Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
2	4.936e-07	0.0007949	b1237	hns	-13.24	0.001473	195 -- 222	26 -- 57	global DNA-binding transcriptional dual regulator H-NS	_____________194______________________________223\n_____________\|________________________________\|\n5'-CUC...AGAUU___ACAA_________________________UGAAC...UAG-3'\n______________ACU____UGAGC__GAAGCACUUAAA__AUUC\n______________\|\|\|____\|:\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGA____AUUCG__CUUCGUGAAUUU__UAAG\n3'-UUU...UACUU___ACGA_____UU____________UU____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	212 -- 218	32 -- 38	-22.6274 kcal/mol	3.10903 kcal/mol	6.27605 kcal/mol	194 223@LB@ \| \|@LB@5'-CUC...AGAUU ACAA UGAAC...UAG-3'@LB@ ACU UGAGC GAAGCACUUAAA AUUC@LB@ \|\|\| \|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGA AUUCG CUUCGUGAAUUU UAAG@LB@3'-UUU...UACUU ACGA UU UU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -22.6274 kcal/mol@LB@Unfolding Energy - mRNA 3.10903 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 195 -- 222@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 32 -- 38@LB@
175	0.01993	0.3669	b0183	rnhB	-5.94	0.199165	195 -- 215	23 -- 41	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________194___________________216\n_____________\|_____________________\|\n5'-AAU...GAGUU_____AA___UC_________UAUCC...UCC-3'\n______________AGCAC__UGA__GAAUUUGUU\n______________\|\|\|\|\|__\|:\|__:\|\|\|\|:\|\|\|\n______________UCGUG__AUU__UUUAAGCAA\n3'-UUU...GUUCU_____A____U__________UGUGG...CAA-5'\n_____________\|_____________________\|\n_____________42____________________22\n	209 -- 215	23 -- 29	-11.3649 kcal/mol	3.77136 kcal/mol	1.64896 kcal/mol	194 216@LB@ \| \|@LB@5'-AAU...GAGUU AA UC UAUCC...UCC-3'@LB@ AGCAC UGA GAAUUUGUU@LB@ \|\|\|\|\| \|:\| :\|\|\|\|:\|\|\|@LB@ UCGUG AUU UUUAAGCAA@LB@3'-UUU...GUUCU A U UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -11.3649 kcal/mol@LB@Unfolding Energy - mRNA 3.77136 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 195 -- 215@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 23 -- 29@LB@
116	0.009699	0.2693	b2708	srlQ	-8.08	0.057211	196 -- 214	36 -- 49	D-arabinose 5-phosphate isomerase	_____________195_________________215\n_____________\|___________________\|\n5'-UAC...GGAGA______UGAGU________ACUGA...GCG-3'\n______________GAGCAA_____GAAGCACU\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UUCGUU_____CUUCGUGA\n3'-UUU...ACGAA___________________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________50__________________35\n	208 -- 214	36 -- 42	-17.2491 kcal/mol	3.12814 kcal/mol	6.03645 kcal/mol	195 215@LB@ \| \|@LB@5'-UAC...GGAGA UGAGU ACUGA...GCG-3'@LB@ GAGCAA GAAGCACU@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCGUU CUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -17.2491 kcal/mol@LB@Unfolding Energy - mRNA 3.12814 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 36 -- 42@LB@
163	0.0182	0.3566	b0397	sbcC	-8.10	0.056577	196 -- 210	26 -- 43	exonuclease dsDNA ATP-dependent	_____________195________________211\n_____________\|__________________\|\n5'-GAA...AACAC__________________UCAGC...UUG-3'\n______________GAAGCAU___GAAAAUUC\n______________\|\|\|\|\|\|:___:\|\|\|\|\|\|\|\n______________CUUCGUG___UUUUUAAG\n3'-UUU...UCGUU_______AAU________CAAUG...CAA-5'\n_____________\|__________________\|\n_____________44_________________25\n	204 -- 210	26 -- 32	-13.6528 kcal/mol	1.79109 kcal/mol	3.75931 kcal/mol	195 211@LB@ \| \|@LB@5'-GAA...AACAC UCAGC...UUG-3'@LB@ GAAGCAU GAAAAUUC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|\|@LB@ CUUCGUG UUUUUAAG@LB@3'-UUU...UCGUU AAU CAAUG...CAA-5'@LB@ \| \|@LB@ 44 25@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -13.6528 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 3.75931 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 26 -- 43@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 26 -- 32@LB@
178	0.02074	0.3753	b4324	uxuR	-9.92	0.017203	196 -- 210	8 -- 22	fructuronate-inducible hexuronate regulon transcriptional repressor; autorepressor	_____________195_____________211\n_____________\|_______________\|\n5'-UAC...ACACA______U________CCACC...UGC-3'\n______________ACACCA_GAAAUCUG\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UGUGGU_CUUUAGAC\n3'-UUU...AGCAA______C________UACACAA-5'\n_____________\|_______________\|\n_____________23______________7\n	203 -- 209	9 -- 15	-19.4171 kcal/mol	1.94047 kcal/mol	7.56026 kcal/mol	195 211@LB@ \| \|@LB@5'-UAC...ACACA U CCACC...UGC-3'@LB@ ACACCA GAAAUCUG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGUGGU CUUUAGAC@LB@3'-UUU...AGCAA C UACACAA-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -19.4171 kcal/mol@LB@Unfolding Energy - mRNA 1.94047 kcal/mol@LB@Unfolding Energy - sRNA 7.56026 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
