# STOCKHOLM 1.0
#=GF ID Afu_309
#=GF AC RF01512
#=GF DE A. fumigatus sRNA Afu_309
#=GF AU Osuch I
#=GF GA 48.0
#=GF NC 47.9
#=GF TC 49.3
#=GF SE INFERNAL
#=GF SS Predicted; WAR; Clustal_alifold;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 20.50 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 18346967
#=GF RT Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT novel mechanism for regulation of protein synthesis.
#=GF RA Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA Haas H, Huttenhofer A
#=GF RL Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ 10

AM921953.1/1-318           ACCAAUUGAACAAACACGGAUCUGUGUCCAGCGAUCCUGAGCAUGGAAC-UGUUUCUCUUCACGGAGGGGCUGCUUCUGUGUCUCGGUUG--AUUGCUG-GACAGUUCGACGACUUAAGGAGCCAUUCCCUU----------GUGGAUGGU-UUUU----AUUUCCGGUCGACAGAUC-UCAGAUCGA-AUGCUGGCAUU
AAIW01000350.1/3989-4323   UCCUCAACACAAACCACAGAUCUGUGUCCAGUAGUCCUGUUCCAGCUGC-UGGUCGUCCUUCGUGAUGGCUAGUAGCUGUGUUUCGGUUG--AUU-CUG-GACAGUUCGACGACCUAUGGAGCCAUCACUUU-----------CUUAUGAU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAGCGAGAUACAGUGACC
ABRJ01000032.1/26170-26452 CUCAUCACAACAAACCCAGAUCUGUGUCCAGCAGUCCUGAUCCAACCAG-AGU-----AUUCGU-----GCUCUGGUUGUGUUUCGGUUGUUAUUGCUG-GACAGCUCGACGAUUCAUGGAGCCAUCAAGGAUUA---CCCCUCAAAUGGU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAGAGAACCUCAGCG---
AM920437.1/3101326-3101627 ACCAA-------ACACCGGAUCUGUGUCCAGAUUUCCUGUCCA--CGGA-CUCCAGUC-----UGACUGGUUUCUG---UGUGACGGUUG--AGAGCUG-GGCAUUUCGACGAGCUU-GGAGCCAUCAUUUU---------CGUGGAUGGC-CUUUA-CGGUUUCCGGUCGACAGAUC-UCAGAAUAA-GUGUCUGCGCC
EU780991.1/1-296           A---------------CGGACCUGUGCCCAGCGCUCCUCUGCCGCCAGC-UCGU----GCUUGC----ACUUGUAGGC-AGCUAGGGUUG--AGUGCUGAGGCAGUUCGGCA-ACCAAGGAGCCAUCCAGGACUUUACGUUCUUCCAUGAU-GUCA----AUUUCCAUCCGACAGGUCACCAGA-A---GAACCGAACUC
BN001307.1/2431637-2431325 AUGAACAGAACACACACGGAUCUGUGUUCGGCGAUCCUGAUCG--CAGAAAGA-----GUUUAC-----UCUUCUG---UGUUUCGGUCG--AUUGCUG-GACAGUUCGACGACCAAAGGAGGCACCCAUUC--------UCUCGUUUGGU-GUCCAUUGUUUUCCGGUCGACAGAUC-UCAGAUUAA-AUGUCGGCAUU
FQ790321.1/369500-369214   AUCAA------AACACCAGAUUUGUGUCCAGCGUCCCUUUGCCA-------GAACUGCUUGUCAGCG---------AUGGUUUAAGGUUG--UAUGCUGAGGCAGUUCGAUCGUCUAUGGAGCCAUCAACCUACCA-AGGUAAUUUAUGAU-GUCA----AUAUCCGAUCGACAAAUC-UCAGAAUGAUCGGUCCUU---
AM270079.1/209972-209642   CAGAACAGAACACACACGGAUCUGUGUUCAGCGAUCCCGUUCAUGGAGG-GU--GCGGCUUCGGCUGUUAUUUCUUU-GUGUUUCGGUUG--AACGCUG-GACAGUUCGACGACUUAAGGAGCCAUUCAUCU---------UGUGGAUGGU-UUUUG--CACUUCCGGUCGACAGAUC-UCAGAUUAA-AGGUUGGCGCU
AP007155.1/3180884-3180570 CUUUUUCGAACACACACGGAUCUGUGUCCAGCGAUCCUGAGCGUGGAGG-C---------UUG---------UCUUCUGCGUCUCGGUUG--AUUACUG-GACAGUUCGACGACUUAAGGAGCCAUCACAUU---------CAUGGAUGGUCGAUU----AUUUCCGGUCGACAGAUC-UCAGAUUAA-AGGUCGACAUU
AASO01001520.1/4391-4721   ACCAA-------ACCACAGAUCUGUGCCCAGCAAUCCUGUUCGAGCGGU-CGACCAUCAUUCGUGGUGGUCUUCGGCUGUGUUUCGGUUG--AUU-CUG-GACAGUUCGACGACCUAUGGAGCCAUCACUAUUU-----AAAUUUCAUGGU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAUUGAGAUGCAGCGGUC
#=GC SS_cons               :::::::::::::::::((((((((<<<<<<-<<<<<<<<<<<<<<<<<.-<<<-<<<<____>>>>.>>>->>>>>>->>->>>>>-->..>>>->>>.>>>,,,,,,,<<<<<--<<<-<<<________........________>>>.->>>....------>>>>>))))))).)::::::::.::<<<---<<<
#=GC RF                    aucAauagAAcAaacaCaGAuCUGUGuCCAGCgcuCCugugCcagccgg.uggcucgccUUugggcg.gccUccggcuGgGUcacgGUUG..agcGCUG.GaCAGUUCGACGaccuAuGgAgcCAUCaauuu........ucuUuuAUGgu.guCa....AUUUCCgguCGACAGaUC.uCAGAuugA.augccgucgcc

AM921953.1/1-318           AGGAU--UA--CU-UGGUCUUGAGCUCCC---GA---------UA--------GGUGAGCUCGGCUUGAGGGCCUAG-UA-GCCAGCGGCGUCAUAUUCCUGAUCCCUUUACC-----------------GAUUUGGCCGUCGGCUUGUGAGGUUAGGGAAAAACCAUGAC-UAGCCAACAUAU
AAIW01000350.1/3989-4323   AGGAG--UUCACU-CUGCCUUGAGCUUCC---GU---------CA--------GGUGAGCUCGGUGAGAUGGCCUGG-U-UGCUGAAGACGCCAUAUUCCGUCUCCCUUUACCGAUGUGCCCCUUCUUGGGGCCAGGCCGUCGGCUGAUGAGGUUAGGGACUAACCAUGGC--AGCCAACAUCC
ABRJ01000032.1/26170-26452 --GC---CCAGUU-UUUCCUUUUUUGCC---------------UU---------GUGUGAAAGGGAAUUUAACACU---CUGCCUUGAGC-------------UCCCUCCCCG------------------UUUCGACGGGCUGGUGAAUUCGGUAAGGU-------------GGCUGGGUUCC
AM920437.1/3101326-3101627 UUGUG--AU--GC-GGGUCUUGAGCUCCC---AC----------U--------GGUGAGCUCGGCUUGACAGCUUGG-U-GUCGGACGGCGUCAUAUUUCAUAUCUCUUUGCCG------------------AUUGGCCGUUGGCCGCUGAGGUUAGGGAAUAACCAUGAC-UUGCCAACAUAU
EU780991.1/1-296           CGGUG--UGAACC-UC-----GUUCG-CC---GC---------AA--------GGCUUGAGCUUGGGGAGCGCCGGAUGAUGUAGGGGAAGUCAUAUUCCAAU-CCGUUCGCCG--------------------AGGACGUCGUCCUAUGAGGCUGGGG-GAAACCAUGACAAUUGCCACAUUU
BN001307.1/2431637-2431325 GGGUGGUUCACUU-UGGUCUUGAGCUCCC---UC---------AU--------GGUGAGCUCGGCUGGGGUUCCUGG-U-GUC-GACGGCGUCAUAUUCCUGUUCCCUUUGCC-----------------GAUUUGGCCGUCGGCUGAUGAGGUCAGGGAGAAACCAUGGC-UAGCCAACAUUC
FQ790321.1/369500-369214   ---------AUGA-AA--C-UUGAGUCGC---UU---------CG--------GCUGAUUCGG--UGGAUGA--GU---GUACUGAAGACGUCAGAUUCCAAAUCUGUUUGCC--------------------UAGGCUGUUAGCCCUUGAGGUUGCGGAAUAACCCUCUC---GUCUACAUUU
AM270079.1/209972-209642   GGGUG--UUCACUCGGGUCUUGAGCUCCCU-UGU---------UUUCGAACUUGGUGAGCUCGGCUGGAGUUCCUGG-UU-GCUGACGGCGUCAUAUUCCUACUCCCUUCACC-----------------GAAUUGGCCGUCGGUCACUGAGGUUAGGGAAAAACCAUGAC-CUGCCAACAUUA
AP007155.1/3180884-3180570 GGGUG--UUCGCUCUGGUCUUGAGCUCCCUUC--CUUUCGGGGUU--------GGUGAGCUCGGCUGGAGAGCCUGG-U-GCUCGGCGGCGUCAUAUUCCUACUCCCUUUACC-----------------GAUUUGGCCGUCGGCCCAUGAGGUUAGGGAAAAACCAUGGC-CAGCCAACAUAC
AASO01001520.1/4391-4721   AGGAG--UACACU-CUGCCUUGAGCUCCC---AU---------UU--------GGUGAGCUCGGUGAGAUGGCCUGA-UAUGCUGAAGACGCCAUAUUCCACCUCCCUUCACCGAUACAUCCCUUUAUGGGAUUAGGCCGUCGGCUGAUGAGGUUAGGGAAAAACCAUGGC--AGCCAAC----
#=GC SS_cons               <<<--..------.-<<<<--<<<<<<<<...__.........__........>>->>>>>>>>>>------>>>>>.>->>>::::<<<<<<<<--------<<<<<--<<<.................-----<<<<___>>>>----->>>->>>>>------>>>>>.-->>>:::::::
#=GC RF                    ggGuG..uuaacu.ucgcCUUgagcuCCC...gu.........uu........GGUGagcucGgcggGAuagCccgg.caggcuGaaGgCGcCAuAUUCCaaauCCcuUugCC.................GauUuGgCcGUCgGcCgaUGAGGcUagGGaaaAACCaUGgC.uaGcCaACAUuu
//
