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
172	0.008479	0.1735	b4395	ytjC	-10.99	0.163500	244 -- 268	34 -- 71	phosphatase	_____________243____________________________________269\n_____________\|______________________________________\|\n5'-UCC...GUGGA____CG________________________________GUCUG...AGC-3'\n______________ACGC__AGCGA__CGU______AUUCAGGG_____CCA\n______________\|\|:\|__\|\|\|:\|__\|\|\|______\|:\|\|\|\|\|\|_____\|\|\|\n______________UGUG__UCGUU__GCA______UGAGUCCC_____GGU\n3'-UUU...UCUGA____UG_____AA___ACAAAG________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	259 -- 265	42 -- 48	-22.1302 kcal/mol	6.3498 kcal/mol	4.79237 kcal/mol	243 269@LB@ \| \|@LB@5'-UCC...GUGGA CG GUCUG...AGC-3'@LB@ ACGC AGCGA CGU AUUCAGGG CCA@LB@ \|\|:\| \|\|\|:\| \|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGUG UCGUU GCA UGAGUCCC GGU@LB@3'-UUU...UCUGA UG AA ACAAAG CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -22.1302 kcal/mol@LB@Unfolding Energy - mRNA 6.3498 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 244 -- 268@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
180	0.009034	0.1747	b3146	rsmI	-12.76	0.071583	191 -- 238	34 -- 76	16S rRNA C1402 2'-O-ribose methyltransferase SAM-dependent	_____________190____________________________________________________239\n_____________\|______________________________________________________\|\n5'-CAG...AAUAC____G____AAUGAAACA___C_______GC_GAUAAUU_______________GCUUU...AGG-3'\n______________GGAC_ACAC_________ACA_CAA_UCG__G_______CUCAGGG_____CCA\n______________:\|\|\|_\|\|\|\|_________\|\|\|_\|\|\|_\|\|\|__\|_______\|\|\|\|\|\|\|_____\|\|\|\n______________UCUG_UGUG_________UGU_GUU_AGC__C_______GAGUCCC_____GGU\n3'-UUU...CCGUU____A________________C___A___AA_AAAGU_________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________________________\|\n_____________77_____________________________________________________33\n	229 -- 235	42 -- 48	-25.3144 kcal/mol	7.73901 kcal/mol	4.816 kcal/mol	190 239@LB@ \| \|@LB@5'-CAG...AAUAC G AAUGAAACA C GC GAUAAUU GCUUU...AGG-3'@LB@ GGAC ACAC ACA CAA UCG G CUCAGGG CCA@LB@ :\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\| \| \|\|\|\|\|\|\| \|\|\|@LB@ UCUG UGUG UGU GUU AGC C GAGUCCC GGU@LB@3'-UUU...CCGUU A C A AA AAAGU CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -25.3144 kcal/mol@LB@Unfolding Energy - mRNA 7.73901 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 191 -- 238@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 42 -- 48@LB@
181	0.009071	0.1747	b3962	sthA	-14.30	0.031527	83 -- 114	34 -- 76	pyridine nucleotide transhydrogenase soluble	_____________82___________________________________________115\n_____________\|____________________________________________\|\n5'-UAC...GAAAC____AAA___AA_______________________AU__AG___GAUAA...CAG-3'\n______________AGAC___GCA__GGC____________CGCUCAGG__AU__CCA\n______________\|\|\|\|___:\|\|__:\|\|____________\|:\|\|\|\|\|\|__\|\|__\|\|\|\n______________UCUG___UGU__UCG____________GUGAGUCC__UA__GGU\n3'-UUU...CCGUU____AUG___G____UUAAGCAACAAA________CC__AA___ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________77___________________________________________33\n	99 -- 105	43 -- 49	-23.8174 kcal/mol	4.70621 kcal/mol	4.816 kcal/mol	82 115@LB@ \| \|@LB@5'-UAC...GAAAC AAA AA AU AG GAUAA...CAG-3'@LB@ AGAC GCA GGC CGCUCAGG AU CCA@LB@ \|\|\|\| :\|\| :\|\| \|:\|\|\|\|\|\| \|\| \|\|\|@LB@ UCUG UGU UCG GUGAGUCC UA GGU@LB@3'-UUU...CCGUU AUG G UUAAGCAACAAA CC AA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -23.8174 kcal/mol@LB@Unfolding Energy - mRNA 4.70621 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 83 -- 114@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 43 -- 49@LB@
