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
116	0.005119	0.155	b2513	yfgM	-8.84	0.371642	84 -- 101	60 -- 75	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________83_________________102\n_____________\|__________________\|\n5'-GGC...GAAGU_____ACG__________AGUGA...UUG-3'\n______________GGCUA___GCACAGCAGU\n______________\|:\|\|\|___:\|\|\|\|\|\|\|:\|\n______________CUGAU___UGUGUCGUUA\n3'-UUU...CGUUU_____G____________AGCAA...GCA-5'\n_____________\|__________________\|\n_____________76_________________59\n	95 -- 101	60 -- 66	-19.484 kcal/mol	7.35825 kcal/mol	3.28851 kcal/mol	83 102@LB@ \| \|@LB@5'-GGC...GAAGU ACG AGUGA...UUG-3'@LB@ GGCUA GCACAGCAGU@LB@ \|:\|\|\| :\|\|\|\|\|\|\|:\|@LB@ CUGAU UGUGUCGUUA@LB@3'-UUU...CGUUU G AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -19.484 kcal/mol@LB@Unfolding Energy - mRNA 7.35825 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 84 -- 101@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 60 -- 66@LB@
141	0.006483	0.1605	b2474	tmcA	-12.94	0.065378	86 -- 105	35 -- 54	elongator methionine tRNA (ac4C34) acetyltransferase	_____________85___________________106\n_____________\|____________________\|\n5'-GAU...AGACA__________U__CAC____CAGCA...UUG-3'\n______________GUUUCACUCA_GG___UUCU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|:\n______________CAAAGUGAGU_CC___AAGG\n3'-UUU...AGCAA__________C__CUA____UACGA...GCA-5'\n_____________\|____________________\|\n_____________55___________________34\n	89 -- 95	45 -- 51	-18.4772 kcal/mol	3.58569 kcal/mol	1.95269 kcal/mol	85 106@LB@ \| \|@LB@5'-GAU...AGACA U CAC CAGCA...UUG-3'@LB@ GUUUCACUCA GG UUCU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ CAAAGUGAGU CC AAGG@LB@3'-UUU...AGCAA C CUA UACGA...GCA-5'@LB@ \| \|@LB@ 55 34@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -18.4772 kcal/mol@LB@Unfolding Energy - mRNA 3.58569 kcal/mol@LB@Unfolding Energy - sRNA 1.95269 kcal/mol@LB@@LB@Position - mRNA 86 -- 105@LB@Position - sRNA 35 -- 54@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 45 -- 51@LB@
48	0.001595	0.1153	b4567	yjjZ	-9.54	0.291590	92 -- 131	37 -- 74	uncharacterized protein	_____________91_______________________________________132\n_____________\|________________________________________\|\n5'-CGG...UGAUU____AU_________AG___UACC__AUAG__A_______AUCUG...GGA-3'\n______________GCUA__CAUAGCGAU__GUU____CG____CA_GGGAUUU\n______________:\|\|\|__\|\|:\|\|\|:\|\|__\|\|\|____\|:____\|\|_\|\|\|\|\|\|\|\n______________UGAU__GUGUCGUUA__CAA____GU____GU_CCCUAAA\n3'-UUU...GUUUC____GU_________AG___CAAA__GA____C_______GGUAC...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________36\n	125 -- 131	37 -- 43	-26.8907 kcal/mol	12.5776 kcal/mol	4.77887 kcal/mol	91 132@LB@ \| \|@LB@5'-CGG...UGAUU AU AG UACC AUAG A AUCUG...GGA-3'@LB@ GCUA CAUAGCGAU GUU CG CA GGGAUUU@LB@ :\|\|\| \|\|:\|\|\|:\|\| \|\|\| \|: \|\| \|\|\|\|\|\|\|@LB@ UGAU GUGUCGUUA CAA GU GU CCCUAAA@LB@3'-UUU...GUUUC GU AG CAAA GA C GGUAC...GCA-5'@LB@ \| \|@LB@ 75 36@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -26.8907 kcal/mol@LB@Unfolding Energy - mRNA 12.5776 kcal/mol@LB@Unfolding Energy - sRNA 4.77887 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 37 -- 74@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 37 -- 43@LB@
