Command-line arguments: -R -D 1 -m 10 -S 100 -P 0.0 -z 3 -y 3 -N 1 -L (amphimedon:0.00001427247692,(((((caenorhabditis:0.0157570080921343,loa:0.0157570080921343):0.0157570080921343,(ixodes:0.000568811298595544,(strigamia:0.000762789807885291,((((acyrthosiphon:0.125526921782279,pediculus:0.125526921782279):1,rhodnius:0.125526921782279):0.151743602421245,((nasonia:0.134217728,(apis:0.262144,(solenopsis:0.4096,atta:0.4096):0.64):0.512):0.150059981796789,((tribolium:0.0716956400810709,dendroctonus:0.0716956400810709):0.490746327796876,(((drosophila:0.457946721791957,megaselia:0.457946721791957):0.1073741824,aedes:0.0491716548351717):0.874689659154622,(bombyx:0.221746825986691,(danaus:0.293085901946853,heliconius:0.293085901946853):0.756593287202541):0.193959655640918):0.818052146050858):0.572433402239946):0.945741609003176):0.0679570226589353,daphnia:0.00129443906881319):0.589282127110592):0.745698608863796):0.4364950285422):0.598559006606478,((lottia:0.00264358728275486,crassostrea:0.00264358728275486):0.268059327217945,(helobdella:0. Seq 0: drosophila Seq 1: nematostella Seq 2: rhodnius Seq 3: nasonia Seq 4: lottia Seq 5: tetraodon Seq 6: aedes Seq 7: bombyx Seq 8: daphnia Seq 9: mnemiopsis Seq 10: tribolium Seq 11: danaus Seq 12: pediculus Seq 13: ixodes Seq 14: strongylocentrotus Seq 15: amphimedon Seq 16: helobdella Input phylogenetic tree: (amphimedon:0.000014,(((((caenorhabditis:0.015757,loa:0.015757):0.015757,(ixodes:0.000569,(strigamia:0.000763,((((acyrthosiphon:0.125527,pediculus:0.125527):1.000000,rhodnius:0.125527):0.151744,((nasonia:0.134218,(apis:0.262144,(solenopsis:0.409600,atta:0.409600):0.640000):0.512000):0.150060,((tribolium:0.071696,dendroctonus:0.071696):0.490746,(((drosophila:0.457947,megaselia:0.457947):0.107374,aedes:0.049172):0.874690,(bombyx:0.221747,(danaus:0.293086,heliconius:0.293086):0.756593):0.193960):0.818052):0.572433):0.945742):0.067957,daphnia:0.001294):0.589282):0.745699):0.436495):0.598559,((lottia:0.002644,crassostrea:0.002644):0.268059,(helobdella:0.001618,capitella:0.001618):0.437958):0.209715):0.529427,(strongylocentrotus:0.000238,((xenopus:0.018900,(((homo:0.362697,ictidomys:0.362697):0.929009,(tursiops:0.416978,ailuropoda:0.416978):0.808074):0.083072,(meleagris:0.319378,ficedula:0.319378):0.087642):0.675209):0.438447,((takifugu:0.521804,tetraodon:0.521804):0.393035,gasterosteus:0.205087):0.040405):0.028718):0.330618):0.370468,(mnemiopsis:0.000029,nematostella:0.000029):1.000000):0.489652) GSL Random number seed: 739 Beta: 20.000000 Full Score: 40.178077 No. of moves: colour 0, single window 226, shift 678, total 904 --------------- Motif 1: Bin size (no. of windows) =2 Top Window Score=2.77415e-36 -- GACTTAAAAG seq 1 pos -29 score 2.774e-36 [rev] actcaCTTTTAAGTCggtgt |-GACTTAAAAG seq 2 pos -29 |- acttaCTTTTAAGTCtactg |-GACTTAAAAG seq 3 pos -29 |- acttaCTTTTAAGTCctgaa |-GACTTAAAAG seq 4 pos -29 |- gcttaCTTTTAAGTCttctt |-GACTTAAAAG seq 5 pos -29 |- acttaCTTTTAAGTCtacaa |-GACTTAAAAG seq 6 pos -29 |- gcttaCTTTTAAGTCcttcc |-GACTTAAAAG seq 7 pos -29 |- acttaCTTTTAAGTCctaat |-GACTTGTGAG seq 8 pos -29 |- aaataCTCACAAGTCttgaa |-GACTTAAAAG seq 11 pos -29 |- acttaCTTTTAAGTCgtaaa `-GACTTAAAAG seq 12 pos -29 `- acttaCTTTTAAGTCtaaca -- GACTTAAACA seq 