Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
47	0.002119	0.1452	b0694	kdpE	-6.96	0.113004	177 -- 189	26 -- 38	response regulator in two-component regulatory system with KdpD	_____________176___________190\n_____________\|_____________\|\n5'-ACG...CCUGA_____________CAUGA...CGC-3'\n______________ACUUGAAGAAUUU\n______________\|\|\|\|:\|\|:\|\|\|\|:\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	179 -- 185	30 -- 36	-10.6038 kcal/mol	2.21135 kcal/mol	1.43364 kcal/mol	176 190@LB@ \| \|@LB@5'-ACG...CCUGA CAUGA...CGC-3'@LB@ ACUUGAAGAAUUU@LB@ \|\|\|\|:\|\|:\|\|\|\|:@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -10.6038 kcal/mol@LB@Unfolding Energy - mRNA 2.21135 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 30 -- 36@LB@
190	0.02239	0.3796	b0724	sdhB	-6.89	0.117799	143 -- 176	24 -- 60	succinate dehydrogenase FeS subunit	_____________142____________________________________177\n_____________\|______________________________________\|\n5'-UUU...GAACC_________GCCC____UUCC____C____________ACUUA...UGA-3'\n______________GAAAC_UGC____GGCA_____CGC___GAAGAUUCGU\n______________\|\|\|\|\|_\|\|\|____:\|\|\|_____\|:\|___:\|\|:\|\|\|\|\|\|\n______________CUUUG_ACG____UCGU_____GUG___UUUUUAAGCA\n3'-UUU...CCCUA_____A___AAU_____UCUUC___AAU__________AUGUG...CAA-5'\n_____________\|______________________________________\|\n_____________61_____________________________________23\n	170 -- 176	24 -- 30	-22.9017 kcal/mol	9.73835 kcal/mol	6.27609 kcal/mol	142 177@LB@ \| \|@LB@5'-UUU...GAACC GCCC UUCC C ACUUA...UGA-3'@LB@ GAAAC UGC GGCA CGC GAAGAUUCGU@LB@ \|\|\|\|\| \|\|\| :\|\|\| \|:\| :\|\|:\|\|\|\|\|\|@LB@ CUUUG ACG UCGU GUG UUUUUAAGCA@LB@3'-UUU...CCCUA A AAU UCUUC AAU AUGUG...CAA-5'@LB@ \| \|@LB@ 61 23@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -22.9017 kcal/mol@LB@Unfolding Energy - mRNA 9.73835 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 143 -- 176@LB@Position - sRNA 24 -- 60@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 24 -- 30@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein	_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@LB@
141	0.01363	0.3114	b0767	pgl	-6.62	0.137481	178 -- 199	36 -- 55	6-phosphogluconolactonase	_____________177____________________200\n_____________\|______________________\|\n5'-UCA...GUCAG_____A__U__A__________CAUGA...AUG-3'\n______________UUGCU_AA_GC_AAGGAGCAUU\n______________\|\|\|\|\|_\|\|_\|\|_\|\|\|:\|\|\|\|:\|\n______________AACGA_UU_CG_UUCUUCGUGA\n3'-UUU...CUUUG_____A________________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	193 -- 199	36 -- 42	-19.0667 kcal/mol	6.27112 kcal/mol	6.17795 kcal/mol	177 200@LB@ \| \|@LB@5'-UCA...GUCAG A U A CAUGA...AUG-3'@LB@ UUGCU AA GC AAGGAGCAUU@LB@ \|\|\|\|\| \|\| \|\| \|\|\|:\|\|\|\|:\|@LB@ AACGA UU CG UUCUUCGUGA@LB@3'-UUU...CUUUG A AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.62 kcal/mol@LB@Hybridization Energy -19.0667 kcal/mol@LB@Unfolding Energy - mRNA 6.27112 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 178 -- 199@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
7	4.438e-05	0.02042	b0794	ybhF	-10.77	0.009494	150 -- 165	11 -- 26	putative ABC transporter ATPase	_____________149______________166\n_____________\|________________\|\n5'-UAC...UGAUG________________GCCAG...GUU-3'\n______________CGUUACGCCAGGGAAU\n______________\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|\n______________GCAAUGUGGUCCUUUA\n3'-UUU...UUUAA________________GACUA...CAA-5'\n_____________\|________________\|\n_____________27_______________10\n	157 -- 163	13 -- 19	-25.1629 kcal/mol	6.0475 kcal/mol	8.34814 kcal/mol	149 166@LB@ \| \|@LB@5'-UAC...UGAUG GCCAG...GUU-3'@LB@ CGUUACGCCAGGGAAU@LB@ \|\|\|\|\|\|:\|\|\|\|\|:\|\|\|@LB@ GCAAUGUGGUCCUUUA@LB@3'-UUU...UUUAA GACUA...CAA-5'@LB@ \| \|@LB@ 27 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -25.1629 kcal/mol@LB@Unfolding Energy - mRNA 6.0475 kcal/mol@LB@Unfolding Energy - sRNA 8.34814 kcal/mol@LB@@LB@Position - mRNA 150 -- 165@LB@Position - sRNA 11 -- 26@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 13 -- 19@LB@
