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	Additional homologs
150	0.02489	0.526	b2088	insE1	-9.25	0.136086	235 -- 276	1 -- 55	IS3 transposase A	b0298 b0373 b0540 b1027	_____________234_____________________________________________________277\n_____________\|_______________________________________________________\|\n5'-ACC...ACCCC_______________CC_______UU__C____________CCC___________UUGCU...CUG-3'\n______________GUAAACAG_CAUUCG____UGAAU__CG______AGUGAAG____UGA____AGC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|:____\|\|\|\|\|__\|\|______\|:\|:\|\|\|____\|\|\|____\|\|\|\n______________CAUUUGUC_GUAAGU____ACUUA__GC______UUAUUUC____ACU____UCG\n3'-UUU...AUCCC________U______CUUU_____CU__CAUUAU_______AAUU___ACUA___-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	261 -- 267	15 -- 21	-23.7484 kcal/mol	8.16492 kcal/mol	6.33758 kcal/mol	234 277@LB@ \| \|@LB@5'-ACC...ACCCC CC UU C CCC UUGCU...CUG-3'@LB@ GUAAACAG CAUUCG UGAAU CG AGUGAAG UGA AGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\| \|\| \|:\|:\|\|\| \|\|\| \|\|\|@LB@ CAUUUGUC GUAAGU ACUUA GC UUAUUUC ACU UCG@LB@3'-UUU...AUCCC U CUUU CU CAUUAU AAUU ACUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.7484 kcal/mol@LB@Unfolding Energy - mRNA 8.16492 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 235 -- 276@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 15 -- 21@LB@
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein		______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
149	0.02481	0.526	b2108	yehA	-13.80	0.014025	228 -- 241	1 -- 14	putative fimbrial-like adhesin protein		_____________227____________242\n_____________\|______________\|\n5'-GUU...UUAUA______________UAUGC...UUG-3'\n______________UUAAUGAUGAUGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	235 -- 241	1 -- 7	-16.5389 kcal/mol	2.69058 kcal/mol	0.0473494 kcal/mol	227 242@LB@ \| \|@LB@5'-GUU...UUAUA UAUGC...UUG-3'@LB@ UUAAUGAUGAUGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -16.5389 kcal/mol@LB@Unfolding Energy - mRNA 2.69058 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 228 -- 241@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
169	0.02775	0.531	b2110	yehC	-5.87	0.481945	191 -- 199	20 -- 28	putative periplasmic pilin chaperone		_____________190_______200\n_____________\|_________\|\n5'-CAG...CUCCA_________CAUGG...CCG-3'\n______________GGUAAUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUAUUU\n3'-UUU...UACUG_________AUUUC...UCG-5'\n_____________\|_________\|\n_____________29________19\n	193 -- 199	20 -- 26	-7.96952 kcal/mol	1.36589 kcal/mol	0.737257 kcal/mol	190 200@LB@ \| \|@LB@5'-CAG...CUCCA CAUGG...CCG-3'@LB@ GGUAAUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUAUUU@LB@3'-UUU...UACUG AUUUC...UCG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -7.96952 kcal/mol@LB@Unfolding Energy - mRNA 1.36589 kcal/mol@LB@Unfolding Energy - sRNA 0.737257 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 20 -- 26@LB@
