Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
103	0.004595	0.1538	b3554	yiaF	-10.61	0.191588	8 -- 38	46 -- 75	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein		_____________7_________________________________39\n_____________\|_________________________________\|\n____5'-AAUCUCU_______AAAAA_________GCACUA______UUUAA...AGC-3'\n______________GGCUACA_____GGCAA__CG______UCAUUU\n______________\|:\|\|\|\|\|_____:\|\|\|\|__\|\|______\|\|\|:\|:\n______________CUGAUGU_____UCGUU__GC______AGUGAG\n3'-UUU...CGUUU_______GUG_______AA__AACAA_______UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________76________________________________45\n	8 -- 14	69 -- 75	-17.9003 kcal/mol	3.5618 kcal/mol	3.72616 kcal/mol	7 39@LB@ \| \|@LB@ 5'-AAUCUCU AAAAA GCACUA UUUAA...AGC-3'@LB@ GGCUACA GGCAA CG UCAUUU@LB@ \|:\|\|\|\|\| :\|\|\|\| \|\| \|\|\|:\|:@LB@ CUGAUGU UCGUU GC AGUGAG@LB@3'-UUU...CGUUU GUG AA AACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 76 45@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -17.9003 kcal/mol@LB@Unfolding Energy - mRNA 3.5618 kcal/mol@LB@Unfolding Energy - sRNA 3.72616 kcal/mol@LB@@LB@Position - mRNA 8 -- 38@LB@Position - sRNA 46 -- 75@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 69 -- 75@LB@
105	0.004683	0.1538	b3349	slyD	-10.61	0.192215	166 -- 197	39 -- 73	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)		_____________165_________________________________198\n_____________\|___________________________________\|\n5'-UGU...ACAAU___________U____UUCCCAU________A___AUCAU...ACU-3'\n______________CUGCGC_CA_C_AUUC________GCUCAGG_GAU\n______________\|\|:\|:\|_\|\|_\|_\|\|\|\|________:\|\|\|\|\|\|_\|\|\|\n______________GAUGUG_GU_G_UAAG________UGAGUCC_CUA\n3'-UUU...UUUCU______U__C_U____CAACAAAG_______C___AAGGU...GCA-5'\n_____________\|___________________________________\|\n_____________74__________________________________38\n	187 -- 193	43 -- 49	-23.2642 kcal/mol	7.88699 kcal/mol	4.77295 kcal/mol	165 198@LB@ \| \|@LB@5'-UGU...ACAAU U UUCCCAU A AUCAU...ACU-3'@LB@ CUGCGC CA C AUUC GCUCAGG GAU@LB@ \|\|:\|:\| \|\| \| \|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ GAUGUG GU G UAAG UGAGUCC CUA@LB@3'-UUU...UUUCU U C U CAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 74 38@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -23.2642 kcal/mol@LB@Unfolding Energy - mRNA 7.88699 kcal/mol@LB@Unfolding Energy - sRNA 4.77295 kcal/mol@LB@@LB@Position - mRNA 166 -- 197@LB@Position - sRNA 39 -- 73@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
89	0.003963	0.1538	b1252	tonB	-10.58	0.194225	25 -- 43	64 -- 82	membrane spanning protein in TonB-ExbB-ExbD transport complex		_____________24___________________44\n_____________\|____________________\|\n5'-AGU...UGAAA_________U__________AAAGA...AUC-3'\n______________GGGCGAAGA_CUGCA_ACGG\n______________\|\|\|\|:\|\|\|\|_\|\|:\|\|_\|\|:\|\n______________CCCGUUUCU_GAUGU_UGUC\n3'-UUU...CUCUA_______________G____GUUAA...GCA-5'\n_____________\|____________________\|\n_____________83___________________63\n	25 -- 31	76 -- 82	-25.6168 kcal/mol	4.83236 kcal/mol	10.2054 kcal/mol	24 44@LB@ \| \|@LB@5'-AGU...UGAAA U AAAGA...AUC-3'@LB@ GGGCGAAGA CUGCA ACGG@LB@ \|\|\|\|:\|\|\|\| \|\|:\|\| \|\|:\|@LB@ CCCGUUUCU GAUGU UGUC@LB@3'-UUU...CUCUA G GUUAA...GCA-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -25.6168 kcal/mol@LB@Unfolding Energy - mRNA 4.83236 kcal/mol@LB@Unfolding Energy - sRNA 10.2054 kcal/mol@LB@@LB@Position - mRNA 25 -- 43@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 76 -- 82@LB@
