AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_synecho_reg_300.orf -o164_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 RCY50395 244 Synechocystis #2 RCY05450 300 Synechocystis #3 RCY38242 51 Synechocystis #4 RCY51764 52 Synechocystis #5 RCY11976 132 Synechocystis #6 RCY02336 194 Synechocystis #7 RCY33232 300 Synechocystis #8 RCY47152 92 Synechocystis #9 RCY08136 202 Synechocystis #10 RCY44540 300 Synechocystis #11 RCY35506 141 Synechocystis #12 RCY39748 135 Synechocystis #13 RCY43947 67 Synechocystis Motif number 1 ATTATTTGCTAGGCGATCGCCGAAGGGTTG 1 162 1 AGGCGATCGC 0.704488 -83 CCTCGGACGATGGAGTTGGCGGTGTCACAC 2 13 1 TGGAGTTGGC 0.848098 -288 AAATGGAGTTTGGGCAACGGTCTTCCTTGG 2 64 1 TGGGCAACGG 0.735202 -237 TGATCGCTTCTGGCTTAGGGTAGGTGGTCC 2 101 0 TGGCTTAGGG 0.897312 -200 GCAATCCCCCTGGCGATCGCCAAAGAAAAT 2 193 1 TGGCGATCGC 0.974862 -108 CAATTTTTTGTGGCCATGGCCTTGGGAGAA 3 17 0 TGGCCATGGC 0.987124 -35 GGATGGTGATCGCTCCAATTTTT 3 39 0 TGGTGATCGC 0.83817 -13 CATTGGCAACGGCGGATCAAGAC 4 40 0 TGGCAACGGC 0.891568 -13 CAAAATTTATTGGCAAAGGCCATAAATTAA 5 61 0 TGGCAAAGGC 0.977609 -72 AAGAAATTGATGGCAATGGTACTTCTAGCA 5 89 0 TGGCAATGGT 0.807121 -44 AGGGTTTGGTCAAGGGAAAAAATCAA 5 117 0 TGGTCAAGGG 0.925262 -16 ACCCAATTGTTGCCATAGGGAATTTCCGCC 6 80 1 TGCCATAGGG 0.731474 -115 CCCTACCAAATGGCGATCGCCTCGATGATT 7 145 1 TGGCGATCGC 0.974862 -156 TTATTGAGTTTGGTTTAGGGGAGGTTCACC 7 215 1 TGGTTTAGGG 0.538542 -86 CGGAGAAAGGTGGCATTGGGGTGAACCTCC 7 234 0 TGGCATTGGG 0.963215 -67 CCCTTGGCCATGGACTAGGGTTAACTAATT 10 96 0 TGGACTAGGG 0.83613 -205 CCCTAGTCCATGGCCAAGGGACTTCCCGTA 10 106 1 TGGCCAAGGG 0.989327 -195 CAAGGTAGATTGGCAGTGGGACGAAATAAA 10 235 0 TGGCAGTGGG 0.889588 -66 GATAGGGAACTGCCCAAGGCAAGGTAGATT 10 254 0 TGCCCAAGGC 0.888581 -47 TAATTGTCGAAGGGGGGTAACTGC 11 5 1 TGTCGAAGGG 0.836906 -137 CAATAATGCCTGGCGATCGGCCAACTTGCC 12 52 0 TGGCGATCGG 0.980931 -84 GCAGTATCCTTGGAGATGGGCAAAGTGGAT 12 114 0 TGGAGATGGG 0.947282 -22 ********** Masking position 2 Map Score: 31.3235 Number of sites scoring better than the average of aligned sites = 6194 Number in coding regions = 5667 Number in noncoding regions = 527 Number of orfs with sites within 600 bp upstream = 484 Fraction of orfs with sites within 600 bp upstream = 0.0777385 Motif number 2 CCAAACTCCATTTCTCACCTTGCTAGTAGTCA 2 45 0 TTCTCCCTTG 0.974322 -256 TAGGTGGTCCTTGATTACCAAGGAAGACCGTT 2 79 0 TTATTCCAAG 0.702802 -222 TAGTTTTTTGTTTTTTGCCTAGACCCCCAACA 2 155 1 TTTTTCCTAG 0.947824 -146 AATTTCTTGATTTTTTCCCTTGACCAAACCCT 5 111 1 TTTTTCCTTG 0.972242 -22 AATTTTATGTTTCTTTACCTTTTGTCCCCTAC 7 119 1 TTTTTCCTTT 0.885477 -182 CGCAATCGTTTTATTCTCCATGACAAAATCTC 7 262 1 TTTTCCCATG 0.967183 -39 TAATCTTCCCTTGCTTACCAATTCTGATCAAT 9 73 0 TTCTTCCAAT 0.731488 -130 TGGTTGACTCTTTTGCTCCTTGCTACCCTGCT 9 115 1 TTTGCCCTTG 0.933606 -88 GTTGTTTTAGTTTCGCTCCTTGAGATTTATTT 10 210 1 