AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i176_cobalamin_biosynthesis_1_synecho_reg_300.orf -o176_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 RCY32260 300 Synechocystis #2 RCY49210 300 Synechocystis #3 RCY35846 218 Synechocystis #4 RCY33500 23 Synechocystis #5 RCY02837 200 Synechocystis #6 RCY48630 89 Synechocystis #7 RCY29821 289 Synechocystis #8 RCY44275 57 Synechocystis #9 RCY33343 128 Synechocystis #10 RCY25912 243 Synechocystis Motif number 1 TCAGCTATAATTGCACCAATGATCTTTACA 1 68 0 TTGCACCAAT 0.914926 -233 TACCGCACCTTTGCACCCTTACCCTTTTCA 2 57 0 TTGCACCCTT 0.914921 -244 CCTCAAGCGGTTCCACCAATCATGGGGCAG 2 172 0 TTCCACCAAT 0.948598 -129 CCCAAACAGATTGCCCCAATTCGCTACACT 3 67 1 TTGCCCCAAT 0.981824 -152 GCTCATGGTATTCCCTCAACGTTTTTCCCC 3 168 1 TTCCCTCAAC 0.792702 -51 CCTCAACGTTTTTCCCCCTCCCATTTGCTA 3 181 1 TTTCCCCCTC 0.919559 -38 TTTACTTAACTTCCCCCAAACTTGGGGAGC 7 182 0 TTCCCCCAAA 0.962641 -108 TGCCCCCTAAATCCCCCAATAATGGGTGAC 7 213 0 ATCCCCCAAT 0.96749 -77 AAGTTTTATTTTGCCCCCTAAATCCCCCAA 7 224 0 TTGCCCCCTA 0.937558 -66 TTAGTTTTATCCCCCCTCATCCCCCTTT 9 9 1 ATCCCCCCTC 0.949078 -120 ATCCCCCCTCATCCCCCTTTGAAAGGGGGG 9 19 1 ATCCCCCTTT 0.821542 -110 TAACAATTATTTCCCCCCTTTCAAAGGGGG 9 31 0 TTCCCCCCTT 0.989326 -98 TATTAAAAATTTTCCCCAATCTGCGGAGCA 10 26 0 TTTCCCCAAT 0.94806 -218 ********** Masking position 2 Map Score: 16.561 Number of sites scoring better than the average of aligned sites = 2254 Number in coding regions = 1893 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 318 Fraction of orfs with sites within 600 bp upstream = 0.0510761 Motif number 2 CGCTCTTACCGCACCTTTGCACCCTTACCC 2 63 0 GCACCTTTGC 0.837065 -238 GCTCGGTAAACCCCGGTTGGAAGCAAGGTC 2 117 1 CCCCGGTTGG 0.688452 -184 GGAAAAAGACCAACCTTTGCCCCTCCGACC 2 143 0 CAACCTTTGC 0.954094 -158 GGATGCGAGGCACCCTTGGGGAGTTATCTA 2 225 0 CACCCTTGGG 0.978726 -76 TTTTGGACGTTCACCGTGGGT 3 2 0 TCACCGTGGG 0.854515 -217 ATCCATCCTCCACCCCTGGGTTTTGGACGT 3 22 0 CACCCCTGGG 0.962376 -197 CTATTAACTTCAACGTTTGCTGACTTGGTA 5 53 1 CAACGTTTGC 0.78876 -148 ATTAACTTACTCACCCTGGGAGAAACTGCG 5 180 1 TCACCCTGGG 0.898308 -21 TAAAATTTGACCAACTTTGCAGTCTCCCGG 6 54 1 CCAACTTTGC 0.833834 -36 TTACCAACCATCCCCTAGGCTCCTGAAAA 7 10 0 TCCCCTAGGC 0.689409 -280 GTTTGAAAAGCCCCCCTGGCTCCCCAAGTT 7 164 1 CCCCCCTGGC 0.982373 -126 TAACTTCCCCCAAACTTGGGGAGCCAGGGG 7 176 0 CAAACTTGGG 0.814502 -114 CCCCCCTCATCCCCCTTTGAAAGGGGGGAA 9 21 1 CCCCCTTTGA 0.856378 -108 CGCGCGACATCAACCTTGGCAAGGTTGCGC 10 76 1 CAACCTTGGC 0.977784 -168 ********** Masking position 9 Map Score: 14.1483 Number of sites