Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
59	0.004284	0.2442	b0094	ftsA	-10.23	0.109208	176 -- 218	1 -- 63	ATP-binding cell division FtsK recruitment protein	_____________175________________________________________________________________219\n_____________\|__________________________________________________________________\|\n5'-AAU...GCAAC__________________CA___AG___________________________UCA_____ACG___AGAAA...UCA-3'\n______________AAAAUCAG_______GCA__GGC__AACA________________ACAAUGA___AGGCG___GAC\n______________\|\|\|\|\|\|\|\|_______\|\|\|__\|\|\|__\|\|\|\|________________\|\|\|\|\|:\|___\|\|\|\|:___:\|\|\n______________UUUUAGUC_______CGU__CCG__UUGU________________UGUUAUU___UCCGU___UUG\n3'-UUU...CAACC________ACCGUUA___UA___GG____CUUUUAUUUUAGACAC_______________AUA___-5'\n_____________\|_________________________________________________________________\|\n_____________64________________________________________________________________1\n	198 -- 204	12 -- 18	-27.1283 kcal/mol	4.74085 kcal/mol	12.1605 kcal/mol	175 219@LB@ \| \|@LB@5'-AAU...GCAAC CA AG UCA ACG AGAAA...UCA-3'@LB@ AAAAUCAG GCA GGC AACA ACAAUGA AGGCG GAC@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\|\|: :\|\|@LB@ UUUUAGUC CGU CCG UUGU UGUUAUU UCCGU UUG@LB@3'-UUU...CAACC ACCGUUA UA GG CUUUUAUUUUAGACAC AUA -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.1283 kcal/mol@LB@Unfolding Energy - mRNA 4.74085 kcal/mol@LB@Unfolding Energy - sRNA 12.1605 kcal/mol@LB@@LB@Position - mRNA 176 -- 218@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
88	0.007723	0.2889	b4403	yjtD	-13.82	0.016006	193 -- 211	1 -- 21	putative methyltransferase	_____________192___________________212\n_____________\|_____________________\|\n5'-AUU...GAAGA_________U___________GAUUA...UUG-3'\n______________GUGGCAAUA___GCGUAUAAC\n______________\|\|\|:\|\|\|\|\|___\|\|:\|\|\|\|\|\|\n______________CACUGUUAU___CGUAUAUUG\n3'-UUU...UUAGA_________UUC_________-5'\n_____________\|____________________\|\n_____________22___________________1\n	205 -- 211	1 -- 7	-21.8234 kcal/mol	3.59402 kcal/mol	4.41334 kcal/mol	192 212@LB@ \| \|@LB@5'-AUU...GAAGA U GAUUA...UUG-3'@LB@ GUGGCAAUA GCGUAUAAC@LB@ \|\|\|:\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ CACUGUUAU CGUAUAUUG@LB@3'-UUU...UUAGA UUC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -21.8234 kcal/mol@LB@Unfolding Energy - mRNA 3.59402 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 193 -- 211@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 1 -- 7@LB@
109	0.01013	0.3127	b3805	hemC	-12.29	0.037947	146 -- 209	1 -- 60	hydroxymethylbilane synthase	_____________145_____________________________________________________________________210\n_____________\|_______________________________________________________________________\|\n5'-AAA...CUGAC____CUC_____AGG____UAG_____A________U____________________CAA______UA___AAUGU...GCC-3'\n______________AUCA___UGGCA___AUGU___GAUGG_CC_ACGGA_GAUAA______UGACGGUAA___GCAUGU__GAC\n______________\|\|\|\|___\|\|\|\|\|___\|\|\|:___:\|\|\|\|_\|\|_\|\|:\|\|_:\|\|\|\|______\|\|\|\|::\|\|\|___\|\|\|\|:\|__:\|\|\n______________UAGU___ACCGU___UACG___UUACC_GG_UGUCU_UUAUU______ACUGUUAUU___CGUAUA__UUG\n3'-UUU...CCUUU____C______________________G__U_____U_____UUAGAC_________UC____________-5'\n_____________\|______________________________________________________________________\|\n_____________61_____________________________________________________________________1\n	