Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
152	0.005935	0.1368	b2701	mltB	-9.57	0.138424	83 -- 107	69 -- 92	membrane-bound lytic murein transglycosylase B	_____________82________________________108\n_____________\|_________________________\|\n5'-AGA...GAUAG__AG_G____G_____A________AAGUC...GAA-3'\n______________CG__G_GAAU_AGUUG_GUUAUGUA\n______________\|\|__:_\|\|\|\|_\|:\|\|\|_\|:\|\|\|\|:\|\n______________GC__U_CUUA_UUAAC_CGAUACGU\n3'-UUU...CCGCA__A__G____G_____A________CAUUA...ACG-5'\n_____________\|_________________________\|\n_____________93________________________68\n	101 -- 107	69 -- 75	-19.8359 kcal/mol	5.60429 kcal/mol	4.66371 kcal/mol	82 108@LB@ \| \|@LB@5'-AGA...GAUAG AG G G A AAGUC...GAA-3'@LB@ CG G GAAU AGUUG GUUAUGUA@LB@ \|\| : \|\|\|\| \|:\|\|\| \|:\|\|\|\|:\|@LB@ GC U CUUA UUAAC CGAUACGU@LB@3'-UUU...CCGCA A G G A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -19.8359 kcal/mol@LB@Unfolding Energy - mRNA 5.60429 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 83 -- 107@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 69 -- 75@LB@
81	0.001932	0.08273	b2763	cysI	-12.36	0.027367	234 -- 285	1 -- 58	sulfite reductase beta subunit NAD(P)-binding heme-binding	_____________233_________________________________________________________286\n_____________\|___________________________________________________________\|\n5'-GAA...UGGUC_______AACU_____ACGCC__________AA______A___AA_____AC_______GCGGC...CGG-3'\n______________GAAGGAA____GACAG_____GAGCGC_AUG______GC_UGA____GCA__UACCUGC\n______________:\|\|\|\|\|\|____\|\|\|\|:_____\|\|\|\|\|\|_\|:\|______\|\|_\|\|\|____\|\|\|__:\|\|\|\|\|\|\n______________UUUCCUU____CUGUU_____CUCGCG_UGC______CG_ACU____CGU__GUGGACG\n3'-UUU...AGUUU_______CAUU_____AUAC_______U___GGGUAG__A___GCAA___AA_______-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	279 -- 285	1 -- 7	-40.3147 kcal/mol	11.0832 kcal/mol	16.8724 kcal/mol	233 286@LB@ \| \|@LB@5'-GAA...UGGUC AACU ACGCC AA A AA AC GCGGC...CGG-3'@LB@ GAAGGAA GACAG GAGCGC AUG GC UGA GCA UACCUGC@LB@ :\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\| \|:\| \|\| \|\|\| \|\|\| :\|\|\|\|\|\|@LB@ UUUCCUU CUGUU CUCGCG UGC CG ACU CGU GUGGACG@LB@3'-UUU...AGUUU CAUU AUAC U GGGUAG A GCAA AA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -40.3147 kcal/mol@LB@Unfolding Energy - mRNA 11.0832 kcal/mol@LB@Unfolding Energy - sRNA 16.8724 kcal/mol@LB@@LB@Position - mRNA 234 -- 285@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 1 -- 7@LB@
56	0.0007477	0.04704	b2777	queE	-11.99	0.034574	197 -- 232	45 -- 77	7-carboxy-7-deazaguanine synthase; queosine biosynthesis	_____________196___________________________________233\n_____________\|_____________________________________\|\n5'-AAU...GAGAA____________CC____UU__C_A__U__UCC____CCUGC...UUG-3'\n______________UGCUAUGCAGUA___CGA__AA_G_GA_GU___AGAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|___\|:\|__\|\|_\|_\|\|_\|\|___\|\|\|\|\n______________ACGAUACGUCAU___GUU__UU_C_CU_CA___UCUG\n3'-UUU...UUAAC____________UAA___UU_______U__U______UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________78____________________________________44\n	202 -- 208	66 -- 72	-23.7263 kcal/mol	6.13303 kcal/mol	5.60521 kcal/mol	196 233@LB@ \| \|@LB@5'-AAU...GAGAA CC UU C A U UCC CCUGC...UUG-3'@LB@ UGCUAUGCAGUA CGA AA G GA GU AGAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|:\| \|\| \| \|\| \|\| \|\|\|\|@LB@ ACGAUACGUCAU GUU UU C CU CA UCUG@LB@3'-UUU...UUAAC UAA UU U U UUAUA...ACG-5'@LB@ \| \|@LB@ 78 44@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -23.7263 kcal/mol@LB@Unfolding Energy - mRNA 6.13303 kcal/mol@LB@Unfolding Energy - sRNA 5.60521 kcal/mol@LB@@LB@Position - mRNA 197 -- 232@LB@Position - sRNA 45 -- 77@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
