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
180	0.009034	0.1747	b3146	rsmI	-12.76	0.071583	191 -- 238	34 -- 76	16S rRNA C1402 2'-O-ribose methyltransferase SAM-dependent	_____________190____________________________________________________239\n_____________\|______________________________________________________\|\n5'-CAG...AAUAC____G____AAUGAAACA___C_______GC_GAUAAUU_______________GCUUU...AGG-3'\n______________GGAC_ACAC_________ACA_CAA_UCG__G_______CUCAGGG_____CCA\n______________:\|\|\|_\|\|\|\|_________\|\|\|_\|\|\|_\|\|\|__\|_______\|\|\|\|\|\|\|_____\|\|\|\n______________UCUG_UGUG_________UGU_GUU_AGC__C_______GAGUCCC_____GGU\n3'-UUU...CCGUU____A________________C___A___AA_AAAGU_________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________________________\|\n_____________77_____________________________________________________33\n	229 -- 235	42 -- 48	-25.3144 kcal/mol	7.73901 kcal/mol	4.816 kcal/mol	190 239@LB@ \| \|@LB@5'-CAG...AAUAC G AAUGAAACA C GC GAUAAUU GCUUU...AGG-3'@LB@ GGAC ACAC ACA CAA UCG G CUCAGGG CCA@LB@ :\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\| \| \|\|\|\|\|\|\| \|\|\|@LB@ UCUG UGUG UGU GUU AGC C GAGUCCC GGU@LB@3'-UUU...CCGUU A C A AA AAAGU CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -25.3144 kcal/mol@LB@Unfolding Energy - mRNA 7.73901 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 191 -- 238@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 42 -- 48@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@
62	0.002558	0.1417	b3579	yiaO	-11.31	0.142375	245 -- 258	62 -- 75	2 3-diketo-L-gulonate-binding periplasmic protein	_____________244____________259\n_____________\|______________\|\n5'-ACU...GGCCU________U_____CAUCU...AAA-3'\n______________GGCUGCAU_CAGCA\n______________\|:\|\|:\|\|:_\|\|\|\|\|\n______________CUGAUGUG_GUCGU\n3'-UUU...CGUUU________U_____UAAGC...GCA-5'\n_____________\|______________\|\n_____________76_____________61\n	246 -- 252	68 -- 74	-19.3904 kcal/mol	4.83304 kcal/mol	3.25167 kcal/mol	244 259@LB@ \| \|@LB@5'-ACU...GGCCU U CAUCU...AAA-3'@LB@ GGCUGCAU CAGCA@LB@ \|:\|\|:\|\|: \|\|\|\|\|@LB@ CUGAUGUG GUCGU@LB@3'-UUU...CGUUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 76 61@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -19.3904 kcal/mol@LB@Unfolding Energy - mRNA 4.83304 kcal/mol@LB@Unfolding Energy - sRNA 3.25167 kcal/mol@LB@@LB@Position - mRNA 245 -- 258@LB@Position - sRNA 62 -- 75@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 68 -- 74@LB@
188	0.009562	0.1776	b0147	ligT	-10.24	0.223023	2 -- 33	35 -- 66	2'-5' RNA ligase	_____________1_________________________________34\n_____________\|_________________________________\|\n__________5'-C________GCAGCGG___GC____UU_______CGGCC...CGG-3'\n______________CAGCAGUU________CA__CAGG__GAUUUCC\n______________\|\|\|\|\|:\|\|________\|\|__\|\|\|\|__\|\|\|\|\|\|\|\n______________GUCGUUAA________GU__GUCC__CUAAAGG\n3'-UUU...UGUGU________GCAACAAA__GA____C________UACGA...GCA-5'\n_____________\|_________________________________\|\n_____________67________________________________34\n	27 -- 33	35 -- 41	-25.6384 kcal/mol	10.64 kcal/mol	4.7609 kcal/mol	1 34@LB@ \| \|@LB@ 5'-C GCAGCGG GC UU CGGCC...CGG-3'@LB@ CAGCAGUU CA CAGG GAUUUCC@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GUCGUUAA GU GUCC CUAAAGG@LB@3'-UUU...UGUGU GCAACAAA GA C UACGA...GCA-5'@LB@ \| \|@LB@ 67 34@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -25.6384 kcal/mol@LB@Unfolding Energy - mRNA 10.64 kcal/mol@LB@Unfolding Energy - sRNA 4.7609 kcal/mol@LB@@LB@Position - mRNA 2 -- 33@LB@Position - sRNA 35 -- 66@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 35 -- 41@LB@
88	0.003962	0.1538	b3084	rlmG	-11.78	0.115170	185 -- 197	40 -- 51	23S rRNA m(2)G1835 methyltransferase SAM-dependent	_____________184___________198\n_____________\|_____________\|\n5'-UGU...UUUUA_________A___CCGAU...AAU-3'\n______________UCAUUCAGG_GGG\n______________\|\|\|:\|\|\|\|\|_\|\|:\n______________AGUGAGUCC_CCU\n3'-UUU...AACAA_____________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	187 -- 193	43 -- 49	-16.9089 kcal/mol	3.37488 kcal/mol	1.76028 kcal/mol	184 198@LB@ \| \|@LB@5'-UGU...UUUUA A CCGAU...AAU-3'@LB@ UCAUUCAGG GGG@LB@ \|\|\|:\|\|\|\|\| \|\|:@LB@ AGUGAGUCC CCU@LB@3'-UUU...AACAA AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -16.9089 kcal/mol@LB@Unfolding Energy - mRNA 3.37488 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
