Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
34	0.001111	0.1164	stm2746	N/A	-14.94	0.120804	53 -- 101	36 -- 90	putative excinuclease ATPase subunit	stm4494 stm3753	_____________52_____________________102\n_____________\|______________________\|\n5'-GGA...UUGAA____UA_________U______UCAAG...AUG-3'\n______________GCAA__ACAACAACG__ACAUU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|:__\|\|\|\|:\n______________CGUU__UGUUGUUGU__UGUAG\n3'-UUU...GUUAA____UG_________GU_____UGUUG...UCA-5'\n_____________\|______________________\|\n_____________91_____________________35\n	61 -- 67	76 -- 82	-20.4267 kcal/mol	3.3222 kcal/mol	4.33922 kcal/mol	52 102@LB@ \| \|@LB@5'-GGA...UUGAA UA U UCAAG...AUG-3'@LB@ GCAA ACAACAACG ACAUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|: \|\|\|\|:@LB@ CGUU UGUUGUUGU UGUAG@LB@3'-UUU...GUUAA UG GU UGUUG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.4267 kcal/mol@LB@Unfolding Energy - mRNA 3.3222 kcal/mol@LB@Unfolding Energy - sRNA 4.33922 kcal/mol@LB@@LB@Position - mRNA 53 -- 101@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 76 -- 82@LB@
76	0.003538	0.1596	stm3058	pepP	-14.75	0.129287	129 -- 167	36 -- 78	Xaa-Pro aminopeptidase		_____________128_________________168\n_____________\|___________________\|\n5'-CGA...CUGGC___________CCG_____GCCGC...GCA-3'\n______________GCAAAUGCAGC___GCAGC\n______________\|\|\|\|\|::\|\|:\|___:\|\|:\|\n______________CGUUUGUGUUG___UGUUG\n3'-UUU...GUUAA___________UUG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________79__________________35\n	249 -- 255	80 -- 86	-18.5262 kcal/mol	6.77337 kcal/mol	3.80362 kcal/mol	128 168@LB@ \| \|@LB@5'-CGA...CUGGC CCG GCCGC...GCA-3'@LB@ GCAAAUGCAGC GCAGC@LB@ \|\|\|\|\|::\|\|:\| :\|\|:\|@LB@ CGUUUGUGUUG UGUUG@LB@3'-UUU...GUUAA UUG UAGUG...UCA-5'@LB@ \| \|@LB@ 79 35@LB@@LB@@LB@Energy -14.75 kcal/mol@LB@Hybridization Energy -18.5262 kcal/mol@LB@Unfolding Energy - mRNA 6.77337 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 129 -- 167@LB@Position - sRNA 36 -- 78@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 80 -- 86@LB@
143	0.007336	0.182	stm2276	ubiG	-14.65	0.134291	225 -- 278	36 -- 81	2-octaprenyl-6-hydroxy phenol methylase		_____________224_________________279\n_____________\|___________________\|\n5'-CAC...CGGCA____________CA_____UUUGC...AAU-3'\n______________GUAGAUAUAACG__GCGAC\n______________\|:\|:\|:\|:\|\|\|:__:\|:\|\|\n______________CGUUUGUGUUGU__UGUUG\n3'-UUU...GUUAA____________UG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________82__________________35\n	134 -- 140	80 -- 86	-18.0681 kcal/mol	5.41873 kcal/mol	3.80362 kcal/mol	224 279@LB@ \| \|@LB@5'-CAC...CGGCA CA UUUGC...AAU-3'@LB@ GUAGAUAUAACG GCGAC@LB@ \|:\|:\|:\|:\|\|\|: :\|:\|\|@LB@ CGUUUGUGUUGU UGUUG@LB@3'-UUU...GUUAA UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -18.0681 kcal/mol@LB@Unfolding Energy - mRNA 5.41873 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 225 -- 278@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 80 -- 86@LB@