174	0.02825	0.531	b2154	yeiG	-9.96	0.098977	140 -- 169	15 -- 51	S-formylglutathione hydrolase		_____________139_____________________________________170\n_____________\|_______________________________________\|\n5'-GCU...UACUC____C________________AA______U_________AAAUU...UUC-3'\n______________ACAG_ACAU_______UGAAU__ACGGUA___GAUGAAG\n______________\|\|\|\|_\|\|\|\|_______\|\|\|\|\|__\|\|\|\|\|\|___:\|\|:\|\|\|\n______________UGUC_UGUA_______ACUUA__UGCCAU___UUAUUUC\n3'-UUU...CCAUU_________AGUCUUU_____C_______UAU_______AAUUA...UCG-5'\n_____________\|_______________________________________\|\n_____________52______________________________________14\n	163 -- 169	15 -- 21	-20.0225 kcal/mol	3.74261 kcal/mol	6.32297 kcal/mol	139 170@LB@ \| \|@LB@5'-GCU...UACUC C AA U AAAUU...UUC-3'@LB@ ACAG ACAU UGAAU ACGGUA GAUGAAG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| :\|\|:\|\|\|@LB@ UGUC UGUA ACUUA UGCCAU UUAUUUC@LB@3'-UUU...CCAUU AGUCUUU C UAU AAUUA...UCG-5'@LB@ \| \|@LB@ 52 14@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -20.0225 kcal/mol@LB@Unfolding Energy - mRNA 3.74261 kcal/mol@LB@Unfolding Energy - sRNA 6.32297 kcal/mol@LB@@LB@Position - mRNA 140 -- 169@LB@Position - sRNA 15 -- 51@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 15 -- 21@LB@
99	0.01587	0.5059	b2155	cirA	-12.92	0.022646	275 -- 290	1 -- 16	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter		_____________274______________291\n_____________\|________________\|\n5'-GGA...UUAGC___C____________GAAAC...UGG-3'\n______________GGU_GAUGAUGAUGGC\n______________:\|\|_:\|\|\|\|\|\|\|\|:\|\|\n______________UCA_UUACUACUAUCG\n3'-UUU...UUAUU___A____________-5'\n_____________\|_______________\|\n_____________17______________1\n	284 -- 290	1 -- 7	-19.8516 kcal/mol	6.87927 kcal/mol	0.0492804 kcal/mol	274 291@LB@ \| \|@LB@5'-GGA...UUAGC C GAAAC...UGG-3'@LB@ GGU GAUGAUGAUGGC@LB@ :\|\| :\|\|\|\|\|\|\|\|:\|\|@LB@ UCA UUACUACUAUCG@LB@3'-UUU...UUAUU A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -19.8516 kcal/mol@LB@Unfolding Energy - mRNA 6.87927 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 1 -- 7@LB@
177	0.02886	0.5353	b2206	napA	-7.95	0.233634	77 -- 89	1 -- 13	nitrate reductase periplasmic large subunit		_____________76____________90\n_____________\|_____________\|\n5'-GAC...GAUUG_________A___AGAAG...UUG-3'\n______________UGGUGGUGG_AGC\n______________\|::\|\|:\|\|:_\|\|\|\n______________AUUACUACU_UCG\n3'-UUU...UUUCA_________A___-5'\n_____________\|____________\|\n_____________14___________1\n	79 -- 85	5 -- 11	-12.9311 kcal/mol	4.9403 kcal/mol	0.0446954 kcal/mol	76 90@LB@ \| \|@LB@5'-GAC...GAUUG A AGAAG...UUG-3'@LB@ UGGUGGUGG AGC@LB@ \|::\|\|:\|\|: \|\|\|@LB@ AUUACUACU UCG@LB@3'-UUU...UUUCA A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -12.9311 kcal/mol@LB@Unfolding Energy - mRNA 4.9403 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 5 -- 11@LB@
49	0.00563	0.3739	b2239	glpQ	-9.17	0.140723	61 -- 103	1 -- 49	periplasmic glycerophosphodiester phosphodiesterase		_____________60__________________________________________________104\n_____________\|___________________________________________________\|\n5'-CGG...ACCGU____UUC_____CUG__________CUU______U________________GGCAG...UCA-3'\n______________GGAC___UUCGG____GGAUGGCGG_______UA_GG_UAAUGAU__UGGC\n______________:\|\|\|___\|\|\|:\|____\|:\|\|\|:\|\|\|_______\|\|_:\|_\|\|\|\|\|\|\|__\|:\|\|\n______________UCUG___AAGUC____CUUACUGCC_______AU_UC_AUUACUA__AUCG\n3'-UUU...AUUUG____U_______UUUA_________AUUAUUU__U__A_______CU____-5'\n_____________\|__________________________________________________\|\n_____________50_________________________________________________1\n	93 -- 99	7 -- 13	-28.1898 kcal/mol	12.697 kcal/mol	6.32371 kcal/mol	60 104@LB@ \| \|@LB@5'-CGG...ACCGU UUC CUG CUU U GGCAG...UCA-3'@LB@ GGAC UUCGG GGAUGGCGG UA GG UAAUGAU UGGC@LB@ :\|\|\| \|\|\|:\| \|:\|\|\|:\|\|\| \|\| :\| \|\|\|\|\|\|\| \|:\|\|@LB@ UCUG AAGUC CUUACUGCC AU UC AUUACUA AUCG@LB@3'-UUU...AUUUG U UUUA AUUAUUU U A CU -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -28.1898 kcal/mol@LB@Unfolding Energy - mRNA 12.697 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 61 -- 103@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 7 -- 13@LB@
