Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
151	0.01691	0.3749	b2442	intZ	-12.49	0.088679	278 -- 291	17 -- 31	CPZ-55 prophage; putative phage integrase	b2349	_____________277_________________292\n_____________\|___________________\|\n5'-ACA...AAACU____________C_G____CGGGG...UGC-3'\n______________CACCGAU__UCA_U_ACGC\n______________\|\|\|\|:\|\|__\|\|\|_\|_\|\|:\|\n______________GUGGUUA__AGU_A_UGUG\n3'-UUU...AAAAU_______UG___C_G____UACUA...UAG-5'\n_____________\|___________________\|\n_____________32__________________16\n	269 -- 275	180 -- 186	-14.1411 kcal/mol	1.5591 kcal/mol	4.88042 kcal/mol	277 292@LB@ \| \|@LB@5'-ACA...AAACU C G CGGGG...UGC-3'@LB@ CACCGAU UCA U ACGC@LB@ \|\|\|\|:\|\| \|\|\| \| \|\|:\|@LB@ GUGGUUA AGU A UGUG@LB@3'-UUU...AAAAU UG C G UACUA...UAG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -14.1411 kcal/mol@LB@Unfolding Energy - mRNA 1.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.88042 kcal/mol@LB@@LB@Position - mRNA 278 -- 291@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 180 -- 186@LB@
152	0.0171	0.3749	b3605	lldD	-10.23	0.248595	212 -- 221	68 -- 77	L-lactate dehydrogenase FMN-linked		_____________211_______222\n_____________\|_________\|\n5'-UUU...GAAAA_________UAUUU...ACA-3'\n______________ACGCAUGAU\n______________\|\|:\|\|\|\|\|\|\n______________UGUGUACUA\n3'-UUU...GUCAG_________CGUCC...UAG-5'\n_____________\|_________\|\n_____________78________67\n	199 -- 205	163 -- 169	-11.1438 kcal/mol	1.00002 kcal/mol	4.14962 kcal/mol	211 222@LB@ \| \|@LB@5'-UUU...GAAAA UAUUU...ACA-3'@LB@ ACGCAUGAU@LB@ \|\|:\|\|\|\|\|\|@LB@ UGUGUACUA@LB@3'-UUU...GUCAG CGUCC...UAG-5'@LB@ \| \|@LB@ 78 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -11.1438 kcal/mol@LB@Unfolding Energy - mRNA 1.00002 kcal/mol@LB@Unfolding Energy - sRNA 4.14962 kcal/mol@LB@@LB@Position - mRNA 212 -- 221@LB@Position - sRNA 68 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit		_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
154	0.01719	0.3749	b3726	pstA	-9.04	0.409183	290 -- 297	24 -- 31	phosphate ABC transporter permease		_____________289____________298\n_____________\|______________\|\n5'-CAG...CCGUA_________C____U-3'\n______________UUGCGCUGA_GCUC\n______________\|\|:\|:\|::\|_:\|\|\|\n______________AAUGUGGUU_UGAG\n3'-UUU...ACUAA_________A____UCAGU...UAG-5'\n_____________\|______________\|\n_____________32_____________23\n	288 -- 294	181 -- 187	-13.2096 kcal/mol	2.6708 kcal/mol	3.40409 kcal/mol	289 298@LB@ \| \|@LB@5'-CAG...CCGUA C U-3'@LB@ UUGCGCUGA GCUC@LB@ \|\|:\|:\|::\| :\|\|\|@LB@ AAUGUGGUU UGAG@LB@3'-UUU...ACUAA A UCAGU...UAG-5'@LB@ \| \|@LB@ 32 23@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.2096 kcal/mol@LB@Unfolding Energy - mRNA 2.6708 kcal/mol@LB@Unfolding Energy - sRNA 3.40409 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 24 -- 31@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 181 -- 187@LB@
