Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
149	0.01599	0.3612	b3236	mdh	-10.77	0.195799	223 -- 232	196 -- 205	malate dehydrogenase NAD(P)-binding	_____________222_____233\n_____________\|_______\|\n5'-GUU...AUGAA_______GUCCU...AUG-3'\n______________AGUCGCA\n______________\|\|\|\|:\|\|\n______________UCAGUGU\n3'-UUU...AUGAG_______GUACU...UAG-5'\n_____________\|_______\|\n_____________206_____195\n	206 -- 212	169 -- 175	-8.87418 kcal/mol	1.40028 kcal/mol	0.26566 kcal/mol	222 233@LB@ \| \|@LB@5'-GUU...AUGAA GUCCU...AUG-3'@LB@ AGUCGCA@LB@ \|\|\|\|:\|\|@LB@ UCAGUGU@LB@3'-UUU...AUGAG GUACU...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -8.87418 kcal/mol@LB@Unfolding Energy - mRNA 1.40028 kcal/mol@LB@Unfolding Energy - sRNA 0.26566 kcal/mol@LB@@LB@Position - mRNA 223 -- 232@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 169 -- 175@LB@
68	0.00659	0.3261	b4080	mdtP	-14.15	0.040423	195 -- 221	144 -- 172	outer membrane factor of efflux pump	_____________194_______________________________222\n_____________\|_________________________________\|\n5'-CUG...CAAGG__C_____A________AUC_____________CGUCU...CUC-3'\n______________AG_CACGC_AUGAU_CA_____GUCAACUUUCA\n______________\|\|_\|\|\|:\|_\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|\|\|\|\|\n______________UC_GUGUG_UACUA_GU_____CAGUUGAAAGU\n3'-UUU...AUGAG__A___________C__CCGUU___________CUUAA...UAG-5'\n_____________\|_________________________________\|\n_____________173_______________________________143\n	215 -- 221	144 -- 150	-24.8993 kcal/mol	3.71866 kcal/mol	8.07675 kcal/mol	194 222@LB@ \| \|@LB@5'-CUG...CAAGG C A AUC CGUCU...CUC-3'@LB@ AG CACGC AUGAU CA GUCAACUUUCA@LB@ \|\| \|\|\|:\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UC GUGUG UACUA GU CAGUUGAAAGU@LB@3'-UUU...AUGAG A C CCGUU CUUAA...UAG-5'@LB@ \| \|@LB@ 173 143@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -24.8993 kcal/mol@LB@Unfolding Energy - mRNA 3.71866 kcal/mol@LB@Unfolding Energy - sRNA 8.07675 kcal/mol@LB@@LB@Position - mRNA 195 -- 221@LB@Position - sRNA 144 -- 172@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 144 -- 150@LB@
69	0.006739	0.3286	b2265	menF	-9.03	0.410924	65 -- 108	52 -- 101	isochorismate synthase 2	_____________64__________109\n_____________\|___________\|\n5'-ACU...CGGGU___________CUUUC...CUC-3'\n______________UAUCGAUAUUC\n______________:\|:\|:\|\|\|:\|\|\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________102_________51\n	285 -- 291	176 -- 182	-9.38108 kcal/mol	0.14396 kcal/mol	3.38772 kcal/mol	64 109@LB@ \| \|@LB@5'-ACU...CGGGU CUUUC...CUC-3'@LB@ UAUCGAUAUUC@LB@ :\|:\|:\|\|\|:\|\|@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 102 51@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -9.38108 kcal/mol@LB@Unfolding Energy - mRNA 0.14396 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 65 -- 108@LB@Position - sRNA 52 -- 101@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 176 -- 182@LB@
28	0.002284	0.2633	b1114	mfd	-18.81	0.004608	253 -- 297	50 -- 95	transcription-repair coupling factor	_____________252______________298\n_____________\|________________\|\n5'-UUC...GCGUC___U____________CGGCG...AAA-3'\n______________UGC_GGGCGAGUUAAC\n______________\|\|\|_:\|\|\|:\|\|\|:\|\|\|\n______________ACG_UCCGUUCAGUUG\n3'-UUU...GUACU________________AAAGU...UAG-5'\n_____________\|________________\|\n_____________96_______________49\n	262 -- 268	149 -- 155	-20.6961 kcal/mol	4.60584 kcal/mol	7.12854 kcal/mol	252 298@LB@ \| \|@LB@5'-UUC...GCGUC U CGGCG...AAA-3'@LB@ UGC GGGCGAGUUAAC@LB@ \|\|\| :\|\|\|:\|\|\|:\|\|\|@LB@ ACG UCCGUUCAGUUG@LB@3'-UUU...GUACU AAAGU...UAG-5'@LB@ \| \|@LB@ 96 49@LB@@LB@@LB@Energy -18.81 kcal/mol@LB@Hybridization Energy -20.6961 kcal/mol@LB@Unfolding Energy - mRNA 4.60584 kcal/mol@LB@Unfolding Energy - sRNA 7.12854 kcal/mol@LB@@LB@Position - mRNA 253 -- 297@LB@Position - sRNA 50 -- 95@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 149 -- 155@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