86	0.003687	0.1509	b0774	bioA	-10.95	0.166636	92 -- 152	44 -- 98	7 8-diaminopelargonic acid synthase PLP-dependent	_____________91_____________________________________________________________153\n_____________\|______________________________________________________________\|\n5'-ACG...ACAAU_____G______C____A__CAU______UCUCCAAA___U__UU_________A_______UGUAG...AAG-3'\n______________GUCCA_CGUGGG_GGUG_GC___GGGGCU________ACG_GU__UUUGUUGUU__AUUCGG\n______________\|:\|\|\|_\|\|\|\|\|\|_\|:\|\|_\|\|___::\|:\|\|________\|\|:_\|:__\|\|:\|\|\|\|\|\|__\|:\|\|:\|\n______________CGGGU_GCACCC_CUAC_CG___UUCUGA________UGU_CG__AAGCAACAA__UGAGUC\n____3'-UUUUUUU_____A______U____C__U________UGUG__________UU_________AG______CCCUA...GCA-5'\n_____________\|______________________________________________________________\|\n_____________99_____________________________________________________________43\n	139 -- 145	52 -- 58	-48.0349 kcal/mol	20.1482 kcal/mol	16.9429 kcal/mol	91 153@LB@ \| \|@LB@5'-ACG...ACAAU G C A CAU UCUCCAAA U UU A UGUAG...AAG-3'@LB@ GUCCA CGUGGG GGUG GC GGGGCU ACG GU UUUGUUGUU AUUCGG@LB@ \|:\|\|\| \|\|\|\|\|\| \|:\|\| \|\| ::\|:\|\| \|\|: \|: \|\|:\|\|\|\|\|\| \|:\|\|:\|@LB@ CGGGU GCACCC CUAC CG UUCUGA UGU CG AAGCAACAA UGAGUC@LB@ 3'-UUUUUUU A U C U UGUG UU AG CCCUA...GCA-5'@LB@ \| \|@LB@ 99 43@LB@@LB@@LB@Energy -10.95 kcal/mol@LB@Hybridization Energy -48.0349 kcal/mol@LB@Unfolding Energy - mRNA 20.1482 kcal/mol@LB@Unfolding Energy - sRNA 16.9429 kcal/mol@LB@@LB@Position - mRNA 92 -- 152@LB@Position - sRNA 44 -- 98@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 52 -- 58@LB@
130	0.005881	0.1577	b0965	yccU	-10.68	0.186123	93 -- 125	46 -- 74	putative CoA-binding protein	_____________92________________________________126\n_____________\|_________________________________\|\n5'-UCA...UACUU___A________A__UAU___CCGC________UCAUU...UGA-3'\n______________ACU_ACAUAUAG_CA___UUC____UUUUGCUC\n______________\|\|\|_\|\|\|:\|:\|\|_\|\|___\|\|\|____\|\|\|::\|\|\|\n______________UGA_UGUGUGUC_GU___AAG____AAAGUGAG\n3'-UUU...GUUUC_______________U_____CAAC________UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________45\n	119 -- 125	46 -- 52	-18.0647 kcal/mol	3.65669 kcal/mol	3.72594 kcal/mol	92 126@LB@ \| \|@LB@5'-UCA...UACUU A A UAU CCGC UCAUU...UGA-3'@LB@ ACU ACAUAUAG CA UUC UUUUGCUC@LB@ \|\|\| \|\|\|:\|:\|\| \|\| \|\|\| \|\|\|::\|\|\|@LB@ UGA UGUGUGUC GU AAG AAAGUGAG@LB@3'-UUU...GUUUC U CAAC UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.0647 kcal/mol@LB@Unfolding Energy - mRNA 3.65669 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 93 -- 125@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 46 -- 52@LB@