99	0.003254	0.1114	b2839	lysR	-9.43	0.148712	276 -- 282	1 -- 7	transcriptional activator of lysA; autorepressor	_____________275_____283\n_____________\|_______\|\n5'-GGC...CGGCA_______UACAC...CAA-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	276 -- 282	1 -- 7	-13.2779 kcal/mol	1.51062 kcal/mol	2.34039 kcal/mol	275 283@LB@ \| \|@LB@5'-GGC...CGGCA UACAC...CAA-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2779 kcal/mol@LB@Unfolding Energy - mRNA 1.51062 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
197	0.008895	0.1548	b2844	yqeF	-5.48	0.714940	222 -- 246	20 -- 39	short chain acyltransferase	_____________221_______________________247\n_____________\|_________________________\|\n5'-CCA...UUGUC_______UACG___A_______G__GCUUU...UCG-3'\n______________GGGGCGU____GAC_CCUAUCG_CU\n______________\|\|:\|\|\|:____:\|\|_\|\|:\|\|\|\|_\|\|\n______________CCUCGCG____UUG_GGGUAGC_GA\n3'-UUU...UUAUA______________C__________ACUGC...ACG-5'\n_____________\|_________________________\|\n_____________40________________________19\n	237 -- 243	22 -- 28	-25.7666 kcal/mol	8.11246 kcal/mol	12.1811 kcal/mol	221 247@LB@ \| \|@LB@5'-CCA...UUGUC UACG A G GCUUU...UCG-3'@LB@ GGGGCGU GAC CCUAUCG CU@LB@ \|\|:\|\|\|: :\|\| \|\|:\|\|\|\| \|\|@LB@ CCUCGCG UUG GGGUAGC GA@LB@3'-UUU...UUAUA C ACUGC...ACG-5'@LB@ \| \|@LB@ 40 19@LB@@LB@@LB@Energy -5.48 kcal/mol@LB@Hybridization Energy -25.7666 kcal/mol@LB@Unfolding Energy - mRNA 8.11246 kcal/mol@LB@Unfolding Energy - sRNA 12.1811 kcal/mol@LB@@LB@Position - mRNA 222 -- 246@LB@Position - sRNA 20 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 22 -- 28@LB@
94	0.002802	0.105	b2905	gcvT	-11.27	0.053451	219 -- 244	68 -- 93	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________218_________________________245\n_____________\|___________________________\|\n5'-CUG...CUCCU_____________CACAC___U_____CGCUC...AAA-3'\n______________UUGUACGAA_CAA_____GCU_UGCGG\n______________\|:\|\|\|\|\|\|\|_\|\|\|_____\|\|\|_\|\|\|:\|\n______________AGCAUGCUU_GUU_____CGA_ACGUC\n3'-UUU...GCCGC_________A___AACA____U_____AUUAA...ACG-5'\n_____________\|___________________________\|\n_____________94__________________________67\n	221 -- 227	85 -- 91	-21.376 kcal/mol	5.42013 kcal/mol	4.68758 kcal/mol	218 245@LB@ \| \|@LB@5'-CUG...CUCCU CACAC U CGCUC...AAA-3'@LB@ UUGUACGAA CAA GCU UGCGG@LB@ \|:\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|@LB@ AGCAUGCUU GUU CGA ACGUC@LB@3'-UUU...GCCGC A AACA U AUUAA...ACG-5'@LB@ \| \|@LB@ 94 67@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -21.376 kcal/mol@LB@Unfolding Energy - mRNA 5.42013 kcal/mol@LB@Unfolding Energy - sRNA 4.68758 kcal/mol@LB@@LB@Position - mRNA 219 -- 244@LB@Position - sRNA 68 -- 93@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 85 -- 91@LB@
122	0.004264	0.1231	b2914	rpiA	-10.11	0.103884	190 -- 234	45 -- 89	ribose 5-phosphate isomerase constitutive	_____________189______________________________________________235\n_____________\|________________________________________________\|\n5'-GAA...CACAG_____A____CA__AC______GAUGA___G_______C_________GGGCG...CAC-3'\n______________GCGAA_CGAU__UG____GCAG_____AUU_AAAAAAG__AGUAGGAU\n______________:\|\|\|\|_\|:\|\|__\|\|____\|\|\|\|_____\|\|\|_\|\|\|\|\|\|\|__\|\|\|\|:\|\|:\n______________UGCUU_GUUA__AC____CGUC_____UAA_UUUUUUC__UCAUUCUG\n3'-UUU...CAGCA_____A____AC__GAUA____AU______G_______CU________UUAUA...ACG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________44\n	