AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i206_nucleases_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 recC 276 recC #2 echA3 48 echA3 #3 Rv0633c 153 hypothetical protein Rv0633c #4 Rv0634c 300 hypothetical protein Rv0634c Motif number 1 CCCAAAGCAACCGCGTCACCCACCAC 1 6 0 CCGCGTCCCC 0.995317 -271 CTTTGGGCAACCGCCTCACACCTACACCGCC 1 30 1 CCGCCTCCAC 0.998125 -247 CACACCTACACCGCCTCCTCCATCTCGAAGT 1 46 1 CCGCCTCTCC 0.995546 -231 GCATGACGAGCCGCCTCGGACGTGACACACT 1 74 0 CCGCCTCGAC 0.9959 -203 CATGCCGACATCGCGGCACGCCCCAGCGCGT 1 100 1 TCGCGGCCGC 0.969367 -177 GTCGAGCGGCCGGCCGCCGACATGCATGCTG 1 242 0 CGGCCGCGAC 0.966398 -35 CGGGCGTCACCCTAGTCGAGCG 1 265 0 GGGCGTCCCC 0.962735 -12 AGGACTGGGCAAGCCTCTCCCGTTCCGGCCC 3 11 1 AAGCCTCCCC 0.941328 -143 GTGTCCAGCGGCGCTTCCGCCAACGATTCGG 3 54 1 GCGCTTCGCC 0.947639 -100 CAGTGCCCAGGCGCCTCTGGGATCCTGTCAG 3 96 1 GCGCCTCGGG 0.980419 -58 TCCGCGGTATCCGCCTCGCCGAGCAACGTTC 4 59 1 CCGCCTCCCG 0.989591 -242 GCAAGGTTGACAGCCTCGCGCGCACCCTTCA 4 95 1 CAGCCTCCGC 0.990047 -206 CCAAAGATACCCACCGCACCCACAGTCAGAC 4 196 1 CCACCGCCCC 0.980247 -105 GCCGCCCAGACCGCGTCTTGGCGTTTGCAGC 4 255 0 CCGCGTCTGG 0.950128 -46 GTCTTGTCCATCGCCGCCCAGACCGCGTCTT 4 267 0 TCGCCGCCAG 0.948962 -34 ******* *** Masking position 7 Map Score: 34.2105 Number of sites scoring better than the average of aligned sites = 9597 Number in coding regions = 8943 Number in noncoding regions = 654 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 2 CTTTGGGCAACCGCCTCACACCTACACCGCCT 1 30 1 CCGCTCACCC 0.899341 -247 GCCGCGATGTCGGCATGACGAGCCGCCTCGGA 1 85 0 CGGCTGACAG 0.925885 -192 CATGCCGACATCGCGGCACGCCCCAGCGCGTT 1 100 1 TCGCGCACCC 0.919415 -177 CGCGAGATCACCGAACGACAAGGGCTACCAGT 1 195 0 CCGACGACAG 0.976075 -82 CGGCGGCCGGCCGCTCGACTAGGGTGACGCCC 1 254 1 CCGCCGACAG 0.995115 -23 GCTGGACACGTCGCTGGACCCGGGCCGGAACG 3 31 0 TCGCGGACCG 0.993841 -123 GGCGGAAGCGCCGCTGGACACGTCGCTGGACC 3 43 0 CCGCGGACCG 0.998633 -111 CGGCGCTTCCGCCAACGATTCGGCAGCCAGCG 3 62 1 GCCACGATCG 0.817119 -92 CGATTCGGCAGCCAGCGACCAGTGCCCAGGCG 3 77 1 GCCACGACAG 0.907487 -77 GGCATTGGGATCGCTGAACTCGTCGTACTCGT 4 13 1 TCGCGAACCG 0.907618 -288 CGCGGAGCATGGGCACGATGACGAGTACGACG 4 33 0 GGGCCGATAC 0.687989 -268 TGCCCATGCTCCGCGGTATCCGCCTCGCCGAG 4 50 1 CCGCGTATCG 0.89912 -251 TCACACGGTACCGCCGGATGACCTTTTGGATA 4 123 1 CCGCGGATAC 0.964801 -178 CACAGTCAGACCCCAAGACTCCGCATTAACGT 4 216 1 CCCCAGACCC 0.958178 -85 GGCGTTTGCAGCCCGGGACACGTTAATGCGGA 4 235 0 GCCCGGACCG 0.994344 -66 GGGCTGCAAACGCCAAGACGCGGTCTGGGCGG 4 253 1 CGCCAGACCG 0.923638 -48 GGTCTGGGCGGCGATGGACAAGACATAGGCTG 4 274 1 GCGAGGACAG 0.973232 -27 **** **** ** Masking position 8 Map Score: 29.1892 Number of sites scoring better than the average of aligned sites = 14374 Number in coding regions = 13291 Number in noncoding regions = 1083 Number of orfs with sites within 600 bp upstream = 737 Fraction of orfs with sites within 600 bp upstream = 0.118375 Motif number 3 GTGGTGGGTGACGCGGTTGCTTTGGGCAAC 1 