9 pos -31 score 4.82e-14 [rev] acgcaTGTTTAAGTCtcgag |-GACTTAAAAA seq 10 pos -30 |- cttacTTTTTAAGTCttgac |-GACTTAAAAA seq 13 pos -31 |- ttactTTTTTAAGTCgcgag `-GACTTAAAAA seq 16 pos -30 `- aatacTTTTTAAGTCttaga -------- WM for this motif --------- // NA Motif_1 PO A C G T cons inf 01 0.00 10.46 0.00 4.13 C 1.14 02 0.00 0.00 1.01 13.48 T 1.64 03 0.00 1.02 0.00 13.12 T 1.63 04 1.02 0.00 0.00 13.12 T 1.63 05 0.00 1.02 0.00 13.12 T 1.63 06 14.59 0.00 0.00 0.00 A 2.00 07 14.59 0.00 0.00 0.00 A 2.00 08 0.00 0.00 14.59 0.00 G 2.00 09 0.00 0.00 0.00 14.59 T 2.00 10 0.00 14.59 0.00 0.00 C 2.00 // ============================== --------------- Motif 2: Bin size (no. of windows) =3 Top Window Score=4.95666e-27 -- TTCGTGTCTT seq 5 pos -42 score 4.957e-27 [rev] tctacAAGACACGAAacggc |-TTCGTGTCGG seq 6 pos -42 |- tccttCCGACACGAAacgag |-TTCGTGTCTT seq 8 pos -42 |- tcttgAAGACACGAAacgtg |-TTCGTGTCGT seq 10 pos -43 |- tcttgACGACACGAAacgtg |-TTCGTGTCTT seq 11 pos -42 |- tcgtaAAGACACGAAacgtg |-TTCGTGTCTG seq 12 pos -42 |- tctaaCAGACACGAAacgag |-TTCGTGTCCT seq 13 pos -44 |- tcgcgAGGACACGAAacgtc |-TTCGTGTCGA seq 14 pos -41 |- tctttTCGACACGAAacgat `-TTCGTGTCTC seq 16 pos -43 `- tcttaGAGACACGAAacgtg -- TTCGTGTCAG seq 2 pos -41 score 2.05e-07 [rev] gtctaCTGACACGAAacgtg `-TTCGTGTCTC seq 9 pos -43 `- gtctcGAGACACGAAacgag -- TTCGTGTCAG seq 1 pos -44 score 2.584e-07 [rev] ggtgtCTGACACGAAacgat `-TTCGTGTCTA seq 15 pos -42 `- ttgccTAGACACGAAacaat -------- WM for this motif --------- // NA Motif_2 PO A C G T cons inf 01 4.94 3.98 2.00 2.00 N 0.11 02 6.93 2.98 1.00 2.00 A 0.33 03 0.00 0.00 13.54 0.00 G 2.00 04 13.54 0.00 0.00 0.00 A 2.00 05 0.00 13.54 0.00 0.00 C 2.00 06 13.54 0.00 0.00 0.00 A 2.00 07 0.00 13.54 0.00 0.00 C 2.00 08 0.00 0.00 13.54 0.00 G 2.00 09 13.54 0.00 0.00 0.00 A 2.00 10 13.54 0.00 0.00 0.00 A 2.00 // ============================== --------------- Motif 3: Bin size (no. of windows) =1 Top Window Score=1.17156e-21 -- CCAATTCACG seq 0 pos -38 score 1.172e-21 [fwd] ttttgCCAATTCACGtttcg |-GTGCACATCG seq 1 pos -55 |- taagcGTGCACATCGtttcg |-AAATCCCACG seq 2 pos -52 |- gcggaAAATCCCACGtttcg |-GGGTCGCACG seq 3 pos -54 |- ttagcGGGTCGCACGtttcg |-GTGTCTATCG seq 4 pos -56 |- taagcGTGTCTATCGtttcg |-GAGTCCGCCG seq 5 pos -53 |- ctagcGAGTCCGCCGtttcg |-GCCGCTCTCG seq 6 pos -53 |- ttggtGCCGCTCTCGtttcg |-GCATTACACG seq 7 pos -54 |- tttcgGCATTACACGtttcg |-GGATAGCACG seq 8 pos -53 |- acagcGGATAGCACGtttcg |-AAGGACCTCG seq 9 pos -54 |- taggtAAGGACCTCGtttcg |-TCAGCACACG seq 10 pos -54 |- cacagTCAGCACACGtttcg |-GCATTACACG seq 11 pos -53 |- ttacgGCATTACACGtttcg |-CGTTGCCTCG seq 12 pos -53 |- ttttgCGTTGCCTCGtttcg |-GTTGAAGACG seq 13 pos -55 |- gcggtGTTGAAGACGtttcg |-GTGCACATCG seq 14 pos -52 |- ttggcGTGCACATCGtttcg |-GCTGACATTG seq 15 pos -53 |- ggttaGCTGACATTGtttcg `-GTTGTTCACG seq 16 pos -54 `- ttttgGTTGTTCACGtttcg -------- WM for this motif --------- // NA Motif_3 PO A C G T cons inf 01 2.00 2.00 11.87 1.00 G 0.67 02 3.00 5.79 3.00 5.00 N 0.06 03 5.77 1.00 5.99 4.00 D 0.20 04 1.00 2.00 5.99 7.84 K 0.35 05 5.98 5.95 1.00 3.80 H 0.21 06 3.87 6.97 2.00 3.93 H 0.13 07 4.00 10.75 2.00 0.00 C 0.73 08 8.73 1.00 0.00 7.00 A 0.74 09 0.00 16.00 0.00 1.02 C 1.67 10 0.00 0.00 17.59 0.00 G 2.00 // ==============================