AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_synecho_reg_100.orf -o110_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 RCY37834 300 Synechocystis #2 RCY04306 300 Synechocystis #3 RCY50074 106 Synechocystis #4 RCY22351 217 Synechocystis #5 RCY16359 57 Synechocystis #6 RCY37028 61 Synechocystis #7 RCY30977 165 Synechocystis #8 RCY10129 213 Synechocystis #9 RCY17386 35 Synechocystis Motif number 1 CGCCCTTTTTAGAAAACAGCAACCAGTAAACAGT 1 33 0 AGAACCAACC 0.913944 -268 CAGTGCCACAGAAAAATACCGCCCTTTTTAGAAA 1 52 0 GAAATCGCCC 0.881509 -249 GGCGTTACCCAGCAAGTTTGGCCTTTGGGAAGCC 1 107 1 AGAATGGCCT 0.795658 -194 TTTGGCCTTTGGGAAGCCCGGACTTTCCTCAGAT 1 123 1 GGAACGGACT 0.708283 -178 TCCCTGTGACAGGAATCCGCAACTCCCTCCCTAA 1 157 1 AGAACCAACT 0.819243 -144 TTGGCACAAAAGCAAACCCCCACAGAATCCTAAA 2 82 0 AGAACCCACA 0.907272 -219 TTATTGCGGCGGAGACCATCAACAAACTTAATAA 2 222 0 GGGACCAACA 0.851219 -79 GTAGTTCCTTGGCATTTTCCCCCAAGGGGGATTA 2 253 0 GGATTCCCCA 0.600249 -48 GAAAATGCCAAGGAACTACCGCCAACGATGAGGA 2 268 1 AGAATCGCCA 0.976701 -33 ATCCGTCAACAGTGACCGTCACCCCATTTTAGG 4 10 0 AGGACCACCC 0.915686 -208 AATAATTGTCAGTAAGTGTCGCCCCCGTAATCCG 4 39 0 AGAATCGCCC 0.97398 -179 ACCCATCCCCGGGGATTATCAACACTGGCGGGGT 4 87 1 GGGATCAACA 0.81187 -131 AAAATCCGGGGCCAAACCCCGCCAGTGTTGATAA 4 102 0 GCAACCGCCA 0.832652 -116 GGCAGAATGGAGCAACAAGCGCCCTTTGCTTAAT 5 12 1 AGAAACGCCC 0.812584 -46 TAAAAAAGCAGAAAAATTTCCCCATAGGTAGAAA 6 21 0 GAAATCCCCA 0.791598 -41 TAAACAAATAAAAAATCCTCACCATTTTACTAGC 7 48 0 AAAACCACCA 0.834038 -118 AACCTAGACCAGCAAGTTTCGCCATTAAACAAAT 7 73 0 AGAATCGCCA 0.976701 -93 GATTTAGTCCGATGAACTACGACTGTACTTGGTT 8 35 1 GAGACCGACT 0.390942 -179 CCGATAGTTAAGCAAATTACAACCAAGTACAGTC 8 55 0 AGAATCAACC 0.889023 -159 CATTGTTAAGGGTAATTAAGACCATGGTAGTTAA 8 154 1 GGAATGACCA 0.873379 -60 AAAATATCTAGAAAGTCTGCCCAGTTCATTACA 8 191 0 AGAATGCCCA 0.823277 -23 ** ** * ***** Masking position 13 Map Score: 19.2573 Number of sites scoring better than the average of aligned sites = 4596 Number in coding regions = 4238 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 366 Fraction of orfs with sites within 600 bp upstream = 0.0587857 Motif number 2 GCGCGAGCGTGAGGACAGTGCCACAGAAAAATACCGC 1 64 0 GGGATGCCGA 0.997938 -237 ACAAACCACAGCGGCCTATGGCTCTAATCAATGGCAC 1 206 0 GGGTTGCCAA 0.990552 -95 ATAGGCCGCTGTGGTTTGTGACCCCAATTAATTGAAA 1 224 1 GGGTTGCCAA 0.990552 -77 GGCAAATTGAGGCAATTTTGGCACAAAAGCAAACCCC 2 96 0 GCATTGCCAA 0.860897 -205 CATAACCTTGGTCAGTATTGTCGCAAAAGCAGACTAA 2 179 0 GCAATGCCAA 0.913019 -122 TCCCCCAAGGGGGATTATTGCGGCGGAGACCATCAAC 2 233 0 GGAATGGCGA 0.933338 -68 ATCCCCCTTGGGGGAAAATGCCAAGGAACTACCGCCA 2 255 1 GGGATGCAGA 0.974448 -46 CCTAAAATGGGGTGACGGTCACTGTTGACGGATTA 