Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
15	0.0001044	0.0245	b0741	pal	-16.61	0.007509	30 -- 75	30 -- 71	peptidoglycan-associated outer membrane lipoprotein	_____________29_____________________________________________76\n_____________\|______________________________________________\|\n5'-GGA...UAACG____U________CUACAGCUCUU__________GGGA________GAAUU...GCG-3'\n______________GCAC_AUGGUAAU___________CUCAGGGGAU____UCCGUGCU\n______________:\|\|\|_\|::\|:\|\|\|___________\|\|\|\|\|\|\|\|\|\|____\|\|\|:\|\|\|\|\n______________UGUG_UGUCGUUA___________GAGUCCCCUA____AGGUACGA\n3'-UUU...UCUGA_____________AGCAACAAAGU__________A___________AUAUU...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________29\n	69 -- 75	30 -- 36	-38.4662 kcal/mol	13.7923 kcal/mol	8.066 kcal/mol	29 76@LB@ \| \|@LB@5'-GGA...UAACG U CUACAGCUCUU GGGA GAAUU...GCG-3'@LB@ GCAC AUGGUAAU CUCAGGGGAU UCCGUGCU@LB@ :\|\|\| \|::\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|@LB@ UGUG UGUCGUUA GAGUCCCCUA AGGUACGA@LB@3'-UUU...UCUGA AGCAACAAAGU A AUAUU...GCA-5'@LB@ \| \|@LB@ 72 29@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -38.4662 kcal/mol@LB@Unfolding Energy - mRNA 13.7923 kcal/mol@LB@Unfolding Energy - sRNA 8.066 kcal/mol@LB@@LB@Position - mRNA 30 -- 75@LB@Position - sRNA 30 -- 71@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 30 -- 36@LB@
16	0.00012	0.02638	b3089	sstT	-15.87	0.012233	203 -- 224	42 -- 75	sodium:serine/threonine symporter	_____________202________________________________225\n_____________\|__________________________________\|\n5'-CAC...AAAAU_________ACG______________________CUAUU...CAU-3'\n______________GACUACGCA______________UUCAC_CGGGG\n______________\|\|\|\|\|\|:\|\|______________\|\|\|\|\|_\|:\|\|\|\n______________CUGAUGUGU______________AAGUG_GUCCC\n3'-UUU...CGUUU_________GUCGUUAAGCAACA_____A_____CUAAA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________41\n	205 -- 211	67 -- 73	-24.6329 kcal/mol	4.00159 kcal/mol	4.76397 kcal/mol	202 225@LB@ \| \|@LB@5'-CAC...AAAAU ACG CUAUU...CAU-3'@LB@ GACUACGCA UUCAC CGGGG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\| \|:\|\|\|@LB@ CUGAUGUGU AAGUG GUCCC@LB@3'-UUU...CGUUU GUCGUUAAGCAACA A CUAAA...GCA-5'@LB@ \| \|@LB@ 76 41@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.6329 kcal/mol@LB@Unfolding Energy - mRNA 4.00159 kcal/mol@LB@Unfolding Energy - sRNA 4.76397 kcal/mol@LB@@LB@Position - mRNA 203 -- 224@LB@Position - sRNA 42 -- 75@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 67 -- 73@LB@
17	0.0001292	0.02674	b1854	pykA	-13.69	0.043994	133 -- 157	36 -- 68	pyruvate kinase II	_____________132_______________________________158\n_____________\|_________________________________\|\n5'-GAA...GCCAU______________A__________________AUGUU...ACG-3'\n______________CGCGGC_____GUU_UUUCAUUC___GGAUUUC\n______________\|:\|:\|\|_____\|\|\|_\|\|\|\|\|:\|\|___\|\|\|\|\|\|\|\n______________GUGUCG_____CAA_AAAGUGAG___CCUAAAG\n3'-UUU...GAUGU______UUAAG___C________UCC_______GUACG...GCA-5'\n_____________\|_________________________________\|\n_____________69________________________________35\n	151 -- 157	36 -- 42	-24.2432 kcal/mol	5.79946 kcal/mol	4.75078 kcal/mol	132 158@LB@ \| \|@LB@5'-GAA...GCCAU A AUGUU...ACG-3'@LB@ CGCGGC GUU UUUCAUUC GGAUUUC@LB@ \|:\|:\|\| \|\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GUGUCG CAA AAAGUGAG CCUAAAG@LB@3'-UUU...GAUGU UUAAG C UCC GUACG...GCA-5'@LB@ \| \|@LB@ 69 35@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -24.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.79946 kcal/mol@LB@Unfolding Energy - sRNA 4.75078 kcal/mol@LB@@LB@Position - mRNA 133 -- 157@LB@Position - sRNA 36 -- 68@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 36 -- 42@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase	_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor	_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