189 -- 195	12 -- 18	-39.6606 kcal/mol	15.2176 kcal/mol	12.1554 kcal/mol	145 210@LB@ \| \|@LB@5'-AAA...CUGAC CUC AGG UAG A U CAA UA AAUGU...GCC-3'@LB@ AUCA UGGCA AUGU GAUGG CC ACGGA GAUAA UGACGGUAA GCAUGU GAC@LB@ \|\|\|\| \|\|\|\|\| \|\|\|: :\|\|\|\| \|\| \|\|:\|\| :\|\|\|\| \|\|\|\|::\|\|\| \|\|\|\|:\| :\|\|@LB@ UAGU ACCGU UACG UUACC GG UGUCU UUAUU ACUGUUAUU CGUAUA UUG@LB@3'-UUU...CCUUU C G U U UUAGAC UC -5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -39.6606 kcal/mol@LB@Unfolding Energy - mRNA 15.2176 kcal/mol@LB@Unfolding Energy - sRNA 12.1554 kcal/mol@LB@@LB@Position - mRNA 146 -- 209@LB@Position - sRNA 1 -- 60@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 12 -- 18@LB@
110	0.01026	0.313	b0063	araB	-12.48	0.034183	202 -- 260	1 -- 55	L-ribulokinase	_____________201___________________________________________________________261\n_____________\|_____________________________________________________________\|\n5'-CGG...AACGA_______U____U_____U____UUU__C_____U___________GCUUU____GUG___UGCGC...GGU-3'\n______________UGGCGAU_GCAA_UGGCC_CGAU___GG_AGUGA__UCUGUG_CGA_____GGCG___GAC\n______________\|\|\|\|:\|\|_\|\|\|\|_\|\|\|\|\|_\|:\|:___\|:_\|:\|:\|__\|\|\|\|\|\|_\|:\|_____\|\|\|:___:\|\|\n______________ACCGUUA_CGUU_ACCGG_GUUG___CU_UUAUU__AGACAC_GUU_____CCGU___UUG\n3'-UUU...UAGUC_______________________U____U_____UU______U___AUUU_____AUA___-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	202 -- 208	49 -- 55	-46.0779 kcal/mol	21.5533 kcal/mol	12.0455 kcal/mol	201 261@LB@ \| \|@LB@5'-CGG...AACGA U U U UUU C U GCUUU GUG UGCGC...GGU-3'@LB@ UGGCGAU GCAA UGGCC CGAU GG AGUGA UCUGUG CGA GGCG GAC@LB@ \|\|\|\|:\|\| \|\|\|\| \|\|\|\|\| \|:\|: \|: \|:\|:\| \|\|\|\|\|\| \|:\| \|\|\|: :\|\|@LB@ ACCGUUA CGUU ACCGG GUUG CU UUAUU AGACAC GUU CCGU UUG@LB@3'-UUU...UAGUC U U UU U AUUU AUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -46.0779 kcal/mol@LB@Unfolding Energy - mRNA 21.5533 kcal/mol@LB@Unfolding Energy - sRNA 12.0455 kcal/mol@LB@@LB@Position - mRNA 202 -- 260@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
116	0.0115	0.3326	b3770	ilvE	-6.73	0.460342	227 -- 277	1 -- 67	branched-chain amino acid aminotransferase	_____________226__________________________________________________________________278\n_____________\|____________________________________________________________________\|\n5'-UUU...UACAU____U______A___G______________C_____________________CG____U_________GUCGC...GCA-3'\n______________UUGG____UCA_UGG_GA___GAUGGUUCG_UGGGAA___________GACG__AAGG_GCAUGUGAU\n______________\|\|\|\|____\|\|\|_\|\|\|_:\|___:\|\|\|\|::\|:_::\|:\|\|___________\|\|\|:__\|\|:\|_\|\|\|\|:\|:\|:\n______________AACC____AGU_ACC_UU___UUACCGGGU_GUCUUU___________CUGU__UUUC_CGUAUAUUG\n3'-UUU...UAUAC____UUUU___C___G__ACG_________U______UAUUUUAGACA____UA______________-5'\n_____________\|___________________________________________________________________\|\n_____________68__________________________________________________________________1\n	269 -- 275	3 -- 9	-35.2937 kcal/mol	16.4013 kcal/mol	12.1612 kcal/mol	226 278@LB@ \| \|@LB@5'-UUU...UACAU U A G C CG U GUCGC...GCA-3'@LB@ UUGG UCA UGG GA GAUGGUUCG UGGGAA GACG AAGG GCAUGUGAU@LB@ \|\|\|\| \|\|\| \|\|\| :\| :\|\|\|\|::\|: ::\|:\|\| \|\|\|: \|\|:\| \|\|\|\|:\|:\|:@LB@ AACC AGU ACC UU UUACCGGGU GUCUUU CUGU UUUC CGUAUAUUG@LB@3'-UUU...UAUAC UUUU C G ACG U UAUUUUAGACA UA -5'@LB@ \| \|@LB@ 68 1@LB@@LB@@LB@Energy -6.73 kcal/mol@LB@Hybridization Energy -35.2937 kcal/mol@LB@Unfolding Energy - mRNA 16.4013 kcal/mol@LB@Unfolding Energy - sRNA 12.1612 kcal/mol@LB@@LB@Position - mRNA 227 -- 277@LB@Position - sRNA 1 -- 67@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 3 -- 9@LB@
161	0.01858	0.3864	b3237	argR	-5.47	0.658327	53 -- 70	1 -- 21	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________52____________________71\n_____________\|_____________________\|\n5'-ACA...AUGCC______C___________UU_UCAAU...UGC-3'\n______________GUGACG____AGGCAUGU__C\n______________\|\|\|\|\|:____\|\|\|\|\|\|:\|__\|\n______________CACUGU____UCCGUAUA__G\n3'-UUU...UUAGA______UAUU________UU_-5'\n_____________\|____________________\|\n_____________22___________________1\n	61 -- 67	4 -- 10	-16.8661 kcal/mol	6.97949 kcal/mol	4.41334 kcal/mol	52 71@LB@ \| \|@LB@5'-ACA...AUGCC C UU UCAAU...UGC-3'@LB@ GUGACG AGGCAUGU C@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\| \|@LB@ CACUGU UCCGUAUA G@LB@3'-UUU...UUAGA UAUU UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -5.47 kcal/mol@LB@Hybridization Energy -16.8661 kcal/mol@LB@Unfolding Energy - mRNA 6.97949 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 4 -- 10@LB@
162	0.01861	0.3864	b2280	nuoJ	-11.65	0.053319	100 -- 143	1 -- 58	NADH:ubiquinone oxidoreductase membrane subunit J	_____________99____________________________________________________________144\n_____________\|_____________________________________________________________\|\n5'-GAU...UCUAC___A_______________AA_______C__________________________A_____AGAGA...UUA-3'\n______________CGG_UGGCAG_GU_AUGGC__UCGACGG_AAA_____________GAUAAGGGCG___AGC\n______________\|:\|_\|\|\|\|\|:_\|:_\|\|\|\|\|__:\|:\|\|:\|_\|\|\|_____________:\|\|\|\|:\|\|\|:___\|:\|\n______________GUC_ACCGUU_CG_UACCG__GGUUGUC_UUU_____________UUAUUUCCGU___UUG\n3'-UUU...UUUUA__________A__U______________U___AUUUUAGACACUG__________AUA___-5'\n_____________\|____________________________________________________________\|\n_____________59___________________________________________________________1\n	133 -- 139	7 -- 13	-36.1441 kcal/mol	12.3456 kcal/mol	12.1476 kcal/mol	99 144@LB@ \| \|@LB@5'-GAU...UCUAC A AA C A AGAGA...UUA-3'@LB@ CGG UGGCAG GU AUGGC UCGACGG AAA GAUAAGGGCG AGC@LB@ \|:\| \|\|\|\|\|: \|: \|\|\|\|\| :\|:\|\|:\| \|\|\| :\|\|\|\|:\|\|\|: \|:\|@LB@ GUC ACCGUU CG UACCG GGUUGUC UUU UUAUUUCCGU UUG@LB@3'-UUU...UUUUA A U U AUUUUAGACACUG AUA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -36.1441 kcal/mol@LB@Unfolding Energy - mRNA 12.3456 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 100 -- 143@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@LB@