4 9 1 GGGAGGCCGT 0.962025 -209 ATCAACACTGGCGGGGTTTGGCCCCGGATTTTTGGCG 4 104 1 GGGTTGCCGG 0.985179 -114 TGGAATCGGACTGGGCAATGACGCTGATACTTTCCCC 4 178 0 CGGATGCCGA 0.982615 -40 AAGTAATTGAGCGGTAATTGACACAGTTTCC 9 15 1 GGGATGCCGT 0.992622 -21 * ** * ** * * ** Masking position 10 Map Score: 14.765 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 580 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 GCGCGCGAGCGTGAGGACAGTGCCACAGAAA 1 72 0 GGAGGACAGT 0.989735 -229 CACAGGGAATCTGAGGAAAGTCCGGGCTTCC 1 134 0 CGAGGAAAGT 0.88047 -167 CAAGACTACGGAGGGGGCAATGAAGTTTCAA 1 255 0 GGGGGGCAAT 0.981764 -46 AGGTTGGGCAGTGTGGGAAGGCAAATTGAGG 2 121 0 GGTGGGAAGG 0.92928 -180 TAATCCCCCTTGGGGGAAAATGCCAAGGAAC 2 253 1 TGGGGAAAAT 0.818723 -48 TTTAAGCTAGTCGAGGGCAGTTAGACCCCTC 3 17 0 TGAGGGCAGT 0.947531 -90 AGATAAAGGGTGGAAAAGTTTGATCGAC 3 89 0 GGTGGAAAAG 0.86444 -18 CCACTACCATGGGGGGAAAGTATCAGCGTCA 4 166 1 GGGGGAAAGT 0.980273 -52 AATGGAATCGGACTGGGCAATGACGCTGATA 4 186 0 GCTGGGCAAT 0.799931 -32 CATTTTACTAGCGAGGACAATTTGACTCTAA 7 29 0 GGAGGACAAT 0.980656 -137 CTTTGGCTGAGGGAGGCCAGTAATTA 7 150 1 GGAGGCCAGT 0.967394 -16 * ********* Masking position 9 Map Score: 11.1202 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 858 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 AGTCAGCAGAAAAACCCTGTTAACT 1 6 1 GCAGAAAAAC 0.859615 -295 GGACAGTGCCACAGAAAAATACCGCCCTTT 1 59 0 ACAGAAAAAT 0.753265 -242 TGGGCGTTACCCAGCAAGTTTGGCCTTTGG 1 105 1 CCAGCAAGTT 0.844282 -196 CAATGGCACACTAGAAAAAGAGAGTTAGGG 1 185 0 CTAGAAAAAG 0.819716 -116 ACTGCCCAACCTAGAAAAACTGTATTCTGC 2 140 1 CTAGAAAAAC 0.924176 -161 TATCAGTCAACCAGCAAAATTTAAGCTAGT 3 37 0 CCAGCAAAAT 0.951362 -70 AAACCATGGCCTAGAATAATTGTCAGTAAG 4 57 0 CTAGAATAAT 0.719836 -161 TTCCCCATAGGTAGAAAATTAATTACT 6 8 0 GTAGAAAATT 0.759597 -54 AAGTAAAAAAGCAGAAAAATTTCCCCATAG 6 28 0 GCAGAAAAAT 0.923836 -34 ATTGTCCTCGCTAGTAAAATGGTGAGGATT 7 39 1 CTAGTAAAAT 0.754164 -127 ACAACCTAGACCAGCAAGTTTCGCCATTAA 7 79 0 CCAGCAAGTT 0.844282 -87 AAAGAACTTCCCATAAAAATAGAGCAAATT 7 124 0 CCATAAAAAT 0.702253 -42 TTTTAATTCACTAGAAGGATTAATGCAGAG 8 101 1 CTAGAAGGAT 0.716316 -113 AAAATATCTAGAAAGTCTGCCCAGTTC 8 197 0 CTAGAAAGTC 0.771614 -17 ********** Masking position 6 Map Score: 9.26381 Number of sites scoring better than the average of aligned sites = 1338 Number in coding regions = 1119 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 5 AGCTTGCAACGAAGTCGATCGGTACGATAAGT 2 14 0 GAAGTCGCGG 0.949711 -287 ACAGAATCCTAAAATTCTCCGGGGGAAACGCA 2 63 0 AAAATTCCGG 0.859912 -238 ATCGTTGGCGGTAGTTCCTTGGCATTTTCCCC 2 265 0 GTAGTTCTGG 0.981846 -36 TGATATTCACTAAGTTCCGTGGCCTGGGTCGA 3 62 1 TAAGTTCTGG 0.91593 -45 ATTTTTATGGGAAGTTCTTTGGCTGAGGGAGG 