155	0.01733	0.3749	b3542	dppC	-14.36	0.036537	40 -- 62	74 -- 93	dipeptide/heme ABC transporter permease		_____________39_______________________________________________________63\n_____________\|________________________________________________________\|\n5'-GGG...UCGUC____U__U___C__________UA___C_____GA_______C_____________AGAAG...UCG-3'\n______________AACU_GC_GGU__GAUCUGCUG__CGG_GUGGU___AC_CCG_GUAUUC_GUCAUA\n______________\|\|\|:_\|\|_\|\|\|__:\|\|\|\|\|\|\|\|__\|\|\|_\|\|\|:\|___\|\|_\|\|:_:\|\|:\|\|_\|\|\|\|:\|\n______________UUGG_CG_CCA__UUAGACGAC__GCC_CACUA___UG_GGU_UAUGAG_CAGUGU\n_____3'-UUUUUU____U__U___UA_________C__________AAA__U__________U______GUACU...UAG-5'\n_____________\|________________________________________________________\|\n_____________94_______________________________________________________73\n	146 -- 152	200 -- 206	-46.3163 kcal/mol	15.5571 kcal/mol	18.3074 kcal/mol	39 63@LB@ \| \|@LB@5'-GGG...UCGUC U U C UA C GA C AGAAG...UCG-3'@LB@ AACU GC GGU GAUCUGCUG CGG GUGGU AC CCG GUAUUC GUCAUA@LB@ \|\|\|: \|\| \|\|\| :\|\|\|\|\|\|\|\| \|\|\| \|\|\|:\| \|\| \|\|: :\|\|:\|\| \|\|\|\|:\|@LB@ UUGG CG CCA UUAGACGAC GCC CACUA UG GGU UAUGAG CAGUGU@LB@ 3'-UUUUUU U U UA C AAA U U GUACU...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -46.3163 kcal/mol@LB@Unfolding Energy - mRNA 15.5571 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 40 -- 62@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 200 -- 206@LB@
156	0.01739	0.3749	b4332	yjiJ	-7.83	0.625728	95 -- 115	80 -- 101	DUF1228 family putative inner membrane MFS superfamily transporter		_____________94_______116\n_____________\|________\|\n5'-AAC...GGUUU________ACAUC...UUU-3'\n______________GUCGCAUA\n______________\|\|\|:\|\|:\|\n______________CAGUGUGU\n3'-UUU...UGAGU________ACUAC...UAG-5'\n_____________\|________\|\n_____________102______79\n	23 -- 29	167 -- 173	-9.78459 kcal/mol	1.62979 kcal/mol	0.409692 kcal/mol	94 116@LB@ \| \|@LB@5'-AAC...GGUUU ACAUC...UUU-3'@LB@ GUCGCAUA@LB@ \|\|\|:\|\|:\|@LB@ CAGUGUGU@LB@3'-UUU...UGAGU ACUAC...UAG-5'@LB@ \| \|@LB@ 102 79@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -9.78459 kcal/mol@LB@Unfolding Energy - mRNA 1.62979 kcal/mol@LB@Unfolding Energy - sRNA 0.409692 kcal/mol@LB@@LB@Position - mRNA 95 -- 115@LB@Position - sRNA 80 -- 101@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 167 -- 173@LB@
157	0.01768	0.3749	b1216	chaA	-11.60	0.134178	242 -- 292	18 -- 65	calcium/sodium:proton antiporter		_____________241_______________293\n_____________\|_________________\|\n5'-AUU...AAUGU_________C___A___UUUCU...GCC-3'\n______________UACCGAUAU_CAG_CAC\n______________:\|\|\|:\|\|\|:_\|\|\|_\|\|\|\n______________GUGGUUAUG_GUC_GUG\n3'-UUU...AAAAU_________A___A___UGUAC...UAG-5'\n_____________\|_________________\|\n_____________66________________17\n	120 -- 126	178 -- 184	-16.2011 kcal/mol	3.68451 kcal/mol	4.86651 kcal/mol	241 293@LB@ \| \|@LB@5'-AUU...AAUGU C A UUUCU...GCC-3'@LB@ UACCGAUAU CAG CAC@LB@ :\|\|\|:\|\|\|: \|\|\| \|\|\|@LB@ GUGGUUAUG GUC GUG@LB@3'-UUU...AAAAU A A UGUAC...UAG-5'@LB@ \| \|@LB@ 66 17@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.2011 kcal/mol@LB@Unfolding Energy - mRNA 3.68451 kcal/mol@LB@Unfolding Energy - sRNA 4.86651 kcal/mol@LB@@LB@Position - mRNA 242 -- 292@LB@Position - sRNA 18 -- 65@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 178 -- 184@LB@
