Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
114	0.01806	0.5155	b3033	yqiB	-9.53	0.119911	174 -- 206	15 -- 50	DUF1249 protein YqiB	_____________173__________________________________207\n_____________\|____________________________________\|\n5'-UGG...AUCAU__A_____AAA_____________C___________CGUUA...GCG-3'\n______________CA_GCGUU___AAAUGAGUG__GG__AUAAAUGAAG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|:\|\|__\|\|__\|\|\|\|\|\|:\|\|\|\n______________GU_UGUAA___UUUACUUAC__CC__UAUUUAUUUC\n3'-UUU...CAUUU__C_____GUC_________UG__AU__________AAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	200 -- 206	15 -- 21	-20.8588 kcal/mol	5.00376 kcal/mol	6.32253 kcal/mol	173 207@LB@ \| \|@LB@5'-UGG...AUCAU A AAA C CGUUA...GCG-3'@LB@ CA GCGUU AAAUGAGUG GG AUAAAUGAAG@LB@ \|\| :\|:\|\| \|\|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|:\|\|\|@LB@ GU UGUAA UUUACUUAC CC UAUUUAUUUC@LB@3'-UUU...CAUUU C GUC UG AU AAUUA...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -20.8588 kcal/mol@LB@Unfolding Energy - mRNA 5.00376 kcal/mol@LB@Unfolding Energy - sRNA 6.32253 kcal/mol@LB@@LB@Position - mRNA 174 -- 206@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 15 -- 21@LB@
19	0.0008973	0.1482	b3964	yijD	-17.08	0.001951	152 -- 223	2 -- 55	DUF1422 family inner membrane protein	_____________151______________________________________________________________________224\n_____________\|________________________________________________________________________\|\n5'-ACU...UCGCC______A___GAAAACCGCAAU_____CG_______UGAAG____A________AC___CA___CAA_____AGGUA...UGC-3'\n______________GUGAAC_AGA____________UAUUC__GGAAAUG_____GACG_GUAAUGAA__AAG__AAU___GAUAG\n______________\|\|:\|\|\|_\|\|\|____________:\|\|\|\|__:\|\|\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|__\|\|\|__\|\|\|___\|\|\|\|\|\n______________CAUUUG_UCU____________GUAAG__UCUUUAC_____CUGC_CAUUAUUU__UUC__UUA___CUAUC\n3'-UUU...AUCCC____________________________________UUA_______________AU___AA___CUA_____G-5'\n_____________\|________________________________________________________________________\|\n_____________56_______________________________________________________________________1\n	199 -- 205	20 -- 26	-31.4266 kcal/mol	8.00944 kcal/mol	6.33752 kcal/mol	151 224@LB@ \| \|@LB@5'-ACU...UCGCC A GAAAACCGCAAU CG UGAAG A AC CA CAA AGGUA...UGC-3'@LB@ GUGAAC AGA UAUUC GGAAAUG GACG GUAAUGAA AAG AAU GAUAG@LB@ \|\|:\|\|\| \|\|\| :\|\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\| \|\|\| \|\|\| \|\|\|\|\|@LB@ CAUUUG UCU GUAAG UCUUUAC CUGC CAUUAUUU UUC UUA CUAUC@LB@3'-UUU...AUCCC UUA AU AA CUA G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -17.08 kcal/mol@LB@Hybridization Energy -31.4266 kcal/mol@LB@Unfolding Energy - mRNA 8.00944 kcal/mol@LB@Unfolding Energy - sRNA 6.33752 kcal/mol@LB@@LB@Position - mRNA 152 -- 223@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 20 -- 26@LB@
30	0.002455	0.2686	b4551	yheV	-11.67	0.043500	186 -- 213	38 -- 63	DUF2387 family putative metal-binding protein	_____________185__________________________214\n_____________\|____________________________\|\n5'-AUC...AAUUU______A_______G_U____A__C___AACGU...UUG-3'\n______________GAGUAG_GGGUAAA_A_GGCA_UC_GAA\n______________:\|:\|\|\|_\|\|\|\|\|\|\|_\|_\|:\|\|_\|\|_\|\|\|\n______________UUUAUC_CCCAUUU_U_CUGU_AG_CUU\n3'-UUU...CCAAC______________G______A__U___UACUU...UCG-5'\n_____________\|____________________________\|\n_____________64___________________________37\n	193 -- 199	51 -- 57	-22.6178 kcal/mol	4.69416 kcal/mol	6.25833 kcal/mol	185 214@LB@ \| \|@LB@5'-AUC...AAUUU A G U A C AACGU...UUG-3'@LB@ GAGUAG GGGUAAA A GGCA UC GAA@LB@ :\|:\|\|\| \|\|\|\|\|\|\| \| \|:\|\| \|\| \|\|\|@LB@ UUUAUC CCCAUUU U CUGU AG CUU@LB@3'-UUU...CCAAC G A U UACUU...UCG-5'@LB@ \| \|@LB@ 64 37@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -22.6178 kcal/mol@LB@Unfolding Energy - mRNA 4.69416 kcal/mol@LB@Unfolding Energy - sRNA 6.25833 kcal/mol@LB@@LB@Position - mRNA 186 -- 213@LB@Position - sRNA 38 -- 63@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