7 134 1 GAAGTTCTGG 0.985999 -32 AAGTACAGTCGTAGTTCATCGGACTAAATCTA 8 33 0 GTAGTTCCGG 0.991127 -181 ATCAAAGTAATTGAGCGGTAATTGACAC 9 7 1 GTAATTGCGG 0.927841 -29 ******* *** Masking position 3 Map Score: 3.10261 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 154 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TCACGCTCGCGCGCACTGGGCGTTACCCAG 1 89 1 GCGCACTGGG 0.908351 -212 CTAATCAATGGCACACTAGAAAAAGAGAGT 1 190 0 GCACACTAGA 0.936957 -111 AAACAGCATTGCAGAATACAGTTTTTCTAG 2 150 0 GCAGAATACA 0.833941 -151 TGTCGCAAAAGCAGACTAAAACAGCATTGC 2 168 0 GCAGACTAAA 0.959391 -133 TCCAATGGAATCGGACTGGGCAATGACGCT 4 190 0 TCGGACTGGG 0.91427 -28 TGGCAGAATGGAGCAACAAGCG 5 3 1 GCAGAATGGA 0.887958 -55 GGCCGACTAAGGTTAAGAACA 5 47 0 GCCGACTAAG 0.876928 -11 TTCTAGATGTTCAGACTACAACCTAGACCA 7 96 0 TCAGACTACA 0.893145 -70 TCGTAGTTCATCGGACTAAATCTACCCTTT 8 27 0 TCGGACTAAA 0.883577 -187 ********** Masking position 5 Map Score: 2.91251 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 301 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 AGTTTGGCCTTTGGGAAGCCCGGACTTTCC 1 121 1 TTGGGAAGCC 0.927952 -180 AAAAGAGAGTTAGGGAGGGAGTTGCGGATT 1 170 0 TAGGGAGGGA 0.946019 -131 TTCCCAAGACTACGGAGGGGGCAATGAAGT 1 260 0 TACGGAGGGG 0.968645 -41 GTTGGGCAGTGTGGGAAGGCAAATTGAGGC 2 120 0 GTGGGAAGGC 0.87277 -181 ACAGTTTTTCTAGGTTGGGCAGTGTGGGAA 2 133 0 TAGGTTGGGC 0.788593 -168 GGTTGGGAGGGGTCTAACTGCC 3 3 1 TTGGGAGGGG 0.979407 -104 ATTCACTAAGTTCCGTGGCCTGGGTCGATC 3 66 1 TTCCGTGGCC 0.736366 -41 GTTGACGGATTACGGGGGCGACACTTACTG 4 34 1 TACGGGGGCG 0.86884 -184 ACCATTTTACTAGCGAGGACAATTTGACTC 7 32 0 TAGCGAGGAC 0.848234 -134 TTCTTTGGCTGAGGGAGGCCAGTAATTA 7 148 1 GAGGGAGGCC 0.979124 -18 ********** Masking position 8 Map Score: 4.25923 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 1035 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 8 CCCTTTTTAGAAAACAGCAACCAGTAAACA 1 35 0 AAAACAGCAA 0.954683 -266 CAATTTTGGCACAAAAGCAAACCCCCACAG 2 91 0 ACAAAAGCAA 0.917404 -210 AAAGCAGACTAAAACAGCATTGCAGAATAC 2 161 0 AAAACAGCAT 0.954683 -140 CAGTATTGTCGCAAAAGCAGACTAAAACAG 2 174 0 GCAAAAGCAG 0.934398 -127 TAGTATAAGTAAAAAAGCAGAAAAATTTCC 6 34 0 AAAAAAGCAG 0.953967 -28 AGAATTGTGAGAAACGGCATCTCTGCATTA 8 121 0 GAAACGGCAT 0.86461 -93 ********** Masking position 4 Map Score: 0.807456 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 204 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 ********** No masking Map Score: 8.05345e-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 10 ********** No masking Map Score: 8.05345e-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: 8.05345e-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