AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_synecho_reg_100.orf -o293_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 RCY10363 283 Synechocystis #2 RCY45270 150 Synechocystis #3 RCY53977 169 Synechocystis #4 RCY06830 23 Synechocystis #5 RCY08607 154 Synechocystis #6 RCY23989 257 Synechocystis #7 RCY21643 109 Synechocystis #8 RCY09697 66 Synechocystis #9 RCY14174 300 Synechocystis #10 RCY42662 233 Synechocystis #11 RCY39566 239 Synechocystis Motif number 1 TCCCAGACATCATTGGCCACTCCAGGGATTTGTC 1 158 0 CTGGCCACCA 0.87045 -126 CTGGCTCCAGCGGTGGCAAAGCCTAATGATCCTA 3 63 0 CTGGCAACCT 0.962271 -107 GAATGTATCCCAAGGGCAATGCTAGTTGGACGGT 3 102 0 CGGGCAACTA 0.987202 -68 GGATAACTGCTCCGGGAAATTTCAGGTAAATCAC 6 111 0 TGGGAAATCA 0.889393 -147 TGGCGATCGGGGCAAGCTCAAGCCGAATTC 6 238 0 TGGGCAATCA 0.970115 -20 CAATTTTTCCCACGGGAAACATCAAGATTTAATA 8 16 0 CGGGAAATCA 0.950268 -51 GCGATCGCCGCCTGGGGAATCCCAGAAAAAATTA 9 30 1 CGGGGAACCA 0.993474 -271 GAAATGCCCACCGGGGCAAAATTTTCCGCCATTG 9 149 1 CGGGCAATTT 0.911498 -152 CCATTGACAGCCAGGGGAATTCCTCGATAAAACT 9 177 1 CGGGGAACCT 0.987406 -124 GCGGAGCTGCTTTGGGGAATAACTTGGCCGGCTG 9 256 0 TGGGGAAACT 0.722205 -45 GGCACCCGACTAAGGGAAACACCAGTAATCTGCC 10 194 1 TGGGAAACCA 0.968768 -40 TTTTCTAGACTTTGGGCAACTCTAAACTTTTTGT 11 115 1 TGGGCAACTA 0.970115 -125 AGCCAGTCACCGTTGGCAAAACCTTAACAAAAAG 11 141 0 CTGGCAACCT 0.962271 -99 AAGGCAAATTCAGGGGGAAAACTACCAGCCAGTC 11 167 0 CGGGGAACTA 0.975287 -73 TATATCGTGATTGGGGCAAGGCAAATTCAGGGGG 11 184 0 TGGGCAACAA 0.907975 -56 * ****** *** Masking position 9 Map Score: 22.3294 Number of sites scoring better than the average of aligned sites = 1646 Number in coding regions = 1523 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 CCGATTTTCACCCCAATCGCCAACCCAGAGA 1 106 0 CCCCATCGCC 0.993831 -178 AAACTTCTAACCCCAAGCTCCCAGACATCAT 1 179 0 CCCCAGCTCC 0.984743 -105 ATTTCTATGGCTCCTGTCTCCCCCACAGATT 1 240 1 CTCCGTCTCC 0.920005 -44 TGCCCCATGGCATTGTTGCGGA 1 272 0 GCCCATGGCA 0.777837 -12 CATTTTTTCGCTACAGTGGCCAATTGTTTCT 2 46 1 CTACGTGGCC 0.613201 -105 GGGTTCTATCCCCCAGTTTCCTAACC 3 6 0 CCCCGTTTCC 0.896385 -164 GTAGAATGTATCCCAAGGGCAATGCTAGTTG 3 108 0 TCCCAGGGCA 0.664888 -62 GGAGCGCCACCCACGATCTCTTGTTGCTATA 5 49 0 CCACATCTCT 0.660119 -106 TTGATGTCAACGCCTAGCGCACTTTTTTTCT 5 80 0 CGCCAGCGCA 0.904319 -75 GGACGTTCAACCCCTGAGGCAATCCAGTGGG 6 78 1 CCCCGAGGCA 0.873515 -180 CTTGAGCTTGCCCCGATCGCCA 6 246 1 CCCCATCGCC 0.993834 -12 TTCTGGGATTCCCCAGGCGGCGATCGCCAGA 9 26 0 CCCCGGCGGC 0.975794 -275 GAAAATTTTGCCCCGGTGGGCATTTCTCATT 9 144 0 CCCCGTGGGC 