Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
130	0.02238	0.5385	b4365	yjjQ	-17.31	0.005324	260 -- 274	14 -- 28	putative transcriptional regulator	_____________259_____________275\n_____________\|_______________\|\n5'-AGG...CAAGC_______________CAUGA...AUG-3'\n______________AGGGUUAAAAGAGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UCCCAAUUUUCUCCA\n3'-CGC...GAAGU_______________CGGCG...AAG-5'\n_____________\|_______________\|\n_____________29______________13\n	268 -- 274	14 -- 20	-23.2971 kcal/mol	2.73817 kcal/mol	3.24497 kcal/mol	259 275@LB@ \| \|@LB@5'-AGG...CAAGC CAUGA...AUG-3'@LB@ AGGGUUAAAAGAGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UCCCAAUUUUCUCCA@LB@3'-CGC...GAAGU CGGCG...AAG-5'@LB@ \| \|@LB@ 29 13@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -23.2971 kcal/mol@LB@Unfolding Energy - mRNA 2.73817 kcal/mol@LB@Unfolding Energy - sRNA 3.24497 kcal/mol@LB@@LB@Position - mRNA 260 -- 274@LB@Position - sRNA 14 -- 28@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 14 -- 20@LB@
128	0.02183	0.5385	b0874	ybjE	-9.13	0.148469	198 -- 230	59 -- 85	putative transporter	_____________197_______________________________231\n_____________\|_________________________________\|\n5'-GGG...GGGUU________UUCUG____GUUAAUC____U____CCCCU...UAA-3'\n______________UUCAUGUU_____GGCU_______AUUC_GGUU\n______________\|\|\|\|:\|\|\|_____\|\|\|\|_______\|\|\|\|_:\|\|\|\n______________AAGUGCAA_____CCGA_______UAAG_UCAA\n3'-CGC...UUUUC_________________AAUCAA_____C____CUCUU...AAG-5'\n_____________\|_________________________________\|\n_____________86________________________________58\n	199 -- 205	78 -- 84	-15.801 kcal/mol	4.95896 kcal/mol	1.70749 kcal/mol	197 231@LB@ \| \|@LB@5'-GGG...GGGUU UUCUG GUUAAUC U CCCCU...UAA-3'@LB@ UUCAUGUU GGCU AUUC GGUU@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|\|\| :\|\|\|@LB@ AAGUGCAA CCGA UAAG UCAA@LB@3'-CGC...UUUUC AAUCAA C CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -15.801 kcal/mol@LB@Unfolding Energy - mRNA 4.95896 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 198 -- 230@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 78 -- 84@LB@
112	0.0191	0.5385	b0854	potF	-9.27	0.140763	36 -- 50	64 -- 78	putrescine ABC transporter periplasmic binding protein	_____________35______________51\n_____________\|_______________\|\n5'-UAC...AACCC_____AA________UUGCG...ACA-3'\n______________UGGCU__AGUUAUUC\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAAG\n3'-CGC...GUGCA_____AA________CUCAA...AAG-5'\n_____________\|_______________\|\n_____________79______________63\n	44 -- 50	64 -- 70	-15.0609 kcal/mol	5.5152 kcal/mol	0.273858 kcal/mol	35 51@LB@ \| \|@LB@5'-UAC...AACCC AA UUGCG...ACA-3'@LB@ UGGCU AGUUAUUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACCGA UCAAUAAG@LB@3'-CGC...GUGCA AA CUCAA...AAG-5'@LB@ \| \|@LB@ 79 63@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.0609 kcal/mol@LB@Unfolding Energy - mRNA 5.5152 kcal/mol@LB@Unfolding Energy - sRNA 0.273858 kcal/mol@LB@@LB@Position - mRNA 36 -- 50@LB@Position - sRNA 64 -- 78@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 64 -- 70@LB@
39	0.007274	0.5385	b1636	pdxY	-13.08	0.030384	230 -- 254	60 -- 84	pyridoxamine kinase	_____________229_______________________255\n_____________\|_________________________\|\n5'-UAU...CAGUC________U__A____C__G_____AACAG...UCU-3'\n______________UCACGUUG_UU_UGGU_AU_CGGGU\n______________\|\|\|\|\|\|\|\|_:\|_\|:\|\|_\|\|_\|\|:\|\|\n______________AGUGCAAC_GA_AUCA_UA_GCUCA\n3'-CGC...UUUCA________C__A____A__A_____ACUCU...AAG-5'\n_____________\|_________________________\|\n_____________85________________________59\n	231 -- 237	77 -- 83	-19.8659 kcal/mol	5.09201 kcal/mol	1.69371 kcal/mol	229 255@LB@ \| \|@LB@5'-UAU...CAGUC U A C G AACAG...UCU-3'@LB@ UCACGUUG UU UGGU AU CGGGU@LB@ \|\|\|\|\|\|\|\| :\| \|:\|\| \|\| \|\|:\|\|@LB@ AGUGCAAC GA AUCA UA GCUCA@LB@3'-CGC...UUUCA C A A A ACUCU...AAG-5'@LB@ \| \|@LB@ 85 59@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.8659 kcal/mol@LB@Unfolding Energy - mRNA 5.09201 kcal/mol@LB@Unfolding Energy - sRNA 1.69371 kcal/mol@LB@@LB@Position - mRNA 230 -- 254@LB@Position - sRNA 60 -- 84@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 77 -- 83@LB@
