AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_hsp60_hsp10_tpal_reg_100.orf -o257_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00362 118 AE000520 #2 RTP00772 204 AE000520 Motif number 1 ACTACTACCGGTGCTCCTTCCTGTTCTCCTC 1 17 1 GTGCTCTTCC 0.999119 -102 GCTCCTTCCTGTTCTCCTCCCTTGCCCTCTC 1 29 1 GTTCTCTCCC 0.989222 -90 TTGCCCTCTCCTGCTGCATCCTTCTCGCTCA 1 50 1 CTGCTCATCC 0.984118 -69 ACTGTGCCTTGTGCTAGTCCCTGAGCGAGAA 1 71 0 GTGCTGTCCC 0.992674 -48 ACAAGGCACAGTGCTCCGTTACACTCGGCCG 1 90 1 GTGCTCGTTA 0.920346 -29 CCGGTCACATGTGCTTCTTCCGTCCTATCCC 2 18 1 GTGCTCTTCC 0.999119 -187 ATCCCTACCCGCGATCCTTTCCTCACCCGTG 2 44 1 GCGATCTTTC 0.955069 -161 GAAACCCACCGTGCTGCTCGCCTTTGACTCG 2 106 1 GTGCTCTCGC 0.995029 -99 TCCCCGCCCTCCGCTTCTTTCAAAACGCACC 2 180 1 CCGCTCTTTC 0.985089 -25 ***** ***** Masking position 5 Map Score: 19.9206 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 273 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 CCTGTTCTCCTCCCTTGCCCTCTCCTGCTG 1 36 1 TCCCTTGCCC 0.977672 -83 TTCCTTACCGGTCACATGTG 2 1 1 TTCCTTACCG 0.92963 -204 CTTCCGTCCTATCCCTACCCGCGATCCTTT 2 34 1 ATCCCTACCC 0.992163 -171 CCGCGATCCTTTCCTCACCCGTGCCTACGA 2 52 1 TTCCTCACCC 0.995127 -153 ATCTCCCCACATCCCCGCACACAGAAACCC 2 83 1 ATCCCCGCAC 0.98679 -122 TGACTCGGATATCATCTACCTTCTTTTCTA 2 130 1 ATCATCTACC 0.808718 -75 CTTTTCTACGATCACCGACCAACAGATTTC 2 152 1 ATCACCGACC 0.972219 -53 ACCAACAGATTTCCCCGCCCTCCGCTTCTT 2 169 1 TTCCCCGCCC 0.998507 -36 ********** Masking position 3 Map Score: 13.2728 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 449 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 CCATCAACTACTACCGGTGCTCCTTCCTG 1 10 1 ACTACCGGTG 0.924163 -109 GTTCTCCTCCCTTGCCCTCTCCTGCTGCAT 1 39 1 CTTGCCCTCT 0.898495 -80 CTCCGTTACACTCGGCCGTGTGTCAA 1 103 1 CTCGGCCGTG 0.900221 -16 TTCCTTACCGGTCACATGTGCTT 2 4 1 CTTACCGGTC 0.981319 -201 CCGTCCTATCCCTACCCGCGATCCTTTCCT 2 37 1 CCTACCCGCG 0.990973 -168 CGATCCTTTCCTCACCCGTGCCTACGAAAT 2 55 1 CTCACCCGTG 0.994515 -150 CACACAGAAACCCACCGTGCTGCTCGCCTT 2 100 1 CCCACCGTGC 0.961268 -105 CACCGTGCTGCTCGCCTTTGACTCGGATAT 2 112 1 CTCGCCTTTG 0.941521 -93 CTTTTCTACGATCACCGACCAACAGATTTC 2 152 1 ATCACCGACC 0.809091 -53 AACAGATTTCCCCGCCCTCCGCTTCTTTCA 2 172 1 CCCGCCCTCC 0.991539 -33 ********** Masking position 6 Map Score: 10.8792 Number of sites scoring better than the average of aligned sites = 1209 Number in coding regions = 1053 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 CCATCAACTACTACCGGTGCTCCTTCCTGT 1 11 1 CTACCGGTGC 0.856419 -108 ACCGGTGCTCCTTCCTGTTCTCCTCCCTTG 1 23 1 CTTCCTGTTC 0.976431 -96 TCCTGTTCTCCTCCCTTGCCCTCTCCTGCT 1 35 1 CTCCCTTGCC 0.968112 -84 TCTCCTGCTGCATCCTTCTCGCTCAGGGAC 1 56 1 CATCCTTCTC 0.980263 -63 ACATGTGCTTCTTCCGTCCTATCCCTACCC 2 24 1 CTTCCGTCCT 0.950523 -181 CCCTACCCGCGATCCTTTCCTCACCCGTGC 2 46 1 GATCCTTTCC 0.839209 -159 ATCCTTTCCTCACCCGTGCCTACGAAATCT 2 57 1 CACCCGTGCC 0.95304 -148 AGAAACCCACCGTGCTGCTCGCCTTTGACT 2 105 1 CGTGCTGCTC 0.756783 -100 CGGATATCATCTACCTTCTTTTCTACGATC 2 135 1 CTACCTTCTT 0.834498 -70 ATTTCCCCGCCCTCCGCTTCTTTCAAAACG 2 177 1 CCTCCGCTTC 0.859517 -28 ********** Masking position 5 Map Score: 3.74165 Number of sites scoring better than the average of aligned sites = 2126 Number in coding regions = 1896 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 5 ********** No masking Map Score: 7.55607e-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 6 ********** No masking Map Score: 7.55607e-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 7 ********** No masking Map Score: 7.55607e-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