Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
27	0.0002115	0.02687	b2607	trmD	-14.32	0.001383	229 -- 258	48 -- 75	tRNA m(1)G37 methyltransferase SAM-dependent	_____________228____________________________259\n_____________\|______________________________\|\n5'-UCG...GUUUC___________C__G___U_A_________GGGUA...UCC-3'\n______________CUGAAAUGUUC_GC_CAA_U_CCGAUUACG\n______________\|\|:\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|_\|\|\|\|\|\|\|\|\|\n______________GAUUUUAUAAG_CG_GUU_A_GGCUAAUGC\n3'-AUU...CCGCC___________U______U___________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	252 -- 258	48 -- 54	-28.476 kcal/mol	6.50272 kcal/mol	7.67232 kcal/mol	228 259@LB@ \| \|@LB@5'-UCG...GUUUC C G U A GGGUA...UCC-3'@LB@ CUGAAAUGUUC GC CAA U CCGAUUACG@LB@ \|\|:\|\|\|\|:\|\|\| \|\| \|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ GAUUUUAUAAG CG GUU A GGCUAAUGC@LB@3'-AUU...CCGCC U U ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -28.476 kcal/mol@LB@Unfolding Energy - mRNA 6.50272 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 229 -- 258@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 48 -- 54@LB@
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent	_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
91	0.002527	0.0977	b4393	trpR	-12.48	0.007130	9 -- 21	43 -- 55	transcriptional repressor tryptophan-binding	_____________8_____________22\n_____________\|_____________\|\n___5'-GAGACGCG_____________AACGU...AUC-3'\n______________CGGUUAUGUGAAG\n______________\|\|:\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUUC\n3'-AUU...UUUAG_____________AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	15 -- 21	43 -- 49	-16.824 kcal/mol	1.08541 kcal/mol	3.2693 kcal/mol	8 22@LB@ \| \|@LB@ 5'-GAGACGCG AACGU...AUC-3'@LB@ CGGUUAUGUGAAG@LB@ \|\|:\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUUC@LB@3'-AUU...UUUAG AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -16.824 kcal/mol@LB@Unfolding Energy - mRNA 1.08541 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 9 -- 21@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 43 -- 49@LB@
120	0.003999	0.1172	b2582	trxC	-9.28	0.072721	206 -- 219	4 -- 16	thioredoxin 2	_____________205____________220\n_____________\|______________\|\n5'-CUC...AUGAA____G_________AUUGU...UUG-3'\n______________UACC_UUUGUACCC\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________AUGG_AGACAUGGG\n3'-AUU...GUAGA______________AUG-5'\n_____________\|______________\|\n_____________17_____________3\n	213 -- 219	4 -- 10	-18.1109 kcal/mol	2.27225 kcal/mol	6.59015 kcal/mol	205 220@LB@ \| \|@LB@5'-CUC...AUGAA G AUUGU...UUG-3'@LB@ UACC UUUGUACCC@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGG AGACAUGGG@LB@3'-AUU...GUAGA AUG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -18.1109 kcal/mol@LB@Unfolding Energy - mRNA 2.27225 kcal/mol@LB@Unfolding Energy - sRNA 6.59015 kcal/mol@LB@@LB@Position - mRNA 206 -- 219@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 4 -- 10@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
107	0.003396	0.1101	b3871	typA	-9.79	0.052081	283 -- 294	47 -- 59	GTP-binding protein	_____________282___________295\n_____________\|_____________\|\n5'-UGC...CCAAC_____________UCGACU-3'\n______________AAUCCGGU_ACGU\n______________\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUAGGCUA_UGCA\n3'-AUU...UCGGU________A____CUUCA...AUG-5'\n_____________\|_____________\|\n_____________60____________46\n	284 -- 290	52 -- 58	-13.0383 kcal/mol	1.68034 kcal/mol	1.56852 kcal/mol	282 295@LB@ \| \|@LB@5'-UGC...CCAAC UCGACU-3'@LB@ AAUCCGGU ACGU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ UUAGGCUA UGCA@LB@3'-AUU...UCGGU A CUUCA...AUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -13.0383 kcal/mol@LB@Unfolding Energy - mRNA 1.68034 kcal/mol@LB@Unfolding Energy - sRNA 1.56852 kcal/mol@LB@@LB@Position - mRNA 283 -- 294@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 52 -- 58@LB@