34	0.0005364	0.05552	b4244	pyrI	-10.55	0.196904	198 -- 215	60 -- 77	aspartate carbamoyltransferase regulatory subunit		_____________197________________216\n_____________\|__________________\|\n5'-UUC...AAAUA_____G_______A____AAAUU...UCA-3'\n______________GAGAU_ACACACG_UAAU\n______________:\|\|\|:_\|\|\|\|\|\|:_:\|\|\|\n______________UUCUG_UGUGUGU_GUUA\n3'-UUU...CCCGU_____A_______C____AGCAA...GCA-5'\n_____________\|__________________\|\n_____________78_________________59\n	204 -- 210	65 -- 71	-15.1619 kcal/mol	1.32522 kcal/mol	3.29036 kcal/mol	197 216@LB@ \| \|@LB@5'-UUC...AAAUA G A AAAUU...UCA-3'@LB@ GAGAU ACACACG UAAU@LB@ :\|\|\|: \|\|\|\|\|\|: :\|\|\|@LB@ UUCUG UGUGUGU GUUA@LB@3'-UUU...CCCGU A C AGCAA...GCA-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 1.32522 kcal/mol@LB@Unfolding Energy - sRNA 3.29036 kcal/mol@LB@@LB@Position - mRNA 198 -- 215@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 65 -- 71@LB@
187	0.009506	0.1776	b1243	oppA	-10.52	0.199375	11 -- 17	40 -- 46	oligopeptide ABC transporter periplasmic binding protein		_____________10______18\n_____________\|_______\|\n5'-UGU...CUCGA_______GACAC...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	11 -- 17	40 -- 46	-13.6251 kcal/mol	1.75344 kcal/mol	1.35582 kcal/mol	10 18@LB@ \| \|@LB@5'-UGU...CUCGA GACAC...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -13.6251 kcal/mol@LB@Unfolding Energy - mRNA 1.75344 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 40 -- 46@LB@
43	0.00107	0.08759	b4036	lamB	-10.48	0.202041	185 -- 197	39 -- 51	maltose outer membrane porin (maltoporin)		_____________184___________198\n_____________\|_____________\|\n5'-CGC...AGCAA_G_______A___AGAAU...GUU-3'\n______________U_ACUCAGG_GAU\n______________\|_\|\|\|\|\|\|\|_\|\|\|\n______________A_UGAGUCC_CUA\n3'-UUU...AACAA_G_______C___AAGGU...GCA-5'\n_____________\|_____________\|\n_____________52____________38\n	187 -- 193	43 -- 49	-14.6452 kcal/mol	2.36402 kcal/mol	1.79807 kcal/mol	184 198@LB@ \| \|@LB@5'-CGC...AGCAA G A AGAAU...GUU-3'@LB@ U ACUCAGG GAU@LB@ \| \|\|\|\|\|\|\| \|\|\|@LB@ A UGAGUCC CUA@LB@3'-UUU...AACAA G C AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -14.6452 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
145	0.006641	0.1605	b3316	rpsS	-10.41	0.208024	125 -- 141	61 -- 77	30S ribosomal subunit protein S19		_____________124_______________142\n_____________\|_________________\|\n5'-GCG...AAGGU____AG__C________CAAGC...CUU-3'\n______________AAGA__AC_CGCAGCAA\n______________\|\|\|\|__\|\|_\|:\|\|\|\|\|\|\n______________UUCU__UG_GUGUCGUU\n3'-UUU...CCCGU____GA__U________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________78________________60\n	135 -- 141	61 -- 67	-16.0034 kcal/mol	2.33428 kcal/mol	3.25748 kcal/mol	124 142@LB@ \| \|@LB@5'-GCG...AAGGU AG C CAAGC...CUU-3'@LB@ AAGA AC CGCAGCAA@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ UUCU UG GUGUCGUU@LB@3'-UUU...CCCGU GA U AAGCA...GCA-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -16.0034 kcal/mol@LB@Unfolding Energy - mRNA 2.33428 kcal/mol@LB@Unfolding Energy - sRNA 3.25748 kcal/mol@LB@@LB@Position - mRNA 125 -- 141@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 61 -- 67@LB@
