Synechocystis #7 RCY44500 158 Synechocystis #8 RCY37504 210 Synechocystis Motif number 1 AATTTTACGGCAGTTCCCCCCTTCTCAAGG 1 127 1 CAGTTCCCCC 0.897174 -174 TTTAATCCCCCCTAGCCCCCCTTGAGAAGG 1 146 0 CCTAGCCCCC 0.94779 -155 ACCATAAATAGCCTTCGCCTTTGTGCCCTA 2 102 1 GCCTTCGCCT 0.907422 -199 TGCCCTAATCGACATCCACCCTTGTCCCCT 2 125 1 GACATCCACC 0.849209 -176 TTGTTGTGCCCCGATCGCCCTTGCTTGGTT 2 203 1 CCGATCGCCC 0.967956 -98 TAAAAACTAAGTTTTCCCCCAGAAATC 2 284 1 GTTTTCCCCC 0.652047 -17 TTAACTAGCGGACAGCGCCCGGTTGAGGGT 3 51 1 GACAGCGCCC 0.967896 -250 CATTAGGGAAGGCAGGCCCCTAGGGATTGT 4 129 1 GGCAGGCCCC 0.791325 -47 CCAAATCATTCGCTGCCCCCTGGGCATTAA 5 52 1 CGCTGCCCCC 0.952914 -242 AATTCCCAAGGCGATCGCCCCTAAAATCCA 5 118 0 GCGATCGCCC 0.982015 -176 ACATCACTAAGCCTGCCACTAAAATTCCCA 5 140 0 GCCTGCCACT 0.682985 -154 TTTTTTTGTCGAGAACCCCCTAGAATTGTG 5 203 0 GAGAACCCCC 0.757881 -91 CTGTGAGGTAGCCTCCGCCCATATTGCTTT 5 258 1 GCCTCCGCCC 0.934631 -36 AAGTCCATTGCCCATCGACCCACATTTGGC 6 102 1 CCCATCGACC 0.884355 -62 ATTGGTAATCGGTAGCCCCC 7 1 0 GGTAGCCCCC 0.917162 -158 GATATAAAACCCCTTCCCCTTTATCTACTG 7 128 1 CCCTTCCCCT 0.88485 -31 GACCATCTAGGCGATCGCCCAAAGGAAAAT 8 73 0 GCGATCGCCC 0.982015 -138 ********** Masking position 9 Map Score: 19.5433 Number of sites scoring better than the average of aligned sites = 4093 Number in coding regions = 3730 Number in noncoding regions = 363 Number of orfs with sites within 600 bp upstream = 373 Fraction of orfs with sites within 600 bp upstream = 0.0599101 Motif number 2 GCAAACCAAGCAAGGGCGATCGGGGCACAAC 2 205 0 CAAGGCGATC 0.871853 -96 CCGCATCTCTCCTTGTTGGTCCGGTGTAGGC 2 234 0 CCTTGTGGTC 0.941642 -67 TTCCAACCAGCCTTGGCCATGAAGGTTAACT 3 20 1 CCTTGCCATG 0.864964 -281 TTGACTTTCACCTTGCCCATCTGGCTAAGTA 3 164 0 CCTTGCCATC 0.984557 -137 AGGTGAAAGTCAATGGTGATCATTGGTTAAC 3 182 1 CAATGTGATC 0.946104 -119 TGAATCATAACCATGTCCATAATG 3 287 1 CCATGCCATA 0.74663 -14 CAATTAATCACCTAGCTAATCCATAGTTGAA 4 34 1 CCTAGTAATC 0.85614 -142 AAAGAAGCAACAATGACAATCCCTAGGGGCC 4 143 0 CAATGCAATC 0.913859 -33 ACTAAAATTCCCAAGGCGATCGCCCCTAAAA 5 122 0 CCAAGCGATC 0.955696 -172 AGGCAAAGTCCATTGCCCATCGACCCACATT 6 97 1 CATTGCCATC 0.966746 -67 GTGAGTGTTTCATTGGTAATCGGTAGCCCCC 7 11 0 CATTGTAATC 0.899705 -148 TATCCAGATCCATTGTTGATCAGTCAAGAAA 8 24 0 CATTGTGATC 0.964866 -187 TGGGCGATCGCCTAGATGGTCGAAAAGTGCT 8 82 1 CCTAGTGGTC 0.851561 -129 ***** ***** Masking