184	0.02285	0.4143	b4312	fimB	-10.59	0.091292	169 -- 221	1 -- 58	tyrosine recombinase/inversion of on/off regulator of fimA	_____________168________________________________________________________________222\n_____________\|__________________________________________________________________\|\n5'-AUG...ACAGC_____C___UC______UA_____G________________________AGAAUA____UG_____AAAAA...GUA-3'\n______________UAGUG_GCG__UGUAAU____UAA_GGAAAA___________ACGAUGA______AGGC__AUAAC\n______________:\|\|\|\|_\|\|:__\|\|:\|\|\|____:\|\|_:\|\|\|\|\|___________\|\|:\|\|:\|______\|\|\|\|__\|\|\|\|\|\n______________GUCAC_CGU__ACGUUA____GUU_UCUUUU___________UGUUAUU______UCCG__UAUUG\n3'-UUU...UUUUA_________U_______CCGG___G______AUUUUAGACAC_________________UA_____-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	198 -- 204	12 -- 18	-31.4649 kcal/mol	8.72248 kcal/mol	12.1476 kcal/mol	168 222@LB@ \| \|@LB@5'-AUG...ACAGC C UC UA G AGAAUA UG AAAAA...GUA-3'@LB@ UAGUG GCG UGUAAU UAA GGAAAA ACGAUGA AGGC AUAAC@LB@ :\|\|\|\| \|\|: \|\|:\|\|\| :\|\| :\|\|\|\|\| \|\|:\|\|:\| \|\|\|\| \|\|\|\|\|@LB@ GUCAC CGU ACGUUA GUU UCUUUU UGUUAUU UCCG UAUUG@LB@3'-UUU...UUUUA U CCGG G AUUUUAGACAC UA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -31.4649 kcal/mol@LB@Unfolding Energy - mRNA 8.72248 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 169 -- 221@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
199	0.02539	0.4256	b2094	gatA	-8.91	0.199733	27 -- 47	1 -- 21	galactitol-specific enzyme IIA component of PTS	_____________26_____________________48\n_____________\|______________________\|\n5'-UUA...UGAUG____AUCU______________AUCCC...AUG-3'\n______________GUGA____UGAAGGCGUG_GAC\n______________\|\|\|\|____\|:\|\|\|\|\|:\|:_:\|\|\n______________CACU____AUUUCCGUAU_UUG\n3'-UUU...UUAGA____GUU___________A___-5'\n_____________\|_____________________\|\n_____________22____________________1\n	38 -- 44	5 -- 11	-17.7737 kcal/mol	4.45083 kcal/mol	4.41334 kcal/mol	26 48@LB@ \| \|@LB@5'-UUA...UGAUG AUCU AUCCC...AUG-3'@LB@ GUGA UGAAGGCGUG GAC@LB@ \|\|\|\| \|:\|\|\|\|\|:\|: :\|\|@LB@ CACU AUUUCCGUAU UUG@LB@3'-UUU...UUAGA GUU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -17.7737 kcal/mol@LB@Unfolding Energy - mRNA 4.45083 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 27 -- 47@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
26	0.00144	0.1863	b4406	yaeP	-8.75	0.213688	187 -- 204	2 -- 20	UPF0253 family protein	_____________186_________________205\n_____________\|___________________\|\n5'-ACC...AGUGC_____G_____________AAAAA...UGC-3'\n______________UGACA__GAGGGCAUGUGG\n______________\|\|\|\|\|__:\|:\|\|\|\|\|:\|::\n______________ACUGU__UUUCCGUAUAUU\n3'-UUU...UAGAC_____UA____________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	197 -- 203	3 -- 9	-20.0716 kcal/mol	7.09254 kcal/mol	4.22649 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...AGUGC G AAAAA...UGC-3'@LB@ UGACA GAGGGCAUGUGG@LB@ \|\|\|\|\| :\|:\|\|\|\|\|:\|::@LB@ ACUGU UUUCCGUAUAUU@LB@3'-UUU...UAGAC UA G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.0716 kcal/mol@LB@Unfolding Energy - mRNA 7.09254 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@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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usability assessment

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service.

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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