TTCGCCCTTG 0.92933 -91 ACTGCCAATCTACCTTGCCTTGGGCAGTTCCC 10 248 1 TACTTCCTTG 0.791405 -53 GATTTTTTCATTCTTCACCAAGCTATCTTTCA 11 98 1 TTTTCCCAAG 0.938597 -44 CTTGGTTGCGTTATTTTCCATTCTGCTAGGCA 12 24 1 TTTTTCCATT 0.848862 -112 ** *** ***** Masking position 1 Map Score: 8.54559 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 630 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 GAAGGGTTGAGGAAGATTACAATGGGATCAATCCCATA 1 183 1 GAATTTGGAT 0.738048 -62 GGTGATCTTGGCAATTTTCTTTGGCGATCGCCAGGGGG 2 198 0 GAATTGGGAT 0.975166 -103 GGTACTTCTAGCAAAATTTATTGGCAAAGGCCATAAAT 5 64 0 GAATTGGAAA 0.918357 -69 AAAGACAATGGCAAAGTTCCATGGCTAATCCCTCATTC 6 12 1 GAATTGGTAA 0.978538 -183 AACTAAATTTGAAACTTAGAAAGGTTAATACTGGTTTT 7 21 1 GAATAGGTAA 0.959416 -280 CAAAAGTTGAGCAAAATTAGCCGGGGATATGGGAACTG 8 37 1 GAATTGGGAT 0.975166 -56 CTCAATCACCGAAAACTTGAATGGCTAAATCAAACGCA 9 35 0 GAATTGGTAA 0.978538 -168 CAAGAAACGTGTAATATAAGCAGGGTAGCAAGGAGCAA 9 127 0 GAATAGGTAG 0.920377 -76 CAAATAAATAGTTAATTTAATGGGATAG 9 185 1 GTATTGGTAG 0.833152 -18 CGAATGCAGTGTTCTCCGGGGAATTCAGATAGG 10 278 0 GAGTTGGGAA 0.937056 -23 GGCTAGAATAGTTAATTATTCAGGAGAAAAATAGGTCA 11 47 0 GTATAGGGAA 0.909726 -95 ATAACTTAATGAAAGATAGCTTGGTGAAGAATGAAAAA 11 101 0 GAATAGGGAA 0.97825 -41 * ** ** ** *** Masking position 17 Map Score: 11.5114 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 305 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 CTGATGTATCTGTGGATTGGTTTCATGAACG 1 54 1 TGTGGATTGT 0.875229 -191 GTCCTTGTTGGGGGTCTAGGCAAAAAACAAA 2 161 0 GGGGTCTAGC 0.91443 -140 GCGATCGCCAGGGGGATTGCCGTCCTTGTTG 2 182 0 GGGGGATTGC 0.962923 -119 TCGTGATTTGTGGGTCTTGATCCGCCGTTGC 4 27 1 TGGGTCTTGT 0.978897 -26 TGGCAACAATTGGGTCTTGGCTAAACTTCTT 6 64 0 TGGGTCTTGC 0.983531 -131 CCTCGATGATTGTGGCTTGATCAACTTCGAG 7 164 1 TGTGGCTTGT 0.947217 -137 TCATTAGATGTGGGTATAGTTATTGAGTTTG 7 196 1 TGGGTATAGT 0.851405 -105 TTCGCCAGTTAGGGGCTTGGTTGCGTTTGAT 9 14 1 AGGGGCTTGT 0.9498 -189 CTGCTTAGCATGGGGGTTGTCCTTTCAGTTT 10 34 0 TGGGGGTTGC 0.964161 -267 ********* * Masking position 7 Map Score: 7.01856 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 483 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 TGGAGTTTGGGCAACGGTCTTCCTTGGTAAT 2 67 1 GCAACGGCTT 0.956207 -234 ATTTTTTGTGGCCATGGCCTTGGGAGAACCT 3 14 0 GCCATGGCTT 0.980941 -38 AAATTTATTGGCAAAGGCCATAAATTAACAC 5 58 0 GCAAAGGCAT 0.848179 -75 GAAATTGATGGCAATGGTACTTCTAGCAAAA 5 86 0 GCAATGGACT 0.976879 -47 ATGGAACTTTGCCATTGTCTTTG 6 3 0 GCCATTGCTT 0.944035 -192 TGAGGGATTAGCCATGGAACTTTGCCATTGT 6 16 0 GCCATGGACT 0.985298 -179 AGATTGTCGAGCAATTGTCCTATTTCACTTT 7 64 1 GCAATTGCCT 0.964547 -237 CTAGTCCATGGCCAAGGGACTTCCCGTAGGA 10 108 1 GCCAAGGACT 0.966837 -193 GACAATTTGAGCTACTGCACTAACTAAACTA 12 83 1 GCTACTGACT 0.739054 -53 ******* *** Masking position 4 Map Score: 6.5195 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 