scoring better than the average of aligned sites = 3643 Number in coding regions = 3309 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 3 CTAAATTGTCATTTTCGCTTTTATTATCATAGAAAATT 1 153 0 ATTCCTTAAC 0.977744 -148 ATTGCGTAAAATTTTCACAATTAAGACCATTTTAAATA 1 205 0 ATTCCATAAC 0.988201 -96 GATCAAGTATTTCTGCTCAGTCATCACCTTTAGTCACT 5 17 1 TTTCCATAAC 0.977744 -184 TTGCCATAGATTTTAGTCAATTAAAAACCTCGAATCTT 5 135 1 TTTGCATAAC 0.879097 -66 AAAACCTCGAATCTTAACAATCATTAACTTACTCACCC 5 158 1 ATTACATAAC 0.903403 -43 ATCTAAATCATTAATCCCAGTTACCAACCATCCCCTAG 7 22 0 TTACCATAAC 0.873825 -268 CGACATTTATATATTCTCTGTAAACAGCCTTAAATTTA 7 120 1 ATTCCTTAAC 0.977744 -170 GTTAATTGCTCTATGATCATCGCCCTATTTT 8 4 1 AATCCTTAAC 0.873825 -54 TTAATTAAATTTCCTCACTAAAAATCGGCCAAGCTT 9 103 0 ATTCCATAAC 0.988201 -26 ** * * ** * * * * Masking position 11 Map Score: 7.71851 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 36 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GATACACTCTCAACCATCCTTCAAAGCCTTC 1 22 1 CACCATCCTT 0.729137 -279 AAGCCTTCTGCATTCAAGCTTCCTGTAAAGA 1 45 1 CATCAAGCTT 0.862842 -256 AACCTTTGCCCCTCCGACCTTGCTTCCAACC 2 131 0 CCCCGACCTT 0.92409 -170 GGCAGGAAAAAGACCAACCTTTGCCCCTCCG 2 146 0 AGCCAACCTT 0.959429 -155 TAATCGCTAACAGGCAAGCTTAGGGAAGAAA 3 127 0 CAGCAAGCTT 0.883676 -92 TCATGGTATTCCCTCAACGTTTTTCCCCCTC 3 170 1 CCTCAACGTT 0.911592 -49 GTCACTATTAACTTCAACGTTTGCTGACTTG 5 49 1 ACTCAACGTT 0.82355 -152 TACCTAACTATGTCCAAGCTTATTGTCCCCA 6 25 0 TGCCAAGCTT 0.772719 -65 TTACCGGGAGACTGCAAAGTTGGTCAAATTT 6 56 0 ACGCAAAGTT 0.526033 -34 TACTTAACTTCCCCCAAACTTGGGGAGCCAG 7 179 0 CCCCAAACTT 0.938265 -111 CACTAAAAATCGGCCAAGCTTAAATTTTAGA 9 93 0 CGCCAAGCTT 0.968199 -36 CGAACGCGCGACATCAACCTTGGCAAGGTTG 10 72 1 ACTCAACCTT 0.937143 -172 TCAGTGGTAGAGCGCAACCTTGCCAAGGTTG 10 86 0 AGGCAACCTT 0.924167 -158 ** ******** Masking position 10 Map Score: 8.12213 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 602 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 GCTATAATTGCACCAATGATCTTTACAGGAA 1 64 0 CACCAATGAC 0.939258 -237 CAAGCGGTTCCACCAATCATGGGGCAGGAAA 2 168 0 CACCAATCAG 0.945629 -133 AAACAGATTGCCCCAATTCGCTACACTAGCT 3 70 1 CCCCAATTCC 0.907994 -149 AAGATTGTCAACCCAATAAAGCTAGTGTAGC 3 89 0 ACCCAATAAG 0.873105 -130 CCAACCCCAGTGACGAGATAGCAAA 3 204 0 CCCCAGTGAG 0.972471 -15 AGGGAATTGTAACCAATGCCGAAACCGCCCC 5 84 1 AACCAATGCG 0.743818 -117 GCCGAAACCGCCCCAATGCTAGCATTAACCT 5 101 1 CCCCAATGCA 0.907983 -100 AGCTTATTGTCCCCAGTAAACCGGAAAAA 6 9 0 CCCCAGTAAC 0.920652 -81 ACTTAACTTCCCCCAAACTTGGGGAGCCAGG 7 178 0 CCCCAAACTG 0.765623 -112 