Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
50	0.004849	0.3217	b1079	flgH	-12.97	0.070541	130 -- 141	23 -- 34	flagellar protein of basal-body outer-membrane L ring	_____________129____________________142\n_____________\|______________________\|\n5'-ACU...CGAUC__A_____CA____________ACUCU...GGG-3'\n______________AG_UGCUG__AAAACUGACGCA\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________UC_ACGAC__UUUUGACUGCGU\n3'-UUU...UUUUA________UA____________ACCCC...UAG-5'\n_____________\|______________________\|\n_____________35_____________________22\n	135 -- 141	23 -- 29	-26.3449 kcal/mol	4.56982 kcal/mol	12.5314 kcal/mol	129 142@LB@ \| \|@LB@5'-ACU...CGAUC A CA ACUCU...GGG-3'@LB@ AG UGCUG AAAACUGACGCA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UC ACGAC UUUUGACUGCGU@LB@3'-UUU...UUUUA UA ACCCC...UAG-5'@LB@ \| \|@LB@ 35 22@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -26.3449 kcal/mol@LB@Unfolding Energy - mRNA 4.56982 kcal/mol@LB@Unfolding Energy - sRNA 12.5314 kcal/mol@LB@@LB@Position - mRNA 130 -- 141@LB@Position - sRNA 23 -- 34@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 23 -- 29@LB@
140	0.01495	0.3575	b2415	ptsH	-9.89	0.288161	112 -- 122	24 -- 34	phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr)	_____________111____________123\n_____________\|______________\|\n5'-UUG...CAAUA_____UA_______ACCGC...UUA-3'\n______________CAGGC__AAGUCGA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\n______________GUCCG__UUCAGUU\n3'-UUU...ACUAC______________GAAAG...UAG-5'\n_____________\|______________\|\n_____________35_____________23\n	138 -- 144	150 -- 156	-14.4294 kcal/mol	3.35524 kcal/mol	6.54796 kcal/mol	111 123@LB@ \| \|@LB@5'-UUG...CAAUA UA ACCGC...UUA-3'@LB@ CAGGC AAGUCGA@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ GUCCG UUCAGUU@LB@3'-UUU...ACUAC GAAAG...UAG-5'@LB@ \| \|@LB@ 35 23@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -14.4294 kcal/mol@LB@Unfolding Energy - mRNA 3.35524 kcal/mol@LB@Unfolding Energy - sRNA 6.54796 kcal/mol@LB@@LB@Position - mRNA 112 -- 122@LB@Position - sRNA 24 -- 34@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 150 -- 156@LB@
154	0.01719	0.3749	b3726	pstA	-9.04	0.409183	290 -- 297	24 -- 31	phosphate ABC transporter permease	_____________289____________298\n_____________\|______________\|\n5'-CAG...CCGUA_________C____U-3'\n______________UUGCGCUGA_GCUC\n______________\|\|:\|:\|::\|_:\|\|\|\n______________AAUGUGGUU_UGAG\n3'-UUU...ACUAA_________A____UCAGU...UAG-5'\n_____________\|______________\|\n_____________32_____________23\n	288 -- 294	181 -- 187	-13.2096 kcal/mol	2.6708 kcal/mol	3.40409 kcal/mol	289 298@LB@ \| \|@LB@5'-CAG...CCGUA C U-3'@LB@ UUGCGCUGA GCUC@LB@ \|\|:\|:\|::\| :\|\|\|@LB@ AAUGUGGUU UGAG@LB@3'-UUU...ACUAA A UCAGU...UAG-5'@LB@ \| \|@LB@ 32 23@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.2096 kcal/mol@LB@Unfolding Energy - mRNA 2.6708 kcal/mol@LB@Unfolding Energy - sRNA 3.40409 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 24 -- 31@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 181 -- 187@LB@
