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
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
53	0.002649	0.1727	b2289	lrhA	-9.83	0.149509	112 -- 119	68 -- 75	transcriptional repressor of flagellar motility and chemotaxis genes	_____________111______120\n_____________\|________\|\n5'-CUG...AAACU________GGCAC...CCG-3'\n______________GCCAGGGA\n______________:\|\|\|\|\|\|\|\n______________UGGUCCCU\n3'-UUU...GGUUG________UUAGA...GUG-5'\n_____________\|________\|\n_____________76_______67\n	113 -- 119	68 -- 74	-14.981 kcal/mol	1.464 kcal/mol	3.68273 kcal/mol	111 120@LB@ \| \|@LB@5'-CUG...AAACU GGCAC...CCG-3'@LB@ GCCAGGGA@LB@ :\|\|\|\|\|\|\|@LB@ UGGUCCCU@LB@3'-UUU...GGUUG UUAGA...GUG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.981 kcal/mol@LB@Unfolding Energy - mRNA 1.464 kcal/mol@LB@Unfolding Energy - sRNA 3.68273 kcal/mol@LB@@LB@Position - mRNA 112 -- 119@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 68 -- 74@LB@
68	0.00345	0.1727	b3168	infB	-10.64	0.105292	126 -- 148	49 -- 77	translation initiation factor IF-2	_____________125___________________________149\n_____________\|_____________________________\|\n5'-AAG...CCGGA______________A______________UAUUU...CUG-3'\n______________GCACU_____GAUU_UGGCUGC_CCGUAA\n______________:\|\|\|:_____:\|\|:_\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UGUGG_____UUAG_ACCGACG_GGCAUU\n3'-UUU...GCGGU_____UCCCU____A_______C______UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	136 -- 142	56 -- 62	-27.6009 kcal/mol	7.61735 kcal/mol	9.34562 kcal/mol	125 149@LB@ \| \|@LB@5'-AAG...CCGGA A UAUUU...CUG-3'@LB@ GCACU GAUU UGGCUGC CCGUAA@LB@ :\|\|\|: :\|\|: \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUGG UUAG ACCGACG GGCAUU@LB@3'-UUU...GCGGU UCCCU A C UAAUA...GUG-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -27.6009 kcal/mol@LB@Unfolding Energy - mRNA 7.61735 kcal/mol@LB@Unfolding Energy - sRNA 9.34562 kcal/mol@LB@@LB@Position - mRNA 126 -- 148@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 56 -- 62@LB@
191	0.01171	0.2159	b4221	tamB	-9.06	0.207346	81 -- 101	52 -- 76	translocation and assembly module for autotransporter export inner membrane subunit	_____________80_________________________102\n_____________\|__________________________\|\n5'-ACC...ACCGG__________________G_______GGAAU...AUC-3'\n______________UACCGGGG___UC__GGC_UGCGCUG\n______________:\|\|\|:\|\|\|___\|\|__\|\|\|_\|\|\|\|\|:\|\n______________GUGGUCCC___AG__CCG_ACGCGGC\n3'-UUU...CGGUU________UUU__AA___________AUUUA...GUG-5'\n_____________\|__________________________\|\n_____________77_________________________51\n	95 -- 101	52 -- 58	-29.4253 kcal/mol	11.0996 kcal/mol	9.26585 kcal/mol	80 102@LB@ \| \|@LB@5'-ACC...ACCGG G GGAAU...AUC-3'@LB@ UACCGGGG UC GGC UGCGCUG@LB@ :\|\|\|:\|\|\| \|\| \|\|\| \|\|\|\|\|:\|@LB@ GUGGUCCC AG CCG ACGCGGC@LB@3'-UUU...CGGUU UUU AA AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -29.4253 kcal/mol@LB@Unfolding Energy - mRNA 11.0996 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 52 -- 58@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
116	0.006112	0.1855	b1260	trpA	-12.39	0.048115	172 -- 199	63 -- 89	tryptophan synthase alpha subunit	_____________171__________________________200\n_____________\|____________________________\|\n5'-GCC...UUCAC______U__AA_____GA__________GAUGG...CAU-3'\n______________GAUAUU_UG__AGCAC__GGGGAAAUCU\n______________:\|\|\|:\|_:\|__\|:\|\|\|__:\|\|\|\|\|\|\|\|\|\n______________UUAUGA_GC__UUGUG__UCCCUUUAGA\n3'-UUU...CGCGC______C__GG_____G___________ACCGA...GUG-5'\n_____________\|____________________________\|\n_____________90___________________________62\n	193 -- 199	63 -- 69	-25.3377 kcal/mol	5.06327 kcal/mol	7.88429 kcal/mol	171 200@LB@ \| \|@LB@5'-GCC...UUCAC U AA GA GAUGG...CAU-3'@LB@ GAUAUU UG AGCAC GGGGAAAUCU@LB@ :\|\|\|:\| :\| \|:\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UUAUGA GC UUGUG UCCCUUUAGA@LB@3'-UUU...CGCGC C GG G ACCGA...GUG-5'@LB@ \| \|@LB@ 90 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -25.3377 kcal/mol@LB@Unfolding Energy - mRNA 5.06327 kcal/mol@LB@Unfolding Energy - sRNA 7.88429 kcal/mol@LB@@LB@Position - mRNA 172 -- 199@LB@Position - sRNA 63 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 63 -- 69@LB@
