############################################################################### # ____ _ _____ ___ ____ _____ __ # # / __ \/ | / / | |__ \ / __ \/ ___/___ ____ ___________/ /_ # # / /_/ / |/ / /| | __/ // / / /\__ \/ _ \/ __ `/ ___/ ___/ __ \ # # / _, _/ /| / ___ |/ __// /_/ /___/ / __/ /_/ / / / /__/ / / / # # /_/ |_/_/ |_/_/ |_/____/_____//____/\___/\__,_/_/ \___/_/ /_/ # # # ############################################################################### # # # RNA2DSearch is an open source bioinformatics pipeline for searching # # for short RNA secondary structures similar to user defined reference # # structures on a genomic scale. # # # # Contact: Russell.Hamilton@bioch.ox.ac.uk # # http://www.rna2dsearch.com # # Department of Biochemistry, # # University of Oxford, OX1 3QU # # Copyright (C) 2008 Russell S. Hamilton # # # ############################################################################### # GNU Licence Details: # # This program is free software; you can redistribute it and/or modify it # # under the terms of the GNU General Public License as published by the Free # # Software Foundation; either version 2 of the License, or (at your option) # # any later version. # # # # This program is distributed in the hope that it will be useful, but WITHOUT # # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or # # FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for # # more details (See http://www.opensource.org/licenses/gpl-license.php). # # # # You should have received a copy of the GNU General Public License along # # with this program; if not, write to the Free Software Foundation, Inc., # # 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # ############################################################################### +---------+-----------------+------+------+------+------+------------------------------------------------------------------------+------------------------------------------------------------------------+ | GENE/TE + NAME | ILSD | ILSF | GLSD | ILSF | SEQUENCE | STRUCTURE BRACKET NOTATION | +---------+-----------------+------+------+------+------+------------------------------------------------------------------------+------------------------------------------------------------------------+ | GLS | GLS | 0.24 | 0.68 | 0.00 | 0.00 | aaguaauuuucgugcucucaacaauugucgccgucacagauuguuguucgagccgaaucuuacu | .(((((..((((.((((.((((((((((.......))).)))))))...))))))))..))))) | | TE19969 | 1360 | 0.10 | 0.39 | 0.24 | 0.61 | agauauucagagagagauuaauuucuuaaaguugacaguaguuuucugagauca | .(((.(((((((((...(((((((....)))))))......)))))))))))). | | TE20325 | 1731 | 0.10 | 0.39 | 0.22 | 0.65 | uguguguugaauauaggccauuugcacaugugcauauguaauucuguaugagaacauaca | .(((((((..(((((((.(((.((((....)))).)))....)))))))...))))))). | | TE19242 | 297 | 0.11 | 0.41 | 0.21 | 0.69 | ugauauaauuauuuacuauuuuugcucauaacgauauuaaagauaacgauauuac | ((((((..((((((..