158	0.01775	0.3749	b1187	fadR	-13.89	0.045798	42 -- 66	152 -- 176	fatty acid metabolism regulon transcriptional regulator		_____________41________________________67\n_____________\|_________________________\|\n5'-AAA...CUUAA______G___G__GUG_________UUGAU...CAG-3'\n______________CGGUCA_GCA_GA___AGGCAAGUC\n______________\|:\|\|\|\|_:\|\|_\|\|___\|\|\|\|\|\|\|\|\|\n______________GUCAGU_UGU_CU___UCCGUUCAG\n3'-UUU...UAUGA______G___A__ACG_________UUGAA...UAG-5'\n_____________\|_________________________\|\n_____________177_______________________151\n	60 -- 66	152 -- 158	-31.5031 kcal/mol	7.04431 kcal/mol	8.02398 kcal/mol	41 67@LB@ \| \|@LB@5'-AAA...CUUAA G G GUG UUGAU...CAG-3'@LB@ CGGUCA GCA GA AGGCAAGUC@LB@ \|:\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ GUCAGU UGU CU UCCGUUCAG@LB@3'-UUU...UAUGA G A ACG UUGAA...UAG-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -13.89 kcal/mol@LB@Hybridization Energy -31.5031 kcal/mol@LB@Unfolding Energy - mRNA 7.04431 kcal/mol@LB@Unfolding Energy - sRNA 8.02398 kcal/mol@LB@@LB@Position - mRNA 42 -- 66@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 152 -- 158@LB@
159	0.01779	0.3749	b2504	yfgG	-11.18	0.162405	230 -- 250	168 -- 187	uncharacterized protein		_____________229___________________251\n_____________\|_____________________\|\n5'-CCU...AAACG________UUAA_________GACCC...UUA-3'\n______________ACACCGAU____CAGUCGCAU\n______________\|\|\|\|\|:\|\|____\|\|\|\|\|:\|\|:\n______________UGUGGUUA____GUCAGUGUG\n3'-UUU...UAAAA________UGA__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	244 -- 250	168 -- 174	-22.7597 kcal/mol	5.28018 kcal/mol	4.88067 kcal/mol	229 251@LB@ \| \|@LB@5'-CCU...AAACG UUAA GACCC...UUA-3'@LB@ ACACCGAU CAGUCGCAU@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|:\|\|:@LB@ UGUGGUUA GUCAGUGUG@LB@3'-UUU...UAAAA UGA UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -22.7597 kcal/mol@LB@Unfolding Energy - mRNA 5.28018 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 168 -- 174@LB@
160	0.01787	0.3749	b3935	priA	-8.27	0.542824	222 -- 250	110 -- 140	Primosome factor n' (replication factor Y)		_____________221_________________________251\n_____________\|___________________________\|\n5'-GAA...UAACC______AU___A_____G_________UAUGC...GCG-3'\n______________CACCGA__UUC_AGUCA_G_AUGAUGC\n______________\|\|\|\|:\|__:\|\|_\|\|\|\|\|_:_\|\|\|\|\|\|\|\n______________GUGGUU__GAG_UCAGU_U_UACUACG\n3'-UUU...AAAAU______AU_________G_G_______UCCGU...UAG-5'\n_____________\|___________________________\|\n_____________141_________________________109\n	193 -- 199	161 -- 167	-24.457 kcal/mol	4.47787 kcal/mol	7.72013 kcal/mol	221 251@LB@ \| \|@LB@5'-GAA...UAACC AU A G UAUGC...GCG-3'@LB@ CACCGA UUC AGUCA G AUGAUGC@LB@ \|\|\|\|:\| :\|\| \|\|\|\|\| : \|\|\|\|\|\|\|@LB@ GUGGUU GAG UCAGU U UACUACG@LB@3'-UUU...AAAAU AU G G UCCGU...UAG-5'@LB@ \| \|@LB@ 141 109@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -24.457 kcal/mol@LB@Unfolding Energy - mRNA 4.47787 kcal/mol@LB@Unfolding Energy - sRNA 7.72013 kcal/mol@LB@@LB@Position - mRNA 222 -- 250@LB@Position - sRNA 110 -- 140@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@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:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching