# STOCKHOLM 1.0 #=GF AU Infernal 0.1 #=GS AP001507.1/288594-288961 WT 1.00 #=GS AB006424.1/2906-3273 WT 1.00 #=GS AE017024.1/157480-157835 WT 1.00 #=GS AE016998.1/163093-163448 WT 1.00 #=GS AP004593.1/258808-259176 WT 1.00 #=GS AL596166.1/50559-50954 WT 1.00 #=GS AF270378.1/2446-2029 WT 1.00 #=GS AC078934.3/32805-32389 WT 1.00 #=GS AE007529.1/1-342 WT 1.00 #=GS AE015944.1/292831-292358 WT 1.00 #=GS AE013165.1/2718-2361 WT 1.00 #=GS AE016953.1/223210-222863 WT 1.00 #=GS AL935254.1/94358-94709 WT 1.00 #=GS AE010557.1/1-209 WT 1.00 #=GS AP001507.1/288594-288961 DE 186..329 172.253250 #=GS AB006424.1/2906-3273 DE 97..241 151.531830 #=GS AE017024.1/157480-157835 DE 61..192 179.467590 #=GS AE016998.1/163093-163448 DE 97..228 179.923904 #=GS AP004593.1/258808-259176 DE 82..227 156.775833 #=GS AL596166.1/50559-50954 DE 189..362 153.721497 #=GS AF270378.1/2446-2029 DE 192..385 148.813217 #=GS AC078934.3/32805-32389 DE 198..390 141.099304 #=GS AE007529.1/1-342 DE 79..215 138.415512 #=GS AE015944.1/292831-292358 DE 202..357 118.595169 #=GS AE013165.1/2718-2361 DE 116..250 143.985779 #=GS AE016953.1/223210-222863 DE 116..241 123.104691 #=GS AL935254.1/94358-94709 DE 105..233 118.056015 #=GS AE010557.1/1-209 DE 37..160 109.025124 AP001507.1/288594-288961 CGCCAGGACUAUUCCACGGACGG........................... #=GR AP001507.1/288594-288961 SS ......<<<<<<<<.................................... AB006424.1/2906-3273 CGCCCGAACUAAGCGCCCGGA--........................... #=GR AB006424.1/2906-3273 SS ......<<<<<<<<.................................... AE017024.1/157480-157835 CGCCAGAACUACA----------........................... #=GR AE017024.1/157480-157835 SS ......<<<<<<<..................................... AE016998.1/163093-163448 CGCCAGAACUACA----------........................... #=GR AE016998.1/163093-163448 SS ......<<<<<<<..................................... AP004593.1/258808-259176 CGCCAGGACUAUUCUUCGGACG-........................... #=GR AP004593.1/258808-259176 SS ......<<<<<<<<.................................... AL596166.1/50559-50954 CGCCAGAACUGAUUGGGACGAAAaugcuuaaaggugaaauuccuggaaag #=GR AL596166.1/50559-50954 SS ......<<<<<<<<.................................... AF270378.1/2446-2029 CGCCUGUGCAAAAUACCUAAAUAguuaucaaguauuaaaaguuaaaauag #=GR AF270378.1/2446-2029 SS ......<<<<<<<<.................................... AC078934.3/32805-32389 CGCCUGUGCAAAUAAAUAUUUGUauuugaagauuaaagguuaauauauga #=GR AC078934.3/32805-32389 SS ......<<<<<<<<.................................... AE007529.1/1-342 CGCCCGAACUUGAGUGAUAUA--........................... #=GR AE007529.1/1-342 SS ......<<<<<<<<.................................... AE015944.1/292831-292358 GGUCUGAG-UAAGUUCCACCAACcaaaucacagauuugggg......... #=GR AE015944.1/292831-292358 SS ......<<.<<<<<.................................... AE013165.1/2718-2361 CGCCUGGACUUAAAGCCUUAA--........................... #=GR AE013165.1/2718-2361 SS ......