AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_synecho_ctra_300.orf -o122_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY08201 100 Synechocystis #2 RCY53401 171 Synechocystis #3 RCY46834 124 Synechocystis #4 RCY13164 111 Synechocystis #5 RCY00205 96 Synechocystis #6 RCY15170 266 Synechocystis #7 RCY43438 300 Synechocystis #8 RCY15995 213 Synechocystis Motif number 1 GTCCCCTGGGCTGACTCTGCCTGGCTTTGCT 1 73 1 CTGACTCGCC 0.979049 -28 TAAAACTTTGCCGACAGGCCCTCGCGTTATC 2 78 1 CCGACAGCCC 0.945749 -94 TGCAGAAAGTCCGGCTCCCCCAGCTTAATTT 2 122 1 CCGGCTCCCC 0.985761 -50 GTTTCTGTGGCCGACTATGCCTTCTTCGTTT 3 48 1 CCGACTAGCC 0.946444 -77 CCTGAGTTGCCCCATACTGCCCCAGGCTAAA 4 54 0 CCCATACGCC 0.946767 -58 AGCGAAAATGCTGACTTTGCCATTTTACCGA 6 53 1 CTGACTTGCC 0.889849 -214 TGCCATTTTACCGATTCTCTCGGATTTTCGG 6 70 1 CCGATTCCTC 0.916722 -197 CTGCAATTTACTCGCTCTCCCCTAGGGTACT 6 102 1 CTCGCTCCCC 0.959589 -165 GCCGGATAACCCCATTTACCCTTTCCCAAAG 6 137 0 CCCATTTCCC 0.955905 -130 CAGCATCTAACCCACTCCCTAGTTTTGAACG 7 119 1 CCCACTCCTA 0.809777 -182 GGAATCTTTGCCCAATCAGCCTGCACAGTGG 7 149 1 CCCAATCGCC 0.958987 -152 ACGACATTACCCCACTGTGCAGGCTGATTGG 7 160 0 CCCACTGGCA 0.91518 -141 GTGAATTGATCCCATTCACCCCCCATCTAGC 7 192 0 CCCATTCCCC 0.992089 -109 TTATGGAAATCTCATTGCCCCCATTGTTCCA 8 69 0 CTCATTGCCC 0.926805 -145 ******* *** Masking position 1 Map Score: 20.519 Number of sites scoring better than the average of aligned sites = 1738 Number in coding regions = 1535 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 2 CCAGGCAGAGTCAGCCCAGGGGACAAAAACTTCC 1 63 0 TCACCGGGAC 0.959195 -38 AGATTTAAGCAAAGCCAGGCAGAGTCAG 1 83 0 TTAGCAGCAG 0.891689 -18 AACAACAAAATTAAGCTGGGGGAGCCGGACTTTC 2 126 0 TTAGCGGGAG 0.987781 -46 ACGATAATCCTCAGCCCTGGGGGGAAACTGTCC 3 102 1 TCACCGGGGG 0.974303 -23 AAATACCCTCTCATCCTGAGGCAGTGTACTTTTT 4 23 0 TCACCAGGAG 0.989103 -89 GAGAGGGTATTTAGCCTGGGGCAGTATGGGGCAA 4 45 1 TTACCGGGAG 0.985625 -67 CAAAGCCAGAGTACCCTAGGGGAGAGCGAGTAAA 6 108 0 GTACCGGGAG 0.798406 -159 CCATTTACCCTTTCCCAAAGCCAGAGTACCCTAG 6 123 0 TTTCCAGCAG 0.931474 -144 TCGCCATTGGCTAGCCATGGGAAGCTAAAATACA 6 169 0 CTACCGGGAG 0.530158 -98 TGAATGCCCCTTTACCTAAGGCAGCGGAGGATGT 8 32 1 TTTCCAGGAG 0.98296 -182 ATTTTGCTCCTTTTCCATCGGAAGACACGGCAAC 8 108 1 TTTCCCGGAG 0.962803 -106 *** ** *** ** Masking position 6 Map Score: 16.3827 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 442 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 AGCTTGTTTTGAAAGCCCTTTAA 2 4 1 TTGTTTTGAA 0.904228 -168 CCCAGCTTAATTTTGTTGTTATTGGGAATT 2 140 1 TTTTGTTGTT 0.813745 -32 TCGTTTTTGGCTGTTTTGATCACGATAATC 3 81 1 CTGTTTTGAT 0.863181 -44 GATATGAAATTCTTGTTGATATC 4 99 1 TCTTGTTGAT 0.887215 -13 ACTTAACAAGCTTTGTTGAAGGTCTTGT 5 79 1 CTTTGTTGAA 0.871468 -18 AGGTGTTTTTTGTTGAAGTTTGTAGGT 6 8 1 TTTTGTTGAA 