146	0.006661	0.1605	b4479	dgoR	-11.67	0.120911	94 -- 106	61 -- 74	D-galactonate catabolism operon transcriptional repressor	_____________93_____________107\n_____________\|______________\|\n5'-UUU...ACAUU______________ACGCG...AAC-3'\n______________AC_ACGCACGGCAA\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\n______________UG_UGUGUGUCGUU\n3'-UUU...GUUUC__A___________AAGCA...GCA-5'\n_____________\|______________\|\n_____________75_____________60\n	100 -- 106	61 -- 67	-16.8512 kcal/mol	1.93692 kcal/mol	3.24589 kcal/mol	93 107@LB@ \| \|@LB@5'-UUU...ACAUU ACGCG...AAC-3'@LB@ AC ACGCACGGCAA@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ UG UGUGUGUCGUU@LB@3'-UUU...GUUUC A AAGCA...GCA-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -16.8512 kcal/mol@LB@Unfolding Energy - mRNA 1.93692 kcal/mol@LB@Unfolding Energy - sRNA 3.24589 kcal/mol@LB@@LB@Position - mRNA 94 -- 106@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 61 -- 67@LB@
44	0.001243	0.09943	b3064	tsaD	-15.06	0.020167	98 -- 131	41 -- 82	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein	_____________97___________________________________________132\n_____________\|____________________________________________\|\n5'-CAU...UAUAA_________G_______GA________________U________CGAAC...UGA-3'\n______________GGGUGAGGA_UAUACAC__GGC_________UUUC_C_CAGGGG\n______________\|\|\|::\|:\|\|_\|\|:\|\|\|\|__:\|\|_________\|\|\|\|_\|_\|\|\|\|\|\|\n______________CCCGUUUCU_AUGUGUG__UCG_________AAAG_G_GUCCCC\n3'-UUU...CUCUA_________G____________UUAAGCAAC____U_A______UAAAG...GCA-5'\n_____________\|____________________________________________\|\n_____________83___________________________________________40\n	108 -- 114	66 -- 72	-38.4936 kcal/mol	9.4641 kcal/mol	13.9685 kcal/mol	97 132@LB@ \| \|@LB@5'-CAU...UAUAA G GA U CGAAC...UGA-3'@LB@ GGGUGAGGA UAUACAC GGC UUUC C CAGGGG@LB@ \|\|\|::\|:\|\| \|\|:\|\|\|\| :\|\| \|\|\|\| \| \|\|\|\|\|\|@LB@ CCCGUUUCU AUGUGUG UCG AAAG G GUCCCC@LB@3'-UUU...CUCUA G UUAAGCAAC U A UAAAG...GCA-5'@LB@ \| \|@LB@ 83 40@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -38.4936 kcal/mol@LB@Unfolding Energy - mRNA 9.4641 kcal/mol@LB@Unfolding Energy - sRNA 13.9685 kcal/mol@LB@@LB@Position - mRNA 98 -- 131@LB@Position - sRNA 41 -- 82@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 66 -- 72@LB@
54	0.00187	0.1218	b3607	cysE	-14.87	0.022582	98 -- 129	42 -- 78	serine acetyltransferase	_____________97_________________________________________130\n_____________\|__________________________________________\|\n5'-CGG...CACGC______GA__________C_____________AACCC_____AACCU...CGA-3'\n______________AAGGAC___GCGCAGCAG__________CACU_____CAGGG\n______________\|\|:\|\|\|___:\|:\|\|\|\|\|:__________\|\|\|\|_____\|\|\|\|\|\n______________UUUCUG___UGUGUCGUU__________GUGA_____GUCCC\n3'-UUU...ACCCG______AUG_________AAGCAACAAA______________CUAAA...