122	0.005462	0.1553	b3143	yraI	-10.36	0.212908	69 -- 81	40 -- 51	putative periplasmic pilin chaperone	b0939 b4316 b0531	_____________68____________82\n_____________\|_____________\|\n5'-GGA...AGAAA____CC_______AGCAG...UGA-3'\n______________UCAC__CAGGGGA\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________AGUG__GUCCCCU\n3'-UUU...AACAA____A________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	75 -- 81	40 -- 46	-16.6795 kcal/mol	4.56539 kcal/mol	1.76028 kcal/mol	68 82@LB@ \| \|@LB@5'-GGA...AGAAA CC AGCAG...UGA-3'@LB@ UCAC CAGGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG GUCCCCU@LB@3'-UUU...AACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.6795 kcal/mol@LB@Unfolding Energy - mRNA 4.56539 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 40 -- 46@LB@
55	0.001955	0.1223	b0840	deoR	-10.34	0.214583	216 -- 260	60 -- 103	deoxyribose-5-phosphate-inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx		_____________215____________________________________________261\n_____________\|______________________________________________\|\n5'-GUG...GUCGC_______G________C__C__CU_____A____AA__________AAGUU...UUU-3'\n______________GAAGAGC_UAUCG_GG_AG_UG__GCAAG_AUUA__ACGCAGCGAU\n______________:\|\|:\|\|\|_:\|\|\|\|_\|\|_\|\|_\|\|__\|\|\|\|:_\|:\|\|__\|\|:\|\|\|\|:\|\|\n______________UUUUUCG_GUAGC_CC_UC_AC__CGUUU_UGAU__UGUGUCGUUA\n_________3'-UU_______G_____A__C__U__C______C____G___________AGCAA...GCA-5'\n_____________\|______________________________________________\|\n_____________104____________________________________________59\n	254 -- 260	60 -- 66	-39.4084 kcal/mol	12.9673 kcal/mol	16.1071 kcal/mol	215 261@LB@ \| \|@LB@5'-GUG...GUCGC G C C CU A AA AAGUU...UUU-3'@LB@ GAAGAGC UAUCG GG AG UG GCAAG AUUA ACGCAGCGAU@LB@ :\|\|:\|\|\| :\|\|\|\| \|\| \|\| \|\| \|\|\|\|: \|:\|\| \|\|:\|\|\|\|:\|\|@LB@ UUUUUCG GUAGC CC UC AC CGUUU UGAU UGUGUCGUUA@LB@ 3'-UU G A C U C C G AGCAA...GCA-5'@LB@ \| \|@LB@ 104 59@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -39.4084 kcal/mol@LB@Unfolding Energy - mRNA 12.9673 kcal/mol@LB@Unfolding Energy - sRNA 16.1071 kcal/mol@LB@@LB@Position - mRNA 216 -- 260@LB@Position - sRNA 60 -- 103@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 60 -- 66@LB@
64	0.002655	0.1417	b0876	ybjD	-10.33	0.215429	171 -- 200	39 -- 78	putative OLD family ATP-dependent endonuclease; DUF2813 family protein		_____________170________________________________________201\n_____________\|__________________________________________\|\n5'-CGU...GCGUA______AAGU_____________________UGG________AUGAU...GGG-3'\n______________AAGGAU____CACAUA___________UUUC____AGGGGAU\n______________\|\|:\|\|:____\|\|\|\|:\|___________\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUG____GUGUGU___________AAAG____UCCCCUA\n3'-UUU...ACCCG______AU________CGUUAAGCAAC____UGAG_______AAGGU...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________38\n	194 -- 200	39 -- 45	-20.0974 kcal/mol	4.99339 kcal/mol	4.77966 kcal/mol	170 201@LB@ \| \|@LB@5'-CGU...GCGUA AAGU UGG AUGAU...GGG-3'@LB@ AAGGAU CACAUA UUUC AGGGGAU@LB@ \|\|:\|\|: \|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUG GUGUGU AAAG UCCCCUA@LB@3'-UUU...ACCCG AU CGUUAAGCAAC UGAG AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -20.0974 kcal/mol@LB@Unfolding Energy - mRNA 4.99339 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 171 -- 200@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 39 -- 45@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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