position 10 Map Score: 11.9293 Number of sites scoring better than the average of aligned sites = 2720 Number in coding regions = 2463 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 3 CCCTAAATCTCCTCACTAAAGCTCCGGCTTAA 1 88 1 CTCACTAAGC 0.957296 -213 GCTGTTTAATCCCCCCTAGCCCCCCTTGAGAA 1 148 0 CCCCCTAGCC 0.958014 -153 CCGTGGTCAACAGCACTAGGACCTTGCAGCTT 2 42 0 CGCACTAGAC 0.792902 -259 CAATTAATCACCTAGCTAATCCATAGTTGAAA 4 34 1 CTAGCTAACC 0.881794 -142 AGGGGCCTGCCTTCCCTAATGCTGAATCATTT 4 118 0 CTCCCTAAGC 0.981319 -58 ACTTTTCACCCAGTCCTAGAGCATA 5 4 0 CGTCCTAGGC 0.890744 -290 CATTGAGCAACATCACTAAGCCTGCCACTAAA 5 147 0 CTCACTAACC 0.980593 -147 CTCTTTGCAGTGTACCTAAACCCACCAAGGCC 6 35 1 TTACCTAACC 0.75354 -129 GACCATTTTCCTGCCCTAATCCAGAGCAAAGG 6 68 1 CGCCCTAACC 0.992264 -96 AAAAGTGCTCCTTAACTAACCCCCCGGCAGAA 8 104 1 CTAACTAACC 0.943051 -107 CGGTCTTCCGCAGTCCTAATCCGCTGTATTCC 8 153 1 CGTCCTAACC 0.967039 -58 * ******* ** Masking position 8 Map Score: 10.0246 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 475 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 AACATGGCACGGGCAAATCAAGCTGCAAGGT 2 23 1 GGGCAAACAA 0.981943 -278 AGGGCGATCGGGGCACAACAATCTAGTATTT 2 193 0 GGGCACACAA 0.98331 -108 GGTCCGGTGTAGGCAAACCAAGCAAGGGCGA 2 217 0 AGGCAAACAA 0.938814 -84 TGAGCCCCATAGGTTAACCAATGATCACCAT 3 194 0 AGGTTAACAA 0.665578 -107 TTAACCTATGGGGCTCAATAAAACTTTCCAA 3 208 1 GGGCTCATAA 0.868058 -93 TACACAGGTGGGGCAAAAAAAATTGATCAAT 4 81 1 GGGCAAAAAA 0.91459 -95 GAAATACCCTGGGAAAAGCAATATGGGCGGA 5 271 0 GGGAAAACAA 0.946872 -23 TGATGGAATAAGGCTCTCCAATTCTAGGTTA 6 136 0 AGGCTCTCAA 0.882728 -28 GAATCTAACAGGGATATAAAACCCCTTCCCC 7 116 1 GGGATATAAA 0.613768 -43 TGTATTCCAAGGGATCTACAAGAGATTTAAG 8 177 1 GGGATCTCAA 0.897365 -34 ******* *** Masking position 10 Map Score: 7.27461 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 552 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 TCAATAAAACTTTCCAAAGGTATTCCCGTC 3 222 1 TTTCCAAAGG 0.965306 -79 CAACAATGACAATCCCTAGGGGCCTGCCTT 4 137 0 AATCCCTAGG 0.823627 -39 CCATGGGTTAATGCCCAGGGGGCAGCGAAT 5 59 0 ATGCCCAGGG 0.967729 -235 TTTTCCATACTTTCCATGGGTTAATGCCCA 5 72 0 TTTCCATGGG 0.941712 -222 TGCCACTAAAATTCCCAAGGCGATCGCCCC 5 127 0 ATTCCCAAGG 0.986146 -167 TTGTGCCTATTTTCCCAAGTCTTTGACACC 5 178 0 TTTCCCAAGT 0.888252 -116 CCATATTGCTTTTCCCAGGGTATTTCCT 5 276 1 TTTCCCAGGG 0.991221 -18 