<<<<<<<<.................................... AE016953.1/223210-222863 CGCCAGACCUGAA----------........................... #=GR AE016953.1/223210-222863 SS ......<<<<<<<..................................... AL935254.1/94358-94709 CGCCAGGACUUUAG---------........................... #=GR AL935254.1/94358-94709 SS ......<<<<<<<..................................... AE010557.1/1-209 CGCCAGAACU-CU----------........................... #=GR AE010557.1/1-209 SS ......<<<<.<<..................................... #=GC SS_cons ::::::<<<<<<<<_________........................... #=GC RF CGCCaGaaCUacgCgCCucaagc........................... AP001507.1/288594-288961 .....................UAACGG...AAUA.GUUGACGAGGA.GAG #=GR AP001507.1/288594-288961 SS ..........................>...>>>>.>>>.........<<< AB006424.1/2906-3273 .....................AAAAGG...CUUA.GUUGACGAGGAuGGA #=GR AB006424.1/2906-3273 SS ..........................>...>>>>.>>>.........<<< AE017024.1/157480-157835 .....................AGUAG-...UGUA.GUUGACGAGGU.GGG #=GR AE017024.1/157480-157835 SS ..............................>>>>.>>>.........<<< AE016998.1/163093-163448 .....................AAUAG-...UGUA.GUUGACGAGGU.GGG #=GR AE016998.1/163093-163448 SS ..............................>>>>.>>>.........<<< AP004593.1/258808-259176 .....................GAUAGGaagGAUA.GUUGACGAGGUaGGA #=GR AP004593.1/258808-259176 SS ..........................>...>>>>.>>>.........<<< AL596166.1/50559-50954 u....................AAAC-A...AUCA.GUUGACGAGGA.GGA #=GR AL596166.1/50559-50954 SS ..........................>...>>>>.>>>.........<<< AF270378.1/2446-2029 uagaacuuuuauagauaacgaUUUGGA...UUUU.GUAGACGAGGA.GGA #=GR AF270378.1/2446-2029 SS ..........................>...>>>>.>>>.........<<< AC078934.3/32805-32389 guggccuuuauagagugcaauAUAUGU...AUUU.GUAGACGAGGA.GGA #=GR AC078934.3/32805-32389 SS ..........................>...>>>>.>>>.........<<< AE007529.1/1-342 .....................GUUCAU...UUAA.GUUGACGAGGA.UGG #=GR AE007529.1/1-342 SS ..........................>...>>>>.>>>.........<<< AE015944.1/292831-292358 .....................UGUC-A...CUUAaGUUGACGAGGA.UGG #=GR AE015944.1/292831-292358 SS ..........................>...>>>>..>>.........<<< AE013165.1/2718-2361 .....................GGC--U...UUAA.GUUGACGAGGG.CAG #=GR AE013165.1/2718-2361 SS ..........................>...>>>>.>>>.........<<< AE016953.1/223210-222863 .....................---CG-...UUCA.GGUGACGAGGAgAGA #=GR AE016953.1/223210-222863 SS ..............................>>>>.>>>.........<<< AL935254.1/94358-94709 .....................AAUC--...UAAA.GUUGACGAGGAuGAC #=GR AL935254.1/94358-94709 SS ..............................>>>>.>>>.........<<< AE010557.1/1-209 .....................UUUU--...AG-A.GUUGACGAGGA.UUG #=GR AE010557.1/1-209 SS ..............................>>.>.>>>.........<<< #=GC SS_cons ....................._____>...>>>>.>>>,,,,,,,,.<<< #=GC RF .....................aauCGG...cguA.GuuGACGAGGA.GGG AP001507.1/288594-288961 GG.UUUAUCGA...AGGUU-.CGGCGGAUG.CCCUCCGGUUGCACAU... #=GR AP001507.1/288594-288961 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AB006424.1/2906-3273 GG.