Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
196	0.02499	0.4226	b3098	yqjD	-9.33	0.238834	67 -- 86	37 -- 57	membrane-anchored ribosome-binding protein	_____________66____________________87\n_____________\|_____________________\|\n5'-UCA...GAGGC_______AAA________C__AUAAG...AAG-3'\n______________GAAGCAA____GGCGAUG_CG\n______________\|\|\|\|\|\|\|____:\|\|:\|\|\|_\|\|\n______________CUUCGUU____UCGUUAC_GC\n3'-UUU...AUGAC_______ACAC_______A__ACGAA...GCG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	77 -- 83	40 -- 46	-18.4137 kcal/mol	5.85817 kcal/mol	3.2267 kcal/mol	66 87@LB@ \| \|@LB@5'-UCA...GAGGC AAA C AUAAG...AAG-3'@LB@ GAAGCAA GGCGAUG CG@LB@ \|\|\|\|\|\|\| :\|\|:\|\|\| \|\|@LB@ CUUCGUU UCGUUAC GC@LB@3'-UUU...AUGAC ACAC A ACGAA...GCG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -18.4137 kcal/mol@LB@Unfolding Energy - mRNA 5.85817 kcal/mol@LB@Unfolding Energy - sRNA 3.2267 kcal/mol@LB@@LB@Position - mRNA 67 -- 86@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 40 -- 46@LB@
200	0.02516	0.4226	b2566	era	-10.17	0.177109	195 -- 210	37 -- 61	membrane-associated 16S rRNA-binding GTPase	_____________194_______________________211\n_____________\|_________________________\|\n5'-UUG...CUGGA_________________________AUAAA...UCU-3'\n______________GCUGGAA______UGAGCA___UCG\n______________:\|\|\|\|\|\|______\|\|\|\|\|\|___\|\|\|\n______________UGACCUU______ACUCGU___AGC\n3'-UUU...CAUUA_______CGUUAC______UAC___ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	195 -- 201	55 -- 61	-17.979 kcal/mol	4.50899 kcal/mol	3.30158 kcal/mol	194 211@LB@ \| \|@LB@5'-UUG...CUGGA AUAAA...UCU-3'@LB@ GCUGGAA UGAGCA UCG@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UGACCUU ACUCGU AGC@LB@3'-UUU...CAUUA CGUUAC UAC ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -17.979 kcal/mol@LB@Unfolding Energy - mRNA 4.50899 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 195 -- 210@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 55 -- 61@LB@
61	0.005602	0.2905	b1778	msrB	-11.92	0.091967	166 -- 177	43 -- 54	methionine sulfoxide reductase B	_____________165__________178\n_____________\|____________\|\n5'-CUU...GUCAC____________CGAUU...GUC-3'\n______________GUAAUGUGAGCA\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________CGUUACACUCGU\n3'-UUU...ACCUU____________UACAG...GCG-5'\n_____________\|____________\|\n_____________55___________42\n	171 -- 177	43 -- 49	-18.0171 kcal/mol	2.89402 kcal/mol	3.19978 kcal/mol	165 178@LB@ \| \|@LB@5'-CUU...GUCAC CGAUU...GUC-3'@LB@ GUAAUGUGAGCA@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ CGUUACACUCGU@LB@3'-UUU...ACCUU UACAG...GCG-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -18.0171 kcal/mol@LB@Unfolding Energy - mRNA 2.89402 kcal/mol@LB@Unfolding Energy - sRNA 3.19978 kcal/mol@LB@@LB@Position - mRNA 166 -- 177@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 43 -- 49@LB@
90	0.009279	0.3393	b0817	mntR	-11.60	0.104050	186 -- 211	37 -- 65	Mn(2+)-responsive manganese regulon transcriptional regulator	_____________185___________________________212\n_____________\|_____________________________\|\n5'-CUU...CACCA_____A________CAA_____C______CGCAG...AUC-3'\n______________UAAUG__GGAAGCA___UGAGU___GUCG\n______________\|\|\|\|:__\|\|\|\|\|\|\|___\|\|\|\|:___\|\|\|\|\n______________AUUAU__CCUUCGU___ACUCG___CAGC\n3'-UUU...GAUUC_____GA_______UAC_____UUA____ACGAA...GCG-5'\n_____________\|_____________________________\|\n_____________66____________________________36\n	192 -- 198	52 -- 58	-22.6144 kcal/mol	7.71005 kcal/mol	3.30549 kcal/mol	185 212@LB@ \| \|@LB@5'-CUU...CACCA A CAA C CGCAG...AUC-3'@LB@ UAAUG GGAAGCA UGAGU GUCG@LB@ \|\|\|\|: \|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|@LB@ AUUAU CCUUCGU ACUCG CAGC@LB@3'-UUU...GAUUC GA UAC UUA ACGAA...GCG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -22.6144 kcal/mol@LB@Unfolding Energy - mRNA 7.71005 kcal/mol@LB@Unfolding Energy - sRNA 3.30549 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 52 -- 58@LB@