AATCCGCTGTATTCCAAGGGATCTACAAGA 8 170 1 ATTCCAAGGG 0.977843 -41 ********** Masking position 5 Map Score: 9.58023 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 665 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 GGGCACAAAGGCGAAGGCTATTTATGGTTT 2 100 0 GCGAAGGCTA 0.984987 -201 GGCAAACCAAGCAAGGGCGATCGGGGCACA 2 207 0 GCAAGGGCGA 0.907565 -94 AAGGAGAGATGCGGCGGCGGTCTAAATTGT 2 251 1 GCGGCGGCGG 0.957429 -50 AACCTTCATGGCCAAGGCTGGTTGGAAGTA 3 17 0 GCCAAGGCTG 0.97271 -284 TTCAGCATTAGGGAAGGCAGGCCCCTAGGG 4 124 1 GGGAAGGCAG 0.895457 -52 CACTAAAATTCCCAAGGCGATCGCCCCTAA 5 124 0 CCCAAGGCGA 0.892567 -170 AGCAATATGGGCGGAGGCTACCTCACAGTT 5 256 0 GCGGAGGCTA 0.969762 -38 CTAATCCAGAGCAAAGGCAAAGTCCATTGC 6 83 1 GCAAAGGCAA 0.925876 -81 TAGATTCTATGCGAAGTCGGTCAGCCCCAT 7 93 0 GCGAAGTCGG 0.944177 -66 ********** Masking position 8 Map Score: 6.06002 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 762 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 GGATGTCGATTAGGGCACAAAGGCGAAGGC 2 112 0 TAGGGCACAA 0.977088 -189 AGATTTTAGTCAGGGGACAAGGGTGGATGT 2 136 0 CAGGGGACAA 0.96821 -165 CAAGGGCGATCGGGGCACAACAATCTAGTA 2 196 0 CGGGGCACAA 0.986132 -105 GATTTCTGGGGGAAAACTTAGTTTTT 2 285 0 TGGGGGAAAA 0.965851 -16 TAACTTTAACTAGCGGACAGCGCCCGGTTG 3 46 1 TAGCGGACAG 0.797726 -255 TAAGTATCTTTGCGGCACAGTGCTCCAGAT 3 140 0 TGCGGCACAG 0.902358 -161 GGTTAACCTATGGGGCTCAATAAAACTTTC 3 206 1 TGGGGCTCAA 0.940416 -95 TATACACAGGTGGGGCAAAAAAAATTGATC 4 79 1 TGGGGCAAAA 0.965849 -97 GCTCTAGGACTGGGTGAAAAGTAGTCATGG 5 14 1 TGGGTGAAAA 0.7119 -280 GGTTAATGCCCAGGGGGCAGCGAATGATTT 5 54 0 CAGGGGGCAG 0.835164 -240 ********** Masking position 9 Map Score: 7.81257 Number of sites scoring better than the average of aligned sites = 1454 Number in coding regions = 1298 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 8 ATTAAAAACTAAGTTTTCCCCCAGAAATC 2 282 1 AAGTTTTCCC 0.82859 -19 GCCCGGTTGAGGGTATTTCGCGGGTAGCCA 3 67 1 GGGTATTTCG 0.930122 -234 AACTTTCCAAAGGTATTCCCGTCTCGTTAG 3 229 1 AGGTATTCCC 0.978976 -72 TTAGAATCAGAGGTAATTCCCGAAATAGTC 3 255 1 AGGTAATTCC 0.945444 -46 GCTTCTTTGAAGGTTTTTCC 4 166 1 AGGTTTTTCC 0.974127 -10 GCTTTTCCCAGGGTATTTCCT 5 283 1 GGGTATTTCC 0.979644 -11 ********** Masking position 4 Map Score: 2.99315 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 268 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TTGTTTTTTCATTTACATTCAC 1 1 1 