663 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 GGGCGAAATTTGGCTGATCATTGCCGATAAAATA 1 114 0 TGTGATCTTC 0.93501 -131 ACGGTCTTCCTTGGTAATCAAGGACCACCTACCC 2 80 1 TGTAATCAGA 0.839635 -221 ATCAGCCACCTAGGTGATCTTGGCAATTTTCTTT 2 214 0 TGTGATCTGC 0.9695 -87 ATCACCTAGGTGGCTGATTCTGATCATTATCCAA 2 230 1 TGTGATTTGT 0.914721 -71 TATTTCACTTTTGATAATTCAGTATATTTTGCTA 7 84 1 TGTAATTAGA 0.818959 -217 GGCGATCGCCTCGATGATTGTGGCTTGATCAACT 7 156 1 TGTGATTTGC 0.964836 -145 ATTCAAGTTTTCGGTGATTGAGATTGATCAGAAT 9 51 1 TGTGATTAGT 0.847635 -152 TTGAACAAACTAGATAATTATTCCAAGAAACGTG 9 154 0 TGTAATTTTC 0.885769 -49 ACAATTAATTTAGGTAATCCTGCTTAGCATGGGG 10 50 0 TGTAATCTGT 0.885885 -251 AACAATCGGGTTGCTAATCTATTCTAGAATAGAT 10 161 1 TGTAATCATC 0.823399 -140 CTGGCTAGAATAGTTAATTATTCAGGAGAAAAAT 11 53 0 TGTAATTTTA 0.796494 -89 CTCGGTATTTTAGTTGATTTTTTAGTTAGCCTTA 13 23 1 TGTGATTTTA 0.863378 -45 * * ***** ** * Masking position 7 Map Score: 7.7995 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 350 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TTATCCAAGGCCTACCAGTTGCCCCTATCCCGT 2 256 1 CCTCAGTTCC 0.997406 -45 GCTCATTTATCCTTTCAGTTCCCATATCCCCGG 8 57 0 CCTCAGTTCC 0.997407 -36 TGGGGGTTGTCCTTTCAGTTTACTGGACTGCCA 10 22 0 CCTCAGTTAC 0.989776 -279 CAAACTTAAACCTAGCAGTTACCCCCCTTCGAC 11 16 0 CCTCAGTTCC 0.997396 -126 *** ***** ** Masking position 7 Map Score: 4.13425 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ACCCTCGGACGATGGAGTTGGCGGTGTCACACTC 2 8 1 GAGGTTGCGG 0.956103 -293 CAGGGGGATTGCCGTCCTTGTTGGGGGTCTAGGCAAA 2 168 0 GCCGTTGGGG 0.996726 -133 GGGAAAAAACGCTGGACGGGATAGGGGCAACTGGTAG 2 267 0 GCCGATGGGG 0.991108 -34 TCCGCCCACAGCCTCCCCCGTTGTCGCTAAGATGGAA 6 104 1 GCCGTTTCGC 0.949021 -91 TTGTCATGGAGAATAAAACGATTGCGGAGAAAGGTGG 7 251 0 GAAGATGCGG 0.843255 -50 TGCTTCGCCAGTTAGGGGCTTGGTTGCG 9 2 1 GCCGTTGGGG 0.996726 -201 GTTTGATTTAGCCATTCAAGTTTTCGGTGATTGAGAT 9 38 1 GCCGTTTCGG 0.991249 -165 TTTCCATTCTGCTAGGCAAGTTGGCCGATCGCCAGGC 12 38 1 GCCGTTGCCG 0.987949 -98 ** * *** **** Masking position 12 Map Score: 4.96015 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 181 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 AATGATCAGCCAAATTTCGCCCAGTTTGCA 1 126 1 CAAATTTCGC 0.939775 -119 CCTTTGCCAATAAATTTTGCTAGAAGTACC 5 72 1 TAAATTTTGC 0.964464 -61 AATTTTCCTCTAACTTTTGCATAGGAGTTC 6 165 1 TAACTTTTGC 0.957448 -30 GATAATTCAGTATATTTTGCTACAATTTTA 7 96 1 TATATTTTGC 0.870057 -205 TAATTTTGCTCAACTTTTGCGGGACTTAGA 8 26 0 CAACTTTTGC 0.972513 -67 ATATCCCCGGCTAATTTTGCTCAACTTTTG 8 37 0 CTAATTTTGC 0.913258 -56 ********** Masking position 5 Map Score: 2.79493 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 165 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ATCAATCCCATAGGAAGAGTGTTATCCGTTA 1 209 1 TAGAAGAGTG 0.970964 -36 ACCTTGCTAGTAGTCAGAGTGTGACACCGCC 2 30 0 TAGCAGAGTG 0.988435 -271 TACTGGTTTTTAGAAAGATTGTCGAGCAATT 