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
75	0.003119	0.1452	b0871	poxB	-11.12	0.154817	181 -- 203	32 -- 50	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________180_____________________204\n_____________\|_______________________\|\n5'-CCG...UAUCA________AGAU___GAA_____AAACA...GUG-3'\n______________CAUUCAGG____GGA___CCAUG\n______________\|\|:\|\|\|\|\|____\|\|\|___\|\|\|\|\|\n______________GUGAGUCC____CCU___GGUAC\n3'-UUU...ACAAA_______________AAA_____GAAUA...GCA-5'\n_____________\|_______________________\|\n_____________51______________________31\n	182 -- 188	43 -- 49	-21.2585 kcal/mol	5.84423 kcal/mol	4.29868 kcal/mol	180 204@LB@ \| \|@LB@5'-CCG...UAUCA AGAU GAA AAACA...GUG-3'@LB@ CAUUCAGG GGA CCAUG@LB@ \|\|:\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GUGAGUCC CCU GGUAC@LB@3'-UUU...ACAAA AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 51 31@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -21.2585 kcal/mol@LB@Unfolding Energy - mRNA 5.84423 kcal/mol@LB@Unfolding Energy - sRNA 4.29868 kcal/mol@LB@@LB@Position - mRNA 181 -- 203@LB@Position - sRNA 32 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
66	0.002697	0.1417	b1306	pspC	-11.06	0.158336	44 -- 64	55 -- 75	psp operon transcription co-activator	_____________43_____________________65\n_____________\|______________________\|\n5'-CCG...GUUAU_______U______________CUGGU...CGG-3'\n______________GGCUGCA_UACAGCAAU_CGUU\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUGAUGU_GUGUCGUUA_GCAA\n3'-UUU...CGUUU_________________A____CAAAG...GCA-5'\n_____________\|______________________\|\n_____________76_____________________54\n	54 -- 60	60 -- 66	-24.9269 kcal/mol	10.2549 kcal/mol	3.6092 kcal/mol	43 65@LB@ \| \|@LB@5'-CCG...GUUAU U CUGGU...CGG-3'@LB@ GGCUGCA UACAGCAAU CGUU@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGAUGU GUGUCGUUA GCAA@LB@3'-UUU...CGUUU A CAAAG...GCA-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -24.9269 kcal/mol@LB@Unfolding Energy - mRNA 10.2549 kcal/mol@LB@Unfolding Energy - sRNA 3.6092 kcal/mol@LB@@LB@Position - mRNA 44 -- 64@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 60 -- 66@LB@
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@
86	0.003687	0.1509	b0774	bioA	-10.95	0.166636	92 -- 152	44 -- 98	7 8-diaminopelargonic acid synthase PLP-dependent	_____________91_____________________________________________________________153\n_____________\|______________________________________________________________\|\n5'-ACG...ACAAU_____G______C____A__CAU______UCUCCAAA___U__UU_________A_______UGUAG...AAG-3'\n______________GUCCA_CGUGGG_GGUG_GC___GGGGCU________ACG_GU__UUUGUUGUU__AUUCGG\n______________\|:\|\|\|_\|\|\|\|\|\|_\|:\|\|_\|\|___::\|:\|\|________\|\|:_\|:__\|\|:\|\|\|\|\|\|__\|:\|\|:\|\n______________CGGGU_GCACCC_CUAC_CG___UUCUGA________UGU_CG__AAGCAACAA__UGAGUC\n____3'-UUUUUUU_____A______U____C__U________UGUG__________UU_________AG______CCCUA...GCA-5'\n_____________\|______________________________________________________________\|\n_____________99_____________________________________________________________43\n	139 -- 145	52 -- 58	-48.0349 kcal/mol	20.1482 kcal/mol	16.9429 kcal/mol	91 153@LB@ \| \|@LB@5'-ACG...ACAAU G C A CAU UCUCCAAA U UU A UGUAG...AAG-3'@LB@ GUCCA CGUGGG GGUG GC GGGGCU ACG GU UUUGUUGUU AUUCGG@LB@ \|:\|\|\| \|\|\|\|\|\| \|:\|\| \|\| ::\|:\|\| \|\|: \|: \|\|:\|\|\|\|\|\| \|:\|\|:\|@LB@ CGGGU GCACCC CUAC CG UUCUGA UGU CG AAGCAACAA UGAGUC@LB@ 3'-UUUUUUU A U C U UGUG UU AG CCCUA...GCA-5'@LB@ \| \|@LB@ 99 43@LB@@LB@@LB@Energy -10.95 kcal/mol@LB@Hybridization Energy -48.0349 kcal/mol@LB@Unfolding Energy - mRNA 20.1482 kcal/mol@LB@Unfolding Energy - sRNA 16.9429 kcal/mol@LB@@LB@Position - mRNA 92 -- 152@LB@Position - sRNA 44 -- 98@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@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@