((((.(((....))).))))....))))))..)))))). | | TE19242 | 297 | 0.11 | 0.41 | 0.21 | 0.69 | ugauauaauuauuuacuauuuuugcucauaacgauauuaaagauaacgauauuac | ((((((..((((((..((((.(((....))).))))....))))))..)))))). | | TE20201 | 3S18 | 0.11 | 0.51 | 0.27 | 0.73 | cccagagaagucaugucgauuuucaguucgagagaauuaaacuuccgacuuuuucugga | .((((((((.....(((((..((.(((((....))))).))..).)))).)))))))). | | TE20132 | 412 | 0.11 | 0.38 | 0.27 | 0.77 | auugcaauugaaugacucgauauguuuauuuaaacauggaaagaaaauuauugcaag | .(((((((..(((...((..(((((((....)))))))....))..)))))))))). | | TE19834 | BS | 0.11 | 0.52 | 0.25 | 0.65 | aaacacauccuucaggccuuugaugacaaggaauacugcaaugguguguuc | .((((((((.(((((..(((((....)))))....))).)).)))))))). | | TE19626 | Burdock | 0.11 | 0.39 | 0.21 | 0.69 | augugucguggagaaaagcggcucaugucgcuuuuaaaguuuucaaagauuacga | .((((((.((((((((((((((....)))))))).....))))))..)).)))). | | TE19938 | Cr1a | 0.10 | 0.42 | 0.26 | 0.79 | uuuguagaucaaauguaucaccgugucaacacgguuuuaugaaacgcagaucaacaau | .((((.((((...(((.((((((((....)))))).....)).)))..)))).)))). | | TE18906 | Doc2 | 0.11 | 0.43 | 0.21 | 0.63 | acuguucagcuauauucuaagauguugcacaagcauuugaccgagucuggcuggaagga | .((.((((((((.((((..(((((((.....)))))))....)))).)))))))).)). | | TE20064 | FB | 0.10 | 0.48 | 0.22 | 0.58 | uuuuauuuuaaagaggugggcuaaggaaauugguuguauuuuaaaagugggc | .((((((((...((((((((((((.....)))))).)))))).)))))))). | | TE19713 | G2 | 0.08 | 0.19 | 0.22 | 0.59 | ugcuggcaauccucuccaaaauacucgaaagaguauuucugcggagaguguugccaguac | (((((((((..((((((.((((((((....))))))))....))))))..))))))))). | | TE19620 | HMS-Beagle | 0.09 | 0.39 | 0.21 | 0.67 | uaaguauauuauuauuauuauauuauuauuauaauauuauuauuauuauuauauuuu | .(((((((.((.((.((..(((((((....)))))))...)).)).)).))))))). | | TE20189 | I-element | 0.02 | 0.00 | 0.22 | 0.67 | augcacaccucccucgucacucuugauuuuucaagagccuucgaucgaguaggugugcac | .(((((((((..((((((.(((((((....))))))).....)).)))).))))))))). | | TE20177 | Idefix | 0.20 | 0.61 | 0.08 | 0.29 | guuuuguaaucauuuagugaaauaaaaacuauaauuuuuuucacuuauaaauauugcaagaa | .(((((((((.(((((((((((.(((........))).)))))))...))))))))))))). | | TE20235 | R1-element | 0.22 | 0.54 | 0.10 | 0.34 | ugcgcacgagugcuccuccgcaauuuuuucccaguugcggaguccgaagcaccgauugcc | .(((..((.((((((((((((((((.......))))))))))...).)))))))..))). | | TE20275 | Rt1a | 0.11 | 0.45 | 0.21 | 0.60 | cguagugcuucuaagugaaccauaccuuccugguguggguaacucaggagugcuacu | .(((((((((((.(((...(((((((.....)))))))...))).))))))))))). | | TE19344 | Rt1a | 0.11 | 0.51 | 0.27 | 0.83 | ggcauaucagcagcaaaggcgaaugcuuuuaaggaccugauugauagcg | .((.(((((((((.((((((....))))))......))).)))))))). | | TE19344 | Rt1a | 0.11 | 0.38 | 0.21 | 0.54 | cguagugcuuuugagugaaccauaccuaccugguguggguaacucaggagugcuacu | .(((((((((((((((...(((((((.....)))))))...))))))))))))))). | | TE20173 | Rt1b | 0.11 | 0.61 | 0.25 | 0.69 | cggcgcucauugauuuggccucugugcgaacggaagcucaaggaauagcacua | .((.(((.(((..((((((.