163	0.01822	0.376	b1073	flgB	-9.73	0.308533	172 -- 220	24 -- 70	flagellar component of cell-proximal portion of basal-body rod	_____________171_______221\n_____________\|_________\|\n5'-UGA...AACAU_________CG-3'\n______________CGCCAAUGC\n______________\|:\|\|\|\|\|:\|\n______________GUGGUUAUG\n3'-UUU...AAAAU_________AGUCA...UAG-5'\n_____________\|_________\|\n_____________71________23\n	292 -- 298	178 -- 184	-11.5881 kcal/mol	1.63005 kcal/mol	3.31726 kcal/mol	171 221@LB@ \| \|@LB@5'-UGA...AACAU CG-3'@LB@ CGCCAAUGC@LB@ \|:\|\|\|\|\|:\|@LB@ GUGGUUAUG@LB@3'-UUU...AAAAU AGUCA...UAG-5'@LB@ \| \|@LB@ 71 23@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -11.5881 kcal/mol@LB@Unfolding Energy - mRNA 1.63005 kcal/mol@LB@Unfolding Energy - sRNA 3.31726 kcal/mol@LB@@LB@Position - mRNA 172 -- 220@LB@Position - sRNA 24 -- 70@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 178 -- 184@LB@
108	0.01175	0.3575	b0723	sdhA	-10.39	0.232370	178 -- 209	28 -- 62	succinate dehydrogenase flavoprotein subunit	_____________177_______________________210\n_____________\|_________________________\|\n5'-GGU...GAAAU__________G_G_AUU________UUGUG...GUG-3'\n______________UGC_CAGUCA_A_A___UGAUGCAG\n______________\|:\|_\|\|\|\|\|\|_\|_\|___\|\|\|\|\|\|\|\|\n______________AUG_GUCAGU_U_U___ACUACGUC\n3'-UUU...UGGUU___A______G_G____________CGUUC...UAG-5'\n_____________\|_________________________\|\n_____________63________________________27\n	225 -- 231	159 -- 165	-22.5908 kcal/mol	8.24888 kcal/mol	4.81331 kcal/mol	177 210@LB@ \| \|@LB@5'-GGU...GAAAU G G AUU UUGUG...GUG-3'@LB@ UGC CAGUCA A A UGAUGCAG@LB@ \|:\| \|\|\|\|\|\| \| \| \|\|\|\|\|\|\|\|@LB@ AUG GUCAGU U U ACUACGUC@LB@3'-UUU...UGGUU A G G CGUUC...UAG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -22.5908 kcal/mol@LB@Unfolding Energy - mRNA 8.24888 kcal/mol@LB@Unfolding Energy - sRNA 4.81331 kcal/mol@LB@@LB@Position - mRNA 178 -- 209@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@LB@
2	4.964e-05	0.08352	b0475	hemH	-12.83	0.075395	238 -- 275	45 -- 93	ferrochelatase	_____________237______________________________________________________________________276\n_____________\|________________________________________________________________________\|\n5'-CGG...AGACU_______________C__________AAACCU_____________C_______C_C_______C___A____UAAAA...GCG-3'\n______________AAAACC____GGUAU___CUGCUGGC______GGGU______ACG_CCGAUGC_C___CACAC_UGA_GCGG\n______________\|\|\|\|\|\|____\|\|\|\|\|___\|\|\|\|\|\|\|\|______\|\|\|\|______\|\|:_\|\|:\|\|:\|_\|___\|\|\|\|\|_\|\|\|_\|\|:\|\n______________UUUUGG____CCAUA___GACGACCG______CCCA______UGU_GGUUAUG_G___GUGUG_ACU_CGUC\n_______3'-UUUU______UCGU_____UUA__________________CUAAAA___________A_UCA_____U___A____CGUUC...UAG-5'\n_____________\|________________________________________________________________________\|\n_____________94_______________________________________________________________________44\n	247 -- 253	178 -- 184	-50.8068 kcal/mol	15.6732 kcal/mol	22.9013 kcal/mol	237 276@LB@ \| \|@LB@5'-CGG...AGACU C AAACCU C C C C A UAAAA...GCG-3'@LB@ AAAACC GGUAU CUGCUGGC GGGU ACG CCGAUGC C CACAC UGA GCGG@LB@ \|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\| \|\|: \|\|:\|\|:\| \| \|\|\|\|\| \|\|\| \|\|:\|@LB@ UUUUGG CCAUA GACGACCG CCCA UGU GGUUAUG G GUGUG ACU CGUC@LB@ 3'-UUUU UCGU UUA CUAAAA A UCA U A CGUUC...UAG-5'@LB@ \| \|@LB@ 94 44@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -50.8068 kcal/mol@LB@Unfolding Energy - mRNA 15.6732 kcal/mol@LB@Unfolding Energy - sRNA 22.9013 kcal/mol@LB@@LB@Position - mRNA 238 -- 275@LB@Position - sRNA 45 -- 93@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 178 -- 184@LB@
