Mercurial > repos > rnateam > targetfinder

diff test-data/targetfinder_test_03.txt @ 1:c9d56748fbde draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit fe9dd99a14770b6c5f26e24893599acb577e304f"
author rnateam
date Thu, 25 Mar 2021 19:53:15 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targetfinder_test_03.txt	Thu Mar 25 19:53:15 2021 +0000
@@ -0,0 +1,252 @@
+No results for Ath-miR395d
+query=Ath-miR395b, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1
+
+target  5' CUCUCUCUCCAAACGCUUCAC 3'
+              ::.:.::::::.::::: 
+query   3' CUCAGGGGGGUUUGUGAAGUC 5'
+
+query=Ath-miR393a, target=AT1G09812.1 | Symbols: no symbol available | no full name available | chr1:3187442-3188854 FOR, score=5.5, range=452-474, strand=1
+
+target  5' CGAUGAAUGCGAUCUCAUUUGGG 3'
+            ::: :::::::::.: :::::.
+query   3' CCUAGUUACGCUAGGG-AAACCU 5'
+
+query=Ath-miR393a, target=AT2G33380.1 | Symbols: AtRD20, PXG3, CLO-3, CLO3, RD20, AtCLO3 | caleosin 3, Arabidopsis thali, score=5.5, range=719-739, strand=1
+
+target  5' AUGGCAAU-CGAUCCUUUUGGA 3'
+             . :::: ::::::.::::::
+query   3' CCUAGUUACGCUAGGGAAACCU 5'
+
+No results for Ath-miR171a
+query=Ath-miR156g, target=AT2G12400.1 | Symbols: no symbol available | no full name available | chr2:5004884-5008442 REV, score=5, range=347-365, strand=1
+
+target  5' GUGUUUACUCUCUUC-GUUU 3'
+           :::.:.::::::::: ::. 
+query   3' CACGAGUGAGAGAAGACAGC 5'
+
+query=Ath-miR156g, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=5, range=948-967, strand=1
+
+target  5' GAGAUCUCUUUCUUCUGUCA 3'
+           : : :: ::.::::::::: 
+query   3' CACGAGUGAGAGAAGACAGC 5'
+
+query=Ath-miR156g, target=AT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R, score=5.5, range=1649-1668, strand=1
+
+target  5' UUGUCUGCUCACUUCUGUCG 3'
+            ::. ..::: :::::::::
+query   3' CACGAGUGAGAGAAGACAGC 5'
+
+query=Ath-miR156g, target=AT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR, score=6, range=82-101, strand=1
+
+target  5' CUGUUUUCUCUCUUCUCUCC 3'
+            ::.:. ::::::::: :: 
+query   3' CACGAGUGAGAGAAGACAGC 5'
+
+query=Ath-miR156g, target=AT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV, score=6, range=570-590, strand=1
+
+target  5' CUUCUUAUUACUCUUCUGUCU 3'
+            : ::.:.: :::::::::: 
+query   3' CACGAGUGA-GAGAAGACAGC 5'
+
+query=Ath-miR156g, target=AT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV, score=6, range=1472-1490, strand=1
+
+target  5' UUCCUCACUUUCUUCU-UCA 3'
+            : ::::::.:::::: :: 
+query   3' CACGAGUGAGAGAAGACAGC 5'
+
+query=Ath-miR395c, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1
+
+target  5' CUCUCUCUCCAAACGCUUCAC 3'
+              ::.:.::::::.::::: 
+query   3' CUCAGGGGGGUUUGUGAAGUC 5'
+
+query=Ath-miRN134, target=AT1G60030.1 | Symbols: NAT7, ATNAT7 | nucleobase-ascorbate transporter 7, ARABIDOPSIS NUCLEOBA, score=5, range=1655-1675, strand=1
+
+target  5' AGAACAAAAUUCAUCCUCGGA 3'
+           ::: : :::::::::: :.::
+query   3' UCUAGGUUUAAGUAGG-GUCU 5'
+
+query=Ath-miRN134, target=AT1G30280.1 | Symbols: no symbol available | no full name available | chr1:10662621-10664668 R, score=6, range=761-779, strand=1
+
+target  5' GGAUCCGAAUUCCUUC-AGA 3'
+           .:::::.::::: :.: :::
+query   3' UCUAGGUUUAAGUAGGGUCU 5'
+
+query=Ath-miRN134, target=AT1G73010.1 | Symbols: PS2, ATPS2, AtPPsPase1, PPsPase1 | pyrophosphate-specific phosphatase1,, score=6, range=1149-1167, strand=1
+
+target  5' AGAUU-GAAUUUAUCCUAAA 3'
+           ::::. .::::.::::.: :
+query   3' UCUAGGUUUAAGUAGGGUCU 5'
+
+query=Ath-miR170, target=AT1G26770.2 | Symbols: ATHEXP ALPHA 1.1, ATEXPA10, AT-EXP10, EXPA10, ATEXP10, EXP10 | expansin, score=5.5, range=321-341, strand=1
+
+target  5' GGUGUUUACCUGGCUCAAUCG 3'
+           :.:.:: :: .:::::::::.