21	0.0001827	0.02926	b1937	fliE	-13.91	0.039102	192 -- 221	38 -- 77	flagellar basal-body component	_____________191________________________________________222\n_____________\|__________________________________________\|\n5'-CUG...UCCGG_____GAGA___U_______A_____________________GAAGG...GUU-3'\n______________GAGAC____AUG_CAGCGAU_____________CAGGGGAUU\n______________:\|\|\|\|____\|::_\|\|\|\|:\|\|_____________\|\|\|\|\|\|\|\|\|\n______________UUCUG____UGU_GUCGUUA_____________GUCCCCUAA\n3'-UUU...CCCGU_____AUG____________AGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________37\n	215 -- 221	38 -- 44	-25.7557 kcal/mol	7.06678 kcal/mol	4.77969 kcal/mol	191 222@LB@ \| \|@LB@5'-CUG...UCCGG GAGA U A GAAGG...GUU-3'@LB@ GAGAC AUG CAGCGAU CAGGGGAUU@LB@ :\|\|\|\| \|:: \|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UUCUG UGU GUCGUUA GUCCCCUAA@LB@3'-UUU...CCCGU AUG AGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 78 37@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -25.7557 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 4.77969 kcal/mol@LB@@LB@Position - mRNA 192 -- 221@LB@Position - sRNA 38 -- 77@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
22	0.0001899	0.02926	b2562	yfhL	-14.77	0.023959	28 -- 42	42 -- 56	putative 4Fe-4S cluster-containing protein	_____________27______________43\n_____________\|_______________\|\n5'-AGC...UCUGC____CA_________AAUGU...UUA-3'\n______________UUGU__CGCUCAGGG\n______________\|\|\|\|__\|:\|\|\|\|\|\|\|\n______________AACA__GUGAGUCCC\n3'-UUU...UAAGC____AA_________CUAAA...GCA-5'\n_____________\|_______________\|\n_____________57______________41\n	36 -- 42	42 -- 48	-19.6539 kcal/mol	2.98712 kcal/mol	1.89561 kcal/mol	27 43@LB@ \| \|@LB@5'-AGC...UCUGC CA AAUGU...UUA-3'@LB@ UUGU CGCUCAGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AACA GUGAGUCCC@LB@3'-UUU...UAAGC AA CUAAA...GCA-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -19.6539 kcal/mol@LB@Unfolding Energy - mRNA 2.98712 kcal/mol@LB@Unfolding Energy - sRNA 1.89561 kcal/mol@LB@@LB@Position - mRNA 28 -- 42@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 42 -- 48@LB@
23	0.0001955	0.02926	b3846	fadB	-13.56	0.047358	39 -- 83	35 -- 77	fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase	_____________38________________________________________________84\n_____________\|_________________________________________________\|\n5'-AGU...ACCUU___U__C_____CUU____CA____________C___A_C_U_______GCCGA...CUG-3'\n______________AAG_CU_CGCAU___AGCA__UCGU____UCAU_CAG_G_G_GAUUUCU\n______________\|\|\|_\|\|_\|:\|\|:___\|\|\|\|__\|\|\|\|____\|\|\|:_\|\|\|_\|_\|_\|\|\|\|\|\|:\n______________UUC_GA_GUGUG___UCGU__AGCA____AGUG_GUC_C_C_CUAAAGG\n3'-UUU...CCCGU___U__U____________UA____ACAA____A_______________UACGA...GCA-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________34\n	77 -- 83	35 -- 41	-27.7125 kcal/mol	9.35112 kcal/mol	4.80542 kcal/mol	38 84@LB@ \| \|@LB@5'-AGU...ACCUU U C CUU CA C A C U