7 49 1 TAGAAGATTG 0.884375 -252 TATACTGAATTATCAAAAGTGAAATAGGACA 7 79 0 TATAAAAGTG 0.701875 -222 AACCCGATTGTTGTCAAAGTGCCAAGGTCGG 10 142 0 TTGCAAAGTG 0.918015 -159 TTAACTATTCTAGCCAGAGTAGAACCTAGAT 11 70 1 TAGCAGAGTA 0.905173 -72 TCCATTCTGCTAGGCAAGTTGGCCGATCGCC 12 40 1 TAGCAAGTTG 0.76617 -96 TCCTTGGAGATGGGCAAAGTGGATTAGTTTA 12 107 0 TGGCAAAGTG 0.943168 -29 *** ******* Masking position 6 Map Score: 1.42584 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 176 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 CAACCCTTCGGCGATCGCCTAGCAAATAAT 1 162 0 GCGATCGCCT 0.993215 -83 ACAGCGTGATATGATCGCTTCTGGCTTAGG 2 112 0 ATGATCGCTT 0.816564 -189 AATCCCCCTGGCGATCGCCAAAGAAAATTG 2 195 1 GCGATCGCCA 0.97802 -106 GGATGGTGATCGCTCCAATTTTTTG 3 37 0 GTGATCGCTC 0.966044 -15 TTAATATTTTGTGCTCGGTTCGGTGTTTTT 5 26 1 GTGCTCGGTT 0.816712 -107 CTACCAAATGGCGATCGCCTCGATGATTGT 7 147 1 GCGATCGCCT 0.993215 -154 ATAATGCCTGGCGATCGGCCAACTTGCCTA 12 50 0 GCGATCGGCC 0.980847 -86 ********** Masking position 5 Map Score: 7.13773 Number of sites scoring better than the average of aligned sites = 6362 Number in coding regions = 5796 Number in noncoding regions = 566 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 12 AACAGTAAGTCTTGATCCTTAGATAATATT 1 21 1 CTTGATCCTT 0.867089 -224 GCGAAATTTGGCTGATCATTGCCGATAAAA 1 116 0 GCTGATCATT 0.838686 -129 TTATCCGTTACCTGATCAATGTGCC 1 230 1 CCTGATCAAT 0.891026 -15 GGTGGCTGATTCTGATCATTATCCAAGGCC 2 238 1 TCTGATCATT 0.951497 -63 CTATTTCACTTTTGATAATTCAGTATATTT 7 83 1 TTTGATAATT 0.535492 -218 ATGATTGTGGCTTGATCAACTTCGAGGTCA 7 169 1 CTTGATCAAC 0.656938 -132 CCCGGCTAATTTTGCTCAACTTTTGCGGGA 8 32 0 TTTGCTCAAC 0.754306 -61 AGTGATTTCCTCTGCTCATTTATCCTTTCA 8 73 0 TCTGCTCATT 0.948353 -20 GCTTACCAATTCTGATCAATCTCAATCACC 9 63 0 TCTGATCAAT 0.919683 -140 GGTTGACTCTTTTGCTCCTTGCTACCCTGC 9 116 1 TTTGCTCCTT 0.895507 -87 TTGTTTTAGTTTCGCTCCTTGAGATTTATT 10 211 1 TTCGCTCCTT 0.617431 -90 ********** Masking position 6 Map Score: 3.30062 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 464 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 13 TGGTAATCAAGGACCACCTACCCTAAGCCA 2 91 1 GGACCACCTA 0.969977 -210 CATGGCCTTGGGAGAACCTAAC 3 3 0 GGAGAACCTA 0.986765 -49 GTGGCATTGGGGTGAACCTCCCCTAAACCA 7 225 0 GGTGAACCTC 0.938453 -76 TAAACTGAAAGGACAACCCCCATGCTAAGC 10 33 1 GGACAACCCC 0.935703 -268 ACTTCCCGTAGGAGCACCGACCTTGGCACT 10 126 1 GGAGCACCGA 0.965332 -175 TCTAGCCAGAGTAGAACCTAGATTTTTTCA 11 78 1 GTAGAACCTA 0.92022 -64 ********** Masking position 6 Map Score: 1.6843 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 96 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 ********** No masking Map Score: -2.15762e-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 15 ********** No masking Map Score: -2.15762e-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