Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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	Additional homologs
176	0.01044	0.208	b0933	ssuB	-9.69	0.158756	203 -- 226	69 -- 90	aliphatic sulfonate ABC transporter ATPase		_____________202______________________227\n_____________\|________________________\|\n5'-AUU...GGUAU_________UC___UGA_______CACGC...AUA-3'\n______________GAAUACUGC__GUC___ACCAGGG\n______________\|\|\|\|\|\|\|\|\|__\|:\|___\|\|\|\|\|\|\|\n______________CUUAUGACG__CGG___UGGUCCC\n3'-UUU...ACGCG______________UUG_______UUUAG...GUG-5'\n_____________\|________________________\|\n_____________91_______________________68\n	220 -- 226	69 -- 75	-28.101 kcal/mol	8.24441 kcal/mol	10.1628 kcal/mol	202 227@LB@ \| \|@LB@5'-AUU...GGUAU UC UGA CACGC...AUA-3'@LB@ GAAUACUGC GUC ACCAGGG@LB@ \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ CUUAUGACG CGG UGGUCCC@LB@3'-UUU...ACGCG UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -28.101 kcal/mol@LB@Unfolding Energy - mRNA 8.24441 kcal/mol@LB@Unfolding Energy - sRNA 10.1628 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 69 -- 75@LB@
75	0.003854	0.1809	b0606	ahpF	-8.17	0.297536	59 -- 82	64 -- 85	alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding		_____________58_______________________83\n_____________\|________________________\|\n5'-UCA...UUGCU___A___GA______UC_______CACCU...CGG-3'\n______________CUG_CGC__AAUACU__GGAAAUU\n______________\|\|\|_\|\|\|__\|\|:\|\|:__\|\|\|\|\|\|:\n______________GAC_GCG__UUGUGG__CCUUUAG\n3'-UUU...CUUAU_______G_______UC_______AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	76 -- 82	64 -- 70	-19.6667 kcal/mol	4.11652 kcal/mol	7.38387 kcal/mol	58 83@LB@ \| \|@LB@5'-UCA...UUGCU A GA UC CACCU...CGG-3'@LB@ CUG CGC AAUACU GGAAAUU@LB@ \|\|\| \|\|\| \|\|:\|\|: \|\|\|\|\|\|:@LB@ GAC GCG UUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -19.6667 kcal/mol@LB@Unfolding Energy - mRNA 4.11652 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 59 -- 82@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 64 -- 70@LB@
169	0.01004	0.2071	b2384	ypdE	-12.38	0.048278	93 -- 137	31 -- 75	aminopeptidase	b4305 b3898	_____________92______________________________________________138\n_____________\|_______________________________________________\|\n5'-AUU...UAUUU_______C__GGG____G_____AUCG___A_______C________CCCGC...UGC-3'\n______________GCCAGGG_AA____GGC_UGCGC____AAG_UGUUGUG_UG_GUUAC\n______________:\|\|\|\|\|\|_\|\|____\|\|\|_\|\|\|\|\|____\|\|:_\|:\|\|:\|\|_\|\|_\|\|\|\|\|\n______________UGGUCCC_UU____CCG_ACGCG____UUU_AUAAUAC_AC_CAAUG\n3'-UUU...GGUUG_______U__AGAA_________GCA____A_______U__U_____UUCCC...GUG-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________30\n	93 -- 99	69 -- 75	-40.1479 kcal/mol	18.4667 kcal/mol	9.29858 kcal/mol	92 138@LB@ \| \|@LB@5'-AUU...UAUUU C GGG G AUCG A C CCCGC...UGC-3'@LB@ GCCAGGG AA GGC UGCGC AAG UGUUGUG UG GUUAC@LB@ :\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|: \|:\|\|:\|\| \|\| \|\|\|\|\|@LB@ UGGUCCC UU CCG ACGCG UUU AUAAUAC AC CAAUG@LB@3'-UUU...GGUUG U AGAA GCA A U U UUCCC...GUG-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -40.1479 kcal/mol@LB@Unfolding Energy - mRNA 18.4667 kcal/mol@LB@Unfolding Energy - sRNA 9.29858 kcal/mol@LB@@LB@Position - mRNA 93 -- 137@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 69 -- 75@LB@
63	0.003148	0.1727	b0131	panD	-12.33	0.049519	276 -- 291	70 -- 84	aspartate 1-decarboxylase		_____________275______________292\n_____________\|________________\|\n5'-AUU...GUUCU_______UUG______AUUUU...UUG-3'\n______________UGCGCCA___ACCAGG\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________ACGCGGU___UGGUCC\n3'-UUU...UUAUG_______UG_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	276 -- 282	78 -- 84	-24.0598 kcal/mol	4.4848 kcal/mol	7.24859 kcal/mol	275 292@LB@ \| \|@LB@5'-AUU...GUUCU UUG AUUUU...UUG-3'@LB@ UGCGCCA ACCAGG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACGCGGU UGGUCC@LB@3'-UUU...UUAUG UG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -24.0598 kcal/mol@LB@Unfolding Energy - mRNA 4.4848 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 276 -- 291@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 78 -- 84@LB@
46	0.002359	0.1727	b4139	aspA	-15.43	0.012067	239 -- 273	37 -- 76	aspartate ammonia-lyase		_____________238_______________________________________274\n_____________\|_________________________________________\|\n5'-GAU...UUGGG_____________CCA____A____________C_______UUCAC...ACU-3'\n______________UACCAGGGAAGUU___GCUG_UGCC______UA_UAUGGUG\n______________:\|\|\|\|\|\|\|\|\|:\|:___\|\|\|\|_:\|\|\|______\|\|_\|\|\|\|:\|\|\n______________GUGGUCCCUUUAG___CGAC_GCGG______AU_AUACUAC\n3'-UUU...CGGUU_____________AAC_________CAUUUA__A_______UCAAU...GUG-5'\n_____________\|_________________________________________\|\n_____________77________________________________________36\n	267 -- 273	37 -- 43	-35.8845 kcal/mol	11.095 kcal/mol	9.35931 kcal/mol	238 274@LB@ \| \|@LB@5'-GAU...UUGGG CCA A C UUCAC...ACU-3'@LB@ UACCAGGGAAGUU GCUG UGCC UA UAUGGUG@LB@ :\|\|\|\|\|\|\|\|\|:\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|:\|\|@LB@ GUGGUCCCUUUAG CGAC GCGG AU AUACUAC@LB@3'-UUU...CGGUU AAC CAUUUA A UCAAU...GUG-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -35.8845 kcal/mol@LB@Unfolding Energy - mRNA 11.095 kcal/mol@LB@Unfolding Energy - sRNA 9.35931 kcal/mol@LB@@LB@Position - mRNA 239 -- 273@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 37 -- 43@LB@
56	0.002848	0.1727	b0797	rhlE	-14.47	0.018687	57 -- 89	53 -- 82	ATP-dependent RNA helicase		_____________56_________________________________90\n_____________\|__________________________________\|\n5'-GAU...AGCAA______U_________U_____A__C________ACAAA...CUG-3'\n______________CGCCAG_CA_CAGGGA_AAUUU_UG_GCUGCGUC\n______________\|\|\|\|\|:_\|\|_\|\|\|\|\|\|_\|\|\|:\|_\|\|_\|\|\|\|\|\|:\|\n______________GCGGUU_GU_GUCCCU_UUAGA_AC_CGACGCGG\n3'-UUU...AUGAC_________G________________________CAUUU...GUG-5'\n_____________\|__________________________________\|\n_____________83_________________________________52\n	83 -- 89	53 -- 59	-38.8186 kcal/mol	7.89252 kcal/mol	16.4547 kcal/mol	56 90@LB@ \| \|@LB@5'-GAU...AGCAA U U A C ACAAA...CUG-3'@LB@ CGCCAG CA CAGGGA AAUUU UG GCUGCGUC@LB@ \|\|\|\|\|: \|\| \|\|\|\|\|\| \|\|\|:\| \|\| \|\|\|\|\|\|:\|@LB@ GCGGUU GU GUCCCU UUAGA AC CGACGCGG@LB@3'-UUU...AUGAC G CAUUU...GUG-5'@LB@ \| \|@LB@ 83 52@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -38.8186 kcal/mol@LB@Unfolding Energy - mRNA 7.89252 kcal/mol@LB@Unfolding Energy - sRNA 16.4547 kcal/mol@LB@@LB@Position - mRNA 57 -- 89@LB@Position - sRNA 53 -- 82@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 53 -- 59@LB@
123	0.00672	0.1913	b0882	clpA	-10.14	0.130927	50 -- 58	66 -- 74	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________49________59\n_____________\|_________\|\n5'-UUU...CACUA_________GGCCA...CGC-3'\n______________CCAGGGGAA\n______________\|\|\|\|\|\|:\|\|\n______________GGUCCCUUU\n3'-UUU...GUUGU_________AGAAC...GUG-5'\n_____________\|_________\|\n_____________75________65\n	52 -- 58	66 -- 72	-13.8898 kcal/mol	0.70189 kcal/mol	3.04768 kcal/mol	49 59@LB@ \| \|@LB@5'-UUU...CACUA GGCCA...CGC-3'@LB@ CCAGGGGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ GGUCCCUUU@LB@3'-UUU...GUUGU AGAAC...GUG-5'@LB@ \| \|@LB@ 75 65@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 0.70189 kcal/mol@LB@Unfolding Energy - sRNA 3.04768 kcal/mol@LB@@LB@Position - mRNA 50 -- 58@LB@Position - sRNA 66 -- 74@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 66 -- 72@LB@
