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
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@
47	0.003222	0.2306	b1667	ydhR	-16.61	0.002759	245 -- 266	34 -- 55	putative monooxygenase	_____________244____________________267\n_____________\|______________________\|\n5'-UUG...CCAUU______C_________G_____CUUAA...AAC-3'\n______________UGGCGA_GCAAUGGCU_AGCAG\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\|:_\|:\|\|\|\n______________ACCGUU_CGUUACCGG_UUGUC\n3'-UUU...UAGUC______A_________G_____UUUUA...UUG-5'\n_____________\|______________________\|\n_____________56_____________________33\n	254 -- 260	40 -- 46	-33.2096 kcal/mol	7.64311 kcal/mol	8.95438 kcal/mol	244 267@LB@ \| \|@LB@5'-UUG...CCAUU C G CUUAA...AAC-3'@LB@ UGGCGA GCAAUGGCU AGCAG@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|: \|:\|\|\|@LB@ ACCGUU CGUUACCGG UUGUC@LB@3'-UUU...UAGUC A G UUUUA...UUG-5'@LB@ \| \|@LB@ 56 33@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -33.2096 kcal/mol@LB@Unfolding Energy - mRNA 7.64311 kcal/mol@LB@Unfolding Energy - sRNA 8.95438 kcal/mol@LB@@LB@Position - mRNA 245 -- 266@LB@Position - sRNA 34 -- 55@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
41	0.002667	0.2088	b2475	ypfJ	-12.17	0.040379	232 -- 266	38 -- 70	putative neutral zinc metallopeptidase	_____________231___________________________________267\n_____________\|_____________________________________\|\n5'-GUC...UGACA_______________GC____CA__UCU_________UCUAU...GCG-3'\n______________AUGUU_GAAGA_CAG__GCAA__GC___GGUGGUCCA\n______________\|\|\|\|\|_\|\|\|:\|_\|\|\|__\|\|\|\|__\|\|___::\|\|\|:\|\|\|\n______________UACAA_CUUUU_GUC__CGUU__CG___UUACCGGGU\n3'-UUU...AAAUA_____C_____A___AC____A_______________UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	260 -- 266	38 -- 44	-27.4905 kcal/mol	8.02084 kcal/mol	7.29667 kcal/mol	231 267@LB@ \| \|@LB@5'-GUC...UGACA GC CA UCU UCUAU...GCG-3'@LB@ AUGUU GAAGA CAG GCAA GC GGUGGUCCA@LB@ \|\|\|\|\| \|\|\|:\| \|\|\| \|\|\|\| \|\| ::\|\|\|:\|\|\|@LB@ UACAA CUUUU GUC CGUU CG UUACCGGGU@LB@3'-UUU...AAAUA C A AC A UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -27.4905 kcal/mol@LB@Unfolding Energy - mRNA 8.02084 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 232 -- 266@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 38 -- 44@LB@
198	0.02539	0.4256	b1624	ydgJ	-9.27	0.170491	217 -- 246	45 -- 70	putative oxidoreductase	_____________216____________________________247\n_____________\|______________________________\|\n5'-GUA...CAUCC________UU______GUA____U______GCAAA...CGG-3'\n______________GUGUUGGG__GAUUGG___UGGU_AUGCGA\n______________:\|\|\|\|\|\|:__:\|\|::\|___\|\|\|:_\|\|\|\|:\|\n______________UACAACCU__UUAGUC___ACCG_UACGUU\n3'-UUU...AAAUA________U______________U______ACCGG...UUG-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	218 -- 224	63 -- 69	-23.4852 kcal/mol	9.77058 kcal/mol	4.44589 kcal/mol	216 247@LB@ \| \|@LB@5'-GUA...CAUCC UU GUA U GCAAA...CGG-3'@LB@ GUGUUGGG GAUUGG UGGU AUGCGA@LB@ :\|\|\|\|\|\|: :\|\|::\| \|\|\|: \|\|\|\|:\|@LB@ UACAACCU UUAGUC ACCG UACGUU@LB@3'-UUU...AAAUA U U ACCGG...UUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -23.4852 kcal/mol@LB@Unfolding Energy - mRNA 9.77058 kcal/mol@LB@Unfolding Energy - sRNA 4.44589 kcal/mol@LB@@LB@Position - mRNA 217 -- 246@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 63 -- 69@LB@
