AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_synecho_reg_100.orf -o231_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 RCY26220 201 Synechocystis #2 RCY36788 79 Synechocystis #3 RCY02011 299 Synechocystis #4 RCY53113 300 Synechocystis Motif number 1 GGGGAGATGGTGTTGTTACCGTAGTATTCT 2 60 0 GGGTGGTTCC 0.95664 -20 CCCGTTGGCCCAAATTACCCTTGGGGTGT 3 1 1 CCTGGCATCC 0.831477 -299 CCCTTGGGGTGTCAGAGGCATACCGGGCCTCCGCAAACT 3 28 1 GCGGGCCGCC 0.992751 -272 GGACAGGGAGGGCAGGAGGTTAATCTGCCCTGTCAATTT 3 91 0 GCGAGGATCC 0.658085 -209 TGCCCTCCCTGTCCTAGGGCGTTAGTCCCCCAAGGCTCA 3 116 1 GCTGGGTTCC 0.995455 -184 CTTTGTTGCCGACATGGTCTCATCTTACCTAGATTTACT 3 155 0 GCTGTCTTCC 0.960396 -145 CTCCTTGGACGCCGGCTTGATCCCTGTCCGCCTTTTTCT 3 239 1 GCGTTGCGCC 0.944464 -61 ATCCCTGTCCGCCTTTTTCTTAATTTTCCCTACCTTTCC 3 258 1 GCTTTCATCC 0.822178 -42 ATCTTTTCCCGCCGGGGGGTCCCCCAGGCCGGTTTGAGA 4 31 0 GCGGGGCAGC 0.595213 -270 CATAATATAAGCCGGGTGCCATTTTTTCCTAGGGCGAGA 4 70 0 GCGTGCTTCC 0.994003 -231 GCTCGGGGAAGACCTGTGGCGGTCAACCCAATTGATCAT 4 106 0 GCTTGGTACC 0.958442 -195 GGTTCACTTAGACCGAGGGAAATGTTTCCCTTCTAGCCC 4 157 0 GCGGGGTTCC 0.998083 -144 GCAGAAATCGGTCTGTGGGCCCTTCTACCCGTGTTATGC 4 198 0 GCGGGGTTCC 0.989978 -103 CCCACAGACCGATTTCTGCAGTCCTTCCCAGCCCTCCAG 4 218 1 GTTTGCCTCC 0.777381 -83 AAACAATGGGGGCAGTGGGCACTAAGTTCACCCCTGGAG 4 251 0 GCGGGGTGTC 0.936318 -50 * * * *** * * ** Masking position 19 Map Score: 22.0697 Number of sites scoring better than the average of aligned sites = 1910 Number in coding regions = 1797 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 CTCCATTGGGCAACGGCGTTAATGCACTGACT 1 37 0 CAGGCGTTAA 0.941552 -165 CGCCGTTGCCCAATGGAGTGATCTAGTTAGAA 1 51 1 CAGGAGTGAT 0.947469 -151 TAGTTAGAATCAATGCAGTTGGTTAATGGAAC 1 74 1 CAGCAGTTGG 0.777068 -128 CGTTCCTCGGCACTGGCTTGGGTAATTCCGTA 1 148 1 CCGGCTTGGG 0.99134 -54 TTCTCCGCTTCTAGGGATTGGGAGCCAGGGGA 2 11 0 CAGGATTGGG 0.984798 -69 GAGGAGAAATCTCCGGAATAGGTAAATTGACA 3 68 1 CCGGAATAGG 0.671403 -232 CCTCCCTGTCCTAGGGCGTTAGTCCCCCAAGG 3 119 1 CAGGCGTTAG 0.975675 -181 CGTTAGTCCCCCAAGGCTCAAGTAAATCTAGG 3 135 1 CAGGCTCAAG 0.886443 -165 AAGCCGGCGTCCAAGGAGTGGGGAAAAAAAAC 3 225 0 CAGGAGTGGG 0.992722 -75 ACTCCTTGGACGCCGGCTTGATCCCTGTCCGC 3 238 1 CCGGCTTGAT 0.937825 -62 CTGGGGGACCCCCCGGCGGGAAAAGATTCTCG 4 43 1 CCGGCGGGAA 0.908478 -258 CCATTTTTTCCTAGGGCGAGAATCTTTTCCCG 4 59 0 CAGGCGAGAA 0.9014 -242 CCCCGCAACGCAATGGCTCGGGGAAGACCTGT 4 128 0 CAGGCTCGGG 0.984273 -173 * * ******** Masking position 1 Map Score: 13.2128 Number of sites scoring better than the average of aligned sites = 2522 Number in coding regions = 2343 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 TACCATGCCGATCGCCAGTGGTCTATAAATA 1 113 1 ATCGCCAGGG 0.925907 -89 CTAGGGATTGGGAGCCAGGGGA 2 2 0 GGAGCCAGGG 0.94601 -78 CTGGCTCCCAATCCCTAGAAGCGGAGAATAT 2 15 1 ATCCCTAGAG 0.465242 -65 AGGGTAATTTGGGCCAACGGG 3 1 0 GGGCCAACGG 0.9762 -299 GGGGTGTCAGAGGCATACCGGGCCTCCGCAA 3 33 1 AGGCATACGG 0.803497 -267 TAGGACAGGGAGGGCAGGAGGTTAATCTGCC 3 101 0 AGGGCAGGGG 0.860517 -199 CTAGGGCGTTAGTCCCCCAAGGCTCAAGTAA 3 129 1 AGTCCCCCAG 0.620905 -171 ATTAAGAAAAAGGCGGACAGGGATCAAGCCG 3 251 0 AGGCGGACGG 0.803075 -49 CCGGCCTGGGGGACCCCCCGGCGGGAAAAGA 4 38 1 GGACCCCCGG 0.948438 -263 CTAGGAAAAAATGGCACCCGGCTTATATTAT 4 77 1 ATGGCACCGG 0.890323 -224 AATTGGGTTGACCGCCACAGGTCTTCCCCGA 