Input and runtime details for job 1654565 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
2	4.208e-07	0.0007412	b2531	iscR	-21.46	0.000012	188 -- 264	2 -- 56	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________187___________________________________________________________________________265\n_____________\|_____________________________________________________________________________\|\n5'-AUG...UUUGA__U___________UG_GACUGACAUCUAAA______U_____GUGACCG__A______________C__A__U___AAGCG...AAC-3'\n______________GG_GAAGUAAGACA__A______________GGGCGC_AUGCC_______CA_UGCUUGACGUUGCG_UC_AC_CUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|\|__\|______________\|:\|\|\|\|_\|:\|\|\|_______\|\|_:\|\|\|\|\|\|\|\|\|\|\|\|:_\|\|_\|\|_\|\|\|\n______________UC_CUUCAUUCUGU__U______________CUCGCG_UGCGG_______GU_GCGAACUGCAACGU_AG_UG_GAC\n3'-UUU...UUUUU______________UA_AC__________________U______________A______________A_________G-5'\n_____________\|_____________________________________________________________________________\|\n_____________57____________________________________________________________________________1\n	244 -- 250	14 -- 20	-58.8762 kcal/mol	20.5805 kcal/mol	16.8438 kcal/mol	187 265@LB@ \| \|@LB@5'-AUG...UUUGA U UG GACUGACAUCUAAA U GUGACCG A C A U AAGCG...AAC-3'@LB@ GG GAAGUAAGACA A GGGCGC AUGCC CA UGCUUGACGUUGCG UC AC CUG@LB@ :\| \|\|\|\|\|\|\|\|\|\|\| \| \|:\|\|\|\| \|:\|\|\| \|\| :\|\|\|\|\|\|\|\|\|\|\|\|: \|\| \|\| \|\|\|@LB@ UC CUUCAUUCUGU U CUCGCG UGCGG GU GCGAACUGCAACGU AG UG GAC@LB@3'-UUU...UUUUU UA AC U A A G-5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -21.46 kcal/mol@LB@Hybridization Energy -58.8762 kcal/mol@LB@Unfolding Energy - mRNA 20.5805 kcal/mol@LB@Unfolding Energy - sRNA 16.8438 kcal/mol@LB@@LB@Position - mRNA 188 -- 264@LB@Position - sRNA 2 -- 56@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 14 -- 20@LB@
185	0.008022	0.1528	b1813	nudL	-20.51	0.000035	188 -- 228	15 -- 56	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	_____________187____________________________________________229\n_____________\|______________________________________________\|\n5'-CCU...CAACU__A__________________AUAC_________G___________AUUUU...CUG-3'\n______________GG_GAAGUAAGAC___GUGGA____CGUAGC_CU_A_CGCUUGAUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|___:\|\|\|\|____\|\|:\|:\|_\|:_\|_\|\|\|\|\|\|\|:\|\n______________UC_CUUCAUUCUG___UACCU____GCGUUG_GG_U_GCGAACUGC\n3'-UUU...UUUUU_____________UUA_____C_________C__G_A_________AACGU...ACG-5'\n_____________\|______________________________________________\|\n_____________57_____________________________________________14\n	221 -- 227	16 -- 22	-41.758 kcal/mol	7.45502 kcal/mol	13.7937 kcal/mol	187 229@LB@ \| \|@LB@5'-CCU...CAACU A AUAC G AUUUU...CUG-3'@LB@ GG GAAGUAAGAC GUGGA CGUAGC CU A CGCUUGAUG@LB@ :\| \|\|\|\|\|\|\|\|\|\| :\|\|\|\| \|\|:\|:\| \|: \| \|\|\|\|\|\|\|:\|@LB@ UC CUUCAUUCUG UACCU GCGUUG GG U GCGAACUGC@LB@3'-UUU...UUUUU UUA C C G A AACGU...ACG-5'@LB@ \| \|@LB@ 57 14@LB@@LB@@LB@Energy -20.51 kcal/mol@LB@Hybridization Energy -41.758 kcal/mol@LB@Unfolding Energy - mRNA 7.45502 kcal/mol@LB@Unfolding Energy - sRNA 13.7937 kcal/mol@LB@@LB@Position - mRNA 188 -- 228@LB@Position - sRNA 15 -- 56@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 16 -- 22@LB@