31	0.00291	0.3081	b1205	ychH	-11.03	0.059536	152 -- 163	53 -- 64	DUF2583 family putative inner membrane protein	_____________151__________164\n_____________\|____________\|\n5'-CAA...CAUAA____G_______UUCCC...UAC-3'\n______________GGAA_AGGGGUA\n______________\|:\|\|_\|\|\|\|\|\|\|\n______________CUUU_UCCCCAU\n3'-UUU...GCCAA____A_______UUGUC...UCG-5'\n_____________\|____________\|\n_____________65___________52\n	157 -- 163	53 -- 59	-13.5677 kcal/mol	2.46117 kcal/mol	0.0747267 kcal/mol	151 164@LB@ \| \|@LB@5'-CAA...CAUAA G UUCCC...UAC-3'@LB@ GGAA AGGGGUA@LB@ \|:\|\| \|\|\|\|\|\|\|@LB@ CUUU UCCCCAU@LB@3'-UUU...GCCAA A UUGUC...UCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.5677 kcal/mol@LB@Unfolding Energy - mRNA 2.46117 kcal/mol@LB@Unfolding Energy - sRNA 0.0747267 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 53 -- 59@LB@
173	0.02817	0.531	b0952	pqiC	-7.60	0.267291	63 -- 71	1 -- 9	DUF330 family putative lipoprotein	_____________62________72\n_____________\|_________\|\n5'-ACG...AACAA_________GGAUA...GCG-3'\n______________GAUGGUGGC\n______________\|\|\|\|:\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	65 -- 71	1 -- 7	-13.4268 kcal/mol	5.80912 kcal/mol	0.0200155 kcal/mol	62 72@LB@ \| \|@LB@5'-ACG...AACAA GGAUA...GCG-3'@LB@ GAUGGUGGC@LB@ \|\|\|\|:\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.60 kcal/mol@LB@Hybridization Energy -13.4268 kcal/mol@LB@Unfolding Energy - mRNA 5.80912 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 63 -- 71@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 1 -- 7@LB@
68	0.00983	0.4523	b1321	ycjX	-10.80	0.066674	34 -- 41	55 -- 62	DUF463 family protein puatative P-loop NTPase	_____________33_______42\n_____________\|________\|\n5'-UGA...UAAAU________ACAUA...CAG-3'\n______________AGUAGGGG\n______________\|:\|\|\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	35 -- 41	55 -- 61	-12.2037 kcal/mol	1.3787 kcal/mol	0.0270923 kcal/mol	33 42@LB@ \| \|@LB@5'-UGA...UAAAU ACAUA...CAG-3'@LB@ AGUAGGGG@LB@ \|:\|\|\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -12.2037 kcal/mol@LB@Unfolding Energy - mRNA 1.3787 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 34 -- 41@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 55 -- 61@LB@
170	0.02787	0.531	b3184	yhbE	-10.77	0.067448	1 -- 31	11 -- 53	EamA family inner membrane putative transporter	______________1__________________________________________32\n______________\|__________________________________________\|\n___________5'-_________GUA_________AUU___________________AGGCC...UGG-3'\n______________AAGCAGACG_____AAGUGAA___CG__________AAGUUAA\n______________\|\|:\|\|\|\|\|:_____\|\|:\|\|\|\|___\|\|__________\|\|\|\|\|\|\|\n______________UUUGUCUGU_____UUUACUU___GC__________UUCAAUU\n3'-UUU...CCCCA_________AAGUC_______ACU__CAUUAUUUAU_______ACUAC...UCG-5'\n_____________\|___________________________________________\|\n_____________54__________________________________________10\n	25 -- 31	11 -- 17	-18.1985 kcal/mol	1.09209 kcal/mol	6.3325 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GUA AUU AGGCC...UGG-3'@LB@ AAGCAGACG AAGUGAA CG AAGUUAA@LB@ \|\|:\|\|\|\|\|: \|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUGUCUGU UUUACUU GC UUCAAUU@LB@3'-UUU...CCCCA AAGUC ACU CAUUAUUUAU ACUAC...UCG-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -18.1985 kcal/mol@LB@Unfolding Energy - mRNA 1.09209 kcal/mol@LB@Unfolding Energy - sRNA 6.3325 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