74	0.003792	0.1804	b2520	yfhM	-12.28	0.050623	263 -- 298	53 -- 91	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein		_____________262_____________________________________299\n_____________\|_______________________________________\|\n5'-CUC...AACAA___UA____________G___U____AAAGA________UU-3'\n______________CGA__AC_GCGCCAACA_CGG_GAAA_______UGCGCC\n______________\|\|\|__\|\|_\|\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|_______\|\|\|\|\|\|\n______________GCU__UG_CGCGGUUGU_GUC_CUUU_______ACGCGG\n3'-UUU...CACGC___UA__A_________G___C____AGAACCG______CAUUU...GUG-5'\n_____________\|_______________________________________\|\n_____________92______________________________________52\n	272 -- 278	75 -- 81	-39.9109 kcal/mol	10.9563 kcal/mol	16.677 kcal/mol	262 299@LB@ \| \|@LB@5'-CUC...AACAA UA G U AAAGA UU-3'@LB@ CGA AC GCGCCAACA CGG GAAA UGCGCC@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|\|\|\|\|@LB@ GCU UG CGCGGUUGU GUC CUUU ACGCGG@LB@3'-UUU...CACGC UA A G C AGAACCG CAUUU...GUG-5'@LB@ \| \|@LB@ 92 52@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -39.9109 kcal/mol@LB@Unfolding Energy - mRNA 10.9563 kcal/mol@LB@Unfolding Energy - sRNA 16.677 kcal/mol@LB@@LB@Position - mRNA 263 -- 298@LB@Position - sRNA 53 -- 91@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 75 -- 81@LB@
47	0.002359	0.1727	b1520	yneE	-16.33	0.007995	225 -- 237	50 -- 62	bestrophin family putative inner membrane protein		_____________224___________238\n_____________\|_____________\|\n5'-CGU...AACAC_____________UUUUU...UCU-3'\n______________UGGCUGCGCCGUA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________ACCGACGCGGCAU\n3'-UUU...UUAGA_____________UUAAU...GUG-5'\n_____________\|_____________\|\n_____________63____________49\n	231 -- 237	50 -- 56	-27.5123 kcal/mol	5.30923 kcal/mol	5.87004 kcal/mol	224 238@LB@ \| \|@LB@5'-CGU...AACAC UUUUU...UCU-3'@LB@ UGGCUGCGCCGUA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ ACCGACGCGGCAU@LB@3'-UUU...UUAGA UUAAU...GUG-5'@LB@ \| \|@LB@ 63 49@LB@@LB@@LB@Energy -16.33 kcal/mol@LB@Hybridization Energy -27.5123 kcal/mol@LB@Unfolding Energy - mRNA 5.30923 kcal/mol@LB@Unfolding Energy - sRNA 5.87004 kcal/mol@LB@@LB@Position - mRNA 225 -- 237@LB@Position - sRNA 50 -- 62@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 50 -- 56@LB@
162	0.009519	0.2068	b4167	nnr	-8.70	0.240671	167 -- 176	76 -- 85	bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase		_____________166________177\n_____________\|__________\|\n5'-ACU...AUUUU__________UGAUU...UGC-3'\n______________UUGCGCUAAC\n______________:\|\|\|\|\|:\|\|\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	170 -- 176	76 -- 82	-14.3794 kcal/mol	0.586298 kcal/mol	5.09564 kcal/mol	166 177@LB@ \| \|@LB@5'-ACU...AUUUU UGAUU...UGC-3'@LB@ UUGCGCUAAC@LB@ :\|\|\|\|\|:\|\|\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -14.3794 kcal/mol@LB@Unfolding Energy - mRNA 0.586298 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 167 -- 176@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 76 -- 82@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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