+query   3' CUAUAACUGUGCCGAGUUAGU 5'
+
+query=Ath-miR170, target=AT1G10340.1 | Symbols: no symbol available | no full name available | chr1:3390475-3392633 REV, score=6, range=716-736, strand=1
+
+target  5' UAUAUUGUUAGGGCUCGAUCA 3'
+            :::::: .: :::::.::::
+query   3' CUAUAACUGUGCCGAGUUAGU 5'
+
+query=Ath-miR861, target=AT2G41190.1 | Symbols: no symbol available | no full name available | chr2:17167279-17170559 R, score=5.5, range=1974-1994, strand=1
+
+target  5' GACCUUGGGGACAUAUUCUUC 3'
+           : :::::..:::::::.: ::
+query   3' CAGGAACUUCUGUAUAGGUAG 5'
+
+query=Ath-miRN132, target=AT1G56660.1 | Symbols: no symbol available | no full name available | chr1:21237839-21241014 F, score=5, range=477-497, strand=1
+
+target  5' AGAGAAGAAACACGAGGAGUU 3'
+           :: :: : :::::::::: ::
+query   3' UCGCUACGUUGUGCUCCUGAA 5'
+
+query=Ath-miR156c, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1
+
+target  5' GAGAUCUCUUUCUUCUGUCA 3'
+           : : :: ::.::::::::::
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT2G12400.1 | Symbols: no symbol available | no full name available | chr2:5004884-5008442 REV, score=5, range=347-365, strand=1
+
+target  5' GUGUUUACUCUCUUC-GUUU 3'
+           :::.:.::::::::: ::. 
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV, score=5, range=1472-1490, strand=1
+
+target  5' UUCCUCACUUUCUUCU-UCA 3'
+            : ::::::.:::::: :::
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R, score=6, range=1649-1668, strand=1
+
+target  5' UUGUCUGCUCACUUCUGUCG 3'
+            ::. ..::: ::::::::.
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR, score=6, range=82-101, strand=1
+
+target  5' CUGUUUUCUCUCUUCUCUCC 3'
+            ::.:. ::::::::: :: 
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV, score=6, range=570-590, strand=1
+
+target  5' CUUCUUAUUACUCUUCUGUCU 3'
+            : ::.:.: :::::::::: 
+query   3' CACGAGUGA-GAGAAGACAGU 5'
+
+query=Ath-miR156c, target=AT2G44740.1 | Symbols: CYCP4;1 | cyclin p4;1 | chr2:18441828-18443405 REVERSE LENGTH=1169, score=6, range=68-88, strand=1
+
+target  5' UUUUUCUUUCUCUCUCUGUCA 3'
+            : .:: .::::: :::::::
+query   3' CACGAGUGAGAGA-AGACAGU 5'
+
+query=Ath-miR156e, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1
+
+target  5' GAGAUCUCUUUCUUCUGUCA 3'
+           : : :: ::.::::::::::
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT2G12400.1 | Symbols: no symbol available | no full name available | chr2:5004884-5008442 REV, score=5, range=347-365, strand=1
+
+target  5' GUGUUUACUCUCUUC-GUUU 3'
+           :::.:.::::::::: ::. 
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV, score=5, range=1472-1490, strand=1
+
+target  5' UUCCUCACUUUCUUCU-UCA 3'
+            : ::::::.:::::: :::
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R, score=6, range=1649-1668, strand=1
+
+target  5' UUGUCUGCUCACUUCUGUCG 3'
+            ::. ..::: ::::::::.
