# STOCKHOLM 1.0
#=GF ID PhotoRC-I
#=GF AC RF01716
#=GF DE PhotoRC-I RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 45.0
#=GF NC 37.7
#=GF TC 51.6
#=GF SE Published; PMID:20230605;
#=GF SS Published; PMID:20230605;
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 22.48 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 20230605
#=GF RT Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT archaea and their metagenomes.
#=GF RA Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL Genome Biol. 2010;11:R31.
#=GF WK PhotoRC_RNA_motifs
#=GF ** seedtax: Bacteria; unclassified sequences
#=GF SQ 65

AACY023623377.1/287-246        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY020357826.1/692-649        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
BX569694.1/85338-85295         AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020002466.1/34-75          AGGCAGGACUUCU--GUCCUUUCUUAAACC-GUCCCCUCG-GGGGC
AACY020555888.1/1588-1547      UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY023381520.1/1204-1161      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020230102.1/641-682        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AANP01000006.1/165195-165236   UGGCAGGGCAUCCCUGCCCUUCCGU-AACU--GCUCUUCG-GAGUU
AACY023856811.1/682-725        AGGCAGGGCUUUCCUGCCCUUCCUUAAAUC-GUUCCUUCG-GGAAC
AACY020358569.1/853-811        AGGCAGGGCCCCCU-GCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AAUA01000001.1/704108-704066   CGGCAGGGCUUCCU-GCCCUUCCGU-AACCCGUCUCUUCG-GAGAC
AACY023836901.1/556-515        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
BX569694.1/302425-302468       AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020238074.1/633-592        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY022984900.1/632-589        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAGC
AACY020529854.1/1240-1199      UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY022410753.1/109-66         AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020523621.1/456-415        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY022923429.1/153-110        AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022976215.1/127-170        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023834750.1/421-380        CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCCUCG-GAGCU
CP000110.1/311054-311011       AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGGAC
AACY022383745.1/671-628        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023810594.1/196-237        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023869287.1/634-676        AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY020489273.1/1935-1892      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CP000110.1/510580-510623       AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGGAC
AACY022913798.1/22-63          CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023829657.1/1220-1179      CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023841191.1/1433-1392      UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
CP000435.1/2093117-2093075     CGGCAGGGCAUCCU-GCCCUUCCGU-AACC-GUCUCCUUGUGAGAC
AACY020970686.1/333-290        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CT971583.1/1915281-1915241     UGGCAGGGCAUCCU-GCCCUUCCGU-AACC--GCUCUUCG-GAGCA
AACY022150842.1/460-501        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY020529150.1/730-771        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY020363125.1/1324-1281      AGGCAGGGCGUCCCUGCCCUUCCUUAAAUC-GUUCCUUCG-GGAAC
AAOK01000001.1/197766-197807   UGGCAGGGCAUUCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCC
AACY021570204.1/746-787        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023816053.1/812-853        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
CP000435.1/372998-372956       CGGCAGGGCAUCCU-GCCCUUCCGU-AACC-GUCUCCUUGUGAGAC
AACY021375498.1/405-363        AGGCAGGGCUACCU-GCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AANP01000005.1/140760-140801   UGGCAGGGCAUCCCUGCCCUUCCGU-AACU--GCUCUUCG-GAGCU
AACY021170829.1/357-400        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CP000097.1/1945369-1945412     AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY023021307.1/72-115         AGGCAGGGCGUCCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022012151.1/406-363        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY021975488.1/320-279        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCUUCG-GAGAC
AACY023861064.1/1393-1436      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022150667.1/535-576        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AAUA01000004.1/159482-159440   CGGCAGGGCUUCCU-GCCCUUCCGU-AACCCGUCUCUUCG-GAGAC
AACY022192565.1/241-199        AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
ACNY01000005.1/1126774-1126731 AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020542254.1/1310-1353      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY021083976.1/176-133        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023406904.1/1134-1177      AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AAOK01000002.1/170526-170567   UGGCAGGGCAUUCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCC
CP000097.1/1741889-1741846     AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY022905865.1/478-437        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AATZ01000004.1/136676-136719   AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY023521750.1/1115-1073      AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY023988443.1/35-78          AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023863310.1/1225-1182      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AF156980.1/155-195             UGGCAGGGCAUCCU-GCCCUUCCGU-AACC--GCUCUUCG-GAGCA
AATZ01000002.1/657722-657679   AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY022125101.1/820-863        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUCCCUUCG-GGGAU
#=GC SS_cons                   :<<-<<<<<______>>>>>->>:::::::.<<<<<____.>>>>>
#=GC RF                        aGGCAGGGCuUCCCUGCCCUUCCuUAAACC.GuCCCUUCG.GGGaC
//