0.970613 -157 TCGAGGAATTCCCCTGGCTGTCAATGGCGGA 9 173 0 CCCCGGCTGT 0.829705 -128 ATTCTTTCCTCGCCAATCTCTTTAGGTTTTG 10 125 0 CGCCATCTCT 0.777637 -109 TTTACCCCCATGTCATGGCAGATTA 10 219 0 CCCCATGTCA 0.954599 -15 **** ****** Masking position 4 Map Score: 16.3688 Number of sites scoring better than the average of aligned sites = 4333 Number in coding regions = 3933 Number in noncoding regions = 400 Number of orfs with sites within 600 bp upstream = 363 Fraction of orfs with sites within 600 bp upstream = 0.0583039 Motif number 3 AAGATGGCGGTGAATTTTTACGAAAACGTTA 1 30 0 TGAATTTTTC 0.865151 -254 GGAGTCTAAACCGATTTTCACCCCAATCGCC 1 116 0 CCGATTTTCC 0.919666 -168 CTCTATCCTTAGCATTTTTTCGCTACAGTGG 2 34 1 AGCATTTTTC 0.761111 -117 GCTACAGTGGCCAATTGTTTCTGAGAAGCGT 2 55 1 CCAATTGTTC 0.902033 -96 TCCTAACAATACAATTTTCGCTGATTATTTC 3 37 0 ACAATTTTCC 0.81867 -133 AAAAATCCGCCCAATTTTTAAATTCTGATTC 6 20 0 CCAATTTTTA 0.752157 -238 AAAAATTGGGCGGATTTTTACAAATCGTCAC 6 32 1 CGGATTTTTC 0.958866 -226 TTTTCCTCACACAATTCTTCCTCTCAGGATA 6 140 0 ACAATTCTTC 0.830909 -118 AAGCTCAAGCCGAATTCTCCCATCGTTGACG 6 224 0 CGAATTCTCC 0.899844 -34 CACTAAATTTTCAATTTTTCCCACGGGAAAC 8 30 0 TCAATTTTTC 0.881686 -37 CCAACTCTCTCTAATTTTTTCTGGGATTCCC 9 44 0 CTAATTTTTC 0.913506 -257 GTGGGCATTTCTCATTTTTGCTAACGAAACT 9 129 0 CTCATTTTTC 0.785423 -172 CTCCCCATGTCGAATTTTTCCCGAGCCGTTG 10 49 0 CGAATTTTTC 0.978803 -185 ATTTCTCTTCCCAGTTTTTGCTCCCCATGTC 10 69 0 CCAGTTTTTC 0.879187 -165 CCAATCATAGCGGATTCTTTCCTCGCCAATC 10 138 0 CGGATTCTTC 0.914729 -96 ********* * Masking position 6 Map Score: 13.2343 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 832 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 TCATTGGCCACTCCAGGGATTTGTCAGGCTTGTCA 1 148 0 CTCCATTGTC 0.719567 -136 GCTCCTGTCTCCCCCACAGATTTTCCGCAACAATG 1 249 1 CCCCCATTTC 0.972467 -35 TGCCCCATGGCATTGTTGCGGAAAATC 1 267 0 CCCCAATGTT 0.756216 -17 GTAAATCACGCCCCACTGGATTGCCTCAGGGGTTG 6 85 0 CCCCAATGCC 0.986942 -173 ATGGTTGCTTCCCCCATCCACAGTCGTGGTTTAGA 6 178 1 CCCCCAAGTC 0.978801 -80 AGTTTGAAAACCGCAGGATAAAGCCAGTGTGATGT 7 13 1 CCGCAAAGCC 0.872574 -97 GACTGTTTTGCCCCCCTAATCATCCTCAAAATAGT 7 77 1 CCCCCTATCC 0.952209 -33 GCAAAATTTTCCGCCATTGACAGCCAGGGGAATTC 9 164 1 CCGCCAAGCC 0.935489 -137 TACGGCCCCACACCCAAAGTTTTTCTGCTGTGTGC 9 216 0 CACCCTTTTC 0.772379 -85 CCAAGTTATTCCCCAAAGCAGCTCCGCCCTTTGAC 9 263 1 CCCCAACTCC 0.848067 -38 CTTAAATTAACCTCCAATAAATTTCTCTTCCCAGT 10 85 0 CCTCCATTTC 0.717054 -149 CTAAGGGAAACACCAGTAATCTGCCATGACATGGG 10 203 1 CACCATTGCC 0.878951 -31 ACAGCAAAGCCCCCCTTTGTTTGTATTTGGGGTTA 