166	0.009748	0.2068	b1261	trpB	-12.89	0.038353	88 -- 97	52 -- 61	tryptophan synthase beta subunit	_____________87_________98\n_____________\|__________\|\n5'-UGG...AAACC__________GACUU...UCA-3'\n______________GGCUGCGCCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCGACGCGGC\n3'-UUU...UAGAA__________AUUUA...GUG-5'\n_____________\|__________\|\n_____________62_________51\n	91 -- 97	52 -- 58	-23.3299 kcal/mol	5.56351 kcal/mol	4.87533 kcal/mol	87 98@LB@ \| \|@LB@5'-UGG...AAACC GACUU...UCA-3'@LB@ GGCUGCGCCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCGACGCGGC@LB@3'-UUU...UAGAA AUUUA...GUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -23.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.56351 kcal/mol@LB@Unfolding Energy - sRNA 4.87533 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
144	0.008344	0.2033	b3159	yhbV	-10.12	0.132236	144 -- 228	15 -- 82	U32 peptidase family protein	_____________143______________________________________________________________________________________229\n_____________\|________________________________________________________________________________________\|\n5'-GUG...AUGUC__AA_____G__AACCAC__________AUAUCA________GGCA_______AAA___AUGAAAUAUUCCUU_______________GGUAC...AUC-3'\n______________CG__GGCAC_CA______UCUUGGC_GC______CCGUAAAU____GUGA_GA___GCA______________AGGGC_CAGUGCUGU\n______________\|\|__::\|\|\|_\|\|______\|\|\|\|\|\|\|_\|\|______\|\|\|\|\|\|\|\|____:\|\|\|_\|\|___:\|\|______________\|\|\|\|\|_\|\|\|::\|\|\|\|\n______________GC__UUGUG_GU______AGAACCG_CG______GGCAUUUA____UACU_CU___UGU______________UCCCG_GUCGUGACA\n3'-UUU...AUGAC__GG________CCCUUU_______A__C_____________AUAA____A__CAA______________________U_________AAAAG...GUG-5'\n_____________\|________________________________________________________________________________________\|\n_____________83_______________________________________________________________________________________14\n	177 -- 183	48 -- 54	-52.1529 kcal/mol	19.8598 kcal/mol	22.1763 kcal/mol	143 229@LB@ \| \|@LB@5'-GUG...AUGUC AA G AACCAC AUAUCA GGCA AAA AUGAAAUAUUCCUU GGUAC...AUC-3'@LB@ CG GGCAC CA UCUUGGC GC CCGUAAAU GUGA GA GCA AGGGC CAGUGCUGU@LB@ \|\| ::\|\|\| \|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\| :\|\|\| \|\| :\|\| \|\|\|\|\| \|\|\|::\|\|\|\|@LB@ GC UUGUG GU AGAACCG CG GGCAUUUA UACU CU UGU UCCCG GUCGUGACA@LB@3'-UUU...AUGAC GG CCCUUU A C AUAA A CAA U AAAAG...GUG-5'@LB@ \| \|@LB@ 83 14@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -52.1529 kcal/mol@LB@Unfolding Energy - mRNA 19.8598 kcal/mol@LB@Unfolding Energy - sRNA 22.1763 kcal/mol@LB@@LB@Position - mRNA 144 -- 228@LB@Position - sRNA 15 -- 82@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
135	0.007679	0.1993	b0096	lpxC	-11.14	0.084212	289 -- 298	76 -- 85	UDP-3-O-acyl N-acetylglucosamine deacetylase	_____________288________299\n_____________\|__________\|\n5'-GAA...ACGCC__________CA-3'\n______________CUGCGCCGGC\n______________\|\|\|\|\|\|\|::\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	292 -- 298	76 -- 82	-18.1767 kcal/mol	1.93848 kcal/mol	5.09564 kcal/mol	288 299@LB@ \| \|@LB@5'-GAA...ACGCC CA-3'@LB@ CUGCGCCGGC@LB@ \|\|\|\|\|\|\|::\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.93848 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 76 -- 82@LB@
93	0.005014	0.1855	b0091	murC	-15.25	0.013117	8 -- 30	73 -- 94	UDP-N-acetylmuramate:L-alanine ligase	_____________7_______________________31\n_____________\|_______________________\|\n____5'-CAGCUUA____________U__________CUGGC...GCG-3'\n______________GCGUGGAUGCUG_CGCCAACACC\n______________\|\|\|:\|:\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________CGCGCUUAUGAC_GCGGUUGUGG\n3'-UUU...CCCCA_______________________UCCCU...GUG-5'\n_____________\|_______________________\|\n_____________95______________________72\n	24 -- 30	73 -- 79	-39.1057 kcal/mol	11.3 kcal/mol	12.5321 kcal/mol	7 31@LB@ \| \|@LB@ 5'-CAGCUUA U CUGGC...GCG-3'@LB@ GCGUGGAUGCUG CGCCAACACC@LB@ \|\|\|:\|:\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCUUAUGAC GCGGUUGUGG@LB@3'-UUU...CCCCA UCCCU...GUG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -15.25 kcal/mol@LB@Hybridization Energy -39.1057 kcal/mol@LB@Unfolding Energy - mRNA 11.3 kcal/mol@LB@Unfolding Energy - sRNA 12.5321 kcal/mol@LB@@LB@Position - mRNA 8 -- 30@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 73 -- 79@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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