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
150	0.01679	0.3749	b3550	yiaC	-14.78	0.030008	125 -- 180	123 -- 174	GNAT family putative N-acetyltransferase	_____________124_______________________________________________181\n_____________\|_________________________________________________\|\n5'-AAU...UCUGU_____CU_______G_C________U___G___GA______________GGCUG...GGC-3'\n______________UACUC__UUAUGCA_G_AUGUGGGC_GGU_AAU__UCA____UGUGGUU\n______________\|\|\|\|\|__\|:\|::\|\|_\|_\|\|\|::\|\|\|_:\|\|_\|\|:__\|\|\|____\|\|:\|\|\|:\n______________AUGAG__AGUGUGU_C_UACGUCCG_UCA_UUG__AGU____ACGCCAG\n3'-UUU...UGGUU_____UC_______A__________U___G___AA___CUUA_______UAGGG...UAG-5'\n_____________\|_________________________________________________\|\n_____________175_______________________________________________122\n	134 -- 140	167 -- 173	-39.4647 kcal/mol	14.8163 kcal/mol	12.8033 kcal/mol	124 181@LB@ \| \|@LB@5'-AAU...UCUGU CU G C U G GA GGCUG...GGC-3'@LB@ UACUC UUAUGCA G AUGUGGGC GGU AAU UCA UGUGGUU@LB@ \|\|\|\|\| \|:\|::\|\| \| \|\|\|::\|\|\| :\|\| \|\|: \|\|\| \|\|:\|\|\|:@LB@ AUGAG AGUGUGU C UACGUCCG UCA UUG AGU ACGCCAG@LB@3'-UUU...UGGUU UC A U G AA CUUA UAGGG...UAG-5'@LB@ \| \|@LB@ 175 122@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -39.4647 kcal/mol@LB@Unfolding Energy - mRNA 14.8163 kcal/mol@LB@Unfolding Energy - sRNA 12.8033 kcal/mol@LB@@LB@Position - mRNA 125 -- 180@LB@Position - sRNA 123 -- 174@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 167 -- 173@LB@
129	0.01414	0.3575	b3579	yiaO	-11.03	0.174508	249 -- 273	50 -- 76	2 3-diketo-L-gulonate-binding periplasmic protein	_____________248_________________________274\n_____________\|___________________________\|\n5'-ACU...CGUCC____________C__UA__________UUGUU...AAA-3'\n______________UGGUUUUAUAUU_AU__UUAGUCGUAU\n______________\|\|:\|\|\|\|\|:\|::_\|\|__\|:\|\|\|\|::\|:\n______________ACUAAAAUGUGG_UA__AGUCAGUGUG\n3'-UUU...CGCCC____________U__UG__________UACUA...UAG-5'\n_____________\|___________________________\|\n_____________77__________________________49\n	132 -- 138	168 -- 174	-19.0823 kcal/mol	5.4875 kcal/mol	5.03533 kcal/mol	248 274@LB@ \| \|@LB@5'-ACU...CGUCC C UA UUGUU...AAA-3'@LB@ UGGUUUUAUAUU AU UUAGUCGUAU@LB@ \|\|:\|\|\|\|\|:\|:: \|\| \|:\|\|\|\|::\|:@LB@ ACUAAAAUGUGG UA AGUCAGUGUG@LB@3'-UUU...CGCCC U UG UACUA...UAG-5'@LB@ \| \|@LB@ 77 49@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -19.0823 kcal/mol@LB@Unfolding Energy - mRNA 5.4875 kcal/mol@LB@Unfolding Energy - sRNA 5.03533 kcal/mol@LB@@LB@Position - mRNA 249 -- 273@LB@Position - sRNA 50 -- 76@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 168 -- 174@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase	_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@LB@
144	0.01541	0.3575	b4555	yicS	-14.57	0.033136	213 -- 290	115 -- 187	putative periplasmic protein	_____________212_________________________________________________________________291\n_____________\|___________________________________________________________________\|\n5'-AUU...CAACG______C______UUU____UUUUUUC__U_____C______UCGUAUACGCCG_____C_______CUCAC...AGA-3'\n______________ACACUA_UGCUUA___UCAC_______GC___AUG_CAGGCA____________AGUCG_CUUUUAG\n______________\|\|\|\|:\|_\|:\|\|:\|___\|\|\|\|_______:\|___\|\|\|_\|\|\|\|\|\|____________\|\|\|\|:_\|\|\|\|:\|\|\n______________UGUGGU_AUGAGU___AGUG_______UG___UAC_GUCCGU____________UCAGU_GAAAGUC\n3'-UUU...UAAAA______U______C_______________UAC___________________________U_______UUAAC...UAG-5'\n_____________\|___________________________________________________________________\|\n_____________188_________________________________________________________________114\n	