11 38 0 CCCCCTTGTA 0.833001 -202 TGGTAGTTTTCCCCCTGAATTTGCCTTGCCCCAAT 11 174 1 CCCCCTTGCC 0.991839 -66 ***** * **** Masking position 4 Map Score: 11.881 Number of sites scoring better than the average of aligned sites = 2301 Number in coding regions = 2088 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 5 ATGTTGGGGTTTTTGTAACGTTTTCGTAAAAA 1 15 1 TTTTGTAAGT 0.929891 -269 GGTTAGAAGTTTTTGGTAGGATAGAATCGATT 1 198 1 TTTTGGTAGT 0.978056 -86 GCGAAAATTGTATTGTTAGGATCATTAGGCTT 3 47 1 TATTGTTAGT 0.96646 -123 GCCCACCTGATTTTGGTACGATGGGAGACTGT 7 51 1 TTTTGGTAGT 0.978056 -59 AAAGCCCTTTTATTGTTAAGTTGAGTTAAGTA 9 77 1 TATTGTTAGT 0.96646 -224 ACTCTAAACTTTTTGTTAAGGTTTTGCCAACG 11 133 1 TTTTGTTAGT 0.981739 -107 ******** * * Masking position 8 Map Score: 4.90463 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 8 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TAAAAATTCACCGCCATCTTAACAGTGAGTACAC 1 41 1 CCGATCTACA 0.876418 -243 CCCAAGCTCCCAGACATCATTGGCCACTCCAGGG 1 165 0 CAGATCTGGC 0.983426 -119 AGTTACAAAGCCTCTATCCTTAGCATTTTTTCGC 2 23 1 CCTATCTAGC 0.918115 -128 TAACGCTTCTCAGAAACAATTGGCCACTGTAGCG 2 54 0 CAGACATGGC 0.892693 -97 GGGATAGAACCCGAAATAATCAGCGAAAATTGTA 3 25 1 CCGATATAGC 0.961933 -145 GGTTGAACGTCCGCTACCCTTAGAACTGTGACGA 6 56 0 CCGACCTAGA 0.974997 -202 TTTCCCGGAGCAGTTATCCTGAGAGGAAGAATTG 6 126 1 CAGATCTAGA 0.95897 -132 GGGTGTGGGGCCGTAATCTTCAGCCGGCCAAGTT 9 236 1 CCGATCTAGC 0.992266 -65 AGGAAAGAATCCGCTATGATTGGATCGAAAACCC 10 146 1 CCGATGTGGA 0.907583 -88 AACTACCAGCCAGTCACCGTTGGCAAAACCTTAA 11 148 0 CAGACCTGGC 0.976877 -92 *** *** * *** Masking position 6 Map Score: 8.83725 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 285 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CCCCCACAGATTTTCCGCAACAATGCCATGG 1 259 1 TTTCCGCAAC 0.911148 -25 GCTTTGTAACTGTTGGTCAACTG 2 3 0 TGTGGTCAAC 0.943598 -148 TCCTTAGCATTTTTTCGCTACAGTGGCCAAT 2 39 1 TTTTCGCTAC 0.706297 -112 GGAAAGGCAATTTTGGGCCACA 4 2 0 TTTGGGCCAC 0.974137 -22 ACTTTTTTTCTGGAGCGCCACCCACGATCTC 5 60 0 TGGGCGCCAC 0.858816 -95 CTTTTGGGATTTGATGTCAACGCCTAGCGCA 5 90 0 TTGTGTCAAC 0.897917 -65 ATAGTGATAGTTTGTGTGAACTTTCTTATAA 5 125 1 TTTTGTGAAC 0.629752 -30 AGATCTGCCTTTGCCGTCAACGATGGGAGAA 6 210 1 TTGCGTCAAC 0.855447 -48 TTATATTATTTTTGTCCACTAAATTTTCA 8 48 0 TTTTGTCCAC 0.934785 -19 CCCTGTGTCGCAACCCGCAACTAA 10 4 1 TGTTCGCAAC 0.885046 -230 TAATAAAGTTTTTTGGTCAACGGCTCGGGAA 10 32 1 TTTGGTCAAC 0.970708 -202 TCTTCCCAGTTTTTGCTCCCCATGTCGAATT 10 64 0 TTTGCTCCCC 0.731536 -170 ATTTTCTAGACTTTGGGCAACTCTAAACTTT 11 114 1 CTTGGGCAAC 0.878366 -126 *** ******* Masking position 11 Map Score: 6.3411 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 913 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 CAAGAGCTATCCCGGCGTTCCAAACTTCCC 3 139 1 CCCGGCGTTC 0.985933 -31 AAAATAAATTCTCGGCGTTCCGTGGTCAA 5 10 0 CTCGGCGTTC 0.962542 -145 AGAGATCGTGGGTGGCGCTCCAGAAAAAAA 5 59 1 GGTGGCGCTC 0.956336 -96 TCTAAGGGTAGCGGACGTTCAACCCCTGAG 6 66 1 GCGGACGTTC 0.927897 -192 GGATTCCCCAGGCGGCGATCGCCAGAAAAA 9 22 0 GGCGGCGATC 0.992708 -279 TATACTCAATGGCGACGATCAGGACAGAAA 11 214 1 GGCGACGATC 0.978751 -26 ********** Masking position 9 Map Score: 2.69938 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 882 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 TTGTTGTTCTCTGGGTTGGCGATTGGGGTG 1 99 1 CTGGGTTGGC 0.988995 -185 TGACAAATCCCTGGAGTGGCCAATGATGTC 1 157 1 CTGGAGTGGC 0.920365 -127 GCTAGTTGGACGGTGTTTGCTGGCTCCAGC 3 86 0 CGGTGTTTGC 0.873545 -84 TCACGCCCCACTGGATTGCCTCAGGGGTTG 6 85 0 CTGGATTGCC 0.929842 -173 TGGTTTAGATCTGCCTTTGCCGTCAACGAT 6 204 1 CTGCCTTTGC 0.916303 -54 CTAATTTTTTCTGGGATTCCCCAGGCGGCG 9 35 0 CTGGGATTCC 0.856057 -266 ATCGAAAACCCTGGGTTTGCTTCCGGGCAC 10 169 1 CTGGGTTTGC 0.990905 -65 CAAACAAAGGGGGGCTTTGCTGTATTATCG 11 50 1 GGGGCTTTGC 0.801766 -190 AGTTTTCCCCCTGAATTTGCCTTGCCCCAA 11 178 1 CTGAATTTGC 0.872491 -62 ********** Masking position 7 Map Score: 4.5635 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 707 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 GGCATTGTTGCGGAAAATCTGTGGGGGAGACA 1 254 0 CGAAAACTGT 0.944308 -30 TATATCGATTCTGAAAATAAATTCTCGGCGTT 5 21 0 CGAAAAAAAT 0.672761 -134 GGTGGCGCTCCAGAAAAAAAGTGCGCTAGGCG 5 69 1 CGAAAAAAGT 0.848659 -86 AAGCAACCATCTGAAAATTTTCCTCACACAAT 6 156 0 CGAAAATTTC 0.816883 -102 CGGCGATCGCCAGAAAAATATTCCTACTA 9 8 0 CGAAAATATT 0.919821 -293 TGGGGAATCCCAGAAAAAATTAGAGAGAGTTG 9 42 1 CGAAAAATTA 0.750616 -259 CTGTCAATGGCGGAAAATTTTGCCCCGGTGGG 9 155 0 CGAAAATTTG 0.816883 -146 GGGCACACAGCAGAAAAACTTTGGGTGTGGGG 9 214 1 CGAAAACTTT 0.97198 -87 GAGCCGTTGACCAAAAAACTTTATTAGTTGCG 10 26 0 CAAAAACTTT 0.751901 -208 ACGATCAGGACAGAAAACCATT 11 228 1 CGAAAACATT 0.959504 -12 * ***** **** Masking position 6 Map Score: 2.55775 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 271 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 ********** No masking Map Score: 5.92836e-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 12 ********** No masking Map Score: 5.92836e-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: 5.92836e-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