CCCCTAAATCCCCCAATAATGGGTGACTTTT 7 209 0 CCCCAATAAG 0.978089 -81 TAAAAATTTTCCCCAATCTGCGGAGCAAAGT 10 22 0 CCCCAATCTC 0.945659 -222 ********* * Masking position 5 Map Score: 6.07768 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1179 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 6 TGGTCTTAATTGTGAAAATTTTACGCAATTTATAGTTA 1 214 1 TGTTTTACAA 0.933109 -87 TCGATACTGCTGGTGCGCTCTTACCGCACCTTTGCACC 2 70 0 TGGTTTACCA 0.97075 -231 TTATCTATCTGGGAAATTTGTTACCAAATTCCTCAAGC 2 194 0 GGGTTTACAA 0.970754 -107 ACTGCAAAGTTGGTCAAATTTTACCTAACTATGTCCAA 6 39 0 TGGTTTACAA 0.990809 -51 GCAACGAACGTGGTCCTATTTTACGGACCATCGACATT 7 89 1 TGGTTTACAC 0.986411 -201 CCCCCAATAATGGGTGACTTTTACTTAACTTCCCCCAA 7 193 0 TGGTTTACAA 0.990815 -97 TTATTTTGTTTGGAAGAGATTTACTTACAATGCCTTCT 9 58 1 TGGATTACAC 0.937772 -71 *** * **** ** Masking position 13 Map Score: 2.94275 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 10 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 CCAGTTAGTCAGCAGAAAAACCCTGTTAAC 2 16 0 AGCAGAAAAA 0.929232 -285 CCAATCATGGGGCAGGAAAAAGACCAACCT 2 157 0 GGCAGGAAAA 0.975553 -144 TAGGGAAGAAAGCAGGGGAAGATTGTCAAC 3 108 0 AGCAGGGGAA 0.947049 -111 GTGATGACTGAGCAGAAATACTTGATCAGA 5 14 0 AGCAGAAATA 0.731618 -187 GTCCCCAGTAAACCGGAAAAA 6 2 0 AACCGGAAAA 0.80774 -88 GGTGCAGGGAAAAAAAGATGAA 7 278 0 TGCAGGGAAA 0.94643 -12 TTTTTGTAGTGGCCGGGAAATCTGACTTAC 10 191 1 GGCCGGGAAA 0.970084 -53 ********** Masking position 10 Map Score: 1.56313 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 724 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 AAATTTTACCTAACTATGTCCAAGCTTATTGTCC 6 28 0 TAACTAGCAG 0.859473 -62 ATAGTTAGGTAAAATTTGACCAACTTTGCAGTCT 6 45 1 AAAATTGCAC 0.791818 -45 GATGGTCCGTAAAATAGGACCACGTTCGTTGCAT 7 87 0 AAAATAGCAG 0.980355 -203 ACAGAGAATATATAAATGTCGATGGTCCGTAAAA 7 107 0 TATAAAGCAG 0.812707 -183 AAAAAAGATGAATAAATGTCTAAGAATCTGTTTG 7 256 0 AATAAAGCAG 0.892149 -34 TTAATTACAAAAAATAGGGCGATGATCATAGAGC 8 18 0 AAAATAGCAG 0.980355 -40 TTTCCTCACTAAAAATCGGCCAAGCTTAAATTTT 9 96 0 AAAAATGCAG 0.932118 -33 CAGACTTTTATCAATATGCCAAAGAAAGATTTTT 10 134 1 TCAATAGCAG 0.927512 -110 TTTTATGTCAACAATTTGGCCAGGATTTTTTTGT 10 164 1 ACAATTGCAG 0.927512 -80 ****** * * * * Masking position 12 Map Score: 2.0504 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 296 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 ********** No masking Map Score: -8.85746e-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: -8.85746e-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: -8.85746e-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