228 -- 234	45 -- 51	-27.3521 kcal/mol	11.527 kcal/mol	5.72096 kcal/mol	189 235@LB@ \| \|@LB@5'-GAA...CACAG A CA AC GAUGA G C GGGCG...CAC-3'@LB@ GCGAA CGAU UG GCAG AUU AAAAAAG AGUAGGAU@LB@ :\|\|\|\| \|:\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|\|:@LB@ UGCUU GUUA AC CGUC UAA UUUUUUC UCAUUCUG@LB@3'-UUU...CAGCA A AC GAUA AU G CU UUAUA...ACG-5'@LB@ \| \|@LB@ 90 44@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -27.3521 kcal/mol@LB@Unfolding Energy - mRNA 11.527 kcal/mol@LB@Unfolding Energy - sRNA 5.72096 kcal/mol@LB@@LB@Position - mRNA 190 -- 234@LB@Position - sRNA 45 -- 89@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 45 -- 51@LB@
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor	_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@LB@
143	0.005544	0.1363	b2936	loiP	-13.30	0.014839	83 -- 152	1 -- 41	Phe-Phe periplasmic metalloprotease OM lipoprotein; low salt-inducible; Era-binding heat shock protein	_____________82______________________________________________________________________153\n_____________\|_______________________________________________________________________\|\n5'-UUG...CUCGC___UU______UCUACU_______C____GCGCUUUUCCUUAUAC__AGACUGA____C____________AAACG...AAG-3'\n______________AUG__GCGCAA______CGCCCGU_CGCU________________UG_______GCGU_G_AUUCACCUGC\n______________\|\|\|__\|\|\|\|\|\|______\|\|\|\|\|:\|_\|\|\|\|________________\|\|_______:\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________UAC__CGCGUU______GCGGGUA_GCGA________________AC_______UGCA_C_UAAGUGGACG\n3'-UUU...UGUUA___CU_____________________________________________________A_G__________-5'\n_____________\|______________________________________________________________________\|\n_____________42_____________________________________________________________________1\n	146 -- 152	1 -- 7	-44.3719 kcal/mol	15.78 kcal/mol	15.2922 kcal/mol	82 153@LB@ \| \|@LB@5'-UUG...CUCGC UU UCUACU C GCGCUUUUCCUUAUAC AGACUGA C AAACG...AAG-3'@LB@ AUG GCGCAA CGCCCGU CGCU UG GCGU G AUUCACCUGC@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\|\|:\| \|\|\|\| \|\| :\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ UAC CGCGUU GCGGGUA GCGA AC UGCA C UAAGUGGACG@LB@3'-UUU...UGUUA CU A G -5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -44.3719 kcal/mol@LB@Unfolding Energy - mRNA 15.78 kcal/mol@LB@Unfolding Energy - sRNA 15.2922 kcal/mol@LB@@LB@Position - mRNA 83 -- 152@LB@Position - sRNA 1 -- 41@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
78	0.001866	0.08273	b2952	yggT	-14.70	0.005634	84 -- 104	37 -- 56	putative inner membrane protein; compensates for loss in K+ uptake	_____________83____________________105\n_____________\|_____________________\|\n5'-AGG...UCUCU_____U__C____________AGCCG...ACA-3'\n______________GGGAA_GU_GGACGAUAUGGA\n______________:\|\|\|\|_\|\|_:\|\|\|:\|\|\|\|\|\|\|\n______________UCCUU_CA_UCUGUUAUACCU\n3'-UUU...UUUUU________U____________CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________57____________________36\n	98 -- 104	37 -- 43	-24.1681 kcal/mol	5.76987 kcal/mol	3.6645 kcal/mol	83 105@LB@ \| \|@LB@5'-AGG...UCUCU U C AGCCG...ACA-3'@LB@ GGGAA GU GGACGAUAUGGA@LB@ :\|\|\|\| \|\| :\|\|\|:\|\|\|\|\|\|\|@LB@ UCCUU CA UCUGUUAUACCU@LB@3'-UUU...UUUUU U CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -24.1681 kcal/mol@LB@Unfolding Energy - mRNA 5.76987 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 84 -- 104@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 98 -- 104@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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