(((((....))))).)).)))).)))))).)). | | TE19304 | Rt1b | 0.11 | 0.51 | 0.25 | 0.70 | ucgagaucccccaccagaggagucgguaacccgacccauggugacggaaucucgg | .((((((((..(((((..((.(((((....))))))).)))))..)).)))))). | | TE19740 | Rt1b | 0.11 | 0.54 | 0.25 | 0.61 | gggcgauagagauguucgaaggugcuacuagcgagcacugcuugacuagccguucuaccca | .((.(.(((((..((((((.((((((.(....)))))))..))))...))..)))))))). | | TE20245 | Rt1c | 0.10 | 0.27 | 0.22 | 0.72 | caggccgcaaguugacacuacgcauuaauaaaugcguccgauguuuuaaaaugaagccug | .((((..((..((((.((.(((((((....))))))).....)).))))..))..)))). | | TE19805 | S-element | 0.10 | 0.44 | 0.22 | 0.67 | caaaaguguguaaauuggaauuugauguuuauuuucuuguauauuuaauauuuuua | .((((((((.(((((.((((..(((...)))..)))).....))))))))))))). | | TE19266 | S-element | 0.10 | 0.41 | 0.26 | 0.76 | uggcacugugcauaguuucuuaauauauuuauauuauauccaauuauacuagucuu | .((.((((.(.((((((...((((((....)))))).....)))))).))))))). | | TE19273 | S-element | 0.10 | 0.50 | 0.20 | 0.65 | aacaaaauaauuaaaaaauuuaugauuaaacuuagguuuaguguuuugug | .((((((((.(((((.((((((....)))).))...))))))))))))). | | TE20228 | S2 | 0.09 | 0.37 | 0.19 | 0.52 | ucgaggaguuugagauuuggcauucagagaaugaaugcagaacaauauuuaaacauuuuga | .(((((.((((((((((..(((((((.....))))))).....))).))))))).))))). | | TE19915 | Stalker2 | 0.11 | 0.42 | 0.23 | 0.71 | ugcauggccuuuaaguuugguuuuuauaaccgaaacagcuagagacucaugcu | .((((((.(((((..(((((((.....))))))).....))))).).))))). | | TE18944 | Tc1 | 0.22 | 0.63 | 0.10 | 0.33 | gauggaaaguugauuugcuaaaaaaaaauuauaaaauguuuauuuuuuuuuaagucagauuucaug | .((((((..((((((((..((((((((((........)))).))))))..)))))))).)))))). | | TE18945 | Tc1 | 0.10 | 0.32 | 0.26 | 0.72 | uuuuuguuuuuggucacuugcugcaaaagugcgcgaaauuaggcgguaacaaaaau | ((((((((..(.(((..((((.(((....))))))).....))).).)))))))). | | TE19334 | Transpac | 0.09 | 0.48 | 0.23 | 0.81 | aauuuaaguuuauuuguaaaauuucaagaaauuuauaggcaguauuuuucaagua | .(((((((..((((.((.((((((....))))))....))))))..))).)))). | | TE19261 | X-element | 0.07 | 0.34 | 0.23 | 0.61 | ccggccgaucagucuccucacuucaauuuugaagguguuuaagagacugauugcugu | .((((.((((((((((..(((((((....)))).))).....)))))))))))))). | | TE18952 | aurora-element | 0.11 | 0.42 | 0.23 | 0.63 | agguccugccuacuugccgugucaguggaugacgcgauggaaaagaugguggaggacua | .((((((.(((((((..(((((((.....)))))))......))).))).).)))))). | | TE19926 | baggins | 0.11 | 0.52 | 0.23 | 0.78 | uuagaagcacucugcuuguggagcauccgcuccaaaggacgcagcaugccuac | .(((..(((..((((((.((((((....))))))...)).))))..)))))). | | TE20203 | blood | 0.10 | 0.46 | 0.20 | 0.74 | gguuaacaaaagugauugggacauuugguuaccauauuucacuuauugcuucaaua | .((((((((((((((.((((((.....))).)))....)))))).))).)).))). | | TE19364 | copia | 0.20 | 0.73 | 0.12 | 0.48 | uggcagcuggugcaaaaauagaagagauggauaaaauuucucauuuacugaucacauugccu | .(((((.((((.((.((((.((.(((((.......)))))))))))..))))))..))))). | | TE19469 | copia | 0.12 | 0.58 | 0.22 | 0.71 | aaauaauuuucguuuauggcaugagagguuuggccauauaagcaauggcaaauuauua | .(((((((((((((((((((.