tmRNA example

Example from tmRNA database.

pairing_mask aaaaaaa--------------bbbbb-bbbb-----ddddddccceeeee---ffffffgggggg---hhhhhhhh--gggggg-----------hhhhhhhh---------------------------------------------------------------------------------------------iiiiiiiiijjjjjj---------------------------------------jjjjjjiiiiiiiii------------kkkkkkkk---llllllmmmmmm-----------nnnnnnnmmmmmm--oooo----oooo-llllll------kkkkkkkk-----------nnnnnnn------------ppp------ppp---------------qqqqqqqqqqrrrrrr-sssssssssrrrrrrqqqqqqqqqq---------sssssssss--ttttttyuuuuu--vvvv---wwwwwxxxxvvvv--uuuuuytttttt--zzzzz--AAAAAzzzzz---AAAAABBBBB-CCCCC-BBBBB----CCCCC--xxxx-wwww-w--fff-fff------eeeeecccdddddd-------bbbbbbbbb----DDDDD-------DDDDDaaaaaaa----
Aqu.aeo.     GGGGGCGga-aaggauu-cgaCGGGG-ACaggcg---GUCCc---cGAGGa--GCAGGCCGGG-------UGGCU-----CCCGuaac--------AGCCG---------------------cuaaaacagcucccgaagcugaacuc---------------------------------------------------gcucuC-GCUGCcuaauuaaa----------------------------cgGCAGC-G---------------------CGUCC-----CCGGUA--GGUU----------uGCGGGU-GGCC-----------------UACCGGa-------GGGCGucag-----agacACCCGCuc-------------------------------------gGGCUACU--CGGUc---GCACGGG---GCUG--AGUAGCUgacacc--uaaCCCGUGC----UaCCC-UCGGG-gaGCUu---GCCC-GUGGGCga-CCCGA-GGGgAaau-----------------------------------------------ccugaaCAC--GGGC-uaaGCC-UGUaga--gCCUC-----GGAUguggcc-gccGUCCUCGg-acGCGGGuucgauuCCCGCCGCCUCCacca
The.mar.     GGGGGCGaa--cggguu-cgaCGGGG-AUGGagu---CCCC-----UGGGaa-gCGAGCCGAGGu---cCCCACCU---CCUCGuaaaaa-----AGGUGGGacaa---------------agaauaagugccaacgaaccuguu------------------------------------------------------gcuguu-GCCGCuuaauaga----------------------------uaaGCGGC-----------------------CGUCCUC---UCCGA----AGUu----------GGCUGG-GCU-------------------UCGGA-----aGAGGGCGugag-----agauCCAGCCua--------------------------------------CCGAUUCA-GcUUc---GCCUUCC---GGcC-UGAAUCGGgaaaac--ucaGGAAGGCug---UGGG-AGaGGacacCCu---GCCC-GUGGGagg-UCcCU-CCCGagagcg-----------------------------------------------aaaaCAC--GGGC-ugcGCU-CGgaga-agCCCA-----GGGGc-----cuCCAUCUUCGg-acGGGGGuucgaauCCCCCCGCCUCCacca
The.the.     GGGGGUGaa-acggucu-cgaCGGGG-GUCgccga-gGGCGu----GGCU---GCGCGCCGAGG----uGCGGGUg--gCCUCGuaaaa-------ACCCGCaac----------------ggcauaacugccaacaccaacuac------------------------------------------------------gcucUC-GCGGcuuaau---------------------------------gaCCGC-GA--------------------CCUCGC----CCGGU---AGCCcu---------GCCGGG-GGCU-----------------cACCGGa-----aGCGGGGacac------aaaCCCGGCua--------------------------------------GCCCGGG--GccAc---GCCCUC----UaaC--CCCGGGCgaagcu--ugaaGGGGGCuc---gCUC-CUGGC--cGCCc---GUCC-GCGGGCcaaGCCAG-GAGgacac-----------------------------------------------gcgaaaCGC--GGAC-uacGCG-CGUaga---GGCC-----CGCCgua----gaGACCUUCGg-acGGGGGuucgacuCCCCCCACCUCCacca
Dei.rad.     GGGGGUGac-ccgguuu-cgaCAGGG-Gaacugaa--GGUG-----aUGUu--GCGUGUCGAGG----uGCCGUUg--gCCUCGuaaaca------AACGGCaaagc--------------cauuuaacuggcaaccagaacuac------------------------------------------------------gcUCUC-GCUgcuu--------------------------------------aAGU-GAGA------------------UGACga-----CCGUG-caGCCc----------GGCCUUUGGCgu----------------CGCGG--------aaGUCAcuaaa----aaaGAAGGCUag--------------------------------------CcCa------GGCgauuCUCCAUA---GCCgac---gGcGaaacu-----uUAUGGAGcuacGGCCu--GCGa-gaACCu---gCCC-ACUGGUga-gCGC--cGGCCcgacaau--------------------------------------------caaacAGU--GGGa-uacACA-CGUaga-c-GCA------CGCUgga----cggaCCUUUGg-acGGCGGuucgacuCCGCCCACCUCCacca