32	0.0009536	0.09599	b0637	rsfS	-12.32	0.003012	197 -- 230	23 -- 59	ribosomal silencing factor	_____________196___________________________________231\n_____________\|_____________________________________\|\n5'-AUU...GGGGA________A_______________CC____U______AUCGA...UCA-3'\n______________AAACUUGC__GGGUA__AAGCACU__AGGA_UUUGUU\n______________\|\|\|\|\|\|\|\|__::\|:\|__\|\|\|\|\|\|\|__\|::\|_\|\|:\|\|\|\n______________UUUGAACG__UUCGU__UUCGUGA__UUUU_AAGCAA\n3'-UUU...CCUAC________AA_____UC_______AU____U______UGUGG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________22\n	211 -- 217	36 -- 42	-25.7611 kcal/mol	7.16036 kcal/mol	6.27609 kcal/mol	196 231@LB@ \| \|@LB@5'-AUU...GGGGA A CC U AUCGA...UCA-3'@LB@ AAACUUGC GGGUA AAGCACU AGGA UUUGUU@LB@ \|\|\|\|\|\|\|\| ::\|:\| \|\|\|\|\|\|\| \|::\| \|\|:\|\|\|@LB@ UUUGAACG UUCGU UUCGUGA UUUU AAGCAA@LB@3'-UUU...CCUAC AA UC AU U UGUGG...CAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -12.32 kcal/mol@LB@Hybridization Energy -25.7611 kcal/mol@LB@Unfolding Energy - mRNA 7.16036 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 197 -- 230@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@LB@
84	0.005596	0.2146	b4065	yjcE	-5.39	0.265673	197 -- 210	9 -- 22	putative cation/proton antiporter	_____________196____________211\n_____________\|______________\|\n5'-UAU...AGGGA____AU________UCUUC...UGC-3'\n______________ACGC__GGAAAUCU\n______________\|\|:\|__\|\|\|\|\|\|\|\|\n______________UGUG__CCUUUAGA\n3'-UUU...AGCAA____GU________CUACACAA-5'\n_____________\|______________\|\n_____________23_____________8\n	203 -- 209	10 -- 16	-15.8377 kcal/mol	2.89158 kcal/mol	7.5588 kcal/mol	196 211@LB@ \| \|@LB@5'-UAU...AGGGA AU UCUUC...UGC-3'@LB@ ACGC GGAAAUCU@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ UGUG CCUUUAGA@LB@3'-UUU...AGCAA GU CUACACAA-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.8377 kcal/mol@LB@Unfolding Energy - mRNA 2.89158 kcal/mol@LB@Unfolding Energy - sRNA 7.5588 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 10 -- 16@LB@
91	0.006547	0.2317	b1323	tyrR	-8.26	0.051378	202 -- 222	3 -- 23	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase	_____________201___________________223\n_____________\|_____________________\|\n5'-UCG...UCCCA______U________UU____AAGAC...UUG-3'\n______________UGCGUC_GGAAGUCU__UGUG\n______________\|:\|::\|_\|\|\|\|:\|\|\|__\|\|\|\|\n______________AUGUGG_CCUUUAGA__ACAC\n3'-UUU...AAGCA______U________CU____AA-5'\n_____________\|_____________________\|\n_____________24____________________2\n	209 -- 215	10 -- 16	-19.6247 kcal/mol	3.79223 kcal/mol	7.5769 kcal/mol	201 223@LB@ \| \|@LB@5'-UCG...UCCCA U UU AAGAC...UUG-3'@LB@ UGCGUC GGAAGUCU UGUG@LB@ \|:\|::\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ AUGUGG CCUUUAGA ACAC@LB@3'-UUU...AAGCA U CU AA-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -19.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.79223 kcal/mol@LB@Unfolding Energy - sRNA 7.5769 kcal/mol@LB@@LB@Position - mRNA 202 -- 222@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 10 -- 16@LB@
107	0.009263	0.2693	b3034	nudF	-7.86	0.065629	202 -- 214	42 -- 54	ADP-ribose pyrophosphatase	_____________201___________215\n_____________\|_____________\|\n5'-AUU...AACAA_________C___CAACC...UUU-3'\n______________UGCUUAAGC_AGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\n______________ACGAAUUCG_UCU\n3'-UUU...UUUGA_________U___UCGUG...CAA-5'\n_____________\|_____________\|\n_____________55____________41\n	204 -- 210	46 -- 52	-15.7149 kcal/mol	1.83586 kcal/mol	6.01534 kcal/mol	201 215@LB@ \| \|@LB@5'-AUU...AACAA C CAACC...UUU-3'@LB@ UGCUUAAGC AGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ ACGAAUUCG UCU@LB@3'-UUU...UUUGA U UCGUG...CAA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -15.7149 kcal/mol@LB@Unfolding Energy - mRNA 1.83586 kcal/mol@LB@Unfolding Energy - sRNA 6.01534 kcal/mol@LB@@LB@Position - mRNA 202 -- 214@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 46 -- 52@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein	_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@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)

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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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