11 1 ACGCGGTTGC 0.913576 -266 TGTAGGTGTGAGGCGGTTGCCCAAAGCAAC 1 26 0 AGGCGGTTGC 0.933273 -251 GTCACGTCCGAGGCGGCTCGTCATGCCGAC 1 79 1 AGGCGGCTCG 0.905705 -198 AACGCGCTGGGGCGTGCCGCGATGTCGGCA 1 102 0 GGCGTGCCGC 0.70912 -175 GGATTTCATCAACGCGCTGGGGCGTGCCGC 1 112 0 AACGCGCTGG 0.802103 -165 GCATGCATGTCGGCGGCCGGCCGCTCGACT 1 244 1 CGGCGGCCGG 0.982304 -33 CGTCGCTGGACCCGGGCCGGAACGGGAGAG 3 25 0 CCCGGGCCGG 0.890363 -129 GCCGCTGGACACGTCGCTGGACCCGGGCCG 3 36 0 ACGTCGCTGG 0.920409 -118 GTTGGCGGAAGCGCCGCTGGACACGTCGCT 3 48 0 GCGCCGCTGG 0.969558 -106 GGGCACTGGTCGCTGGCTGCCGAATCGTTG 3 74 0 CGCTGGCTGC 0.967508 -80 AGGATCCCAGAGGCGCCTGGGCACTGGTCG 3 92 0 AGGCGCCTGG 0.911763 -62 ATTAACGTGTCCCGGGCTGCAAACGCCAAG 4 240 1 CCCGGGCTGC 0.983656 -61 AACGCCAAGACGCGGTCTGGGCGGCGATGG 4 261 1 CGCGGTCTGG 0.89146 -40 CGCGGTCTGGGCGGCGATGGACAAGACATA 4 271 1 GCGGCGATGG 0.673479 -30 ACAAGACATAGGCTGGTTGC 4 291 1 GGCTGGTTGC 0.813429 -10 ********** Masking position 9 Map Score: 16.0584 Number of sites scoring better than the average of aligned sites = 38326 Number in coding regions = 35947 Number in noncoding regions = 2379 Number of orfs with sites within 600 bp upstream = 1110 Fraction of orfs with sites within 600 bp upstream = 0.178285 Motif number 4 GCCTCCTCCATCTCGAAGTGTGTCACGTCC 1 58 1 TCTCGAAGTG 0.828408 -219 CGTGCCGCGATGTCGGCATGACGAGCCGCC 1 90 0 TGTCGGCATG 0.951363 -187 CATGCCGACATCGCGGCACGCCCCAGCGCG 1 100 1 TCGCGGCACG 0.886635 -177 CTGGGTCAGATATCGAACCGTTCCGGGATT 1 137 0 TATCGAACCG 0.730661 -140 CGGGCCTTCTTGTCGACCTGGAACTGGGTC 1 160 0 TGTCGACCTG 0.986052 -117 GCCTCTCCCGTTCCGGCCCGGGTCCAGCGA 3 23 1 TTCCGGCCCG 0.915253 -131 TCAGCTAACTTCTCGGTCCGATGTCACTGT 3 123 1 TCTCGGTCCG 0.949958 -31 CGCGCGAGGCTGTCAACCTTGCGCTGCGAA 4 87 0 TGTCAACCTT 0.620651 -214 TAGAGGTTGATGACGACCTTATCCAAAAGG 4 144 0 TGACGACCTT 0.782351 -157 TCAACCTCTATCTCGACCCTCTTCAGCATG 4 164 1 TCTCGACCCT 0.975014 -137 CATTAACGTGTCCCGGGCTGCAAACGCCAA 4 239 1 TCCCGGGCTG 0.912615 -62 CCAGACCGCGTCTTGGCGTTTGCAGCCCGG 4 251 0 TCTTGGCGTT 0.508469 -50 ********** Masking position 1 Map Score: 4.76815 Number of sites scoring better than the average of aligned sites = 10632 Number in coding regions = 9746 Number in noncoding regions = 886 Number of orfs with sites within 600 bp upstream = 644 Fraction of orfs with sites within 600 bp upstream = 0.103437 Motif number 5 CGCCTCACACCTACACCGCCTCCTCCATCTCGA 1 41 1 CTAACCCTCC 0.56357 -236 CCATCTCGAAGTGTGTCACGTCCGAGGCGGCTC 1 65 1 GTGGTCCTCC 0.853454 -212 GGTTCGATATCTGACCCAGTTCCAGGTCGACAA 1 148 1 CTGCCCGTCC 0.983767 -129 CCCTAGTCGAGCGGCCGGCCGCCGACATGCATG 1 245 0 GCGCCGCGCC 0.914606 -32 CTGCGGGCGCACAAGATCCCCCAATGCTG 2 7 1 GCGACAGTCC 0.989429 -42 ATCCCCCAATGCTGATCTGATTCAATCGAGAGC 2 26 1 GCTATCGTTC 0.457821 -23 AACGGGAGAGGCTTGCCCAGTCCT 3 2 0 GCTGCCATCC 0.800128 -152 CTCTCCCGTTCCGGCCCGGGTCCAGCGACGTGT 3 25 1 CCGCCCGTCC 0.99419 -129 AGCGGCGCTTCCGCCAACGATTCGGCAGCCAGC 3 60 1 CCGCAAGTTC 0.697325 -94 CCAGCGACCAGTGCCCAGGCGCCTCTGGGATCC 