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
81	0.008086	0.3318	b3114	tdcE	-10.99	0.130865	237 -- 290	38 -- 86	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase	_____________236_____________________________________________________291\n_____________\|_______________________________________________________\|\n5'-AGA...UGUAC____A___A____U_____UUAA_____CGG_______AAACGAAAU________CGCGA...UUA-3'\n______________GCCG_CGC_UGGC_UGGCU____AGGUA___ACUGGAA__________UAAUGUC\n______________\|\|\|:_\|:\|_:\|\|\|_\|\|\|\|\|____\|:\|\|\|___\|\|\|\|\|\|\|__________:\|\|\|\|\|\|\n______________CGGU_GUG_GCCG_ACCGA____UUCAU___UGACCUU__________GUUACAG\n_______3'-UUUU____C___G___________________UA________CGUUACACUC_______CACGA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________87______________________________________________________37\n	284 -- 290	38 -- 44	-39.8415 kcal/mol	13.9412 kcal/mol	14.9106 kcal/mol	236 291@LB@ \| \|@LB@5'-AGA...UGUAC A A U UUAA CGG AAACGAAAU CGCGA...UUA-3'@LB@ GCCG CGC UGGC UGGCU AGGUA ACUGGAA UAAUGUC@LB@ \|\|\|: \|:\| :\|\|\| \|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGGU GUG GCCG ACCGA UUCAU UGACCUU GUUACAG@LB@ 3'-UUUU C G UA CGUUACACUC CACGA...GCG-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -39.8415 kcal/mol@LB@Unfolding Energy - mRNA 13.9412 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 237 -- 290@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
82	0.008223	0.3318	b1654	grxD	-11.69	0.100410	189 -- 207	43 -- 58	glutaredoxin-4	_____________188_________________208\n_____________\|___________________\|\n5'-AAA...UUUGA________GACAA______CCACU...CUG-3'\n______________GGAAGCAA_____UGAGCA\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________CCUUCGUU_____ACUCGU\n3'-UUU...UAUGA________AC_________UACAG...GCG-5'\n_____________\|___________________\|\n_____________59__________________42\n	190 -- 196	51 -- 57	-19.1647 kcal/mol	4.26252 kcal/mol	3.20949 kcal/mol	188 208@LB@ \| \|@LB@5'-AAA...UUUGA GACAA CCACU...CUG-3'@LB@ GGAAGCAA UGAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCUUCGUU ACUCGU@LB@3'-UUU...UAUGA AC UACAG...GCG-5'@LB@ \| \|@LB@ 59 42@LB@@LB@@LB@Energy -11.69 kcal/mol@LB@Hybridization Energy -19.1647 kcal/mol@LB@Unfolding Energy - mRNA 4.26252 kcal/mol@LB@Unfolding Energy - sRNA 3.20949 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 43 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 51 -- 57@LB@
83	0.008249	0.3318	b0183	rnhB	-13.04	0.059790	42 -- 55	44 -- 58	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________41______________56\n_____________\|_______________\|\n5'-AAU...UUGCA_______________CGCAA...UCC-3'\n______________GGAAG_AGUGUGAGC\n______________\|\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________CCUUC_UUACACUCG\n3'-UUU...UAUGA_____G_________UUACA...GCG-5'\n_____________\|_______________\|\n_____________59______________43\n	49 -- 55	44 -- 50	-21.6429 kcal/mol	5.39444 kcal/mol	3.20799 kcal/mol	41 56@LB@ \| \|@LB@5'-AAU...UUGCA CGCAA...UCC-3'@LB@ GGAAG AGUGUGAGC@LB@ \|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ CCUUC UUACACUCG@LB@3'-UUU...UAUGA G UUACA...GCG-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -21.6429 kcal/mol@LB@Unfolding Energy - mRNA 5.39444 kcal/mol@LB@Unfolding Energy - sRNA 3.20799 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 44 -- 50@LB@