GCCGA...CUG-3'@LB@ AAG CU CGCAU AGCA UCGU UCAU CAG G G GAUUUCU@LB@ \|\|\| \|\| \|:\|\|: \|\|\|\| \|\|\|\| \|\|\|: \|\|\| \| \| \|\|\|\|\|\|:@LB@ UUC GA GUGUG UCGU AGCA AGUG GUC C C CUAAAGG@LB@3'-UUU...CCCGU U U UA ACAA A UACGA...GCA-5'@LB@ \| \|@LB@ 78 34@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -27.7125 kcal/mol@LB@Unfolding Energy - mRNA 9.35112 kcal/mol@LB@Unfolding Energy - sRNA 4.80542 kcal/mol@LB@@LB@Position - mRNA 39 -- 83@LB@Position - sRNA 35 -- 77@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 35 -- 41@LB@
24	0.0002076	0.02926	b3459	panM	-18.00	0.002751	9 -- 48	38 -- 75	PanD autocleavage accelerator panothenate synthesis	_____________8___________________________________________49\n_____________\|___________________________________________\|\n___5'-AAAAUAAC_______A_G___GGAAU_____ACUA________________AUGCU...UUG-3'\n______________GGC_ACA_A_GGC_____AAUUC______UCAUUCAGGGGAUU\n______________\|:\|_\|\|\|_\|_:\|\|_____\|\|\|\|\|______\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________CUG_UGU_U_UCG_____UUAAG______AGUGAGUCCCCUAA\n3'-UUU...CGUUU___A___G_G_____________CAACAA______________AGGUA...GCA-5'\n_____________\|___________________________________________\|\n_____________76__________________________________________37\n	42 -- 48	38 -- 44	-31.5918 kcal/mol	8.81239 kcal/mol	4.77946 kcal/mol	8 49@LB@ \| \|@LB@ 5'-AAAAUAAC A G GGAAU ACUA AUGCU...UUG-3'@LB@ GGC ACA A GGC AAUUC UCAUUCAGGGGAUU@LB@ \|:\| \|\|\| \| :\|\| \|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ CUG UGU U UCG UUAAG AGUGAGUCCCCUAA@LB@3'-UUU...CGUUU A G G CAACAA AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -31.5918 kcal/mol@LB@Unfolding Energy - mRNA 8.81239 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 9 -- 48@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 38 -- 44@LB@
25	0.0002079	0.02926	b4064	ghxP	-13.58	0.046769	115 -- 151	38 -- 73	guanine/hypoxanthine permease high affinity; guanine/hypoxanthine:H+ symporter	_____________114____________________________________152\n_____________\|______________________________________\|\n5'-UCG...CAAAC___GA_____G__GAUAAC________GG_________GUCCG...UAA-3'\n______________CUG___GCAG_AA______GUUUCGCU__CAGGGGAUU\n______________\|\|:___:\|\|\|_\|\|______\|\|\|\|\|:\|\|__\|\|\|\|\|\|\|\|\|\n______________GAU___UGUC_UU______CAAAGUGA__GUCCCCUAA\n3'-UUU...UUUCU___GUG____G__AAGCAA___________________AGGUA...GCA-5'\n_____________\|______________________________________\|\n_____________74_____________________________________37\n	145 -- 151	38 -- 44	-32.2199 kcal/mol	13.8672 kcal/mol	4.77333 kcal/mol	114 152@LB@ \| \|@LB@5'-UCG...CAAAC GA G GAUAAC GG GUCCG...UAA-3'@LB@ CUG GCAG AA GUUUCGCU CAGGGGAUU@LB@ \|\|: :\|\|\| \|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ GAU UGUC UU CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUUCU GUG G AAGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 74 37@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -32.2199 kcal/mol@LB@Unfolding Energy - mRNA 13.8672 kcal/mol@LB@Unfolding Energy - sRNA 4.77333 kcal/mol@LB@@LB@Position - mRNA 115 -- 151@LB@Position - sRNA 38 -- 73@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 38 -- 44@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)

Job resubmission

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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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