(....).....)))))).....))))).)))))))). | | TE18972 | diver | 0.09 | 0.50 | 0.23 | 0.75 | ggagccgaccuuauggcacaacucuuguugccuggaacuaagauuggcuug | .(((((((.((((.(((((((...))).))))......)))).))))))). | | TE20264 | gypsy2 | 0.19 | 0.52 | 0.11 | 0.46 | ucugcgaaaaguuccgcgaagaugcacuacguguguuuguuucgggacuuaagcguagu | .(((((..((((((((.((((((((((...)))))))).)).))))))))...))))). | | TE19930 | gypsy3 | 0.11 | 0.59 | 0.23 | 0.67 | aggucagauagcgcuaauugcaggagcaauuuucugcgcucucauuugcaucg | .(((((((((((((.((((((....))))))....)))))...))))).))). | | TE19103 | gypsy | 0.11 | 0.52 | 0.21 | 0.60 | ccuggcagcggaaagcugacacuuccuaccgggaguguugcuucacgcugcaaga | .((.((((((..((((.(((((((((....)))))))))))))..)))))).)). | | TE19800 | hopper2 | 0.11 | 0.34 | 0.21 | 0.57 | auugacaugacagacauauuaauauuguccucauauuaaaaaaugagcuggaugucaac | .(((((((..(((.(((.(((((((.(....))))))))...)))..))).))))))). | | TE19901 | hopper | 0.11 | 0.45 | 0.23 | 0.70 | cguugugauucugcgcccuuacgaguucaucugcuugcugucuucggccguuuauaaua | .(((((((...((.(((..(((((((......))))).)).....))))).))))))). | | TE19870 | invader2 | 0.10 | 0.42 | 0.26 | 0.77 | uauaaguuggaaauuucgaaaagaucaggugaucuuaaaugucaggauggucgaauugua | .((((.((((..(((..((.((((((....)))))).....))..)))..)))).)))). | | TE20319 | invader3 | 0.06 | 0.31 | 0.24 | 0.76 | aguauaucauugcuaucucgcucuuacuuauaagcuagcauuaagagauaagaauguaca | .((((((..((..(((((((((((((....))))..))).....)))))).)))))))). | | TE19234 | invader4 | 0.10 | 0.47 | 0.24 | 0.65 | aagucguuaguuaucaagcgaacauauaaauauucgcaugaauguaauggugacuc | .((((((((..(((((.(((((.((....)).))))).)).)))...)))))))). | | TE20045 | jockey | 0.11 | 0.45 | 0.23 | 0.67 | gugauacgcucgcggauuaacaaggggcucugaggagcuucggauauuccucagcgaucac | .((((.((((.(.(((.((....(((((((....)))))))...)).))).))))))))). | | TE19239 | mariner2 | 0.10 | 0.32 | 0.18 | 0.52 | ucaauuagagaagguuuggaauggccaaucuguuccauugugauuuuuucuauugu | .((((.((((((((((((((((((.....))))))))....)))))))))))))). | | TE20135 | mdg1 | 0.22 | 0.55 | 0.10 | 0.29 | caugaucaaaaggaguaaccacagugacugaaugucaucuguauggucgacuauuuuuaaguuauu | .(((((..((((((((.(((((((((((.....)))).))))..)))..))).)))))..))))). | | TE20171 | mdg3 | 0.11 | 0.46 | 0.19 | 0.57 | guuuuccaguugaugcucucgcucucgccaaagagacgauaaccgauuacgaugggaaaac | .((((((.((((.((.(((((.((((......))))))).....)).)))))).)))))). | | TE19900 | qbert | 0.09 | 0.39 | 0.23 | 0.79 | uuaucgguauauucccgaauuuugaauuuauuaagaacaguguggauauugauau | .((((((((...(((((..((((((.....))))))....)).))))))))))). | | TE20199 | roo | 0.09 | 0.31 | 0.21 | 0.73 | ucauggaccgcguuggcagaaggcauucccucugcgccucaaugcugcucugugc | .(((((((.(((((((((((.((....)).)))))....)))))).).)))))). | | TE19253 | transib4 | 0.11 | 0.50 | 0.25 | 0.70 | gcgccuguauggauuuccguuucuaauuuaggauuguacaauuucaauacgggacgg | .((((((((((((.((.((.(((((...))))).))...)).))).))))))).)). | +---------+-----------------+------+------+------+------+------------------------------------------------------------------------+------------------------------------------------------------------------+