10	6.564e-05	0.0231	b3458	livK	-17.14	0.005196	153 -- 196	35 -- 71	leucine transporter subunit	_____________152____________________________________________197\n_____________\|______________________________________________\|\n5'-UGU...UGUUA______AAAAACAA_____CACAACA______GAAU__________GACUA...CGA-3'\n______________ACACAU________AGCAA_________UCAC____GGGGAUUUUU\n______________\|\|\|\|\|:________\|\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|::\n______________UGUGUG________UCGUU_________AGUG____CCCCUAAAGG\n3'-UUU...UCUGA___________________AAGCAACAA____AGU___________UACGA...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________34\n	190 -- 196	35 -- 41	-26.3585 kcal/mol	4.43917 kcal/mol	4.78171 kcal/mol	152 197@LB@ \| \|@LB@5'-UGU...UGUUA AAAAACAA CACAACA GAAU GACUA...CGA-3'@LB@ ACACAU AGCAA UCAC GGGGAUUUUU@LB@ \|\|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|::@LB@ UGUGUG UCGUU AGUG CCCCUAAAGG@LB@3'-UUU...UCUGA AAGCAACAA AGU UACGA...GCA-5'@LB@ \| \|@LB@ 72 34@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -26.3585 kcal/mol@LB@Unfolding Energy - mRNA 4.43917 kcal/mol@LB@Unfolding Energy - sRNA 4.78171 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 35 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 35 -- 41@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@
28	0.0004009	0.04965	b3511	hdeD	-17.16	0.005105	126 -- 176	35 -- 75	acid-resistance membrane protein	_____________125__________________________________________________177\n_____________\|____________________________________________________\|\n5'-GAG...AAAUC________U_UUA__CG________G__AUAGAUUGAUAG____________UUCUU...UCG-3'\n______________GACUGCAU_C___GA__CGUU_UUU_GC____________CAGGGGAUUUUC\n______________\|\|\|\|:\|\|:_\|___:\|__\|\|\|\|_\|\|\|_:\|____________\|\|\|\|\|\|\|\|\|\|:\|\n______________CUGAUGUG_G___UU__GCAA_AAA_UG____________GUCCCCUAAAGG\n3'-UUU...CGUUU________U_UCG__AA____C___G__A_______________________UACGA...GCA-5'\n_____________\|____________________________________________________\|\n_____________76___________________________________________________34\n	170 -- 176	35 -- 41	-34.0299 kcal/mol	12.0619 kcal/mol	4.80541 kcal/mol	125 177@LB@ \| \|@LB@5'-GAG...AAAUC U UUA CG G AUAGAUUGAUAG UUCUU...UCG-3'@LB@ GACUGCAU C GA CGUU UUU GC CAGGGGAUUUUC@LB@ \|\|\|\|:\|\|: \| :\| \|\|\|\| \|\|\| :\| \|\|\|\|\|\|\|\|\|\|:\|@LB@ CUGAUGUG G UU GCAA AAA UG GUCCCCUAAAGG@LB@3'-UUU...CGUUU U UCG AA C G A UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.0299 kcal/mol@LB@Unfolding Energy - mRNA 12.0619 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 126 -- 176@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 35 -- 41@LB@
37	0.0006599	0.0618	b3399	yrfG	-16.99	0.005777	176 -- 197	35 -- 56	GMP/IMP nucleotidase	_____________175____________________198\n_____________\|______________________\|\n5'-UAG...GCAAA___C_______U__A_______CUCAU...AGC-3'\n______________UUG_UUCACUC_GG_GAUUUCC\n______________\|\|\|_\|\|\|\|\|\|\|_\|\|_\|\|\|\|\|\|\|\n______________AAC_AAGUGAG_CC_CUAAAGG\n3'-UUU...UAAGC___A_______U__C_______UACGA...GCA-5'\n_____________\|______________________\|\n_____________57_____________________34\n	191 -- 197	35 -- 41	-24.095 kcal/mol	5.08619 kcal/mol	2.02101 kcal/mol	175 198@LB@ \| \|@LB@5'-UAG...GCAAA C U A CUCAU...AGC-3'@LB@ UUG UUCACUC GG GAUUUCC@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ AAC AAGUGAG CC CUAAAGG@LB@3'-UUU...UAAGC A U C UACGA...GCA-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -16.99 kcal/mol@LB@Hybridization Energy -24.095 kcal/mol@LB@Unfolding Energy - mRNA 5.08619 kcal/mol@LB@Unfolding Energy - sRNA 2.02101 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