76	0.007246	0.3134	b4174	hflK	-10.43	0.160892	249 -- 292	51 -- 90	modulator for HflB protease specific for phage lambda cII repressor	_____________248_____________________________________________293\n_____________\|_______________________________________________\|\n5'-AGA...CGUGG__________AA___________AACUC____GGAAA______A___AGGCGGUC-3'\n______________GGAAG_CAGC__ACCUGGC_GGC_____UGAG______UGGAA_CAA\n______________::\|\|\|_\|\|\|\|__\|\|\|:\|\|\|_\|\|\|_____\|:\|\|______\|\|\|\|\|_\|\|\|\n______________UUUUC_GUCG__UGGGCCG_CCG_____AUUC______ACCUU_GUU\n___________3'-_____G_____________A____________AUUAUG_____C___ACACU...GCG-5'\n______________\|______________________________________________\|\n______________90_____________________________________________50\n	260 -- 266	74 -- 80	-34.0568 kcal/mol	9.12339 kcal/mol	14.5017 kcal/mol	248 293@LB@ \| \|@LB@5'-AGA...CGUGG AA AACUC GGAAA A AGGCGGUC-3'@LB@ GGAAG CAGC ACCUGGC GGC UGAG UGGAA CAA@LB@ ::\|\|\| \|\|\|\| \|\|\|:\|\|\| \|\|\| \|:\|\| \|\|\|\|\| \|\|\|@LB@ UUUUC GUCG UGGGCCG CCG AUUC ACCUU GUU@LB@ 3'- G A AUUAUG C ACACU...GCG-5'@LB@ \| \|@LB@ 90 50@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -34.0568 kcal/mol@LB@Unfolding Energy - mRNA 9.12339 kcal/mol@LB@Unfolding Energy - sRNA 14.5017 kcal/mol@LB@@LB@Position - mRNA 249 -- 292@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 74 -- 80@LB@
109	0.01153	0.3513	b0826	moeB	-14.46	0.034286	118 -- 145	37 -- 63	molybdopterin synthase sulfurylase	_____________117__________________________146\n_____________\|____________________________\|\n5'-CUU...UUAUC_________C_____CGC________G_AAGUG...GCG-3'\n______________GUGCUGGAA_GCGAU___GGCAAUGU_G\n______________:\|:\|\|\|\|\|\|_\|\|:\|\|___:\|\|\|\|\|\|\|_\|\n______________UAUGACCUU_CGUUA___UCGUUACA_C\n3'-UUU...UUCAU_______________CAC________G_ACGAA...GCG-5'\n_____________\|____________________________\|\n_____________64___________________________36\n	137 -- 143	39 -- 45	-30.0553 kcal/mol	12.2918 kcal/mol	3.30267 kcal/mol	117 146@LB@ \| \|@LB@5'-CUU...UUAUC C CGC G AAGUG...GCG-3'@LB@ GUGCUGGAA GCGAU GGCAAUGU G@LB@ :\|:\|\|\|\|\|\| \|\|:\|\| :\|\|\|\|\|\|\| \|@LB@ UAUGACCUU CGUUA UCGUUACA C@LB@3'-UUU...UUCAU CAC G ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -30.0553 kcal/mol@LB@Unfolding Energy - mRNA 12.2918 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 118 -- 145@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 39 -- 45@LB@
91	0.009487	0.3393	b4148	sugE	-13.59	0.048204	42 -- 77	12 -- 46	multidrug efflux system protein	_____________41___________________________________78\n_____________\|____________________________________\|\n5'-CGC...ACGAC___U_________CG__UGUU__________UA___ACAAA...UUA-3'\n______________AGC_GUGUCGUGC__UU____UUUUCUGCGA__GUC\n______________\|\|\|_:\|\|\|\|\|\|\|\|__\|:____\|\|:\|\|:\|\|\|\|__\|\|\|\n______________UCG_UACAGCACG__AG____AAGAGGCGCU__CAG\n3'-UUU...UACAC___U_________AA__UCC___________CC___AAGGA...GCG-5'\n_____________\|____________________________________\|\n_____________47___________________________________11\n	