37	0.002433	0.2088	b2825	ppdB	-7.88	0.305516	133 -- 146	40 -- 54	putative prepilin peptidase-dependent protein	_____________132_____________147\n_____________\|_______________\|\n5'-CAU...CAACG_______________GGUGG...CGU-3'\n______________GGCGA_GUGGUGGCU\n______________\|\|\|:\|_\|:::\|\|\|\|:\n______________CCGUU_CGUUACCGG\n3'-UUU...AGUCA_____A_________GUUGU...UUG-5'\n_____________\|_______________\|\n_____________55______________39\n	140 -- 146	40 -- 46	-19.4494 kcal/mol	6.98652 kcal/mol	4.58617 kcal/mol	132 147@LB@ \| \|@LB@5'-CAU...CAACG GGUGG...CGU-3'@LB@ GGCGA GUGGUGGCU@LB@ \|\|\|:\| \|:::\|\|\|\|:@LB@ CCGUU CGUUACCGG@LB@3'-UUU...AGUCA A GUUGU...UUG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -19.4494 kcal/mol@LB@Unfolding Energy - mRNA 6.98652 kcal/mol@LB@Unfolding Energy - sRNA 4.58617 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 40 -- 46@LB@
24	0.001299	0.182	b1267	yciO	-12.11	0.041783	4 -- 24	36 -- 58	putative RNA binding protein	_____________3_______________________25\n_____________\|_______________________\|\n________5'-GCG_____C_________C_______GAACG...CAA-3'\n______________CAGUG_CA__GCAAU_GCCCAAU\n______________\|\|\|\|\|_\|\|__\|\|\|\|\|_\|\|\|\|\|\|:\n______________GUCAC_GU__CGUUA_CGGGUUG\n3'-UUU...UUUUA_____C__UA_____C_______UCUUU...UUG-5'\n_____________\|_______________________\|\n_____________59______________________35\n	18 -- 24	36 -- 42	-24.2706 kcal/mol	1.86377 kcal/mol	10.2972 kcal/mol	3 25@LB@ \| \|@LB@ 5'-GCG C C GAACG...CAA-3'@LB@ CAGUG CA GCAAU GCCCAAU@LB@ \|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ GUCAC GU CGUUA CGGGUUG@LB@3'-UUU...UUUUA C UA C UCUUU...UUG-5'@LB@ \| \|@LB@ 59 35@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.86377 kcal/mol@LB@Unfolding Energy - sRNA 10.2972 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 36 -- 58@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
63	0.004757	0.2539	b1342	ydaN	-13.10	0.024145	140 -- 198	7 -- 70	putative Zn(II) transporter	_____________139_______________________________________________________________199\n_____________\|_________________________________________________________________\|\n5'-CGU...AUGAG______CGU__________CA_____A____A___UAC_______UGCGU_______________CUGUG...AUG-3'\n______________AUGUUG___AA_CAG_GGC_____GA_GGCU_GAC___AAAAUAA______UGAUGAUGGAGGCA\n______________\|\|\|\|\|\|___\|\|_\|\|\|_\|\|\|_____:\|_\|\|\|:_:\|\|___\|\|\|\|\|\|\|______\|\|\|::\|\|::\|\|\|\|\|\n______________UACAAC___UU_GUC_CCG_____UU_CCGG_UUG___UUUUAUU______ACUGUUAUUUCCGU\n3'-UUU...AAAUA______CUU__A___A___UUACG__A____G___UC________UUAGAC______________AUAUUG-5'\n_____________\|_________________________________________________________________\|\n_____________71________________________________________________________________6\n	192 -- 198	7 -- 13	-39.9747 kcal/mol	14.7113 kcal/mol	12.1606 kcal/mol	139 199@LB@ \| \|@LB@5'-CGU...AUGAG CGU CA A A UAC UGCGU CUGUG...AUG-3'@LB@ AUGUUG AA CAG GGC GA GGCU GAC AAAAUAA UGAUGAUGGAGGCA@LB@ \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|::\|\|::\|\|\|\|\|@LB@ UACAAC UU GUC CCG UU CCGG UUG UUUUAUU ACUGUUAUUUCCGU@LB@3'-UUU...AAAUA CUU A A UUACG A G UC UUAGAC AUAUUG-5'@LB@ \| \|@LB@ 71 6@LB@@LB@@LB@Energy -13.10 kcal/mol@LB@Hybridization Energy -39.9747 kcal/mol@LB@Unfolding Energy - mRNA 14.7113 kcal/mol@LB@Unfolding Energy - sRNA 12.1606 kcal/mol@LB@@LB@Position - mRNA 140 -- 198@LB@Position - sRNA 7 -- 70@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