0.95137 -259 TCGTGGTGGATATTTTTGATCCAAAC 7 7 0 TATTTTTGAT 0.88986 -294 AAAGTAAAATTTTCGTTGATTTTGTACAAA 7 60 0 TTTCGTTGAT 0.866227 -241 ACCCACTCCCTAGTTTTGAACGGAATCTTT 7 128 1 TAGTTTTGAA 0.700833 -173 ATTCAACCTATTTTTCTGATAAAACA 8 7 0 TTTTTCTGAT 0.848253 -207 ACATATCAAGTTTTTTTGATGTAAGATTAT 8 167 1 TTTTTTTGAT 0.970205 -47 TTCCATCAAGTTTTTTTGATGAGTTGTC 8 196 1 TTTTTTTGAT 0.970205 -18 ********** Masking position 7 Map Score: 12.1039 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 367 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 CACGGTGAGAGGAGCAAAAAACGATAATAC 1 26 0 GGAGCAAAAA 0.836791 -75 GTCAGCCCAGGGGACAAAAACTTCCTGAAG 1 58 0 GGGACAAAAA 0.928391 -43 AGTTTTGGCCGGGAAACTAAAACTTTGCCG 2 61 1 GGGAAACTAA 0.691422 -111 AGAAAAGGGGAAAATTCCCAATAACA 2 156 0 GGGGAAAATT 0.839384 -16 CAGCCCTGGGGGGAAACTGTCC 3 113 1 GGGAAACTGT 0.778722 -12 TATTTAGCCTGGGGCAGTATGGGGCAACTC 4 52 1 GGGGCAGTAT 0.92763 -60 GGAACAAATTTTAGCCCTTT 5 1 1 GGAACAAATT 0.436651 -96 TCCCGTACCAGGGAAAATAACCTGTATGAT 5 35 1 GGGAAAATAA 0.876426 -62 CTCTGGCTTTGGGAAAGGGTAAATGGGGTT 6 131 1 GGGAAAGGGT 0.63238 -136 TTACTTTTTGGGGGCAAGAATTTGGCTACA 7 83 1 GGGGCAAGAA 0.945786 -218 GTTAGATGCTGGGGAAATGTAGCCAAATTC 7 100 0 GGGGAAATGT 0.963596 -201 GCAGGCTGATTGGGCAAAGATTCCGTTCAA 7 143 0 TGGGCAAAGA 0.706603 -158 CCTGCACAGTGGGGTAATGTCGTAGCTAGA 7 168 1 GGGGTAATGT 0.846042 -133 TGGAACAATGGGGGCAATGAGATTTCCATA 8 69 1 GGGGCAATGA 0.980123 -145 CGATGGAAAAGGAGCAAAATAGAGTACTTT 8 98 0 GGAGCAAAAT 0.853555 -116 ********** Masking position 6 Map Score: 10.4144 Number of sites scoring better than the average of aligned sites = 5110 Number in coding regions = 4478 Number in noncoding regions = 632 Number of orfs with sites within 600 bp upstream = 587 Fraction of orfs with sites within 600 bp upstream = 0.094282 Motif number 5 AAGCAAAGCCAGGCAGAGTCAGCCCAGGGG 1 75 0 AGGCAGAGTC 0.991992 -26 AAAACGAAGAAGGCATAGTCGGCCACAGAA 3 50 0 AGGCATAGTC 0.959575 -75 TCTCATCCTGAGGCAGTGTACTTTTTCCTG 4 19 0 AGGCAGTGTA 0.954678 -93 ATCGGTAAAATGGCAAAGTCAGCATTTTCG 6 55 0 TGGCAAAGTC 0.91488 -212 CCTTTCCCAAAGCCAGAGTACCCTAGGGGA 6 119 0 AGCCAGAGTA 0.967492 -148 TCCCATGGCTAGCCAATGGCGATCGTAAAG 6 181 1 AGCCAATGGC 0.900806 -86 GGGGAAATGTAGCCAAATTCTTGCCCCCAA 7 90 0 AGCCAAATTC 0.804558 -211 CCTTTACCTAAGGCAGCGGAGGATGTGAAT 8 40 1 AGGCAGCGGA 0.909302 -174 ********** Masking position 5 Map Score: 5.55913 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 368 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 TTTTAGTTTCCCGGCCAAAACTTGGCACTA 2 53 0 CCGGCCAAAA 0.879157 -119 GTGATCAAAACAGCCAAAAACGAGAAAACG 3 74 0 CAGCCAAAAA 0.968639 -51 GGAAGCAGCAGGAAAAAGTACACTG 4 6 1 CAGCAGGAAA 0.929052 -106 CTACAAACTTCAACAAAAAACACCT 6 6 0 CAACAAAAAA 0.882949 -261 GTTGGGTTTACAAGCGAAAATGCTGACTTT 6 41 1 CAAGCGAAAA 