66 -- 72	17 -- 23	-35.5696 kcal/mol	9.46718 kcal/mol	12.5096 kcal/mol	41 78@LB@ \| \|@LB@5'-CGC...ACGAC U CG UGUU UA ACAAA...UUA-3'@LB@ AGC GUGUCGUGC UU UUUUCUGCGA GUC@LB@ \|\|\| :\|\|\|\|\|\|\|\| \|: \|\|:\|\|:\|\|\|\| \|\|\|@LB@ UCG UACAGCACG AG AAGAGGCGCU CAG@LB@3'-UUU...UACAC U AA UCC CC AAGGA...GCG-5'@LB@ \| \|@LB@ 47 11@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -35.5696 kcal/mol@LB@Unfolding Energy - mRNA 9.46718 kcal/mol@LB@Unfolding Energy - sRNA 12.5096 kcal/mol@LB@@LB@Position - mRNA 42 -- 77@LB@Position - sRNA 12 -- 46@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 17 -- 23@LB@
13	0.000833	0.2153	b1531	marA	-8.74	0.292618	190 -- 205	38 -- 57	multiple antibiotic resistance transcriptional regulator	_____________189__________________206\n_____________\|____________________\|\n5'-AAG...AAAAA____________________CAGAC...AGC-3'\n______________GAGGUA___UGA_CGAUGUC\n______________\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\n______________CUUCGU___ACU_GUUACAG\n3'-UUU...AUGAC______UAC___C_______CACGA...GCG-5'\n_____________\|____________________\|\n_____________58___________________37\n	199 -- 205	38 -- 44	-15.3925 kcal/mol	3.44101 kcal/mol	3.2161 kcal/mol	189 206@LB@ \| \|@LB@5'-AAG...AAAAA CAGAC...AGC-3'@LB@ GAGGUA UGA CGAUGUC@LB@ \|\|:\|:\| \|\|\| \|:\|\|\|\|\|@LB@ CUUCGU ACU GUUACAG@LB@3'-UUU...AUGAC UAC C CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -15.3925 kcal/mol@LB@Unfolding Energy - mRNA 3.44101 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
35	0.003076	0.2776	b1678	ldtE	-14.38	0.035403	2 -- 13	49 -- 60	murein L D-transpeptidase	_____________1____________14\n_____________\|____________\|\n__________5'-U____________AUUCG...GCC-3'\n______________CUGGAAGCGAUG\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________GACCUUCGUUAC\n3'-UUU...AUUAU____________ACUCG...GCG-5'\n_____________\|____________\|\n_____________61___________48\n	7 -- 13	49 -- 55	-19.7187 kcal/mol	2.33169 kcal/mol	3.00762 kcal/mol	1 14@LB@ \| \|@LB@ 5'-U AUUCG...GCC-3'@LB@ CUGGAAGCGAUG@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ GACCUUCGUUAC@LB@3'-UUU...AUUAU ACUCG...GCG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -19.7187 kcal/mol@LB@Unfolding Energy - mRNA 2.33169 kcal/mol@LB@Unfolding Energy - sRNA 3.00762 kcal/mol@LB@@LB@Position - mRNA 2 -- 13@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 49 -- 55@LB@
80	0.007461	0.3134	b0925	ldtD	-10.36	0.165445	187 -- 206	37 -- 61	murein L D-transpeptidase	_____________186_______________________207\n_____________\|_________________________\|\n5'-AAG...UAAAA__A______________G_______CUUAA...CUG-3'\n______________AC_GGGGGCA_____AG_GAUGUUG\n______________\|\|_\|\|::\|\|\|_____\|\|_:\|\|\|\|:\|\n______________UG_CCUUCGU_____UC_UUACAGC\n3'-UUU...CAUUA__A_______UACAC__G_______ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	200 -- 206	37 -- 43	-19.2999 kcal/mol	5.64293 kcal/mol	3.30158 kcal/mol	186 207@LB@ \| \|@LB@5'-AAG...UAAAA A G CUUAA...CUG-3'@LB@ AC GGGGGCA AG GAUGUUG@LB@ \|\| \|\|::\|\|\| \|\| :\|\|\|\|:\|@LB@ UG CCUUCGU UC UUACAGC@LB@3'-UUU...CAUUA A UACAC G ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -19.2999 kcal/mol@LB@Unfolding Energy - mRNA 5.64293 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 37 -- 43@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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