106	0.009895	0.3118	b3962	sthA	-8.25	0.262922	71 -- 97	8 -- 33	pyridine nucleotide transhydrogenase soluble	_____________70___________________________98\n_____________\|____________________________\|\n5'-UAC...GGGCA_________AACA______AGC______CGCUC...CAG-3'\n______________AAAGUAAGA_____GACAA___AAAGGC\n______________\|\|\|:\|\|\|:\|_____\|\|\|\|\|___\|\|\|\|\|\|\n______________UUUUAUUUU_____CUGUU___UUUCCG\n3'-UUU...UUGUC_________AGACA_____A________UAUAUUG-5'\n_____________\|____________________________\|\n_____________34___________________________7\n	73 -- 79	25 -- 31	-15.3826 kcal/mol	2.09876 kcal/mol	5.02883 kcal/mol	70 98@LB@ \| \|@LB@5'-UAC...GGGCA AACA AGC CGCUC...CAG-3'@LB@ AAAGUAAGA GACAA AAAGGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ UUUUAUUUU CUGUU UUUCCG@LB@3'-UUU...UUGUC AGACA A UAUAUUG-5'@LB@ \| \|@LB@ 34 7@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -15.3826 kcal/mol@LB@Unfolding Energy - mRNA 2.09876 kcal/mol@LB@Unfolding Energy - sRNA 5.02883 kcal/mol@LB@@LB@Position - mRNA 71 -- 97@LB@Position - sRNA 8 -- 33@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 25 -- 31@LB@
159	0.01815	0.3828	b2418	pdxK	-7.58	0.341503	51 -- 77	38 -- 65	pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase	_____________50___________________________78\n_____________\|____________________________\|\n5'-CAU...AACGG____U____UUA___________A____GACAA...GCA-3'\n______________GGAG_GUCA___GUAGUGUAAUG__CCA\n______________\|\|\|:_:\|\|\|___\|:\|:\|\|:\|\|\|\|__\|\|\|\n______________CCUU_UAGU___CGUUACGUUAC__GGU\n3'-UUU...UACAA____U____CAC___________CG___UGUCU...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________37\n	67 -- 73	43 -- 49	-23.6415 kcal/mol	9.38399 kcal/mol	6.67322 kcal/mol	50 78@LB@ \| \|@LB@5'-CAU...AACGG U UUA A GACAA...GCA-3'@LB@ GGAG GUCA GUAGUGUAAUG CCA@LB@ \|\|\|: :\|\|\| \|:\|:\|\|:\|\|\|\| \|\|\|@LB@ CCUU UAGU CGUUACGUUAC GGU@LB@3'-UUU...UACAA U CAC CG UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -23.6415 kcal/mol@LB@Unfolding Energy - mRNA 9.38399 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 51 -- 77@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 43 -- 49@LB@
187	0.02306	0.4145	b1854	pykA	-9.88	0.128920	243 -- 268	12 -- 43	pyruvate kinase II	_____________242______________________________269\n_____________\|________________________________\|\n5'-GAA...CGUUA_________AC____________C________UCUUG...ACG-3'\n______________GGCCCAGCA_______AGAUC_G_GAUAAUAA\n______________\|\|\|\|\|\|:\|\|_______\|:\|\|\|_\|_\|\|:\|\|\|\|\|\n______________CCGGGUUGU_______UUUAG_C_CUGUUAUU\n3'-UUU...CGUUA_________CUUUUAU_____A_A________UCCGU...UUG-5'\n_____________\|________________________________\|\n_____________44_______________________________11\n	262 -- 268	12 -- 18	-24.7448 kcal/mol	4.16838 kcal/mol	10.6985 kcal/mol	242 269@LB@ \| \|@LB@5'-GAA...CGUUA AC C UCUUG...ACG-3'@LB@ GGCCCAGCA AGAUC G GAUAAUAA@LB@ \|\|\|\|\|\|:\|\| \|:\|\|\| \| \|\|:\|\|\|\|\|@LB@ CCGGGUUGU UUUAG C CUGUUAUU@LB@3'-UUU...CGUUA CUUUUAU A A UCCGU...UUG-5'@LB@ \| \|@LB@ 44 11@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -24.7448 kcal/mol@LB@Unfolding Energy - mRNA 4.16838 kcal/mol@LB@Unfolding Energy - sRNA 10.6985 kcal/mol@LB@@LB@Position - mRNA 243 -- 268@LB@Position - sRNA 12 -- 43@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 12 -- 18@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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