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
15	0.0001044	0.0245	b0741	pal	-16.61	0.007509	30 -- 75	30 -- 71	peptidoglycan-associated outer membrane lipoprotein	_____________29_____________________________________________76\n_____________\|______________________________________________\|\n5'-GGA...UAACG____U________CUACAGCUCUU__________GGGA________GAAUU...GCG-3'\n______________GCAC_AUGGUAAU___________CUCAGGGGAU____UCCGUGCU\n______________:\|\|\|_\|::\|:\|\|\|___________\|\|\|\|\|\|\|\|\|\|____\|\|\|:\|\|\|\|\n______________UGUG_UGUCGUUA___________GAGUCCCCUA____AGGUACGA\n3'-UUU...UCUGA_____________AGCAACAAAGU__________A___________AUAUU...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________29\n	69 -- 75	30 -- 36	-38.4662 kcal/mol	13.7923 kcal/mol	8.066 kcal/mol	29 76@LB@ \| \|@LB@5'-GGA...UAACG U CUACAGCUCUU GGGA GAAUU...GCG-3'@LB@ GCAC AUGGUAAU CUCAGGGGAU UCCGUGCU@LB@ :\|\|\| \|::\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|@LB@ UGUG UGUCGUUA GAGUCCCCUA AGGUACGA@LB@3'-UUU...UCUGA AGCAACAAAGU A AUAUU...GCA-5'@LB@ \| \|@LB@ 72 29@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -38.4662 kcal/mol@LB@Unfolding Energy - mRNA 13.7923 kcal/mol@LB@Unfolding Energy - sRNA 8.066 kcal/mol@LB@@LB@Position - mRNA 30 -- 75@LB@Position - sRNA 30 -- 71@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 30 -- 36@LB@
111	0.004903	0.1545	b1735	chbR	-11.17	0.151186	109 -- 138	30 -- 50	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________108____________________________139\n_____________\|______________________________\|\n5'-GAU...GUCCA________AUCAUUUAAU__CG________UGCGC...CUG-3'\n______________CGCUCAGG__________GA__UCCAUGCU\n______________\|:\|\|\|\|\|\|__________\|\|__\|\|\|\|\|\|\|\|\n______________GUGAGUCC__________CU__AGGUACGA\n3'-UUU...ACAAA________C___________AA________AUAUU...GCA-5'\n_____________\|______________________________\|\n_____________51_____________________________29\n	132 -- 138	30 -- 36	-23.5874 kcal/mol	7.28235 kcal/mol	5.13509 kcal/mol	108 139@LB@ \| \|@LB@5'-GAU...GUCCA AUCAUUUAAU CG UGCGC...CUG-3'@LB@ CGCUCAGG GA UCCAUGCU@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GUGAGUCC CU AGGUACGA@LB@3'-UUU...ACAAA C AA AUAUU...GCA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.5874 kcal/mol@LB@Unfolding Energy - mRNA 7.28235 kcal/mol@LB@Unfolding Energy - sRNA 5.13509 kcal/mol@LB@@LB@Position - mRNA 109 -- 138@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 30 -- 36@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@
178	0.008884	0.1747	b0051	rsmA	-9.94	0.250586	2 -- 32	30 -- 58	16S rRNA m(6)A1518 m(6)A1519 dimethyltransferase SAM-dependent	_____________1_______________________________33\n_____________\|_______________________________\|\n__________5'-G__A___AC___GA______UC__C_______AAAAU...UUA-3'\n______________CG_UGU__CAC__UCAGGG__UU_CCGUGCU\n______________\|\|_\|\|\|__\|\|\|__\|\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\n______________GC_ACA__GUG__AGUCCC__AA_GGUACGA\n3'-UUU...GUUAA__A___AA___________CU__A_______AUAUU...GCA-5'\n_____________\|_______________________________\|\n_____________59______________________________29\n	26 -- 32	30 -- 36	-26.3106 kcal/mol	10.5715 kcal/mol	5.79877 kcal/mol	1 33@LB@ \| \|@LB@ 5'-G A AC GA UC C AAAAU...UUA-3'@LB@ CG UGU CAC UCAGGG UU CCGUGCU@LB@ \|\| \|\|\| \|\|\| \|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ GC ACA GUG AGUCCC AA GGUACGA@LB@3'-UUU...GUUAA A AA CU A AUAUU...GCA-5'@LB@ \| \|@LB@ 59 29@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -26.3106 kcal/mol@LB@Unfolding Energy - mRNA 10.5715 kcal/mol@LB@Unfolding Energy - sRNA 5.79877 kcal/mol@LB@@LB@Position - mRNA 2 -- 32@LB@Position - sRNA 30 -- 58@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 30 -- 36@LB@