84	0.008296	0.3318	b0892	rarA	-13.69	0.046473	183 -- 215	37 -- 66	recombination intermediate processing DNA-dependent ATPase	_____________182_________________________________216\n_____________\|___________________________________\|\n5'-CAA...UCAAC____GUA________CCUGA________UC_____CUCGA...AUU-3'\n______________GUAA_____GAGGCA_____GUGAGCAA__UGUCG\n______________\|\|\|\|_____\|\|:\|\|\|_____\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CAUU_____CUUCGU_____CACUCGUU__ACAGC\n3'-UUU...CGAUU____AUGAC______UA__________________ACGAA...GCG-5'\n_____________\|___________________________________\|\n_____________67__________________________________36\n	202 -- 208	42 -- 48	-25.9915 kcal/mol	8.99953 kcal/mol	3.30551 kcal/mol	182 216@LB@ \| \|@LB@5'-CAA...UCAAC GUA CCUGA UC CUCGA...AUU-3'@LB@ GUAA GAGGCA GUGAGCAA UGUCG@LB@ \|\|\|\| \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CAUU CUUCGU CACUCGUU ACAGC@LB@3'-UUU...CGAUU AUGAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 67 36@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -25.9915 kcal/mol@LB@Unfolding Energy - mRNA 8.99953 kcal/mol@LB@Unfolding Energy - sRNA 3.30551 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 37 -- 66@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
85	0.008408	0.3323	b1246	oppD	-9.75	0.205761	38 -- 64	37 -- 61	oligopeptide ABC transporter ATPase	_____________37__________________________65\n_____________\|___________________________\|\n5'-AGC...AAGCA_______U___U__C_________G__CGAAC...ACG-3'\n______________GCUGGGG_GCA_UG_UGAGUGAUG_CG\n______________:\|\|\|\|::_\|\|\|_\|\|_\|\|\|\|::\|\|\|_\|\|\n______________UGACCUU_CGU_AC_ACUCGUUAC_GC\n3'-UUU...CAUUA___________U____________A__ACGAA...GCG-5'\n_____________\|___________________________\|\n_____________62__________________________36\n	55 -- 61	40 -- 46	-27.1525 kcal/mol	14.0993 kcal/mol	3.30158 kcal/mol	37 65@LB@ \| \|@LB@5'-AGC...AAGCA U U C G CGAAC...ACG-3'@LB@ GCUGGGG GCA UG UGAGUGAUG CG@LB@ :\|\|\|\|:: \|\|\| \|\| \|\|\|\|::\|\|\| \|\|@LB@ UGACCUU CGU AC ACUCGUUAC GC@LB@3'-UUU...CAUUA U A ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -27.1525 kcal/mol@LB@Unfolding Energy - mRNA 14.0993 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 38 -- 64@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 40 -- 46@LB@
86	0.008505	0.3323	b0879	macB	-10.85	0.137944	147 -- 181	15 -- 61	macrolide ABC transporter peremase/ATPase	_____________146_____________________________________________182\n_____________\|_______________________________________________\|\n5'-AAU...AAAGG___U__________________AA____________GA__G______CCAAA...CGG-3'\n______________GCU_GAAGC_____GGGCGAUG__GU_______GGU__UU_GUGAGG\n______________:\|\|_\|\|\|\|\|_____\|:\|\|:\|\|\|__\|\|_______\|\|\|__\|:_\|:\|\|\|\|\n______________UGA_CUUCG_____CUCGUUAC__CA_______CCA__AG_CGCUCC\n3'-UUU...CAUUA___C_____UUACA________AG__CGAAAGU___AG__G______CAGAA...GCG-5'\n_____________\|_______________________________________________\|\n_____________62______________________________________________14\n	157 -- 163	40 -- 46	-34.4359 kcal/mol	9.61218 kcal/mol	13.9754 kcal/mol	146 182@LB@ \| \|@LB@5'-AAU...AAAGG U AA GA G CCAAA...CGG-3'@LB@ GCU GAAGC GGGCGAUG GU GGU UU GUGAGG@LB@ :\|\| \|\|\|\|\| \|:\|\|:\|\|\| \|\| \|\|\| \|: \|:\|\|\|\|@LB@ UGA CUUCG CUCGUUAC CA CCA AG CGCUCC@LB@3'-UUU...CAUUA C UUACA AG CGAAAGU AG G CAGAA...GCG-5'@LB@ \| \|@LB@ 62 14@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -34.4359 