271 -- 277	143 -- 149	-34.4495 kcal/mol	11.6435 kcal/mol	13.2932 kcal/mol	212 291@LB@ \| \|@LB@5'-AUU...CAACG C UUU UUUUUUC U C UCGUAUACGCCG C CUCAC...AGA-3'@LB@ ACACUA UGCUUA UCAC GC AUG CAGGCA AGUCG CUUUUAG@LB@ \|\|\|\|:\| \|:\|\|:\| \|\|\|\| :\| \|\|\| \|\|\|\|\|\| \|\|\|\|: \|\|\|\|:\|\|@LB@ UGUGGU AUGAGU AGUG UG UAC GUCCGU UCAGU GAAAGUC@LB@3'-UUU...UAAAA U C UAC U UUAAC...UAG-5'@LB@ \| \|@LB@ 188 114@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -34.4495 kcal/mol@LB@Unfolding Energy - mRNA 11.6435 kcal/mol@LB@Unfolding Energy - sRNA 13.2932 kcal/mol@LB@@LB@Position - mRNA 213 -- 290@LB@Position - sRNA 115 -- 187@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 143 -- 149@LB@
169	0.01937	0.3812	b4557	yidD	-14.07	0.041992	2 -- 13	11 -- 22	membrane protein insertion efficiency factor UPF0161 family inner membrane protein	_____________1______________________14\n_____________\|______________________\|\n__________5'-C____________GUAUCG____UUACA...UCA-3'\n______________UGGGGCAUCCCC_______GUC\n______________\|\|\|\|\|\|\|:\|\|\|\|_______:\|\|\n______________ACCCCGUGGGGG_______UAG\n3'-UUU...UGCGU____________AACGAAG___-5'\n_____________\|_____________________\|\n_____________23____________________11\n	7 -- 13	11 -- 17	-28.608 kcal/mol	8.24927 kcal/mol	10.7363 kcal/mol	1 14@LB@ \| \|@LB@ 5'-C GUAUCG UUACA...UCA-3'@LB@ UGGGGCAUCCCC GUC@LB@ \|\|\|\|\|\|\|:\|\|\|\| :\|\|@LB@ ACCCCGUGGGGG UAG@LB@3'-UUU...UGCGU AACGAAG -5'@LB@ \| \|@LB@ 23 11@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -28.608 kcal/mol@LB@Unfolding Energy - mRNA 8.24927 kcal/mol@LB@Unfolding Energy - sRNA 10.7363 kcal/mol@LB@@LB@Position - mRNA 2 -- 13@LB@Position - sRNA 11 -- 22@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 11 -- 17@LB@
187	0.02173	0.3833	b3679	yidK	-10.16	0.256396	240 -- 256	191 -- 205	putative transporter	_____________239________________________________________257\n_____________\|__________________________________________\|\n5'-UUU...UUACG_________GC______________U____GAA_________AAACA...AAG-3'\n______________CUGCUGGUG__GGUGAU____CACC_GGUG___GGUC_CGCA\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|____\|\|\|\|_::\|:___:\|\|\|_\|:\|\|\n______________GACGACCGC__CCACUA____GUGG_UUAU___UCAG_GUGU\n3'-UUU...UAUUA_________________AAAU_________GAG____U____ACUAC...UAG-5'\n_____________\|__________________________________________\|\n_____________206________________________________________190\n	242 -- 248	197 -- 203	-39.2862 kcal/mol	16.885 kcal/mol	15.3993 kcal/mol	239 257@LB@ \| \|@LB@5'-UUU...UUACG GC U GAA AAACA...AAG-3'@LB@ CUGCUGGUG GGUGAU CACC GGUG GGUC CGCA@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| ::\|: :\|\|\| \|:\|\|@LB@ GACGACCGC CCACUA GUGG UUAU UCAG GUGU@LB@3'-UUU...UAUUA AAAU GAG U ACUAC...UAG-5'@LB@ \| \|@LB@ 206 190@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -39.2862 kcal/mol@LB@Unfolding Energy - mRNA 16.885 kcal/mol@LB@Unfolding Energy - sRNA 15.3993 kcal/mol@LB@@LB@Position - mRNA 240 -- 256@LB@Position - sRNA 191 -- 205@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 197 -- 203@LB@
82	0.008839	0.3575	b3680	yidL	-8.33	0.532337	91 -- 113	142 -- 164	AraC family putative transcriptional regulator	_____________90________________114\n_____________\|_________________\|\n5'-AAC...UGCGU________GCAG_____UUCUU...UGA-3'\n______________CGGGUCAG____UCAGA\n______________\|::\|\|\|\|:____\|\|\|\|\|\n______________GUUCAGUU____AGUCU\n3'-UUU...CGUCC________GAA______UAACG...UAG-5'\n_____________\|_________________\|\n_____________165_______________141\n	97 -- 103	151 -- 157	-14.3717 kcal/mol	4.36777 kcal/mol	4.37859 kcal/mol	90 114@LB@ \| \|@LB@5'-AAC...UGCGU GCAG UUCUU...UGA-3'@LB@ CGGGUCAG UCAGA@LB@ \|::\|\|\|\|: \|\|\|\|\|@LB@ GUUCAGUU AGUCU@LB@3'-UUU...CGUCC GAA UAACG...UAG-5'@LB@ \| \|@LB@ 165 141@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -14.3717 kcal/mol@LB@Unfolding Energy - mRNA 4.36777 kcal/mol@LB@Unfolding Energy - sRNA 4.37859 kcal/mol@LB@@LB@Position - mRNA 91 -- 113@LB@Position - sRNA 142 -- 164@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 151 -- 157@LB@
107	0.01169	0.3575	b3858	yihD	-12.50	0.087903	89 -- 104	63 -- 77	DUF1040 protein YihD	_____________88______________________________105\n_____________\|_______________________________\|\n5'-AUA...UUUAC___CU___________GCC____AUC_____CAUCA...CGA-3'\n______________CGC__GCCAGCACAAC___UGUU___GUCGU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|\|___:\|:\|___\|\|\|\|:\n______________GCG__UGGUCGUGUUG___GCGA___CAGCG\n3'-UUU...UGGUU___U____________AA_____________CCAUU...UAG-5'\n_____________\|_______________________________\|\n_____________78______________________________62\n	98 -- 104	63 -- 69	-31.4348 kcal/mol	4.67185 kcal/mol	17.7932 kcal/mol	88 105@LB@ \| \|@LB@5'-AUA...UUUAC CU GCC AUC CAUCA...CGA-3'@LB@ CGC GCCAGCACAAC UGUU GUCGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\|\| :\|:\| \|\|\|\|:@LB@ GCG UGGUCGUGUUG GCGA CAGCG@LB@3'-UUU...UGGUU U AA CCAUU...UAG-5'@LB@ \| \|@LB@ 78 62@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -31.4348 kcal/mol@LB@Unfolding Energy - mRNA 4.67185 kcal/mol@LB@Unfolding Energy - sRNA 17.7932 kcal/mol@LB@@LB@Position - mRNA 89 -- 104@LB@Position - sRNA 63 -- 77@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 63 -- 69@LB@
124	0.0136	0.3575	b4065	yjcE	-10.85	0.188871	258 -- 289	125 -- 174	putative cation/proton antiporter	_____________257___________290\n_____________\|_____________\|\n5'-UAU...UGGUC_____U_______CCUUU...UGC-3'\n______________ACUCG_GUCAUGC\n______________\|\|\|\|:_\|\|\|\|::\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________175___________124\n	267 -- 273	168 -- 174	-13.2629 kcal/mol	3.88311 kcal/mol	0.283892 kcal/mol	257 290@LB@ \| \|@LB@5'-UAU...UGGUC U CCUUU...UGC-3'@LB@ ACUCG GUCAUGC@LB@ \|\|\|\|: \|\|\|\|::\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 175 124@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.2629 kcal/mol@LB@Unfolding Energy - mRNA 3.88311 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 258 -- 289@LB@Position - sRNA 125 -- 174@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 168 -- 174@LB@
199	0.02363	0.3833	b4141	yjeH	-8.04	0.585705	57 -- 67	64 -- 74	putative transporter	_____________56_____________68\n_____________\|______________\|\n5'-CAG...AAAUC___G_______C__AAAUU...CUG-3'\n______________UAC_CAGUUGC_CA\n______________\|\|\|_\|\|\|\|::\|_\|\|\n______________AUG_GUCAGUG_GU\n3'-UUU...UGGUU___A_______U__ACUAC...UAG-5'\n_____________\|______________\|\n_____________75_____________63\n	163 -- 169	170 -- 176	-11.2481 kcal/mol	2.09942 kcal/mol	0.433965 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAUC G C AAAUU...CUG-3'@LB@ UAC CAGUUGC CA@LB@ \|\|\| \|\|\|\|::\| \|\|@LB@ AUG GUCAGUG GU@LB@3'-UUU...UGGUU A U ACUAC...UAG-5'@LB@ \| \|@LB@ 75 63@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -11.2481 kcal/mol@LB@Unfolding Energy - mRNA 2.09942 kcal/mol@LB@Unfolding Energy - sRNA 0.433965 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 64 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 170 -- 176@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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