5	9.512e-06	0.006694	b4006	purH	-17.40	0.004319	188 -- 204	31 -- 46	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase	_____________187_______________205\n_____________\|_________________\|\n5'-GUA...AAAUC__________A______AACAA...AGC-3'\n______________CAGGGGAUUU_CCAUGC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GUCCCCUAAA_GGUACG\n3'-UUU...AGUGA_________________AAUAU...GCA-5'\n_____________\|_________________\|\n_____________47________________30\n	191 -- 197	37 -- 43	-27.6893 kcal/mol	6.33421 kcal/mol	3.95768 kcal/mol	187 205@LB@ \| \|@LB@5'-GUA...AAAUC A AACAA...AGC-3'@LB@ CAGGGGAUUU CCAUGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCCCCUAAA GGUACG@LB@3'-UUU...AGUGA AAUAU...GCA-5'@LB@ \| \|@LB@ 47 30@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -27.6893 kcal/mol@LB@Unfolding Energy - mRNA 6.33421 kcal/mol@LB@Unfolding Energy - sRNA 3.95768 kcal/mol@LB@@LB@Position - mRNA 188 -- 204@LB@Position - sRNA 31 -- 46@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
18	0.0001516	0.02826	b2817	amiC	-14.62	0.026197	167 -- 204	31 -- 70	N-acetylmuramoyl-L-alanine amidase	_____________166______________________________________205\n_____________\|________________________________________\|\n5'-AGU...CUUGU________UUAGAUUUC___________A__GG_______CAGGA...UCA-3'\n______________UACACAGC_________UUUUGCUCGGG_GA____CAUGU\n______________:\|\|\|\|\|\|\|_________\|\|\|::\|\|\|:\|\|_\|\|____\|\|\|\|:\n______________GUGUGUCG_________AAAGUGAGUCC_CU____GUACG\n3'-UUU...CUGAU________UUAAGCAAC___________C__AAAG_____AAUAU...GCA-5'\n_____________\|________________________________________\|\n_____________71_______________________________________30\n	188 -- 194	43 -- 49	-32.0387 kcal/mol	10.1821 kcal/mol	7.23824 kcal/mol	166 205@LB@ \| \|@LB@5'-AGU...CUUGU UUAGAUUUC A GG CAGGA...UCA-3'@LB@ UACACAGC UUUUGCUCGGG GA CAUGU@LB@ :\|\|\|\|\|\|\| \|\|\|::\|\|\|:\|\| \|\| \|\|\|\|:@LB@ GUGUGUCG AAAGUGAGUCC CU GUACG@LB@3'-UUU...CUGAU UUAAGCAAC C AAAG AAUAU...GCA-5'@LB@ \| \|@LB@ 71 30@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -32.0387 kcal/mol@LB@Unfolding Energy - mRNA 10.1821 kcal/mol@LB@Unfolding Energy - sRNA 7.23824 kcal/mol@LB@@LB@Position - mRNA 167 -- 204@LB@Position - sRNA 31 -- 70@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
49	0.00161	0.1153	b0655	gltI	-14.54	0.027470	112 -- 169	31 -- 74	glutamate/aspartate periplasmic binding protein	_____________111________________________________________________________170\n_____________\|__________________________________________________________\|\n5'-AUU...ACAAC_______AAUAAAGUU____A____AACAACACAAA______CAAC____A_______GUUCU...UGG-3'\n______________ACUGCAC_________GCAG_CGAU___________CACUCA____GGGU_UCCAUGC\n______________\|\|\|:\|\|\|_________:\|\|\|_\|:\|\|___________\|\|\|\|\|\|____\|\|:\|_\|\|\|\|\|\|\|\n______________UGAUGUG_________UGUC_GUUA___________GUGAGU____CCUA_AGGUACG\n3'-UUU...GUUUC_________________________AGCAACAAA________CC______A_______AAUAU...GCA-5'\n_____________\|__________________________________________________________\|\n_____________75_________________________________________________________30\n	163 -- 169	31 -- 37	-33.5884 kcal/mol	11.7902 kcal/mol	7.26183 kcal/mol	111 170@LB@ \| \|@LB@5'-AUU...ACAAC AAUAAAGUU A AACAACACAAA CAAC A GUUCU...UGG-3'@LB@ ACUGCAC GCAG CGAU CACUCA GGGU UCCAUGC@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\| \|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|@LB@ UGAUGUG UGUC GUUA GUGAGU CCUA AGGUACG@LB@3'-UUU...GUUUC AGCAACAAA CC A AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -33.5884 kcal/mol@LB@Unfolding Energy - mRNA 11.7902 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 112 -- 169@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 31 -- 37@LB@