-UUAUCG-...A-AUUU.CG-CGGAU-.CCUCCCGGCUGAGUGUgca #=GR AB006424.1/2906-3273 SS <<......<<...........>>........>>>>><<<<<<........ AE017024.1/157480-157835 GU.UU-AUCG-...AGAUUU.CGGCGGAUG.ACUCCCGGUUGUUCAU... #=GR AE017024.1/157480-157835 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AE016998.1/163093-163448 GU.UU-AUCG-...AGAUUU.CGGCGGAUG.ACUCCCGGUUGUUCAU... #=GR AE016998.1/163093-163448 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AP004593.1/258808-259176 GG.UU-AUCG-...A-AUUUuCGGCGGGUG.CCUCCCGGCUGUC-AU... #=GR AP004593.1/258808-259176 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AL596166.1/50559-50954 GA.UUAAUCGA...A-AUUU.CGGCGGGAG.UCUCCCGGCUGUGCA-... #=GR AL596166.1/50559-50954 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AF270378.1/2446-2029 UAgUG-AUCGAaucAGAU--.CGGCGGAUGcUAUCCCGGAUGUG-G-... #=GR AF270378.1/2446-2029 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AC078934.3/32805-32389 UAgUG-AUCGAau.AGAU--.CGGCGGAUGcUAUCCCGGAUGUG-G-... #=GR AC078934.3/32805-32389 SS <<.<...<<<...........>>>.....>.>>>>><<<<<<........ AE007529.1/1-342 GG.AGAAUCG-...A-AUCUuCGGCGGAUG.CCCCACGGUACCGC--... #=GR AE007529.1/1-342 SS <<.-...<<<...........>>>.....-.>>>>><<.---........ AE015944.1/292831-292358 GG.AGUAUCG-...A-AUCUuCGGCGGGUG.CCCCACGGUACUGC--... #=GR AE015944.1/292831-292358 SS <<.-...<<<...........>>>.....-.>>>>><<.---........ AE013165.1/2718-2361 GG.UUUAUCG-...AGACAU.CGGCGGGUG.CCCUGCGGUCUUCC--... #=GR AE013165.1/2718-2361 SS <<.<...<<<...........>>>.....>.>>>>><<<<<-........ AE016953.1/223210-222863 GC.UU-AUCGA...AGAUU-.CGGCGGGUG.GCUCUAGG--GAC---... #=GR AE016953.1/223210-222863 SS <<.<...<<<...........>>>.....>.>>>>>..<..<........ AL935254.1/94358-94709 GU.UU-AUCGAu..A-AU--.CGACGGGUG.ACGUCAGG--GAC---... #=GR AL935254.1/94358-94709 SS <<.<...<<<...........>>>.....>.>>>>>..<..<........ AE010557.1/1-209 GAaUU-AUCGA...AGUUUU.CGGCGGAUGuUCCAAAGGUGGUU-A-... #=GR AE010557.1/1-209 SS <<.<...<<<...........>>>.....>.>>>>>...<.<........ #=GC SS_cons <<.<---<<<_...______.>>>----->.>>>>><<<<<<_____... #=GC RF GG.UUuAUCGA...AGAUUU.CGGCGGgUG.CCCCCCGGcuGUcCaU... AP001507.1/288594-288961 ...GACAGCCGCAAG-C.UUUUGU...A.AAAAA-CAGAGGGGCGACCUU #=GR AP001507.1/288594-288961 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AB006424.1/2906-3273 gauCACAGCCGUAAG--aAUUUCU...U.CAAA-CCAAGGGGGUGACUCC #=GR AB006424.1/2906-3273 SS .....>>>>>>.......<<<<<<...........<<<<<<<....>>>> AE017024.1/157480-157835 ...CACAACCGCAAG-C.UUUUAC...U.UAAA-UCAUUAAGGUGACUUA #=GR AE017024.1/157480-157835 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AE016998.1/163093-163448 ...CACAACCGCAAG-C.UUUUAC...U.UAAA-UCAUUAAGGUGACUUA #=GR AE016998.1/163093-163448 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AP004593.1/258808-259176 ...CACAGUCG--AAAC.UUUAUC...AcUAAAA-CAGUAGGGUGACCUA #=GR AP004593.1/258808-259176 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AL596166.1/50559-50954 ...UGCAGUCGUUAA--gUCUUACuu.A.CAAA-UCAUUUGGGUGACCAA #=GR AL596166.1/50559-50954 SS .....