57	0.007764	0.4472	b0585	fes	-12.40	0.029926	182 -- 237	1 -- 55	enterobactin/ferrienterobactin esterase	_____________181___________________________________________________________238\n_____________\|_____________________________________________________________\|\n5'-CAU...GCACA_______U__G____________U_______CGU____AGU__GA_____GAGC_______AGUCG...GGU-3'\n______________GUAAACA_GG_GUU_____AUGG_GUGACGG___UAAA___AG__AGUGA____UGGUGGC\n______________\|\|\|\|\|\|\|_\|:_:\|\|_____\|\|\|:_:\|\|\|\|\|\|___\|\|\|\|___\|\|__\|:\|\|\|____\|\|:\|:\|\|\n______________CAUUUGU_CU_UAA_____UACU_UACUGCC___AUUU___UC__UUACU____ACUAUCG\n3'-UUU...AUCCC__________G___GUCUU____________AUU____AUU__AA________________-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	231 -- 237	1 -- 7	-34.1879 kcal/mol	15.4551 kcal/mol	6.33758 kcal/mol	181 238@LB@ \| \|@LB@5'-CAU...GCACA U G U CGU AGU GA GAGC AGUCG...GGU-3'@LB@ GUAAACA GG GUU AUGG GUGACGG UAAA AG AGUGA UGGUGGC@LB@ \|\|\|\|\|\|\| \|: :\|\| \|\|\|: :\|\|\|\|\|\| \|\|\|\| \|\| \|:\|\|\| \|\|:\|:\|\|@LB@ CAUUUGU CU UAA UACU UACUGCC AUUU UC UUACU ACUAUCG@LB@3'-UUU...AUCCC G GUCUU AUU AUU AA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -34.1879 kcal/mol@LB@Unfolding Energy - mRNA 15.4551 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 182 -- 237@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 1 -- 7@LB@
126	0.01995	0.5155	b2452	eutH	-9.16	0.141344	190 -- 206	5 -- 22	ethanolamine transporter	_____________189________________207\n_____________\|__________________\|\n5'-UUG...ACAGG________GC________AUUAA...UCC-3'\n______________GAGUAAAG__GAUGG_GA\n______________:\|:\|\|\|\|\|__:\|\|\|:_\|\|\n______________UUUAUUUC__UUACU_CU\n3'-UUU...CAUUA________AA_____A__AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	191 -- 197	15 -- 21	-11.7395 kcal/mol	2.48279 kcal/mol	0.0977783 kcal/mol	189 207@LB@ \| \|@LB@5'-UUG...ACAGG GC AUUAA...UCC-3'@LB@ GAGUAAAG GAUGG GA@LB@ :\|:\|\|\|\|\| :\|\|\|: \|\|@LB@ UUUAUUUC UUACU CU@LB@3'-UUU...CAUUA AA A AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -11.7395 kcal/mol@LB@Unfolding Energy - mRNA 2.48279 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
105	0.01645	0.5059	b0454	ybaZ	-8.45	0.190978	84 -- 93	47 -- 56	excision repair protein alkyltransferase-like protein ATL	_____________83_________94\n_____________\|__________\|\n5'-AGG...GACCU__________GUAGC...UUC-3'\n______________GGUAAACAGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUCU\n3'-UUU...UAUCC__________GUAAG...UCG-5'\n_____________\|__________\|\n_____________57_________46\n	87 -- 93	47 -- 53	-13.2019 kcal/mol	2.68818 kcal/mol	2.06629 kcal/mol	83 94@LB@ \| \|@LB@5'-AGG...GACCU GUAGC...UUC-3'@LB@ GGUAAACAGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUCU@LB@3'-UUU...UAUCC GUAAG...UCG-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.2019 kcal/mol@LB@Unfolding Energy - mRNA 2.68818 kcal/mol@LB@Unfolding Energy - sRNA 2.06629 kcal/mol@LB@@LB@Position - mRNA 84 -- 93@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 87 -- 93@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)

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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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