Por.gin.     GGGGCUGa--ccggcuu-ugaCAG-C-GUGaugaa-gCGGU-----AUGUaa-GCAUGUAGUGCGu--gGGUGgCU--UGCACUauaaucu---cAGaCAUCaaa----------------aguuuaauuggcgaaaauaa------------------------------------------------------cuaCGCUcUC-GCUgcguaaucgaagaauaguagauuagacgcuucaucgccgccaaAGU-GGcAGCGacgaga---------CAUCGCc----CGAGC-aGCUUu----------UUCCCG-AAGU----------------aGCUCGa---ugguGCGGUGcugac----aaauCGGGAAcc--------------------------------------GCUA------CAGGaugCUUCCu-g-CCUG------UGGUcagauc---gaacGGAAGaua-agGAu-CGuGCauuGGGuc--GUUUCAGcCUCc--GCuCG-cUCacgaaaa----------------------------------------------uuccaaCUG-AAAC-uaaACA-UGUaga-aaGCAU-----AUUGauu-----cCAUGuUUGg-acGAGGGuucaauuCCCUCCAGCUCCacca
Chl.tep.     GGGGAUGa--caggcuaucgaCAGGA-UAggugug-aGAUGU---cGUUG----CACUCCGAGUUucaGCAUGGAC-gGACUCGuuaaaca---aGUCUAUGUa-----------------ccaauagaugcagacgauuauucguau---------------------------------------------------gcaAuG-GCuGccugauua----------gcacaag-uuaauucagaagccaUcGU-CcUgcggugaaugcgcuuacucUGAAgCCg--ccggauGGCauaaccc------gcGCUUG---aGCCu------------------------acGGgUUCGcgcaa-------gUAAGC-----------------------------------------UCCGUACAU-UCaU---gCCCGA---GgGG-GUGUGCGGGuaacc-----aaUCGGG-aua-agGGg-aCGAa---cGCug--CUGGcGGUGUaa---UCGg-aCCacgaaaaac-----------------------------------------------caACCa-CCAGagauGAG-UGugg----UAACu---GCAUCgag----cagUGUCCUGg-acGCGGGuucaaguCCCGCCAUCUCCacca
Chl.tra.     GGGGGUGua-aagguuu-cgaCUUAG-aAAugaag--CGUU-----AAUU---GCAUGCGGAGGgc---GUUGGCUgg-CCUCCuaaaa------AGCCGACaaa----------------acaauaaaugccgaaccuaaggcugaaugcgaaauuauca---------------gcuucgcugaucucgaagaucuaagAGUA-GCUgcuuaauua------------------------------gcaaAGU-UGUUaccuaaauacgggugaccCGGUGU-----UCGcG--AGCUcc---------ACCAGA-GGUU-----------------UuCGAa-------ACACCGuca------uguaUCUGGUua-------------------------------------GAACUUAgguccUUUa-AUUCUCG---AGGaa--aUGAGUUUgaaau--uuaaUGAGAGU---CGUUA-GUCUCu-aUAGg--GGUUUCUAGCUGa-gGAGACaUAACGuauag------------------------------------------------uacCUAG-GAAC-UaaGCA-UGUaga---GGUU-----AGCGggg---aguUUaCUAAGg-acGAGAGuucgacuCUCUCCACCUCCacca
Chl.pne.     GGGGGUGua-uagguuu-cgaCUUGA-aAAugaag--UGUU-----AAUU---GCAUGCGGAGGgc---GUUGGCUgg-CCUCCuaaaa------AGCCAACaaa----------------acaauaaaugccgaaccuaaggcugaaugcgaaauuauua---------------gcuuguuugacucaguagagGAaaGaCUA-GCUGcuuaauua----------------------gcaaaaguuguUAGC-UAGaUaaUCucuagg--uaaccCGGUAU----cUGCG---AGCUcc---------ACCAGA-GGCU------------------UGCAa------aAUACCGuca------uuuaUCUGGUug-------------------------------------GAACuuACuuUcUCUa-AUUCUCA---AGGaA--GUucGUUCgagau---uuuUGAGAGU---CAUUG-GCUgCu-aUAGag-gCUUC-UAGCUAa-gGgAGUcCAAUGuaaac-----------------------------------------------aauuCUA--GAAGauaaGCA-UGUaga---GGUU-----AGCAggg---aguUUgUCAAGg-acGAGAGuucgaguCUCUCCACCUCCauua
Ana.spe.     GGGUCcGu---cgguuu-cgaCAGGU-UGGcgaac--GCUaC---UCUGUgauuCAGGUCgAGAG----UGAGUCUc-CUCU-Gcaaauca----AGGCUCAaaaca--------------aaaguaaaugcgaauaacaucguuaaauuu---------------------------------gcucguaaggacgcUcuagua-GcuGccuaa----------------------------auagccucUuuC-agguucGagc------------GUCUU------CGGUUuga-------------cUCCGUU-aa---g---------------GACUG---------AAGACcaac-----ccccAACGGAugcu------------------------------------CUAGCAAu---GUU---CUCUGGUU-GGC----UUGCUAGcu-aagauuuAAUCAGAGc----------------------------------------------------AUCCUa-CGUUCGGGAUaauGAACGAUUCccGCCUUgaGGGUcagaAAGGC------------uaaACC-UGugaaugaGCGGG---G-GGUcaau---acCCAAUUUGg-acAGCAGuucgacuCUGCUC-GAUCCacca