51	0.001671	0.1153	b3527	yhjJ	-13.34	0.053290	153 -- 204	31 -- 75	putative periplasmic M16 family chaperone	_____________152_____________________________________________________205\n_____________\|_______________________________________________________\|\n5'-CUC...UGACC___A___G_____UU___UAUUACCAGGAUA___GA____________CA_____AGGGC...GGC-3'\n______________GAC_ACG_GCAGU__UUU_____________GUU____UCAGGGG_UU__CAUGC\n______________\|\|\|_\|\|:_:\|\|\|:__\|\|:_____________\|\|\|____\|\|\|\|\|\|\|_\|\|__\|\|\|\|\|\n______________CUG_UGU_UGUCG__AAG_____________CAA____AGUCCCC_AA__GUACG\n3'-UUU...CGUUU___A___G_____UU___CAA_____________AGUG_______U__AG_____AAUAU...GCA-5'\n_____________\|_______________________________________________________\|\n_____________76______________________________________________________30\n	189 -- 195	41 -- 47	-32.6504 kcal/mol	12.0549 kcal/mol	7.26183 kcal/mol	152 205@LB@ \| \|@LB@5'-CUC...UGACC A G UU UAUUACCAGGAUA GA CA AGGGC...GGC-3'@LB@ GAC ACG GCAGU UUU GUU UCAGGGG UU CAUGC@LB@ \|\|\| \|\|: :\|\|\|: \|\|: \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ CUG UGU UGUCG AAG CAA AGUCCCC AA GUACG@LB@3'-UUU...CGUUU A G UU CAA AGUG U AG AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -32.6504 kcal/mol@LB@Unfolding Energy - mRNA 12.0549 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 153 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 41 -- 47@LB@
70	0.002881	0.1417	b4144	yjeI	-14.17	0.033933	177 -- 235	31 -- 99	DUF4156 family lipoprotein	_____________176______________________________________________________________________236\n_____________\|________________________________________________________________________\|\n5'-GCA...CGUCC_________AUU________G__UA______________AA_______________CA______G__G____CGCGC...GCA-3'\n______________AGCUCAUUG______AUGGG_AA__AC_AUGCAC_GUAA__________UACUUAG__GGGAUU_UC_GUGC\n______________\|\|\|:\|\|\|:\|______\|\|\|\|\|_\|\|__\|\|_\|::\|\|\|_\|:\|\|__________:\|\|\|:\|\|__\|\|\|\|\|\|_\|\|_:\|\|\|\n______________UCGGGUAGC______UACCC_UU__UG_UGUGUG_CGUU__________GUGAGUC__CCCUAA_AG_UACG\n_____3'-UUUUUU_________ACCCUC_____G__UC__A______U____AAGCAACAAA__________________G____AAUAU...GCA-5'\n_____________\|________________________________________________________________________\|\n_____________100______________________________________________________________________30\n	213 -- 219	44 -- 50	-46.9384 kcal/mol	12.7048 kcal/mol	20.0691 kcal/mol	176 236@LB@ \| \|@LB@5'-GCA...CGUCC AUU G UA AA CA G G CGCGC...GCA-3'@LB@ AGCUCAUUG AUGGG AA AC AUGCAC GUAA UACUUAG GGGAUU UC GUGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\| \|\| \|::\|\|\| \|:\|\| :\|\|\|:\|\| \|\|\|\|\|\| \|\| :\|\|\|@LB@ UCGGGUAGC UACCC UU UG UGUGUG CGUU GUGAGUC CCCUAA AG UACG@LB@ 3'-UUUUUU ACCCUC G UC A U AAGCAACAAA G AAUAU...GCA-5'@LB@ \| \|@LB@ 100 30@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -46.9384 kcal/mol@LB@Unfolding Energy - mRNA 12.7048 kcal/mol@LB@Unfolding Energy - sRNA 20.0691 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 31 -- 99@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 44 -- 50@LB@
80	0.003376	0.1462	b3098	yqjD	-10.12	0.233597	155 -- 204	31 -- 75	membrane-anchored ribosome-binding protein	_____________154_________________________________________________205\n_____________\|___________________________________________________\|\n5'-UCA...CGCGC______UA__UCA____A___CACUAC_______CCU__A__AAA______CGAAA...AAG-3'\n______________GACUAC__AC___CAAU__GU______UUACUCA___GG_GA___CUAUGU\n______________\|\|\|\|\|\|__\|\|___\|\|\|\|__\|\|______\|:\|\|\|\|\|___\|\|_\|\|___\|:\|\|\|:\n______________CUGAUG__UG___GUUA__CA______AGUGAGU___CC_CU___GGUACG\n3'-UUU...CGUUU______UG__UC_____AG__ACAA_________C_______AAA______AAUAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________76__________________________________________________30\n	181 -- 187	45 -- 51	-24.4421 kcal/mol	7.05998 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UCA...CGCGC UA UCA A CACUAC CCU A AAA CGAAA...AAG-3'@LB@ GACUAC AC CAAU GU UUACUCA GG GA CUAUGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|:\|\|\|\|\| \|\| \|\| \|:\|\|\|:@LB@ CUGAUG UG GUUA CA AGUGAGU CC CU GGUACG@LB@3'-UUU...CGUUU UG UC AG ACAA C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -24.4421 kcal/mol@LB@Unfolding Energy - mRNA 7.05998 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 181 -- 187@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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