198	0.01098	0.197	stm2803	N/A	-14.51	0.140962	192 -- 262	36 -- 101	DNA-binding transcriptional regulator		_____________191___________________________263\n_____________\|_____________________________\|\n5'-GCU...AAAAA________UA___C_____UAU_______UCGCU...CGC-3'\n______________GCAGACCA__UGC__GCGC___CAGCACA\n______________\|\|\|\|\|\|\|\|__\|\|\|__:\|:\|___\|\|:\|\|\|\|\n______________CGUCUGGU__ACG__UGUG___GUUGUGU\n3'-UUU...CUUAG________UA___UU____UU________UGUAG...UCA-5'\n_____________\|_____________________________\|\n_____________102___________________________35\n	213 -- 219	74 -- 80	-31.0005 kcal/mol	8.41541 kcal/mol	13.1066 kcal/mol	191 263@LB@ \| \|@LB@5'-GCU...AAAAA UA C UAU UCGCU...CGC-3'@LB@ GCAGACCA UGC GCGC CAGCACA@LB@ \|\|\|\|\|\|\|\| \|\|\| :\|:\| \|\|:\|\|\|\|@LB@ CGUCUGGU ACG UGUG GUUGUGU@LB@3'-UUU...CUUAG UA UU UU UGUAG...UCA-5'@LB@ \| \|@LB@ 102 35@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -31.0005 kcal/mol@LB@Unfolding Energy - mRNA 8.41541 kcal/mol@LB@Unfolding Energy - sRNA 13.1066 kcal/mol@LB@@LB@Position - mRNA 192 -- 262@LB@Position - sRNA 36 -- 101@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 74 -- 80@LB@
126	0.006333	0.1774	stm1584	ansP	-14.21	0.157463	122 -- 184	36 -- 93	amino acid permease		_____________121_________________185\n_____________\|___________________\|\n5'-AUA...UGUCA________UAUAACA____ACGUA...GUC-3'\n______________GGACAGGC_______GGUA\n______________\|\|\|\|\|\|:\|_______\|\|\|\|\n______________CCUGUCUG_______CCAU\n3'-UUU...UGAUA________UC_________UUACA...UCA-5'\n_____________\|___________________\|\n_____________94__________________35\n	178 -- 184	156 -- 162	-15.5225 kcal/mol	4.18435 kcal/mol	3.12041 kcal/mol	121 185@LB@ \| \|@LB@5'-AUA...UGUCA UAUAACA ACGUA...GUC-3'@LB@ GGACAGGC GGUA@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ CCUGUCUG CCAU@LB@3'-UUU...UGAUA UC UUACA...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -15.5225 kcal/mol@LB@Unfolding Energy - mRNA 4.18435 kcal/mol@LB@Unfolding Energy - sRNA 3.12041 kcal/mol@LB@@LB@Position - mRNA 122 -- 184@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 156 -- 162@LB@
178	0.009774	0.1951	stm2667	pheA	-14.20	0.157815	177 -- 228	36 -- 93	chorismate mutase		_____________176__________________229\n_____________\|____________________\|\n5'-GAC...ACAAA___G______C_________GGAAA...UUG-3'\n______________AAA_GCAACA_UAUGACAUC\n______________\|\|\|_:\|\|\|\|\|_:\|::\|\|\|\|\|\n______________UUU_UGUUGU_GUGUUGUAG\n3'-UUU...UAACG___G______U_________UGUUG...UCA-5'\n_____________\|____________________\|\n_____________94___________________35\n	202 -- 208	69 -- 75	-17.8987 kcal/mol	1.45353 kcal/mol	4.11387 kcal/mol	176 229@LB@ \| \|@LB@5'-GAC...ACAAA G C GGAAA...UUG-3'@LB@ AAA GCAACA UAUGACAUC@LB@ \|\|\| :\|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUU UGUUGU GUGUUGUAG@LB@3'-UUU...UAACG G U UGUUG...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.20 kcal/mol@LB@Hybridization Energy -17.8987 kcal/mol@LB@Unfolding Energy - mRNA 1.45353 kcal/mol@LB@Unfolding Energy - sRNA 4.11387 kcal/mol@LB@@LB@Position - mRNA 177 -- 228@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 69 -- 75@LB@
137	0.006825	0.1774	stm1196	acpP	-14.14	0.161333	197 -- 223	36 -- 60	acyl carrier protein		_____________196___________________________________________224\n_____________\|_____________________________________________\|\n5'-ACU...AGAAC_______GAAA_____C____A____CU__GCGUUAA________AAGUA...UGG-3'\n______________GCGUUAA____AUUAU_GGCG_ACAG__GG_______GCAGGAAG\n______________:\|:\|\|\|\|____\|:\|\|\|_\|:\|:_\|\|\|\|__\|\|_______:\|\|\|\|\|\|\|\n______________UGUAAUU____UGAUA_CUGU_UGUC__CC_______UGUCCUUC\n3'-UUU...CACGA_______AG_______C____C________AUUUACA________ACUUU...UCA-5'\n_____________\|_____________________________________________\|\n_____________61____________________________________________35\n	258 -- 264	137 -- 143	-28.6095 kcal/mol	10.3633 kcal/mol	7.13805 kcal/mol	196 224@LB@ \| \|@LB@5'-ACU...AGAAC GAAA C A CU GCGUUAA AAGUA...UGG-3'@LB@ GCGUUAA AUUAU GGCG ACAG GG GCAGGAAG@LB@ :\|:\|\|\|\| \|:\|\|\| \|:\|: \|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ UGUAAUU UGAUA CUGU UGUC CC UGUCCUUC@LB@3'-UUU...CACGA AG C C AUUUACA ACUUU...