79	0.00332	0.1462	b1845	ptrB	-10.90	0.169644	42 -- 70	35 -- 70	protease II	_____________41____________________________________71\n_____________\|_____________________________________\|\n5'-UCU...AGAAU________C_____AA____________CU_______UCUGU...AGC-3'\n______________CGCACAGC_AUUUG__________CAGG__GAUUUUC\n______________\|:\|\|\|\|\|\|_\|\|\|:\|__________\|\|\|\|__\|\|\|\|\|:\|\n______________GUGUGUCG_UAAGC__________GUCC__CUAAAGG\n3'-UUU...CUGAU________U_____AACAAAGUGA____C________UACGA...GCA-5'\n_____________\|_____________________________________\|\n_____________71____________________________________34\n	64 -- 70	35 -- 41	-24.5069 kcal/mol	8.82337 kcal/mol	4.7817 kcal/mol	41 71@LB@ \| \|@LB@5'-UCU...AGAAU C AA CU UCUGU...AGC-3'@LB@ CGCACAGC AUUUG CAGG GAUUUUC@LB@ \|:\|\|\|\|\|\| \|\|\|:\| \|\|\|\| \|\|\|\|\|:\|@LB@ GUGUGUCG UAAGC GUCC CUAAAGG@LB@3'-UUU...CUGAU U AACAAAGUGA C UACGA...GCA-5'@LB@ \| \|@LB@ 71 34@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -24.5069 kcal/mol@LB@Unfolding Energy - mRNA 8.82337 kcal/mol@LB@Unfolding Energy - sRNA 4.7817 kcal/mol@LB@@LB@Position - mRNA 42 -- 70@LB@Position - sRNA 35 -- 70@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 35 -- 41@LB@
127	0.005686	0.1575	b1176	minC	-17.54	0.003902	3 -- 40	35 -- 74	inhibitor of FtsZ ring polymerization	_____________2________________________________________41\n_____________\|________________________________________\|\n_________5'-AA_G_____________GG____A__G__A_____U______UAAGC...AAG-3'\n______________A_UACG_ACGGCAAU__GUUG_UU_AC__AGGG_AUUUUU\n______________\|_\|\|\|:_\|\|:\|\|\|\|\|__\|\|\|\|_\|\|_\|\|__\|\|\|\|_\|\|\|\|::\n______________U_AUGU_UGUCGUUA__CAAC_AA_UG__UCCC_UAAAGG\n3'-UUU...GUUUC_G____G________AG____A__G__AG____C______UACGA...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________34\n	10 -- 16	60 -- 66	-29.7113 kcal/mol	7.37167 kcal/mol	4.80541 kcal/mol	2 41@LB@ \| \|@LB@ 5'-AA G GG A G A U UAAGC...AAG-3'@LB@ A UACG ACGGCAAU GUUG UU AC AGGG AUUUUU@LB@ \| \|\|\|: \|\|:\|\|\|\|\| \|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|::@LB@ U AUGU UGUCGUUA CAAC AA UG UCCC UAAAGG@LB@3'-UUU...GUUUC G G AG A G AG C UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -29.7113 kcal/mol@LB@Unfolding Energy - mRNA 7.37167 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 3 -- 40@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 60 -- 66@LB@
141	0.006483	0.1605	b2474	tmcA	-12.94	0.065378	86 -- 105	35 -- 54	elongator methionine tRNA (ac4C34) acetyltransferase	_____________85___________________106\n_____________\|____________________\|\n5'-GAU...AGACA__________U__CAC____CAGCA...UUG-3'\n______________GUUUCACUCA_GG___UUCU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|:\n______________CAAAGUGAGU_CC___AAGG\n3'-UUU...AGCAA__________C__CUA____UACGA...GCA-5'\n_____________\|____________________\|\n_____________55___________________34\n	89 -- 95	45 -- 51	-18.4772 kcal/mol	3.58569 kcal/mol	1.95269 kcal/mol	85 106@LB@ \| \|@LB@5'-GAU...AGACA U CAC CAGCA...UUG-3'@LB@ GUUUCACUCA GG UUCU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ CAAAGUGAGU CC AAGG@LB@3'-UUU...AGCAA C CUA UACGA...GCA-5'@LB@ \| \|@LB@ 55 34@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -18.4772 kcal/mol@LB@Unfolding Energy - mRNA 3.58569 kcal/mol@LB@Unfolding Energy - sRNA 1.95269 kcal/mol@LB@@LB@Position - mRNA 86 -- 105@LB@Position - sRNA 35 -- 54@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 45 -- 51@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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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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