65	0.006332	0.3261	b3857	mobA	-11.59	0.134663	143 -- 181	126 -- 173	molybdopterin-guanine dinucleotide synthase	_____________142________________________________________________________182\n_____________\|__________________________________________________________\|\n5'-UCC...AUAGU_______C_____U_U___GA___A__C______AG______________A_______AAUAA...AAC-3'\n______________GAUGCUC__UUAC_C_UGA__CAG_CA_GUUAGC____________GGUC_AUCCCAC\n______________:\|\|:\|\|\|__\|:\|\|_\|_\|\|\|__\|\|\|_\|\|_\|\|:\|:\|____________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAUGAG__AGUG_G_ACU__GUC_GU_CAGUUG____________CCAG_UAGGGUG\n3'-UUU...UGUGG_______UC____U_U___AC___C__U______AAAGUCUUAACG____________ACGUA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________174________________________________________________________125\n	175 -- 181	126 -- 132	-38.7055 kcal/mol	10.57 kcal/mol	15.6637 kcal/mol	142 182@LB@ \| \|@LB@5'-UCC...AUAGU C U U GA A C AG A AAUAA...AAC-3'@LB@ GAUGCUC UUAC C UGA CAG CA GUUAGC GGUC AUCCCAC@LB@ :\|\|:\|\|\| \|:\|\| \| \|\|\| \|\|\| \|\| \|\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAUGAG AGUG G ACU GUC GU CAGUUG CCAG UAGGGUG@LB@3'-UUU...UGUGG UC U U AC C U AAAGUCUUAACG ACGUA...UAG-5'@LB@ \| \|@LB@ 174 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -38.7055 kcal/mol@LB@Unfolding Energy - mRNA 10.57 kcal/mol@LB@Unfolding Energy - sRNA 15.6637 kcal/mol@LB@@LB@Position - mRNA 143 -- 181@LB@Position - sRNA 126 -- 173@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 126 -- 132@LB@
70	0.00686	0.3298	b0761	modE	-10.05	0.269682	248 -- 271	57 -- 77	transcriptional repressor for the molybdenum transport operon modABC	_____________247______272\n_____________\|________\|\n5'-ACC...GAAAA________CUUUU...CCA-3'\n______________GCACUCCC\n______________\|\|\|\|:\|\|\|\n______________CGUGGGGG\n3'-UUU...UACCC________AACGA...UAG-5'\n_____________\|________\|\n_____________78_______56\n	126 -- 132	11 -- 17	-14.7879 kcal/mol	0.633098 kcal/mol	5.13224 kcal/mol	247 272@LB@ \| \|@LB@5'-ACC...GAAAA CUUUU...CCA-3'@LB@ GCACUCCC@LB@ \|\|\|\|:\|\|\|@LB@ CGUGGGGG@LB@3'-UUU...UACCC AACGA...UAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -14.7879 kcal/mol@LB@Unfolding Energy - mRNA 0.633098 kcal/mol@LB@Unfolding Energy - sRNA 5.13224 kcal/mol@LB@@LB@Position - mRNA 248 -- 271@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 11 -- 17@LB@
165	0.01884	0.3812	b3291	mscL	-11.12	0.167422	252 -- 267	193 -- 208	mechanosensitive channel protein high conductance	_____________251_____268\n_____________\|_______\|\n5'-UGU...UGUCG_______AGGGA...UCU-3'\n______________GCUUCAU\n______________\|\|\|\|\|\|\|\n______________CGAAGUA\n3'-UUU...GGGAA_______G-5'\n_____________\|_______\|\n_____________209_____192\n	182 -- 188	2 -- 8	-9.41561 kcal/mol	2.23742 kcal/mol	0.70263 kcal/mol	251 268@LB@ \| \|@LB@5'-UGU...UGUCG AGGGA...UCU-3'@LB@ GCUUCAU@LB@ \|\|\|\|\|\|\|@LB@ CGAAGUA@LB@3'-UUU...GGGAA G-5'@LB@ \| \|@LB@ 209 192@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -9.41561 kcal/mol@LB@Unfolding Energy - mRNA 2.23742 kcal/mol@LB@Unfolding Energy - sRNA 0.70263 kcal/mol@LB@@LB@Position - mRNA 252 -- 267@LB@Position - sRNA 193 -- 208@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 2 -- 8@LB@
200	0.02363	0.3833	b3068	mug	-12.10	0.106144	279 -- 297	1 -- 19	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________278__________________298\n_____________\|____________________\|\n5'-UGG...GGACU___UU_______________CGG-3'\n______________GGU__UCCCUUUGCU_CAUC\n______________\|\|:__:\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCG__GGGGGAACGA_GUAG\n3'-UUU...GUACC___U___________A____-5'\n_____________\|___________________\|\n_____________20__________________1\n	287 -- 293	6 -- 12	-22.9494 kcal/mol	3.41941 kcal/mol	8.43224 kcal/mol	278 298@LB@ \| \|@LB@5'-UGG...GGACU UU CGG-3'@LB@ GGU UCCCUUUGCU CAUC@LB@ \|\|: :\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCG GGGGGAACGA GUAG@LB@3'-UUU...GUACC U A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.9494 kcal/mol@LB@Unfolding Energy - mRNA 3.41941 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 6 -- 12@LB@
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@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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