3 88 1 GTGCCAGGCC 0.957526 -66 CGAGAAGTTAGCTGACAGGATCCCAGAGGCGCC 3 105 0 GCTACAGTCC 0.949067 -49 ACTCGTCATCGTGCCCATGCTCCGCGGTATCCG 4 39 1 GTGCCAGTCC 0.987288 -262 ATCCGCCTCGCCGAGCAACGTTCGCAGCGCAAG 4 67 1 CCGGCACTTC 0.93231 -234 TGACAGCCTCGCGCGCACCCTTCACACGGTACC 4 102 1 GCGGCACTTC 0.960612 -199 *** *** * *** Masking position 13 Map Score: 11.775 Number of sites scoring better than the average of aligned sites = 12797 Number in coding regions = 11836 Number in noncoding regions = 961 Number of orfs with sites within 600 bp upstream = 685 Fraction of orfs with sites within 600 bp upstream = 0.110022 Motif number 6 GTGGTGGGTGACGCGGTTGC 1 1 1 GTGGTGGGTG 0.884412 -276 CCTCCATCTCGAAGTGTGTCACGTCCGAGG 1 62 1 GAAGTGTGTC 0.946967 -215 TGTCACGTCCGAGGCGGCTCGTCATGCCGA 1 78 1 GAGGCGGCTC 0.74268 -199 TTTCATCAACGCGCTGGGGCGTGCCGCGAT 1 109 0 GCGCTGGGGC 0.938301 -168 TGTCGACCTGGAACTGGGTCAGATATCGAA 1 150 0 GAACTGGGTC 0.962585 -127 CTCCCGTTCCGGCCCGGGTCCAGCGACGTG 3 27 1 GGCCCGGGTC 0.502931 -127 GGCAGCCAGCGACCAGTGCCCAGGCGCCTC 3 83 1 GACCAGTGCC 0.631547 -71 GGTCCATGCTGAAGAGGGTCGAGATAGAGG 4 168 0 GAAGAGGGTC 0.974634 -133 GACTGTGGGTGCGGTGGGTATCTTTGGTCC 4 193 0 GCGGTGGGTA 0.933672 -108 ********** Masking position 6 Map Score: 2.96117 Number of sites scoring better than the average of aligned sites = 4682 Number in coding regions = 4292 Number in noncoding regions = 390 Number of orfs with sites within 600 bp upstream = 324 Fraction of orfs with sites within 600 bp upstream = 0.0520398 Motif number 7 CGAGGCGGCTCGTCATGCCGACATCGCGGC 1 87 1 CGTCATGCCG 0.657002 -190 CAACGCGCTGGGGCGTGCCGCGATGTCGGC 1 103 0 GGGCGTGCCG 0.820327 -174 CGACAAGAAGGCCCGTACCGACTGGTAGCC 1 175 1 GCCCGTACCG 0.983307 -102 CCGACTGGTAGCCCTTGTCGTTCGGTGATC 1 192 1 GCCCTTGTCG 0.735886 -85 CACAAGATCCCCCAATGCTGATCTGATTCA 2 20 1 CCCAATGCTG 0.939512 -29 GGAGAGGCTTGCCCAGTCCT 3 1 0 GCCCAGTCCT 0.762232 -153 ACGTCGCTGGACCCGGGCCGGAACGGGAGA 3 26 0 ACCCGGGCCG 0.981478 -128 GCAGCCAGCGACCAGTGCCCAGGCGCCTCT 3 84 1 ACCAGTGCCC 0.839811 -70 GTTCAGCGATCCCAATGCCTG 4 2 0 CCCAATGCCT 0.871074 -299 TCGTCATCGTGCCCATGCTCCGCGGTATCC 4 41 1 GCCCATGCTC 0.972698 -260 GGTATCTTTGGTCCATGCTGAAGAGGGTCG 4 177 0 GTCCATGCTG 0.880614 -124 ACAGTCAGACCCCAAGACTCCGCATTAACG 4 217 1 CCCAAGACTC 0.494031 -84 CATTAACGTGTCCCGGGCTGCAAACGCCAA 4 239 1 TCCCGGGCTG 0.914107 -62 GTCCATCGCCGCCCAGACCGCGTCTTGGCG 4 263 0 GCCCAGACCG 0.981335 -38 ********** Masking position 8 Map Score: 10.652 Number of sites scoring better than the average of aligned sites = 26464 Number in coding regions = 24826 Number in noncoding regions = 1638 Number of orfs with sites within 600 bp upstream = 958 Fraction of orfs with sites within 600 bp upstream = 0.153871 Motif number 8 ********** No masking Map Score: 1.75747e-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: 1.75747e-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: 1.75747e-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