140	0.02329	0.5385	b3026	qseC	-7.47	0.277092	174 -- 202	52 -- 78	quorum sensing sensory histidine kinase in two-component regulatory system with QseB	_____________173___________________________203\n_____________\|_____________________________\|\n5'-AAA...GUGCA____A_______CA_AUU__G________GAAAU...GGA-3'\n______________UGGU_UUGGUUA__C___AG_UGAGAAAU\n______________\|\|\|:_\|\|:\|\|\|\|__\|___\|\|_\|\|\|\|\|\|\|:\n______________ACCG_AAUCAAU__G___UC_ACUCUUUG\n3'-CGC...GUGCA____A_______AA_C____A________AGAGC...AAG-5'\n_____________\|_____________________________\|\n_____________79____________________________51\n	196 -- 202	52 -- 58	-18.6962 kcal/mol	6.8409 kcal/mol	4.38944 kcal/mol	173 203@LB@ \| \|@LB@5'-AAA...GUGCA A CA AUU G GAAAU...GGA-3'@LB@ UGGU UUGGUUA C AG UGAGAAAU@LB@ \|\|\|: \|\|:\|\|\|\| \| \|\| \|\|\|\|\|\|\|:@LB@ ACCG AAUCAAU G UC ACUCUUUG@LB@3'-CGC...GUGCA A AA C A AGAGC...AAG-5'@LB@ \| \|@LB@ 79 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -18.6962 kcal/mol@LB@Unfolding Energy - mRNA 6.8409 kcal/mol@LB@Unfolding Energy - sRNA 4.38944 kcal/mol@LB@@LB@Position - mRNA 174 -- 202@LB@Position - sRNA 52 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 52 -- 58@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@LB@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@LB@
91	0.0156	0.5385	b0881	clpS	-13.09	0.030255	248 -- 265	74 -- 90	regulatory protein for ClpA substrate specificity	_____________247________________266\n_____________\|__________________\|\n5'-GCA...GAAGA___________AC_C___AAAAC...UCA-3'\n______________AAAAGUUCGCG__G_GCU\n______________\|\|\|\|\|\|\|\|:\|\|__\|_\|\|\|\n______________UUUUCAAGUGC__C_CGA\n3'-CGC...AGGCG___________AA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	252 -- 258	80 -- 86	-16.9257 kcal/mol	3.31752 kcal/mol	0.517587 kcal/mol	247 266@LB@ \| \|@LB@5'-GCA...GAAGA AC C AAAAC...UCA-3'@LB@ AAAAGUUCGCG G GCU@LB@ \|\|\|\|\|\|\|\|:\|\| \| \|\|\|@LB@ UUUUCAAGUGC C CGA@LB@3'-CGC...AGGCG AA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -16.9257 kcal/mol@LB@Unfolding Energy - mRNA 3.31752 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 248 -- 265@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 80 -- 86@LB@
190	0.03345	0.5559	b4090	rpiB	-6.75	0.355761	259 -- 286	57 -- 78	ribose 5-phosphate isomerase B/allose 6-phosphate isomerase	_____________258__________________________287\n_____________\|____________________________\|\n5'-AAC...AAUAG____ACA________AGCG___C_____AGUGA...AAG-3'\n______________UGGC___UUUAGUUG____UGG_GUUGA\n______________\|\|\|\|___\|\|\|\|\|\|\|:____:\|:_\|\|\|\|\|\n______________ACCG___AAAUCAAU____GCU_CAACU\n3'-CGC...GUGCA_______________AA___________CUUUG...AAG-5'\n_____________\|____________________________\|\n_____________79___________________________56\n	267 -- 273	67 -- 73	-15.2709 kcal/mol	7.30632 kcal/mol	1.21856 kcal/mol	258 287@LB@ \| \|@LB@5'-AAC...AAUAG ACA AGCG C AGUGA...AAG-3'@LB@ UGGC UUUAGUUG UGG GUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|: :\|: \|\|\|\|\|@LB@ ACCG AAAUCAAU GCU CAACU@LB@3'-CGC...GUGCA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 79 56@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -15.2709 kcal/mol@LB@Unfolding Energy - mRNA 7.30632 kcal/mol@LB@Unfolding Energy - sRNA 1.21856 kcal/mol@LB@@LB@Position - mRNA 259 -- 286@LB@Position - sRNA 57 -- 78@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 67 -- 73@LB@
161	0.02817	0.5559	b0852	rimK	-8.21	0.210781	44 -- 79	81 -- 107	ribosomal protein S6 modification protein	_____________43___________________________________80\n_____________\|____________________________________\|\n5'-AAC...CGCCG____A_______CGAUCAU______C___CAA____UAAAG...AUC-3'\n______________GGAU_CCUGGAG_______AUCCGC_GAA___UCAU\n______________\|\|\|\|_\|\|\|\|\|\|\|_______\|\|\|\|\|\|_:\|\|___\|\|\|:\n______________CCUA_GGACCUC_______UAGGCG_UUU___AGUG\n_________3'-CG_________________________U___CA_____CAACC...AAG-5'\n_____________\|____________________________________\|\n_____________108__________________________________80\n	49 -- 55	97 -- 103	-27.5385 kcal/mol	7.46513 kcal/mol	11.8593 kcal/mol	43 80@LB@ \| \|@LB@5'-AAC...CGCCG A CGAUCAU C CAA UAAAG...AUC-3'@LB@ GGAU CCUGGAG AUCCGC GAA UCAU@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|:@LB@ CCUA GGACCUC UAGGCG UUU AGUG@LB@ 3'-CG U CA CAACC...AAG-5'@LB@ \| \|@LB@ 108 80@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -27.5385 kcal/mol@LB@Unfolding Energy - mRNA 7.46513 kcal/mol@LB@Unfolding Energy - sRNA 11.8593 kcal/mol@LB@@LB@Position - mRNA 44 -- 79@LB@Position - sRNA 81 -- 107@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 97 -- 103@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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