TGTTTTTTAT 0.746982 -300 AGTTGGGTTTTGGCTGTTTAATCCCCCCTAGC 1 160 0 TGCTGTTTAT 0.897902 -141 GAATCTTAAGTTGTTGATTTATGACAAATTCC 1 218 0 TGTTGATTAT 0.924066 -83 AAGGATTAATTGTTTAATGAAAAATTAT 1 283 0 TATTGTTTAT 0.884139 -18 GGGGGAAAACTTAGTTTTTAATAACAATTTAG 2 272 0 TAGTTTTTAT 0.793568 -29 CCCGAAATAGTCAGTGAATCATAACCATGTCC 3 273 1 TAGTGAATAT 0.714119 -28 ATGGATTAGCTAGGTGATTAATTGATCAACGA 4 26 0 TGGTGATTAT 0.968879 -150 TGAATCATTTTTGGTGATTGATCAATTTTTTT 4 96 0 TGGTGATTAT 0.968879 -80 TTGAGCATTGTGAGTGTTTCATTGGTAATCGG 7 19 0 TAGTGTTTAT 0.951273 -140 * ******* ** Masking position 5 Map Score: 3.84002 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 86 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 AAATAGCCTTCGCCTTTGTGCCCTAATCGA 2 107 1 CGCCTTTGTG 0.899782 -194 CTAAAATCTCCGCTATGGTGGCCAGCCAGT 2 157 1 CGCTATGGTG 0.928914 -144 CGCCGCATCTCTCCTTGTTGGTCCGGTGTA 2 237 0 CTCCTTGTTG 0.941852 -64 CAAGGTGAAAGTCAATGGTGATCATTGGTT 3 180 1 GTCAATGGTG 0.956324 -121 CCTAGGGATTGTCATTGTTGCTTCTTTGAA 4 147 1 GTCATTGTTG 0.887178 -29 AGTGATGTTGCTCAATGGTGTCAAAGACTT 5 162 1 CTCAATGGTG 0.949885 -132 AAAATGGTCCGGCCTTGGTGGGTTTAGGTA 6 47 0 GGCCTTGGTG 0.981905 -117 ********** Masking position 6 Map Score: 3.44968 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 954 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 AAGACTAGGTATTTATCCCCCTAAATCTCC 1 70 1 ATTTATCCCC 0.965257 -231 GTTTTGGCTGTTTAATCCCCCCTAGCCCCC 1 156 0 TTTAATCCCC 0.922054 -145 TCATTAAACAATTAATCCTT 1 291 1 ATTAATCCTT 0.63197 -10 TTCATCGGACATCTATCCCTGGCTACCCGC 3 86 0 ATCTATCCCT 0.924357 -215 AGTGCTCCAGATTTATCTCTAAAGATTTTC 3 122 0 ATTTATCTCT 0.854796 -179 TCGTTGATCAATTAATCACCTAGCTAATCC 4 26 1 ATTAATCACC 0.860174 -150 AAAAAAATTGATCAATCACCAAAAATGATT 4 96 1 ATCAATCACC 0.776962 -80 GGAAGGGGTTTTATATCCCTGTTAGATTCT 7 115 0 TTATATCCCT 0.701504 -44 GGTGGTTTTATCTCTTAAATCTCTT 8 196 0 TTTTATCTCT 0.755385 -15 ********** Masking position 5 Map Score: 2.00765 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 674 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 12 ********** No masking Map Score: 5.79336e-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 13 ********** No masking Map Score: 5.79336e-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 14 ********** No masking Map Score: 5.79336e-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