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR, score=6, range=82-101, strand=1
+
+target  5' CUGUUUUCUCUCUUCUCUCC 3'
+            ::.:. ::::::::: :: 
+query   3' CACGAGUGAGAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV, score=6, range=570-590, strand=1
+
+target  5' CUUCUUAUUACUCUUCUGUCU 3'
+            : ::.:.: :::::::::: 
+query   3' CACGAGUGA-GAGAAGACAGU 5'
+
+query=Ath-miR156e, target=AT2G44740.1 | Symbols: CYCP4;1 | cyclin p4;1 | chr2:18441828-18443405 REVERSE LENGTH=1169, score=6, range=68-88, strand=1
+
+target  5' UUUUUCUUUCUCUCUCUGUCA 3'
+            : .:: .::::: :::::::
+query   3' CACGAGUGAGAGA-AGACAGU 5'
+
+No results for Ath-miR395a
+No results for Ath-miR165b
+No results for Ath-miR2111a
+query=Ath-miR171c, target=AT2G32800.1 | Symbols: LecRK-S.2, AP4.3A | L-type lectin receptor kinase S.2 | chr2:13916440-1, score=6, range=1659-1679, strand=1
+
+target  5' GUUGAUUUUGGUACGGCUUAU 3'
+             :::: ::::.::::::.: 
+query   3' GCACUAUAACCGUGCCGAGUU 5'
+
+query=Ath-miR393b, target=AT1G09812.1 | Symbols: no symbol available | no full name available | chr1:3187442-3188854 FOR, score=4.5, range=453-474, strand=1
+
+target  5' GAUGAAUGCGAUCUCAUUUGGG 3'
+           ::: :::::::::.: :::::.
+query   3' CUAGUUACGCUAGGG-AAACCU 5'
+
+query=Ath-miR393b, target=AT2G33380.1 | Symbols: AtRD20, PXG3, CLO-3, CLO3, RD20, AtCLO3 | caleosin 3, Arabidopsis thali, score=4.5, range=720-739, strand=1
+
+target  5' UGGCAAU-CGAUCCUUUUGGA 3'
+            . :::: ::::::.::::::
+query   3' CUAGUUACGCUAGGGAAACCU 5'
+
+query=Ath-miR393b, target=AT1G20070.1 | Symbols: no symbol available | no full name available | chr1:6958010-6959148 REV, score=5, range=72-91, strand=1
+
+target  5' UAUCAAAACGAUCC-UUUGGA 3'
+            :::::  :::::: ::::::
+query   3' CUAGUUACGCUAGGGAAACCU 5'
+
+query=Ath-miR393b, target=AT1G63300.1 | Symbols: no symbol available | no full name available | chr1:23481907-23486220 F, score=6, range=1397-1416, strand=1
+
+target  5' GAUCCAUG-GGUUCUUUUGGA 3'
+           :::: ::: :.:.:.::::::
+query   3' CUAGUUACGCUAGGGAAACCU 5'
+
+No results for Ath-miR829
+No results for Ath-miR2111b
+query=Ath-miRN146, target=AT1G62620.1 | Symbols: no symbol available | no full name available | chr1:23182644-23185151 F, score=6, range=242-263, strand=1
+
+target  5' CAUUCAAGCGUCUAUAGAUCUC 3'
+            :::: :: :::::::.:.:.:
+query   3' CUAAGCUC-CAGAUAUUUGGGG 5'
+
+No results for Ath-miR165a
+No results for Ath-miR168a
+query=Ath-miRN118, target=AT1G78720.1 | Symbols: no symbol available | no full name available | chr1:29605457-29607678 F, score=5.5, range=523-542, strand=1
+
+target  5' GCUAUUCUUAUCAUAGUUCA 3'
+           ::.: : :.::::.::.:::
+query   3' CGGUUAAAGUAGUGUCGAGU 5'
+
+query=Ath-miRN118, target=AT1G01200.1 | Symbols: RABA3, ATRABA3, ATRAB-A3 | ARABIDOPSIS RAB GTPASE HOMOLOG A3, RAB GTPas, score=6, range=484-503, strand=1
+
+target  5' GGCAAACUCGUCAAAGCUCA 3'
+           : :::  ::.::: ::::::
+query   3' CGGUUAAAGUAGUGUCGAGU 5'
+
+query=Ath-miR395f, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1
+
+target  5' CUCUCUCUCCAAACGCUUCAC 3'
+              ::.:.::::::.::::: 
+query   3' CUCAGGGGGGUUUGUGAAGUC 5'
+
+No results for Ath-miR851
+No results for Ath-miR395e
+No results for Ath-miRN143