148	0.02477	0.526	b2262	menB	-9.56	0.118602	261 -- 300	25 -- 56	dihydroxynaphthoic acid synthetase		_____________260______________________________________300\n_____________\|________________________________________\|\n5'-CGU...CCGAA___UUCGA__________UU_____AAAUCCACC_______-3'\n______________GGU_____GGACAUUC_G__AUGAA_________GACGGUA\n______________\|\|\|_____:\|\|\|\|\|\|\|_\|__\|\|\|\|\|_________\|\|\|\|\|\|\|\n______________CCA_____UCUGUAAG_C__UACUU_________CUGCCAU\n3'-UUU...UAUCC___UUUG_________U_UU_____A_______________UAUUU...UCG-5'\n_____________\|_________________________________________\|\n_____________57________________________________________24\n	294 -- 300	25 -- 31	-24.8577 kcal/mol	9.0019 kcal/mol	6.29869 kcal/mol	260 300@LB@ \| \|@LB@5'-CGU...CCGAA UUCGA UU AAAUCCACC -3'@LB@ GGU GGACAUUC G AUGAA GACGGUA@LB@ \|\|\| :\|\|\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCA UCUGUAAG C UACUU CUGCCAU@LB@3'-UUU...UAUCC UUUG U UU A UAUUU...UCG-5'@LB@ \| \|@LB@ 57 24@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -24.8577 kcal/mol@LB@Unfolding Energy - mRNA 9.0019 kcal/mol@LB@Unfolding Energy - sRNA 6.29869 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 25 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 25 -- 31@LB@
190	0.03178	0.5492	b2266	elaB	-7.52	0.274944	163 -- 222	3 -- 61	putative membrane-anchored DUF883 family ribosome-binding protein		_____________162_____________________________________________________________223\n_____________\|_______________________________________________________________\|\n5'-ACU...UGUCU____UUAGU______U_____C_C_______GA___AG____UC___UC______________CACGU...AUC-3'\n______________AUAG_____GACAGG__UUUA_G_AAAUGGA__ACG__AAUG__UAA__AGUU__UGGUGAUA\n______________\|\|\|\|_____:\|\|\|\|:__\|\|:\|_\|_\|\|\|\|\|:\|__\|\|\|__\|\|\|:__\|\|\|__\|\|\|\|__\|\|:\|\|\|\|\|\n______________UAUC_____UUGUCU__AAGU_C_UUUACUU__UGC__UUAU__AUU__UCAA__ACUACUAU\n3'-UUU...AACUU____CCCAU______GU______________AC___CA____UU_________UU________CG-5'\n_____________\|_______________________________________________________________\|\n_____________62______________________________________________________________2\n	216 -- 222	3 -- 9	-26.4945 kcal/mol	12.6276 kcal/mol	6.34398 kcal/mol	162 223@LB@ \| \|@LB@5'-ACU...UGUCU UUAGU U C C GA AG UC UC CACGU...AUC-3'@LB@ AUAG GACAGG UUUA G AAAUGGA ACG AAUG UAA AGUU UGGUGAUA@LB@ \|\|\|\| :\|\|\|\|: \|\|:\| \| \|\|\|\|\|:\| \|\|\| \|\|\|: \|\|\| \|\|\|\| \|\|:\|\|\|\|\|@LB@ UAUC UUGUCU AAGU C UUUACUU UGC UUAU AUU UCAA ACUACUAU@LB@3'-UUU...AACUU CCCAU GU AC CA UU UU CG-5'@LB@ \| \|@LB@ 62 2@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -26.4945 kcal/mol@LB@Unfolding Energy - mRNA 12.6276 kcal/mol@LB@Unfolding Energy - sRNA 6.34398 kcal/mol@LB@@LB@Position - mRNA 163 -- 222@LB@Position - sRNA 3 -- 61@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 3 -- 9@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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