>>>>>>.......<-<<<<...........<<<<<<<....>>>> AF270378.1/2446-2029 ...CACAUUCGUUAGCU.UAUUAA...G.UAAA-UCAUUAAGGUGACUUA #=GR AF270378.1/2446-2029 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AC078934.3/32805-32389 ...CUCAUUCGUUAGCU.UAUUAA...G.UAAAA-CAUUAGGGUGACUUA #=GR AC078934.3/32805-32389 SS .....>>>>>>.....<.<<<<<<...........<<<<<<<....>>>> AE007529.1/1-342 ...ACUAC-CGUUAG-C.GGUUGG...-.UAAAA-GCAGAAAGUGAUUUC #=GR AE007529.1/1-342 SS .....---.>>.......<<<<<<...........<<<<<<<....>>>> AE015944.1/292831-292358 ...ACUAC-CGUUAA--aGAUUGA...-.CAAAA-CCAAGGAGUAAUUUU #=GR AE015944.1/292831-292358 SS .....---.>>.......<<<<<<...........<<<<<<<....>>>> AE013165.1/2718-2361 ...UGCGACCGUUAGAG.GACUG-...G.UAAAA-CCACA-GGCGAC-UG #=GR AE013165.1/2718-2361 SS .....->>>>>.....<.<<<<<............<<<<<.<....>.>> AE016953.1/223210-222863 ...UGCACU--CUAC--aGAUAACaaaG.AAAAA-C-UAAUUGUGAAGUU #=GR AE016953.1/223210-222863 SS .....>..>.........<<<<<<...........<.<<<<<....>>>> AL935254.1/94358-94709 ...UGCACU--CUACAG.GUCAAUu..A.CAAAA-ACCGACUGUGAGGUU #=GR AL935254.1/94358-94709 SS .....>..>.......<.<<<<<<...........<<<<<<<....>>>> AE010557.1/1-209 ...--C-A-----AC--cAUUAUCa..A.CAAAA-ACACAGAGCAAUUUG #=GR AE010557.1/1-209 SS .....>.>..........<<<<<<...........<<<<<<<....>>>> #=GC SS_cons ...__>>>>>>,,,,,<.<<<<<<...-.------<<<<<<<____>>>> #=GC RF ...CaCagCCGCUAGcC.GuUuGC...g.CAAAAUCCccaGGGUGACCug AP001507.1/288594-288961 CUGGACAAA.G..GCAAAAG #=GR AP001507.1/288594-288961 SS >>>..........>>>>>>> AB006424.1/2906-3273 UUGAACAAA.G..AGAAAUC #=GR AB006424.1/2906-3273 SS >>>..........>>>>>>. AE017024.1/157480-157835 GUGGACAAA.G..GUGAAAG #=GR AE017024.1/157480-157835 SS >>>..........>>>>>>> AE016998.1/163093-163448 GUGGACAAA.G..GUGAAAG #=GR AE016998.1/163093-163448 SS >>>..........>>>>>>> AP004593.1/258808-259176 UUGCACAAAaG..GAUAAAG #=GR AP004593.1/258808-259176 SS >>>..........>>>>>>> AL596166.1/50559-50954 GUGGACAGA.GuaGUAAUGA #=GR AL596166.1/50559-50954 SS >>>..........>>>>->. AF270378.1/2446-2029 GUGGACAAA.G..UUAAUAA #=GR AF270378.1/2446-2029 SS >>>..........>>>>>>> AC078934.3/32805-32389 AUGGACAAA.G..UUAAUAA #=GR AC078934.3/32805-32389 SS >>>..........>>>>>>> AE007529.1/1-342 UGUCACAAA.G..CCAAUC- #=GR AE007529.1/1-342 SS >>>..........>>>>>>. AE015944.1/292831-292358 UGGUACAAA.-..UCAAUCA #=GR AE015944.1/292831-292358 SS >>>..........>>>>>>. AE013165.1/2718-2361 UGGCAUAGA.G..-CAGUCC #=GR AE013165.1/2718-2361 SS >>>...........>>>>>> AE016953.1/223210-222863 A-GAACAAA.GcgGUUAUCA #=GR AE016953.1/223210-222863 SS >.>..........>>>>>>. AL935254.1/94358-94709 GGUGACAGA.UauAUUGACC #=GR AL935254.1/94358-94709 SS >>>..........>>>>>>> AE010557.1/1-209 UGUAACAAA.G.aGAUAAUA #=GR AE010557.1/1-209 SS >>>..........>>>>>>. #=GC SS_cons >>>------.-..>>>>>>> #=GC RF gGGgACAAA.G..GCaAaCG //