108	0.004771	0.1538	b2594	rluD	-7.24	0.588975	189 -- 206	62 -- 78	23S rRNA pseudouridine(1911 1915 1917) synthase	_____________188________________207\n_____________\|__________________\|\n5'-CCC...ACGAA____C_G___________CAACG...GUU-3'\n______________GAAG_A_UAUAUAUGGCA\n______________:\|\|\|_\|_\|\|:\|:\|::\|\|\|\n______________UUUC_U_AUGUGUGUCGU\n3'-UUU...ACCCG______G___________UAAGC...GCA-5'\n_____________\|__________________\|\n_____________79_________________61\n	200 -- 206	62 -- 68	-13.9289 kcal/mol	3.43926 kcal/mol	3.2555 kcal/mol	188 207@LB@ \| \|@LB@5'-CCC...ACGAA C G CAACG...GUU-3'@LB@ GAAG A UAUAUAUGGCA@LB@ :\|\|\| \| \|\|:\|:\|::\|\|\|@LB@ UUUC U AUGUGUGUCGU@LB@3'-UUU...ACCCG G UAAGC...GCA-5'@LB@ \| \|@LB@ 79 61@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.9289 kcal/mol@LB@Unfolding Energy - mRNA 3.43926 kcal/mol@LB@Unfolding Energy - sRNA 3.2555 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 62 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
150	0.006982	0.1638	b3581	sgbH	-9.48	0.297019	138 -- 176	34 -- 74	3-keto-L-gulonate 6-phosphate decarboxylase	_____________137________________________________________177\n_____________\|__________________________________________\|\n5'-UUU...UAUCA__GU_________UC__A___CCG__C_______C_______CGCCC...AAG-3'\n______________AC__UAU_CAGCA__UC_UUG___CA_UUCAGGG___UUUCA\n______________\|\|__:\|:_\|\|\|\|\|__\|\|_\|\|\|___\|\|_:\|\|\|\|\|\|___\|\|:\|\|\n______________UG__GUG_GUCGU__AG_AAC___GU_GAGUCCC___AAGGU\n3'-UUU...GUUUC__AU___U_____UA__C___AAA__________CUA_____ACGAA...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________33\n	164 -- 170	42 -- 48	-24.4875 kcal/mol	10.188 kcal/mol	4.81599 kcal/mol	137 177@LB@ \| \|@LB@5'-UUU...UAUCA GU UC A CCG C C CGCCC...AAG-3'@LB@ AC UAU CAGCA UC UUG CA UUCAGGG UUUCA@LB@ \|\| :\|: \|\|\|\|\| \|\| \|\|\| \|\| :\|\|\|\|\|\| \|\|:\|\|@LB@ UG GUG GUCGU AG AAC GU GAGUCCC AAGGU@LB@3'-UUU...GUUUC AU U UA C AAA CUA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.4875 kcal/mol@LB@Unfolding Energy - mRNA 10.188 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 42 -- 48@LB@
162	0.007731	0.1668	b4202	rpsR	-9.58	0.287294	60 -- 77	62 -- 76	30S ribosomal subunit protein S18	_____________59_________________78\n_____________\|__________________\|\n5'-CGG...AAACC____CAU___U_______UAACG...UCA-3'\n______________AGGC___UAC_CACAGUA\n______________\|\|:\|___\|\|\|_\|\|\|\|\|:\|\n______________UCUG___AUG_GUGUCGU\n3'-UUU...CCGUU__________U_______UAAGC...GCA-5'\n_____________\|__________________\|\n_____________77_________________61\n	71 -- 77	62 -- 68	-14.2281 kcal/mol	1.39912 kcal/mol	3.25371 kcal/mol	59 78@LB@ \| \|@LB@5'-CGG...AAACC CAU U UAACG...UCA-3'@LB@ AGGC UAC CACAGUA@LB@ \|\|:\| \|\|\| \|\|\|\|\|:\|@LB@ UCUG AUG GUGUCGU@LB@3'-UUU...CCGUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.2281 kcal/mol@LB@Unfolding Energy - mRNA 1.39912 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 60 -- 77@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 62 -- 68@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@
170	0.008354	0.1723	b3294	rplQ	-12.86	0.068031	178 -- 204	31 -- 54	50S ribosomal subunit protein L17	_____________177_________________________205\n_____________\|___________________________\|\n5'-UAU...UUAAG________G__AA____AAGG______GCCAU...UCA-3'\n______________GUUUUACU_AG__GGAU____UCAUGC\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|____:\|\|\|\|\|\n______________CAAAGUGA_UC__CCUA____GGUACG\n3'-UUU...AGCAA________G__C_____AA________AAUAU...GCA-5'\n_____________\|___________________________\|\n_____________55__________________________30\n	179 -- 185	47 -- 53	-21.6424 kcal/mol	4.376 kcal/mol	4.40484 kcal/mol	177 205@LB@ \| \|@LB@5'-UAU...UUAAG G AA AAGG GCCAU...UCA-3'@LB@ GUUUUACU AG GGAU UCAUGC@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\| :\|\|\|\|\|@LB@ CAAAGUGA UC CCUA GGUACG@LB@3'-UUU...AGCAA G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 55 30@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -21.6424 kcal/mol@LB@Unfolding Energy - mRNA 4.376 kcal/mol@LB@Unfolding Energy - sRNA 4.40484 kcal/mol@LB@@LB@Position - mRNA 178 -- 204@LB@Position - sRNA 31 -- 54@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 47 -- 53@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