146	0.005604	0.1342	b1637	tyrS	-10.18	0.040102	30 -- 71	2 -- 50	tyrosyl-tRNA synthetase	_____________29________________________________________________72\n_____________\|_________________________________________________\|\n5'-CAU...UACCA_______AAU___U_CG________U__U____________________AAAAG...CGA-3'\n______________GCGUGAA____GA_G__UGGAAGAU_GA_CGUCUUGC______ACCCUG\n______________:\|\|\|\|\|\|____:\|_\|__\|\|:\|\|\|\|\|_\|\|_\|:\|\|\|\|:\|______\|\|\|\|\|:\n______________UGCACUU____UU_C__ACUUUCUA_CU_GUAGAAUG______UGGGAU\n3'-AUU...GCUAA_______CAUU__C_AG________U__U________GAGACA______G-5'\n_____________\|_________________________________________________\|\n_____________51________________________________________________1\n	30 -- 36	44 -- 50	-35.883 kcal/mol	13.0482 kcal/mol	12.6769 kcal/mol	29 72@LB@ \| \|@LB@5'-CAU...UACCA AAU U CG U U AAAAG...CGA-3'@LB@ GCGUGAA GA G UGGAAGAU GA CGUCUUGC ACCCUG@LB@ :\|\|\|\|\|\| :\| \| \|\|:\|\|\|\|\| \|\| \|:\|\|\|\|:\| \|\|\|\|\|:@LB@ UGCACUU UU C ACUUUCUA CU GUAGAAUG UGGGAU@LB@3'-AUU...GCUAA CAUU C AG U U GAGACA G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -35.883 kcal/mol@LB@Unfolding Energy - mRNA 13.0482 kcal/mol@LB@Unfolding Energy - sRNA 12.6769 kcal/mol@LB@@LB@Position - mRNA 30 -- 71@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 44 -- 50@LB@
39	0.0004396	0.03766	b3669	uhpA	-8.50	0.116685	77 -- 96	47 -- 66	response regulator in two-component regulatory system wtih UhpB	_____________76___________________97\n_____________\|____________________\|\n5'-UCA...CGUAA______C_______CG____UUAAC...UUG-3'\n______________UCAGUC_GAUCCGA__AUGU\n______________\|\|\|\|:\|_:\|\|\|\|\|\|__\|:\|\|\n______________AGUCGG_UUAGGCU__UGCA\n3'-AUU...UUAUA______U_______AA____CUUCA...AUG-5'\n_____________\|____________________\|\n_____________67___________________46\n	84 -- 90	53 -- 59	-21.6061 kcal/mol	5.63687 kcal/mol	7.4916 kcal/mol	76 97@LB@ \| \|@LB@5'-UCA...CGUAA C CG UUAAC...UUG-3'@LB@ UCAGUC GAUCCGA AUGU@LB@ \|\|\|\|:\| :\|\|\|\|\|\| \|:\|\|@LB@ AGUCGG UUAGGCU UGCA@LB@3'-AUU...UUAUA U AA CUUCA...AUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -21.6061 kcal/mol@LB@Unfolding Energy - mRNA 5.63687 kcal/mol@LB@Unfolding Energy - sRNA 7.4916 kcal/mol@LB@@LB@Position - mRNA 77 -- 96@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 53 -- 59@LB@
185	0.008247	0.1556	b4195	ulaC	-8.57	0.111851	181 -- 191	40 -- 50	L-ascorbate-specific enzyme IIA component of PTS	_____________180_________192\n_____________\|___________\|\n5'-GCG...GCAGG___________GGACG...UGG-3'\n______________AUGUGAAGUAA\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UGCACUUCAUU\n3'-AUU...GCUAA___________UUCCA...AUG-5'\n_____________\|___________\|\n_____________51__________39\n	185 -- 191	40 -- 46	-13.163 kcal/mol	1.2893 kcal/mol	3.32158 kcal/mol	180 192@LB@ \| \|@LB@5'-GCG...GCAGG GGACG...UGG-3'@LB@ AUGUGAAGUAA@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UGCACUUCAUU@LB@3'-AUU...GCUAA UUCCA...AUG-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -13.163 kcal/mol@LB@Unfolding Energy - mRNA 1.2893 kcal/mol@LB@Unfolding Energy - sRNA 3.32158 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 40 -- 46@LB@
196	0.008709	0.1558	b2498	upp	-7.14	0.244299	249 -- 259	45 -- 56	uracil phosphoribosyltransferase	_____________248__________260\n_____________\|____________\|\n5'-GGC...UGGGA____________GCAAG...CCG-3'\n______________CUGA_UGCGUGA\n______________\|:\|\|_\|:\|\|\|\|\|\n______________GGCU_AUGCACU\n3'-AUU...GUUUA____A_______UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	253 -- 259	45 -- 51	-12.6155 kcal/mol	3.20986 kcal/mol	2.27945 kcal/mol	248 260@LB@ \| \|@LB@5'-GGC...UGGGA GCAAG...CCG-3'@LB@ CUGA UGCGUGA@LB@ \|:\|\| \|:\|\|\|\|\|@LB@ GGCU AUGCACU@LB@3'-AUU...GUUUA A UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -12.6155 kcal/mol@LB@Unfolding Energy - mRNA 3.20986 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 249 -- 259@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 253 -- 259@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)

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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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