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________41\n	108 -- 114	61 -- 67	-27.0645 kcal/mol	7.42824 kcal/mol	4.76487 kcal/mol	97 130@LB@ \| \|@LB@5'-CGG...CACGC GA C AACCC AACCU...CGA-3'@LB@ AAGGAC GCGCAGCAG CACU CAGGG@LB@ \|\|:\|\|\| :\|:\|\|\|\|\|: \|\|\|\| \|\|\|\|\|@LB@ UUUCUG UGUGUCGUU GUGA GUCCC@LB@3'-UUU...ACCCG AUG AAGCAACAAA CUAAA...GCA-5'@LB@ \| \|@LB@ 79 41@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0645 kcal/mol@LB@Unfolding Energy - mRNA 7.42824 kcal/mol@LB@Unfolding Energy - sRNA 4.76487 kcal/mol@LB@@LB@Position - mRNA 98 -- 129@LB@Position - sRNA 42 -- 78@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 61 -- 67@LB@
194	0.009812	0.1776	b2687	luxS	-7.90	0.495572	99 -- 106	42 -- 49	S-ribosylhomocysteine lyase	_____________98_______107\n_____________\|________\|\n5'-GAA...UCUGA________AUGAU...UCA-3'\n______________AUUCAGGG\n______________\|:\|\|\|\|\|\|\n______________UGAGUCCC\n3'-UUU...CAAAG________CUAAA...GCA-5'\n_____________\|________\|\n_____________50_______41\n	100 -- 106	42 -- 48	-12.5942 kcal/mol	3.05922 kcal/mol	1.63991 kcal/mol	98 107@LB@ \| \|@LB@5'-GAA...UCUGA AUGAU...UCA-3'@LB@ AUUCAGGG@LB@ \|:\|\|\|\|\|\|@LB@ UGAGUCCC@LB@3'-UUU...CAAAG CUAAA...GCA-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -12.5942 kcal/mol@LB@Unfolding Energy - mRNA 3.05922 kcal/mol@LB@Unfolding Energy - sRNA 1.63991 kcal/mol@LB@@LB@Position - mRNA 99 -- 106@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 42 -- 48@LB@
120	0.005393	0.1553	b0523	purE	-13.83	0.040764	102 -- 146	30 -- 75	N5-carboxyaminoimidazole ribonucleotide mutase	_____________101________________________________________________147\n_____________\|__________________________________________________\|\n5'-UGG...UUGCU____U____GC__C____C_____UUCC______UC______________AUUCU...UGA-3'\n______________GAUU_CACA__CA_GCAA__CGUU____UUGCUC______UUUCCGUGCU\n______________\|\|:\|_\|\|\|\|__\|\|_\|\|\|\|__\|\|\|\|____\|::\|\|\|______\|\|\|\|\|:\|\|\|\|\n______________CUGA_GUGU__GU_CGUU__GCAA____AGUGAG______AAAGGUACGA\n3'-UUU...CGUUU____U_____________AA____CAA_______UCCCCU__________AUAUU...GCA-5'\n_____________\|__________________________________________________\|\n_____________76_________________________________________________29\n	140 -- 146	30 -- 36	-29.2897 kcal/mol	7.36654 kcal/mol	8.08958 kcal/mol	101 147@LB@ \| \|@LB@5'-UGG...UUGCU U GC C C UUCC UC AUUCU...UGA-3'@LB@ GAUU CACA CA GCAA CGUU UUGCUC UUUCCGUGCU@LB@ \|\|:\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|::\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGA GUGU GU CGUU GCAA AGUGAG AAAGGUACGA@LB@3'-UUU...CGUUU U AA CAA UCCCCU AUAUU...GCA-5'@LB@ \| \|@LB@ 76 29@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -29.2897 kcal/mol@LB@Unfolding Energy - mRNA 7.36654 kcal/mol@LB@Unfolding Energy - sRNA 8.08958 kcal/mol@LB@@LB@Position - mRNA 102 -- 146@LB@Position - sRNA 30 -- 75@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 30 -- 36@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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service.

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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