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
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity	_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
175	0.008768	0.1747	b0658	ybeX	-12.37	0.086971	210 -- 256	35 -- 75	putative ion transport	_____________209_____________________________________________257\n_____________\|_______________________________________________\|\n5'-UUA...GCGAC___AAUU___________GACACGAUAAG__ACA__AA_________CUCCC...ACC-3'\n______________GAC____CACACAGUAGU___________CA___AG__GGGAUUUUU\n______________\|\|\|____\|\|\|\|\|\|\|:\|:\|___________\|\|___\|\|__\|\|\|\|\|\|\|::\n______________CUG____GUGUGUCGUUA___________GU___UC__CCCUAAAGG\n3'-UUU...CGUUU___AU_____________AGCAACAAA____GAG_____________UACGA...GCA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________34\n	249 -- 255	36 -- 42	-26.9454 kcal/mol	9.77444 kcal/mol	4.80541 kcal/mol	209 257@LB@ \| \|@LB@5'-UUA...GCGAC AAUU GACACGAUAAG ACA AA CUCCC...ACC-3'@LB@ GAC CACACAGUAGU CA AG GGGAUUUUU@LB@ \|\|\| \|\|\|\|\|\|\|:\|:\| \|\| \|\| \|\|\|\|\|\|\|::@LB@ CUG GUGUGUCGUUA GU UC CCCUAAAGG@LB@3'-UUU...CGUUU AU AGCAACAAA GAG UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -26.9454 kcal/mol@LB@Unfolding Energy - mRNA 9.77444 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 210 -- 256@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 36 -- 42@LB@
183	0.009087	0.1747	b3965	trmA	-11.75	0.116675	18 -- 52	35 -- 74	tRNA m(5)U54 methyltransferase SAM-dependent; tmRNA m(5)U341 methyltransferase	_____________17____________________________________________53\n_____________\|_____________________________________________\|\n5'-UCG...UUACC________U____UCCA_________________________C__UAUUA...UUC-3'\n______________GCUGCGCG_CAGC____GAUUCG______CACU____GGAUU_CC\n______________:\|\|:\|:\|:_\|\|\|\|____:\|\|\|\|\|______\|\|\|\|____\|\|\|\|\|_\|\|\n______________UGAUGUGU_GUCG____UUAAGC______GUGA____CCUAA_GG\n3'-UUU...GUUUC_______________________AACAAA____GUCC_____A__UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________34\n	18 -- 24	68 -- 74	-28.5766 kcal/mol	12.0258 kcal/mol	4.80541 kcal/mol	17 53@LB@ \| \|@LB@5'-UCG...UUACC U UCCA C UAUUA...UUC-3'@LB@ GCUGCGCG CAGC GAUUCG CACU GGAUU CC@LB@ :\|\|:\|:\|: \|\|\|\| :\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UGAUGUGU GUCG UUAAGC GUGA CCUAA GG@LB@3'-UUU...GUUUC AACAAA GUCC A UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -28.5766 kcal/mol@LB@Unfolding Energy - mRNA 12.0258 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 18 -- 52@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
185	0.009421	0.1776	b3094	exuR	-10.10	0.235203	51 -- 95	35 -- 75	hexuronate regulon transcriptional repressor; autorepressor	_____________50____________________________________________96\n_____________\|_____________________________________________\|\n5'-CCG...AUAAC___CC_____C____CAUUAAC_______GUA__UUUUA______CUUCA...CUG-3'\n______________GAU__CGCAC_GCAA_______GUUUCGU___AG_____GUUUCC\n______________\|\|:__\|:\|\|\|_\|\|\|\|_______\|\|\|\|\|::___\|\|_____:\|\|\|\|\|\n______________CUG__GUGUG_CGUU_______CAAAGUG___UC_____UAAAGG\n3'-UUU...CGUUU___AU_____U____AAGCAA________AG___CCC________UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________76____________________________________________34\n	73 -- 79	48 -- 54	-21.0703 kcal/mol	6.16224 kcal/mol	4.80541 kcal/mol	50 96@LB@ \| \|@LB@5'-CCG...AUAAC CC C CAUUAAC GUA UUUUA CUUCA...CUG-3'@LB@ GAU CGCAC GCAA GUUUCGU AG GUUUCC@LB@ \|\|: \|:\|\|\| \|\|\|\| \|\|\|\|\|:: \|\| :\|\|\|\|\|@LB@ CUG GUGUG CGUU CAAAGUG UC UAAAGG@LB@3'-UUU...CGUUU AU U AAGCAA AG CCC UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -21.0703 kcal/mol@LB@Unfolding Energy - mRNA 6.16224 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 51 -- 95@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 48 -- 54@LB@
188	0.009562	0.1776	b0147	ligT	-10.24	0.223023	2 -- 33	35 -- 66	2'-5' RNA ligase	_____________1_________________________________34\n_____________\|_________________________________\|\n__________5'-C________GCAGCGG___GC____UU_______CGGCC...CGG-3'\n______________CAGCAGUU________CA__CAGG__GAUUUCC\n______________\|\|\|\|\|:\|\|________\|\|__\|\|\|\|__\|\|\|\|\|\|\|\n______________GUCGUUAA________GU__GUCC__CUAAAGG\n3'-UUU...UGUGU________GCAACAAA__GA____C________UACGA...GCA-5'\n_____________\|_________________________________\|\n_____________67________________________________34\n	27 -- 33	35 -- 41	-25.6384 kcal/mol	10.64 kcal/mol	4.7609 kcal/mol	1 34@LB@ \| \|@LB@ 5'-C GCAGCGG GC UU CGGCC...CGG-3'@LB@ CAGCAGUU CA CAGG GAUUUCC@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GUCGUUAA GU GUCC CUAAAGG@LB@3'-UUU...UGUGU GCAACAAA GA C UACGA...GCA-5'@LB@ \| \|@LB@ 67 34@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -25.6384 kcal/mol@LB@Unfolding Energy - mRNA 10.64 kcal/mol@LB@Unfolding Energy - sRNA 4.7609 kcal/mol@LB@@LB@Position - mRNA 2 -- 33@LB@Position - sRNA 35 -- 66@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 35 -- 41@LB@
17	0.0001292	0.02674	b1854	pykA	-13.69	0.043994	133 -- 157	36 -- 68	pyruvate kinase II	_____________132_______________________________158\n_____________\|_________________________________\|\n5'-GAA...GCCAU______________A__________________AUGUU...ACG-3'\n______________CGCGGC_____GUU_UUUCAUUC___GGAUUUC\n______________\|:\|:\|\|_____\|\|\|_\|\|\|\|\|:\|\|___\|\|\|\|\|\|\|\n______________GUGUCG_____CAA_AAAGUGAG___CCUAAAG\n3'-UUU...GAUGU______UUAAG___C________UCC_______GUACG...GCA-5'\n_____________\|_________________________________\|\n_____________69________________________________35\n	151 -- 157	36 -- 42	-24.2432 kcal/mol	5.79946 kcal/mol	4.75078 kcal/mol	132 158@LB@ \| \|@LB@5'-GAA...GCCAU A AUGUU...ACG-3'@LB@ CGCGGC GUU UUUCAUUC GGAUUUC@LB@ \|:\|:\|\| \|\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GUGUCG CAA AAAGUGAG CCUAAAG@LB@3'-UUU...GAUGU UUAAG C UCC GUACG...GCA-5'@LB@ \| \|@LB@ 69 35@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -24.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.79946 kcal/mol@LB@Unfolding Energy - sRNA 4.75078 kcal/mol@LB@@LB@Position - mRNA 133 -- 157@LB@Position - sRNA 36 -- 68@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 36 -- 42@LB@
109	0.004772	0.1538	b2580	ung	-9.28	0.319241	25 -- 55	36 -- 70	uracil-DNA-glycosylase	_____________24__________________________________56\n_____________\|___________________________________\|\n5'-UCU...AAAAC______U___GUA____G_____AAAU________AUUGU...CCG-3'\n______________CACACA_CAA_____UG__UCGC_____GGAUUUU\n______________\|\|\|\|\|\|_\|\|\|_____\|\|__\|\|:\|_____\|\|\|\|\|\|:\n______________GUGUGU_GUU_____AC__AGUG_____CCUAAAG\n3'-UUU...CUGAU______C___AAGCA__AA____AGUCC_______GUACG...GCA-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	49 -- 55	36 -- 42	-19.0861 kcal/mol	5.04532 kcal/mol	4.7591 kcal/mol	24 56@LB@ \| \|@LB@5'-UCU...AAAAC U GUA G AAAU AUUGU...CCG-3'@LB@ CACACA CAA UG UCGC GGAUUUU@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|:\| \|\|\|\|\|\|:@LB@ GUGUGU GUU AC AGUG CCUAAAG@LB@3'-UUU...CUGAU C AAGCA AA AGUCC GUACG...GCA-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -19.0861 kcal/mol@LB@Unfolding Energy - mRNA 5.04532 kcal/mol@LB@Unfolding Energy - sRNA 4.7591 kcal/mol@LB@@LB@Position - mRNA 25 -- 55@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 36 -- 42@LB@
48	0.001595	0.1153	b4567	yjjZ	-9.54	0.291590	92 -- 131	37 -- 74	uncharacterized protein	_____________91_______________________________________132\n_____________\|________________________________________\|\n5'-CGG...UGAUU____AU_________AG___UACC__AUAG__A_______AUCUG...GGA-3'\n______________GCUA__CAUAGCGAU__GUU____CG____CA_GGGAUUU\n______________:\|\|\|__\|\|:\|\|\|:\|\|__\|\|\|____\|:____\|\|_\|\|\|\|\|\|\|\n______________UGAU__GUGUCGUUA__CAA____GU____GU_CCCUAAA\n3'-UUU...GUUUC____GU_________AG___CAAA__GA____C_______GGUAC...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________36\n	125 -- 131	37 -- 43	-26.8907 kcal/mol	12.5776 kcal/mol	4.77887 kcal/mol	91 132@LB@ \| \|@LB@5'-CGG...UGAUU AU AG UACC AUAG A AUCUG...GGA-3'@LB@ GCUA CAUAGCGAU GUU CG CA GGGAUUU@LB@ :\|\|\| \|\|:\|\|\|:\|\| \|\|\| \|: \|\| \|\|\|\|\|\|\|@LB@ UGAU GUGUCGUUA CAA GU GU CCCUAAA@LB@3'-UUU...GUUUC GU AG CAAA GA C GGUAC...GCA-5'@LB@ \| \|@LB@ 75 36@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -26.8907 kcal/mol@LB@Unfolding Energy - mRNA 12.5776 kcal/mol@LB@Unfolding Energy - sRNA 4.77887 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 37 -- 74@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 37 -- 43@LB@
65	0.002677	0.1417	b0584	fepA	-11.47	0.132508	209 -- 249	37 -- 78	ferrienterobactin outer membrane transporter	_____________208___________________________________________250\n_____________\|_____________________________________________\|\n5'-GAA...AACAA___________U_CCU___C________G____A__U________AUGGG...ACG-3'\n______________GAAGAUU_CAU_C___GGC___UUGUUG__UCA_UC_GGGGAUUU\n______________:\|\|\|\|:\|_\|\|:_\|___:\|\|___\|:\|\|\|\|__\|\|\|_\|\|_\|\|\|\|\|\|\|\|\n______________UUUCUGA_GUG_G___UCG___AGCAAC__AGU_AG_CCCCUAAA\n3'-UUU...ACCCG_______U___U_______UUA______AA___G__U________GGUAC...GCA-5'\n_____________\|_____________________________________________\|\n_____________79____________________________________________36\n	243 -- 249	37 -- 43	-30.6633 kcal/mol	14.4176 kcal/mol	4.77973 kcal/mol	208 250@LB@ \| \|@LB@5'-GAA...AACAA U CCU C G A U AUGGG...ACG-3'@LB@ GAAGAUU CAU C GGC UUGUUG UCA UC GGGGAUUU@LB@ :\|\|\|\|:\| \|\|: \| :\|\| \|:\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UUUCUGA GUG G UCG AGCAAC AGU AG CCCCUAAA@LB@3'-UUU...ACCCG U U UUA AA G U GGUAC...GCA-5'@LB@ \| \|@LB@ 79 36@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -30.6633 kcal/mol@LB@Unfolding Energy - mRNA 14.4176 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 209 -- 249@LB@Position - sRNA 37 -- 78@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 37 -- 43@LB@
115	0.005088	0.155	b4131	cadA	-16.57	0.007707	197 -- 237	37 -- 75	lysine decarboxylase acid-inducible	_____________196__________________________________________238\n_____________\|____________________________________________\|\n5'-CUC...GAUAU______GA___UUAUU_____A_____AA____AU_________AUUUU...UUG-3'\n______________GACUAU__ACG_____GCAAU___UUG__UCAC___GGGGGUUU\n______________\|\|\|\|\|:__\|\|:_____\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|:\|\|\|\n______________CUGAUG__UGU_____CGUUA___AAC__AGUG___CCCCUAAA\n3'-UUU...CGUUU______UG_____________AGC___AA____AGU________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	231 -- 237	37 -- 43	-27.1465 kcal/mol	5.79755 kcal/mol	4.77966 kcal/mol	196 238@LB@ \| \|@LB@5'-CUC...GAUAU GA UUAUU A AA AU AUUUU...UUG-3'@LB@ GACUAU ACG GCAAU UUG UCAC GGGGGUUU@LB@ \|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|\|@LB@ CUGAUG UGU CGUUA AAC AGUG CCCCUAAA@LB@3'-UUU...CGUUU UG AGC AA AGU GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.57 kcal/mol@LB@Hybridization Energy -27.1465 kcal/mol@LB@Unfolding Energy - mRNA 5.79755 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 197 -- 237@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 37 -- 43@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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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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