19	0.0004926	0.08107	b0820	ybiT	-10.62	0.010514	37 -- 84	2 -- 44	ABC-F family putative regulatory ATPase	_____________36________________________________________________85\n_____________\|_________________________________________________\|\n5'-CCU...GUAUU________A___U_______A__CCA__U_A___U______A_______ACGAA...UUG-3'\n______________GGAAGCGC_UUA__AAGUUC_UU___GC_C_CAG_GAAAUC_GAUGUGU\n______________:\|\|\|\|\|:\|_\|\|\|__\|\|:\|\|\|_\|\|___:\|_\|_\|\|\|_\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGUG_AAU__UUUAAG_AA___UG_G_GUC_CUUUAG_CUACACA\n3'-UUU...UUCGU____________UU______C_______U____________A_______A-5'\n_____________\|_________________________________________________\|\n_____________45________________________________________________1\n	38 -- 44	37 -- 43	-34.6599 kcal/mol	11.843 kcal/mol	12.1934 kcal/mol	36 85@LB@ \| \|@LB@5'-CCU...GUAUU A U A CCA U A U A ACGAA...UUG-3'@LB@ GGAAGCGC UUA AAGUUC UU GC C CAG GAAAUC GAUGUGU@LB@ :\|\|\|\|\|:\| \|\|\| \|\|:\|\|\| \|\| :\| \| \|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGUG AAU UUUAAG AA UG G GUC CUUUAG CUACACA@LB@3'-UUU...UUCGU UU C U A A-5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -34.6599 kcal/mol@LB@Unfolding Energy - mRNA 11.843 kcal/mol@LB@Unfolding Energy - sRNA 12.1934 kcal/mol@LB@@LB@Position - mRNA 37 -- 84@LB@Position - sRNA 2 -- 44@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 37 -- 43@LB@
34	0.001265	0.1198	b0826	moeB	-10.82	0.009172	276 -- 295	26 -- 46	molybdopterin synthase sulfurylase	_____________275___________________296\n_____________\|_____________________\|\n5'-CUU...ACGGC_____________________UCGCG-3'\n______________CAGGAGGCGC_UGAAAGAUUC\n______________\|\|:\|\|:\|\|:\|_\|:\|\|\|:\|\|\|\|\n______________GUUCUUCGUG_AUUUUUUAAG\n3'-UUU...AAUUC__________A__________CAAUG...CAA-5'\n_____________\|_____________________\|\n_____________47____________________25\n	289 -- 295	26 -- 32	-23.0973 kcal/mol	6.15128 kcal/mol	6.13041 kcal/mol	275 296@LB@ \| \|@LB@5'-CUU...ACGGC UCGCG-3'@LB@ CAGGAGGCGC UGAAAGAUUC@LB@ \|\|:\|\|:\|\|:\| \|:\|\|\|:\|\|\|\|@LB@ GUUCUUCGUG AUUUUUUAAG@LB@3'-UUU...AAUUC A CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -23.0973 kcal/mol@LB@Unfolding Energy - mRNA 6.15128 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 26 -- 32@LB@
169	0.01902	0.3625	b0858	ybjO	-5.59	0.239654	140 -- 156	25 -- 43	DUF2593 family inner membrane protein	_____________139__________________157\n_____________\|____________________\|\n5'-AUG...UGGCU____A_______________CCAAC...UUA-3'\n______________GAAG_CACU___AAAAUUUG\n______________\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|:\|\n______________CUUC_GUGA___UUUUAAGC\n3'-UUU...UCGUU_________AUU________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________44___________________24\n	150 -- 156	25 -- 31	-11.6219 kcal/mol	2.26879 kcal/mol	3.76226 kcal/mol	139 157@LB@ \| \|@LB@5'-AUG...UGGCU A CCAAC...UUA-3'@LB@ GAAG CACU AAAAUUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ CUUC GUGA UUUUAAGC@LB@3'-UUU...UCGUU AUU AAUGU...CAA-5'@LB@ \| \|@LB@ 44 24@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -11.6219 kcal/mol@LB@Unfolding Energy - mRNA 2.26879 kcal/mol@LB@Unfolding Energy - sRNA 3.76226 kcal/mol@LB@@LB@Position - mRNA 140 -- 156@LB@Position - sRNA 25 -- 43@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 25 -- 31@LB@
66	0.003432	0.1645	b0882	clpA	-7.45	0.084488	282 -- 290	34 -- 42	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________281_______291\n_____________\|_________\|\n5'-UUU...CCGUC_________UUACU...CGC-3'\n______________GAGCACUUG\n______________:\|\|\|\|\|\|\|:\n______________UUCGUGAAU\n3'-UUU...CGUUC_________UUUUU...CAA-5'\n_____________\|_________\|\n_____________43________33\n	284 -- 290	34 -- 40	-10.5586 kcal/mol	1.49281 kcal/mol	1.61613 kcal/mol	281 291@LB@ \| \|@LB@5'-UUU...CCGUC UUACU...CGC-3'@LB@ GAGCACUUG@LB@ :\|\|\|\|\|\|\|:@LB@ UUCGUGAAU@LB@3'-UUU...CGUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 43 33@LB@@LB@@LB@Energy -7.45 kcal/mol@LB@Hybridization Energy -10.5586 kcal/mol@LB@Unfolding Energy - mRNA 1.49281 kcal/mol@LB@Unfolding Energy - sRNA 1.61613 kcal/mol@LB@@LB@Position - mRNA 282 -- 290@LB@Position - sRNA 34 -- 42@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 34 -- 40@LB@
182	0.02157	0.3768	b0887	cydD	-7.84	0.066788	30 -- 38	33 -- 41	glutathione/cysteine ABC transporter export permease/ATPase	_____________29________39\n_____________\|_________\|\n5'-AUU...AUGGC_________UGCGG...UGA-3'\n______________AGCACUUGA\n______________\|\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	32 -- 38	33 -- 39	-10.6359 kcal/mol	1.18174 kcal/mol	1.6188 kcal/mol	29 39@LB@ \| \|@LB@5'-AUU...AUGGC UGCGG...UGA-3'@LB@ AGCACUUGA@LB@ \|\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -10.6359 kcal/mol@LB@Unfolding Energy - mRNA 1.18174 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 30 -- 38@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 33 -- 39@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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