***cm->el_selfsc: -0.089267
cmalign - align sequences to an RNA CM
Infernal 0.7 (December 2005)
Copyright (C) 2001-2005 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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CM file:              ../../round1/seed.cm
Sequence file:        all.out.fa
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Aligning scaffold_3_2136376-2136148_1_37.15
alignment strategy:CYKDivideAndConquer:nb:small
***returning from CYKDivideAndConquer() sc : 37.200298
# STOCKHOLM 1.0
#=GF AU    Infernal 0.7

scaffold_3_2136376-2136148_1_37.15             AUGACCACACUCUACAGGAUCUUUUGUAUAGUUGGUCUCCCGUCAUCGUA
#=GC SS_cons                                   ::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                                        AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUuuGUUACUAGAGAAGUUU

scaffold_3_2136376-2136148_1_37.15             CUCCUACGUUGACAAACCCUAAACGCACGAUGAAGAUAGAGAGGUCCAUC
#=GC SS_cons                                   ::::::::::::::::::::::::((((--------------((((((((
#=GC RF                                        CUCUGAauGUGUAGAGCCCcgAAACCaCGAGGAgGAGAcauAGCGuuCuC

scaffold_3_2136376-2136148_1_37.15             ACCUGAGCGUGAGGCAGGAUCAUCGUCCUACUCCUUUGUGGGcaGGCGCU
#=GC SS_cons                                   ((((,,,,,,,,,,,,<<<<--<<<<<<<<<______>>>>>..->>>>-
#=GC RF                                        uCCuGAGCGUGAAGcCGGCuuucgGcGcuGCuUaauUGCagC..UgCcgu

scaffold_3_2136376-2136148_1_37.15             GAUUCCUCGAUGACCGUGCGCUACCGUAUGGcucuucgugagcAACGGUA
#=GC SS_cons                                   ->>>>,,,,,,,,,,,,<<<<-<<<<<<___............>>>>>>-
#=GC RF                                        uaGCCAUUGAUGAUCGUuCucaccccCcuuu............gGggggu

scaffold_3_2136376-2136148_1_37.15             GCACUGGUGGuUGGAUCAUUCCGAAUGCG
#=GC SS_cons                                   >>>>)))))).))))))-------)))):
#=GC RF                                        gaGagGGaGa.GaaCGCAgUCUGAGuGGu
//

CPU time: 1.40u 0.00s 00:00:01.39 Elapsed: 00:00:02