kcal/mol@LB@Unfolding Energy - mRNA 9.61218 kcal/mol@LB@Unfolding Energy - sRNA 13.9754 kcal/mol@LB@@LB@Position - mRNA 147 -- 181@LB@Position - sRNA 15 -- 61@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.008915	0.3393	b2530	iscS	-12.30	0.079567	175 -- 203	40 -- 68	cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent	_____________174___________________________204\n_____________\|_____________________________\|\n5'-AAG...GCAUU________UAC_____UUAUA________AAAUU...UUG-3'\n______________GAGUGAUG___GGAGU_____GAGCAAUG\n______________:\|\|\|:\|\|:___\|:\|\|:_____\|\|\|\|\|\|\|\|\n______________UUCAUUAU___CUUCG_____CUCGUUAC\n3'-UUU...ACCGA________GAC_____UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________39\n	197 -- 203	40 -- 46	-22.6486 kcal/mol	7.04226 kcal/mol	3.30507 kcal/mol	174 204@LB@ \| \|@LB@5'-AAG...GCAUU UAC UUAUA AAAUU...UUG-3'@LB@ GAGUGAUG GGAGU GAGCAAUG@LB@ :\|\|\|:\|\|: \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UUCAUUAU CUUCG CUCGUUAC@LB@3'-UUU...ACCGA GAC UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -22.6486 kcal/mol@LB@Unfolding Energy - mRNA 7.04226 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@LB@
88	0.008994	0.3393	b0721	sdhC	-13.41	0.051766	40 -- 58	43 -- 60	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________39__________________59\n_____________\|___________________\|\n5'-UCC...CGCAU_____________UUU___UGACG...CCG-3'\n______________CUGGAAGCAGUGU___GCA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|___\|\|\|\n______________GACCUUCGUUACA___CGU\n3'-UUU...AUUAU_____________CU____UACAG...GCG-5'\n_____________\|___________________\|\n_____________61__________________42\n	46 -- 52	48 -- 54	-24.0509 kcal/mol	7.34137 kcal/mol	3.29917 kcal/mol	39 59@LB@ \| \|@LB@5'-UCC...CGCAU UUU UGACG...CCG-3'@LB@ CUGGAAGCAGUGU GCA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\|@LB@ GACCUUCGUUACA CGU@LB@3'-UUU...AUUAU CU UACAG...GCG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -13.41 kcal/mol@LB@Hybridization Energy -24.0509 kcal/mol@LB@Unfolding Energy - mRNA 7.34137 kcal/mol@LB@Unfolding Energy - sRNA 3.29917 kcal/mol@LB@@LB@Position - mRNA 40 -- 58@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 48 -- 54@LB@
89	0.009246	0.3393	b1279	yciS	-12.08	0.086714	189 -- 204	46 -- 61	DUF1049 family inner membrane protein function unknown	_____________188______________205\n_____________\|________________\|\n5'-ACC...ACAUA__G_____________AAUAU...UGU-3'\n______________AC_GGAAGUAAUGUGA\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UG_CCUUCGUUACACU\n3'-UUU...CAUUA__A_____________CGUUA...GCG-5'\n_____________\|________________\|\n_____________62_______________45\n	198 -- 204	46 -- 52	-21.4875 kcal/mol	6.16612 kcal/mol	3.24422 kcal/mol	188 205@LB@ \| \|@LB@5'-ACC...ACAUA G AAUAU...UGU-3'@LB@ AC GGAAGUAAUGUGA@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UG CCUUCGUUACACU@LB@3'-UUU...CAUUA A CGUUA...GCG-5'@LB@ \| \|@LB@ 62 45@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -21.4875 kcal/mol@LB@Unfolding Energy - mRNA 6.16612 kcal/mol@LB@Unfolding Energy - sRNA 3.24422 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 46 -- 61@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 46 -- 52@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@

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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