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -28.6095 kcal/mol@LB@Unfolding Energy - mRNA 10.3633 kcal/mol@LB@Unfolding Energy - sRNA 7.13805 kcal/mol@LB@@LB@Position - mRNA 197 -- 223@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 137 -- 143@LB@
23	0.0005914	0.08814	stm3466	crp	-13.97	0.171291	272 -- 288	36 -- 50	transcriptional regulator Crp		_____________271_______________________________289\n_____________\|_________________________________\|\n5'-ACG...CGAAA______CUAAA________________C_____UAAUA...AGG-3'\n______________GCUAUG_____ACAGACA____AGAUG_UACAG\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|____\|:\|\|\|_\|\|\|\|\|\n______________UGAUAC_____UGUCUGU____UUUAC_AUGUC\n3'-UUU...AUUAG______C___________CCCA___________CUUCA...UCA-5'\n_____________\|_________________________________\|\n_____________51________________________________35\n	21 -- 27	155 -- 161	-20.3438 kcal/mol	4.64329 kcal/mol	5.58455 kcal/mol	271 289@LB@ \| \|@LB@5'-ACG...CGAAA CUAAA C UAAUA...AGG-3'@LB@ GCUAUG ACAGACA AGAUG UACAG@LB@ :\|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|@LB@ UGAUAC UGUCUGU UUUAC AUGUC@LB@3'-UUU...AUUAG C CCCA CUUCA...UCA-5'@LB@ \| \|@LB@ 51 35@LB@@LB@@LB@Energy -13.97 kcal/mol@LB@Hybridization Energy -20.3438 kcal/mol@LB@Unfolding Energy - mRNA 4.64329 kcal/mol@LB@Unfolding Energy - sRNA 5.58455 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 36 -- 50@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 155 -- 161@LB@
165	0.008886	0.1918	stm0281	N/A	-13.47	0.204933	267 -- 289	36 -- 56	type VI secretion system-associated protein		_____________266______________________________________________290\n_____________\|________________________________________________\|\n5'-UGA...UAAUU____A_____A______A__UAU___C_____UGACC_C_______G_AGUGA...ACC-3'\n______________ACGG_ACGGG_UAAAUG_AU___GAG_UGGAA_____G_GUAGUCU_G\n______________\|\|:\|_\|\|:\|\|_\|\|\|\|\|\|_\|:___:\|\|_\|\|:\|\|_____\|_\|\|\|\|\|\|\|_\|\n______________UGUC_UGUCC_AUUUAC_UG___UUC_ACUUU_____C_CAUCAGA_C\n3'-UUU...AUACC__________C______A__UCC_________UUC___________G_GAUGG...UCA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________35\n	219 -- 225	121 -- 127	-29.4304 kcal/mol	8.43831 kcal/mol	11.9516 kcal/mol	266 290@LB@ \| \|@LB@5'-UGA...UAAUU A A A UAU C UGACC C G AGUGA...ACC-3'@LB@ ACGG ACGGG UAAAUG AU GAG UGGAA G GUAGUCU G@LB@ \|\|:\| \|\|:\|\| \|\|\|\|\|\| \|: :\|\| \|\|:\|\| \| \|\|\|\|\|\|\| \|@LB@ UGUC UGUCC AUUUAC UG UUC ACUUU C CAUCAGA C@LB@3'-UUU...AUACC C A UCC UUC G GAUGG...UCA-5'@LB@ \| \|@LB@ 57 35@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -29.4304 kcal/mol@LB@Unfolding Energy - mRNA 8.43831 kcal/mol@LB@Unfolding Energy - sRNA 11.9516 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 36 -- 56@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 121 -- 127@LB@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein		_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@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