13	2.167e-05	0.005627	b0123	cueO	-18.83	0.000188	100 -- 180	1 -- 93	multicopper oxidase (laccase)	_____________99__________________________________________________________________________________________________181\n_____________\|___________________________________________________________________________________________________\|\n5'-CUG...CAUUA________UUA________C______CU___CC___CCGU_______________U___________________A________U______________UUAAG...CGU-3'\n______________UUGU_CGA___AAUUGUGU__UGCGG__UGA__UUC____AAGGGGAAG___GAC_____________AUGCUCA_CGUUUGAU_UUGU_UUCGCCUGC\n______________\|:\|\|_\|\|\|___\|\|\|\|\|\|\|:__\|\|\|:\|__\|:\|__\|\|\|____\|\|::\|\|\|\|\|___\|\|\|_____________\|:\|\|:\|\|_\|\|:\|\|\|\|:_\|\|\|:_\|\|\|:\|\|\|\|\|\n______________AGCA_GCU___UUAACACG__ACGUC__AUU__AAG____UUUUCCUUC___CUG_____________UGCGGGU_GCGAACUG_AACG_AAGUGGACG\n3'-UUU...GCCGC____U___UAG________AU_______________UU___________AUU___UUAUACCUCGCGU_______A________C____U_________-5'\n_____________\|__________________________________________________________________________________________________\|\n_____________94_________________________________________________________________________________________________1\n	174 -- 180	1 -- 7	-64.9216 kcal/mol	25.1682 kcal/mol	20.925 kcal/mol	99 181@LB@ \| \|@LB@5'-CUG...CAUUA UUA C CU CC CCGU U A U UUAAG...CGU-3'@LB@ UUGU CGA AAUUGUGU UGCGG UGA UUC AAGGGGAAG GAC AUGCUCA CGUUUGAU UUGU UUCGCCUGC@LB@ \|:\|\| \|\|\| \|\|\|\|\|\|\|: \|\|\|:\| \|:\| \|\|\| \|\|::\|\|\|\|\| \|\|\| \|:\|\|:\|\| \|\|:\|\|\|\|: \|\|\|: \|\|\|:\|\|\|\|\|@LB@ AGCA GCU UUAACACG ACGUC AUU AAG UUUUCCUUC CUG UGCGGGU GCGAACUG AACG AAGUGGACG@LB@3'-UUU...GCCGC U UAG AU UU AUU UUAUACCUCGCGU A C U -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -64.9216 kcal/mol@LB@Unfolding Energy - mRNA 25.1682 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 100 -- 180@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@LB@
20	4.953e-05	0.008725	b1841	yobA	-18.58	0.000237	158 -- 228	20 -- 76	CopC family protein	_____________157_______________________________________________________________________229\n_____________\|_________________________________________________________________________\|\n5'-GCC...ACAAG_______UCUGUAAAAA___U___AC_________U_____________CUUCAAC____C__U___U_____ACGCG...AGU-3'\n______________GUUAUGC__________AGU_AUU__AAAAAGGAA___AGAUAAUAUGG_______UGCA_GC_CCC_UCGCU\n______________\|:\|\|\|\|\|__________\|\|\|_\|\|\|__\|\|\|\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|\|_______:\|\|\|_:\|_\|\|\|_\|\|\|\|\|\n______________CGAUACG__________UCA_UAA__UUUUUCCUU___UCUGUUAUACC_______GCGU_UG_GGG_AGCGA\n3'-UUU...UAACA____________________U___GU_________CAU___________UC____________C___U_____ACUGC...ACG-5'\n_____________\|_________________________________________________________________________\|\n_____________77________________________________________________________________________19\n	198 -- 204	38 -- 44	-46.9503 kcal/mol	10.9442 kcal/mol	17.4278 kcal/mol	157 229@LB@ \| \|@LB@5'-GCC...ACAAG UCUGUAAAAA U AC U CUUCAAC C U U ACGCG...AGU-3'@LB@ GUUAUGC AGU AUU AAAAAGGAA AGAUAAUAUGG UGCA GC CCC UCGCU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\| :\|\|\| :\| \|\|\| \|\|\|\|\|@LB@ CGAUACG UCA UAA UUUUUCCUU UCUGUUAUACC GCGU UG GGG AGCGA@LB@3'-UUU...UAACA U GU CAU UC C U ACUGC...ACG-5'@LB@ \| \|@LB@ 77 19@LB@@LB@@LB@Energy -18.58 kcal/mol@LB@Hybridization Energy -46.9503 kcal/mol@LB@Unfolding Energy - mRNA 10.9442 kcal/mol@LB@Unfolding Energy - sRNA 17.4278 kcal/mol@LB@@LB@Position - mRNA 158 -- 228@LB@Position - sRNA 20 -- 76@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 38 -- 44@LB@
4	1.28e-06	0.001128	b0884	infA	-17.67	0.000535	178 -- 264	1 -- 71	translation initiation factor IF-1	_____________177_______________________________________________________________________________________265\n_____________\|_________________________________________________________________________________________\|\n5'-UUU...UUACG________ACCCC______UUAGAUGGCCAA_____________U__AA_____G__A___________AA______CUAA____A___UCCGC...CUG-3'\n______________GUAGUGAU_____AGAGGA____________AG_AAGACAAUAU_GA__UGCAA_GU_CCGUU_CUUGA__CGUUGC____UACC_UGU\n______________\|:\|\|\|:\|\|_____\|:\|\|\|\|____________\|\|_\|\|\|\|\|\|\|\|\|\|_\|\|__:\|\|\|\|_\|:_\|\|:\|:_\|\|\|\|\|__\|\|\|\|\|\|____:\|\|\|_\|\|:\n______________CGUCAUUA_____UUUCCU____________UC_UUCUGUUAUA_CU__GCGUU_CG_GGUAG_GAACU__GCAACG____GUGG_ACG\n3'-UUU...CGAUA________AGUUU____________________A__________C__C______G________C_____________UAA_________-5'\n_____________\|________________________________________________________________________________________\|\n_____________72_______________________________________________________________________________________1\n	214 -- 220	40 -- 46	-55.7119 kcal/mol	17.4656 kcal/mol	20.5786 kcal/mol	177 265@LB@ \| \|@LB@5'-UUU...UUACG ACCCC UUAGAUGGCCAA U AA G A AA CUAA A UCCGC...CUG-3'@LB@ GUAGUGAU AGAGGA AG AAGACAAUAU GA UGCAA GU CCGUU CUUGA CGUUGC UACC UGU@LB@ \|:\|\|\|:\|\| \|:\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|: \|\|:\|: \|\|\|\|\| \|\|\|\|\|\| :\|\|\| \|\|:@LB@ CGUCAUUA UUUCCU UC UUCUGUUAUA CU GCGUU CG GGUAG GAACU GCAACG GUGG ACG@LB@3'-UUU...CGAUA AGUUU A C C G C UAA -5'@LB@ \| \|@LB@ 72 1@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -55.7119 kcal/mol@LB@Unfolding Energy - mRNA 17.4656 kcal/mol@LB@Unfolding Energy - sRNA 20.5786 kcal/mol@LB@@LB@Position - mRNA 178 -- 264@LB@Position - sRNA 1 -- 71@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 40 -- 46@LB@
90	0.002477	0.09689	b4020	yjbB	-17.01	0.000941	168 -- 222	1 -- 56	putative Na+/Pi-cotransporter	_____________167________________________________________________________223\n_____________\|__________________________________________________________\|\n5'-UCC...GCUUC_____CA__UA______A____AACC___AA______GUUA___C_____________UUUCU...UGC-3'\n______________AGGAA__UA__ACGAUA_GGAG_____UG__C_UCGU____ACG_UGC_UUCACCUGC\n______________\|\|\|\|\|__\|\|__\|\|:\|\|\|_\|\|\|\|_____:\|__\|_\|\|\|:____\|\|\|_\|\|\|_\|\|\|\|\|\|\|\|\|\n______________UCCUU__AU__UGUUAU_CCUC_____GC__G_AGCG____UGC_ACG_AAGUGGACG\n3'-UUU...UUUUU_____C___UC______A____GCGUU__GG_U____AAC____A___U_________-5'\n_____________\|_________________________________________________________\|\n_____________57________________________________________________________1\n	216 -- 222	1 -- 7	-44.3986 kcal/mol	10.5518 kcal/mol	16.8439 kcal/mol	167 223@LB@ \| \|@LB@5'-UCC...GCUUC CA UA A AACC AA GUUA C UUUCU...UGC-3'@LB@ AGGAA UA ACGAUA GGAG UG C UCGU ACG UGC UUCACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\| :\| \| \|\|\|: \|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUU AU UGUUAU CCUC GC G AGCG UGC ACG AAGUGGACG@LB@3'-UUU...UUUUU C UC A GCGUU GG U AAC A U -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -44.3986 kcal/mol@LB@Unfolding Energy - mRNA 10.5518 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 168 -- 222@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
40	0.000329	0.02897	b2513	yfgM	-16.53	0.001389	180 -- 205	37 -- 63	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________179_________________________206\n_____________\|___________________________\|\n5'-GGC...CUGGG_____________A_______C_____AAUUU...UUG-3'\n______________UUAAGGAAGG_AG_AGGACAG_GUGGA\n______________\|:\|\|::\|\|\|\|_\|\|_\|:\|\|\|\|:_:\|\|\|\|\n______________AGUUUUUUCC_UC_UUCUGUU_UACCU\n3'-UUU...CAUUA__________U__A_______A_____CGCGU...ACG-5'\n_____________\|___________________________\|\n_____________64__________________________36\n	193 -- 199	43 -- 49	-25.2652 kcal/mol	3.41523 kcal/mol	5.31676 kcal/mol	179 206@LB@ \| \|@LB@5'-GGC...CUGGG A C AAUUU...UUG-3'@LB@ UUAAGGAAGG AG AGGACAG GUGGA@LB@ \|:\|\|::\|\|\|\| \|\| \|:\|\|\|\|: :\|\|\|\|@LB@ AGUUUUUUCC UC UUCUGUU UACCU@LB@3'-UUU...CAUUA U A A CGCGU...ACG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -25.2652 kcal/mol@LB@Unfolding Energy - mRNA 3.41523 kcal/mol@LB@Unfolding Energy - sRNA 5.31676 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
6	5.595e-06	0.003285	b2048	cpsG	-15.91	0.002276	49 -- 82	20 -- 54	phosphomannomutase	_____________48__________________________________83\n_____________\|___________________________________\|\n5'-GGG...AUCUC_________________U____UU___GG______ACGGA...GCG-3'\n______________GAAG_AGGAUGAUGUGG_GCGU__CGC__AUCGCU\n______________\|\|\|\|_\|:\|\|::\|\|:\|\|\|_\|\|\|:__\|\|\|__\|\|\|\|\|\|\n______________CUUC_UUCUGUUAUACC_CGCG__GCG__UAGCGA\n3'-UUU...UUUUC____A____________U____UU___GG______ACUGC...ACG-5'\n_____________\|___________________________________\|\n_____________55__________________________________19\n	54 -- 60	42 -- 48	-40.4755 kcal/mol	10.8622 kcal/mol	13.7092 kcal/mol	48 83@LB@ \| \|@LB@5'-GGG...AUCUC U UU GG ACGGA...GCG-3'@LB@ GAAG AGGAUGAUGUGG GCGU CGC AUCGCU@LB@ \|\|\|\| \|:\|\|::\|\|:\|\|\| \|\|\|: \|\|\| \|\|\|\|\|\|@LB@ CUUC UUCUGUUAUACC CGCG GCG UAGCGA@LB@3'-UUU...UUUUC A U UU GG ACUGC...ACG-5'@LB@ \| \|@LB@ 55 19@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -40.4755 kcal/mol@LB@Unfolding Energy - mRNA 10.8622 kcal/mol@LB@Unfolding Energy - sRNA 13.7092 kcal/mol@LB@@LB@Position - mRNA 49 -- 82@LB@Position - sRNA 20 -- 54@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 42 -- 48@LB@
19	4.82e-05	0.008725	b2452	eutH	-15.86	0.002353	187 -- 206	37 -- 56	ethanolamine transporter	_____________186___________________207\n_____________\|_____________________\|\n5'-UUG...CUAAC_______A_____________AUUAA...UCC-3'\n______________AGGGAGU_AAGGCGAUG_GGA\n______________\|\|\|:\|\|\|_\|\|\|:\|:\|\|:_\|\|\|\n______________UCCUUCA_UUCUGUUAU_CCU\n3'-UUU...UUUUU_________________A___CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________57____________________36\n	197 -- 203	41 -- 47	-22.1606 kcal/mol	2.59538 kcal/mol	3.6645 kcal/mol	186 207@LB@ \| \|@LB@5'-UUG...CUAAC A AUUAA...UCC-3'@LB@ AGGGAGU AAGGCGAUG GGA@LB@ \|\|\|:\|\|\| \|\|\|:\|:\|\|: \|\|\|@LB@ UCCUUCA UUCUGUUAU CCU@LB@3'-UUU...UUUUU A CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -15.86 kcal/mol@LB@Hybridization Energy -22.1606 kcal/mol@LB@Unfolding Energy - mRNA 2.59538 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 41 -- 47@LB@
5	2.521e-06	0.001776	b3365	nirB	-15.77	0.002536	156 -- 206	35 -- 88	nitrite reductase large subunit NAD(P)H-binding	_____________155____________________________________________________207\n_____________\|______________________________________________________\|\n5'-AUC...GUUGC_______UUAA__G__G_________________A__UC_______AAAU____AAAGU...UUA-3'\n______________UGAAUCG_____G_UA_GCGGUAAU__AGAAAAG_AA__GAGGCAA____GAGC\n______________:\|\|\|\|\|:_____\|_\|\|_\|\|:\|\|\|\|\|__\|:\|\|\|\|\|_\|\|__:\|\|:\|\|\|____\|\|\|\|\n______________GCUUAGU_____C_AU_CGUCAUUA__UUUUUUC_UU__UUCUGUU____CUCG\n3'-UUU...AGCAU_______UAACA_G__A________AG_______C__CA_______AUAC____CGUUG...ACG-5'\n_____________\|______________________________________________________\|\n_____________89_____________________________________________________34\n	192 -- 198	43 -- 49	-31.7984 kcal/mol	7.74851 kcal/mol	8.27555 kcal/mol	155 207@LB@ \| \|@LB@5'-AUC...GUUGC UUAA G G A UC AAAU AAAGU...UUA-3'@LB@ UGAAUCG G UA GCGGUAAU AGAAAAG AA GAGGCAA GAGC@LB@ :\|\|\|\|\|: \| \|\| \|\|:\|\|\|\|\| \|:\|\|\|\|\| \|\| :\|\|:\|\|\| \|\|\|\|@LB@ GCUUAGU C AU CGUCAUUA UUUUUUC UU UUCUGUU CUCG@LB@3'-UUU...AGCAU UAACA G A AG C CA AUAC CGUUG...ACG-5'@LB@ \| \|@LB@ 89 34@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -31.7984 kcal/mol@LB@Unfolding Energy - mRNA 7.74851 kcal/mol@LB@Unfolding Energy - sRNA 8.27555 kcal/mol@LB@@LB@Position - mRNA 156 -- 206@LB@Position - sRNA 35 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 43 -- 49@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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