72	0.007293	0.3408	b3240	aaeB	-15.57	0.020683	172 -- 248	45 -- 133	p-hydroxybenzoic acid efflux system component	_____________171________________249\n_____________\|__________________\|\n5'-ACU...ACAUA__________________CUGGC...UGG-3'\n______________UUCGCU_UUGCGGUAAAA\n______________\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\|\|\n______________AAGCGA_AGCGCCAUUUU\n3'-UUU...UGUUG______C___________AUCAC...UAG-5'\n_____________\|__________________\|\n_____________134________________44\n	240 -- 246	47 -- 53	-22.573 kcal/mol	5.7072 kcal/mol	6.14031 kcal/mol	171 249@LB@ \| \|@LB@5'-ACU...ACAUA CUGGC...UGG-3'@LB@ UUCGCU UUGCGGUAAAA@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|\|\|\|@LB@ AAGCGA AGCGCCAUUUU@LB@3'-UUU...UGUUG C AUCAC...UAG-5'@LB@ \| \|@LB@ 134 44@LB@@LB@@LB@Energy -15.57 kcal/mol@LB@Hybridization Energy -22.573 kcal/mol@LB@Unfolding Energy - mRNA 5.7072 kcal/mol@LB@Unfolding Energy - sRNA 6.14031 kcal/mol@LB@@LB@Position - mRNA 172 -- 248@LB@Position - sRNA 45 -- 133@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 47 -- 53@LB@
73	0.007584	0.3458	b0059	rapA	-13.35	0.058963	263 -- 277	46 -- 60	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________262_____________278\n_____________\|_______________\|\n5'-GCU...GGAAC_______________UGCGC...UUU-3'\n______________CGUUGUCGCGGUGGA\n______________\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GCGACAGCGCCAUUU\n3'-UUU...UUGAA_______________UAUCA...UAG-5'\n_____________\|_______________\|\n_____________61______________45\n	269 -- 275	48 -- 54	-26.0749 kcal/mol	7.19742 kcal/mol	6.07408 kcal/mol	262 278@LB@ \| \|@LB@5'-GCU...GGAAC UGCGC...UUU-3'@LB@ CGUUGUCGCGGUGGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GCGACAGCGCCAUUU@LB@3'-UUU...UUGAA UAUCA...UAG-5'@LB@ \| \|@LB@ 61 45@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -26.0749 kcal/mol@LB@Unfolding Energy - mRNA 7.19742 kcal/mol@LB@Unfolding Energy - sRNA 6.07408 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 46 -- 60@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
28	0.002284	0.2633	b1114	mfd	-18.81	0.004608	253 -- 297	50 -- 95	transcription-repair coupling factor	_____________252______________298\n_____________\|________________\|\n5'-UUC...GCGUC___U____________CGGCG...AAA-3'\n______________UGC_GGGCGAGUUAAC\n______________\|\|\|_:\|\|\|:\|\|\|:\|\|\|\n______________ACG_UCCGUUCAGUUG\n3'-UUU...GUACU________________AAAGU...UAG-5'\n_____________\|________________\|\n_____________96_______________49\n	262 -- 268	149 -- 155	-20.6961 kcal/mol	4.60584 kcal/mol	7.12854 kcal/mol	252 298@LB@ \| \|@LB@5'-UUC...GCGUC U CGGCG...AAA-3'@LB@ UGC GGGCGAGUUAAC@LB@ \|\|\| :\|\|\|:\|\|\|:\|\|\|@LB@ ACG UCCGUUCAGUUG@LB@3'-UUU...GUACU AAAGU...UAG-5'@LB@ \| \|@LB@ 96 49@LB@@LB@@LB@Energy -18.81 kcal/mol@LB@Hybridization Energy -20.6961 kcal/mol@LB@Unfolding Energy - mRNA 4.60584 kcal/mol@LB@Unfolding Energy - sRNA 7.12854 kcal/mol@LB@@LB@Position - mRNA 253 -- 297@LB@Position - sRNA 50 -- 95@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 149 -- 155@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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