0.775624 -226 GAGTAAATTGCAGGCCGAAAATCCGAGAGA 6 85 0 CAGGCCGAAA 0.879157 -182 CAAAAATATCCACCACGAAAGGTAGCACTG 7 19 1 CACCACGAAA 0.846756 -282 CAAATTCTTGCCCCCAAAAAGTAAAATTTT 7 77 0 CCCCCAAAAA 0.91469 -224 TTGCGGATAACCACCGAAAAGCTCTGGATG 7 232 0 CCACCGAAAA 0.891217 -69 CGGTGGTTATCCGCAAGAAAATCGCATAAA 7 246 1 CCGCAAGAAA 0.928877 -55 AATAATCTTACATCAAAAAAACTTGATATG 8 168 0 CATCAAAAAA 0.840367 -46 GACAACTCATCAAAAAAACTTGATGGA 8 197 0 CATCAAAAAA 0.840367 -17 ********** Masking position 8 Map Score: 9.99164 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 1068 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 7 CGAGAGAATCGGTAAAATGGCAAAGTCAGC 6 62 0 GGTAAAATGG 0.761831 -205 AGGGGAGAGCGAGTAAATTGCAGGCCGAAA 6 95 0 GAGTAAATTG 0.693804 -172 CTTTGGGAAAGGGTAAATGGGGTTATCCGG 6 137 1 GGGTAAATGG 0.988853 -130 CCACTGTGCAGGCTGATTGGGCAAAGATTC 7 150 0 GGCTGATTGG 0.84082 -151 GCTAGATGGGGGGTGAATGGGATCAATTCA 7 192 1 GGGTGAATGG 0.994295 -109 ATGTATTATGGTGTGAATTGATCCCATTCA 7 205 0 GTGTGAATTG 0.887007 -96 CAGAAAAATAGGTTGAATGCCCCTTTACCT 8 19 1 GGTTGAATGC 0.852778 -195 CCGCTGCCTTAGGTAAAGGGGCATTCAACC 8 29 0 AGGTAAAGGG 0.803207 -185 GCAGCGGAGGATGTGAATGGAACAATGGGG 8 52 1 ATGTGAATGG 0.887007 -162 ********** Masking position 6 Map Score: 3.51953 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 849 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 8 TCGGCCACAGAAACCCACCGCCATCTTCGTT 3 31 0 AACCCACCGC 0.988617 -94 TTGATCACGATAATCCTCAGCCCTGGGGGGA 3 96 1 TATCCTCAGC 0.895986 -29 TGGATCAAAAATATCCACCACGAAAGGTAGC 7 14 1 AATCCACCAC 0.96756 -287 ACACCATAATACATCCAGAGCTTTTCGGTGG 7 221 1 AATCCAGAGC 0.937255 -80 TTTCTTGCGGATAACCACCGAAAAGCTCTGG 7 235 0 AAACCACCGA 0.900652 -66 TGTTCCATTCACATCCTCCGCTGCCTTAGGT 8 45 0 AATCCTCCGC 0.990415 -169 * ********* Masking position 3 Map Score: 0.801766 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 571 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 ATCGCAGTTTGGTATTATCGTTTTTTGCTCCT 1 15 1 GGTATTCGTT 0.801311 -86 TTTGCCGACAGGCCCTCGCGTTATCATCGGCA 2 84 1 GGCCCTCGTT 0.979878 -88 GAAACCCACCGCCATCTTCGTTAATCTTCGTG 3 21 0 GCCATCCGTT 0.98741 -104 GGCCGACTATGCCTTCTTCGTTTTCTCGTTTT 3 56 1 GCCTTCCGTT 0.978011 -69 ACAAATTTTAGCCCTTTCCGTTCCCGTACCAG 5 14 1 GCCCTTCGTT 0.99118 -83 AAATCTCATTGCCCCCATTGTTCCATTCACAT 8 62 0 GCCCCCTGTT 0.957741 -152 ****** **** Masking position 11 Map Score: 0.295522 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 275 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ********** No masking Map Score: 3.7902e-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 11 ********** No masking Map Score: 3.7902e-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 12 ********** No masking Map Score: 3.7902e-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