4 112 1 ACCGCCACGG 0.87798 -189 CCGCAACGCAATGGCTCGGGGAAGACCTGTG 4 127 0 ATGGCTCGGG 0.910629 -174 ATTGCGTTGCGGGGCTAGAAGGGAAACATTT 4 146 1 GGGGCTAGAG 0.887869 -155 ACGGGTAGAAGGGCCCACAGACCGATTTCTG 4 205 1 GGGCCCACGA 0.884845 -96 AGTCCTTCCCAGCCCTCCAGGGGTGAACTTA 4 237 1 AGCCCTCCGG 0.961765 -64 GTGAAACAATGGGGGCAGTGGGCACTAAGTT 4 262 0 GGGGGCAGGG 0.949708 -39 ******** ** Masking position 11 Map Score: 9.25185 Number of sites scoring better than the average of aligned sites = 7017 Number in coding regions = 6467 Number in noncoding regions = 550 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 4 TGGAAATATTCTGGAAATGCTACGGAATTAC 1 169 0 CTGGAAATGT 0.98218 -33 TGGTAATTTTCTGGAAATATTCTGGAAATGC 1 180 0 CTGGAAATAT 0.877288 -22 GGAGAAATCTCCGGAATAGGTAAATTGACAG 3 70 1 CCGGAATAGT 0.926053 -230 AAGCAAAGTAAAGGAAAAGTTTTTTTTCCCC 3 207 1 AAGGAAAAGT 0.917374 -93 GGGTTAGGTACGGGGAAAGGTAGGGAAAATT 3 279 0 CGGGGAAAGT 0.980298 -21 GACCCCCCGGCGGGAAAAGATTCTCGCCCTA 4 49 1 CGGGAAAAGT 0.993854 -252 ACTTAGACCGAGGGAAATGTTTCCCTTCTAG 4 160 0 AGGGAAATGT 0.971328 -141 ********* * Masking position 6 Map Score: 5.83644 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 373 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 CCTAGAAGCGGAGAATATGGCACAATCTAGG 2 28 1 GAGATATGGC 0.985777 -52 TAGGTAAGATGAGACCATGTCGGCAACAAAG 3 163 1 GAGACATGTC 0.941101 -137 AGGGAAAATTAAGAAAAAGGCGGACAGGGAT 3 258 0 AAGAAAAGGC 0.897713 -42 AGGCCGGTTTGAGAGAATGGGACTAAATCAA 4 14 0 GAGAAATGGG 0.991747 -287 CTCGCCCTAGGAAAAAATGGCACCCGGCTTA 4 71 1 GAAAAATGGC 0.987258 -230 TCTCGATGGTGAAACAATGGGGGCAGTGGGC 4 270 0 GAAAAATGGG 0.975968 -31 **** ****** Masking position 7 Map Score: 4.01876 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 249 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 TGCATTAACGCCGTTGCCCAATGGAGTGAT 1 43 1 CCGTTGCCCA 0.856165 -159 TCCCCTGGCTCCCAATCCCTAG 2 3 1 CCCTGGCTCC 0.980597 -77 CCCGTTGGCCCAAATTACCCT 3 2 1 CCGTTGGCCC 0.980007 -298 CCCGGTATGCCTCTGACACCCCAAGGGTAA 3 25 0 CTCTGACACC 0.905347 -275 CAGAGGCATACCGGGCCTCCGCAAACTAGA 3 40 1 CCGGGCCTCC 0.928118 -260 TCAAACCGGCCTGGGGGACCCCCCGGCGGG 4 33 1 CTGGGGGACC 0.944869 -268 ATGCTAGGTTCACTTAGACCGAGGGAAATG 4 172 0 CACTTAGACC 0.638493 -129 AGAAATCGGTCTGTGGGCCCTTCTACCCGT 4 205 0 CTGTGGGCCC 0.986379 -96 ACTTAGTGCCCACTGCCCCCATTGTTTCAC 4 263 1 CACTGCCCCC 0.955208 -38 ********** Masking position 9 Map Score: 5.51196 Number of sites scoring better than the average of aligned sites = 2594 Number in coding regions = 2391 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 7 TGACAGGAAATAAGTTACATCT 1 3 0 TAAGTTACAT 0.872527 -199 ATGGTAACAGTAGGTTCCATTAACCAACTG 1 89 0 TAGGTTCCAT 0.972023 -113 TACTTTGCTTTAGGTTAACTCAACTTTGTT 3 187 0 TAGGTTAACT 0.96987 -113 CGTGTTATGCTAGGTTCACTTAGACCGAGG 4 178 0 TAGGTTCACT 0.986399 -123 CAGTGGGCACTAAGTTCACCCCTGGAGGGC 4 248 0 TAAGTTCACC 0.935487 -53 ********** Masking position 5 Map Score: 1.38659 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 63 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ********** No masking Map Score: -1.12023e-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 9 ********** No masking Map Score: -1.12023e-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: -1.12023e-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