82	0.00343	0.1462	b4043	lexA	-10.80	0.176998	163 -- 196	40 -- 72	transcriptional repressor of SOS regulon	_____________162________________________________197\n_____________\|__________________________________\|\n5'-CGC...GUAUA___U_______UAAC___AUAUA___C_______CGGAA...AGC-3'\n______________UAC_CACAGCA____UGU_____CAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|\|\|____:\|\|_____\|\|\|_\|\|\|\|\|\|:\n______________AUG_GUGUCGU____GCA_____GUG_GUCCCCU\n3'-UUU...UUCUG___U_______UAA____ACAAA___A_______AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________73_________________________________39\n	190 -- 196	40 -- 46	-30.123 kcal/mol	14.5591 kcal/mol	4.76217 kcal/mol	162 197@LB@ \| \|@LB@5'-CGC...GUAUA U UAAC AUAUA C CGGAA...AGC-3'@LB@ UAC CACAGCA UGU CAC CAGGGGG@LB@ \|\|\| \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|:@LB@ AUG GUGUCGU GCA GUG GUCCCCU@LB@3'-UUU...UUCUG U UAA ACAAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 73 39@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -30.123 kcal/mol@LB@Unfolding Energy - mRNA 14.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.76217 kcal/mol@LB@@LB@Position - mRNA 163 -- 196@LB@Position - sRNA 40 -- 72@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated	_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
134	0.006141	0.1605	b3413	gntX	-10.72	0.183370	226 -- 267	37 -- 75	DNA catabolic protein	_____________225__________________________________________268\n_____________\|____________________________________________\|\n5'-CCC...AUGCU___________AAU__CACUGG____AGG_______________GUUCG...AUA-3'\n______________GGCUAUGC_CG___GC______CGUU___UCAUU_GGGGGAUUU\n______________\|:\|\|\|::\|_\|:___\|\|______\|\|\|\|___\|\|\|:\|_:\|\|\|\|\|\|\|\|\n______________CUGAUGUG_GU___CG______GCAA___AGUGA_UCCCCUAAA\n3'-UUU...CGUUU________U_______UUAA______CAA_____G_________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	261 -- 267	37 -- 43	-30.3916 kcal/mol	14.8943 kcal/mol	4.77966 kcal/mol	225 268@LB@ \| \|@LB@5'-CCC...AUGCU AAU CACUGG AGG GUUCG...AUA-3'@LB@ GGCUAUGC CG GC CGUU UCAUU GGGGGAUUU@LB@ \|:\|\|\|::\| \|: \|\| \|\|\|\| \|\|\|:\| :\|\|\|\|\|\|\|\|@LB@ CUGAUGUG GU CG GCAA AGUGA UCCCCUAAA@LB@3'-UUU...CGUUU U UUAA CAA G GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -30.3916 kcal/mol@LB@Unfolding Energy - mRNA 14.8943 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 226 -- 267@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 37 -- 43@LB@
130	0.005881	0.1577	b0965	yccU	-10.68	0.186123	93 -- 125	46 -- 74	putative CoA-binding protein	_____________92________________________________126\n_____________\|_________________________________\|\n5'-UCA...UACUU___A________A__UAU___CCGC________UCAUU...UGA-3'\n______________ACU_ACAUAUAG_CA___UUC____UUUUGCUC\n______________\|\|\|_\|\|\|:\|:\|\|_\|\|___\|\|\|____\|\|\|::\|\|\|\n______________UGA_UGUGUGUC_GU___AAG____AAAGUGAG\n3'-UUU...GUUUC_______________U_____CAAC________UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________45\n	119 -- 125	46 -- 52	-18.0647 kcal/mol	3.65669 kcal/mol	3.72594 kcal/mol	92 126@LB@ \| \|@LB@5'-UCA...UACUU A A UAU CCGC UCAUU...UGA-3'@LB@ ACU ACAUAUAG CA UUC UUUUGCUC@LB@ \|\|\| \|\|\|:\|:\|\| \|\| \|\|\| \|\|\|::\|\|\|@LB@ UGA UGUGUGUC GU AAG AAAGUGAG@LB@3'-UUU...GUUUC U CAAC UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.0647 kcal/mol@LB@Unfolding Energy - mRNA 3.65669 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 93 -- 125@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 46 -- 52@LB@
198	0.01016	0.1776	b1764	selD	-10.66	0.187945	118 -- 146	45 -- 71	selenophosphate synthase	_____________117___________________________147\n_____________\|_____________________________\|\n5'-UUU...AGCAA_G______G_____AGACACUC_______UCACU...AGC-3'\n______________A_GCGCAG_AAUUC________UCACUUA\n______________\|_:\|:\|\|\|_\|\|\|\|\|________\|\|\|\|\|:\|\n______________U_UGUGUC_UUAAG________AGUGAGU\n3'-UUU...UCUGA_G______G_____CAACAA_________CCCCU...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________44\n	140 -- 146	45 -- 51	-20.1282 kcal/mol	5.75637 kcal/mol	3.71323 kcal/mol	117 147@LB@ \| \|@LB@5'-UUU...AGCAA G G AGACACUC UCACU...AGC-3'@LB@ A GCGCAG AAUUC UCACUUA@LB@ \| :\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|@LB@ U UGUGUC UUAAG AGUGAGU@LB@3'-UUU...UCUGA G G CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 72 44@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -20.1282 kcal/mol@LB@Unfolding Energy - mRNA 5.75637 kcal/mol@LB@Unfolding Energy - sRNA 3.71323 kcal/mol@LB@@LB@Position - mRNA 118 -- 146@LB@Position - sRNA 45 -- 71@LB@Position Seed - mRNA 140 -- 146@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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