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
100	0.01027	0.3393	b0661	miaB	-11.26	0.118120	162 -- 200	37 -- 86	tRNA-i(6)A37 methylthiotransferase	_____________161_________________________________________________201\n_____________\|___________________________________________________\|\n5'-CGC...UAUGC___CU_______________C________UC____________________AUGAC...AAC-3'\n______________GCC__GCAUUC__CUGGCUA_____UAUU____GCAA___GAGCAA_GUCG\n______________\|\|\|__\|\|\|::\|__\|\|\|\|\|\|\|_____\|\|:\|____\|\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________CGG__CGUGGG__GACCGAU_____AUGA____CGUU___CUCGUU_CAGC\n_______3'-UUUU___U_______CC_______UCAUU____CCUU____ACA______A____ACGAA...GCG-5'\n_____________\|___________________________________________________\|\n_____________87__________________________________________________36\n	173 -- 179	68 -- 74	-35.2592 kcal/mol	9.08526 kcal/mol	14.9108 kcal/mol	161 201@LB@ \| \|@LB@5'-CGC...UAUGC CU C UC AUGAC...AAC-3'@LB@ GCC GCAUUC CUGGCUA UAUU GCAA GAGCAA GUCG@LB@ \|\|\| \|\|\|::\| \|\|\|\|\|\|\| \|\|:\| \|\|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ CGG CGUGGG GACCGAU AUGA CGUU CUCGUU CAGC@LB@ 3'-UUUU U CC UCAUU CCUU ACA A ACGAA...GCG-5'@LB@ \| \|@LB@ 87 36@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -35.2592 kcal/mol@LB@Unfolding Energy - mRNA 9.08526 kcal/mol@LB@Unfolding Energy - sRNA 14.9108 kcal/mol@LB@@LB@Position - mRNA 162 -- 200@LB@Position - sRNA 37 -- 86@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 68 -- 74@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@
110	0.01171	0.3513	b0613	citG	-15.71	0.020947	180 -- 206	37 -- 61	2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase	_____________179_________________________207\n_____________\|___________________________\|\n5'-UGA...CAACC__A________C__C___A________AUGCC...UCA-3'\n______________GC_UGGAGGCA_UG_UGA_CGAUGUCG\n______________:\|_\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|:\|\|\|\|\|\|\n______________UG_ACCUUCGU_AC_ACU_GUUACAGC\n3'-UUU...CAUUA___________U______C________ACGAA...GCG-5'\n_____________\|___________________________\|\n_____________62__________________________36\n	200 -- 206	37 -- 43	-28.5741 kcal/mol	9.5654 kcal/mol	3.30158 kcal/mol	179 207@LB@ \| \|@LB@5'-UGA...CAACC A C C A AUGCC...UCA-3'@LB@ GC UGGAGGCA UG UGA CGAUGUCG@LB@ :\| \|\|\|\|:\|\|\| \|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UG ACCUUCGU AC ACU GUUACAGC@LB@3'-UUU...CAUUA U C ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -15.71 kcal/mol@LB@Hybridization Energy -28.5741 kcal/mol@LB@Unfolding Energy - mRNA 9.5654 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 37 -- 43@LB@
115	0.01202	0.3513	b1881	cheZ	-13.42	0.051545	178 -- 197	37 -- 61	chemotaxis regulator protein phosphatase for CheY	_____________177_______________________198\n_____________\|_________________________\|\n5'-AUU...GAGAA_________________________ACUAU...GGG-3'\n______________ACUGG__GC_AUGUGAG_GAUG_CG\n______________\|\|\|\|\|__\|\|_\|\|\|\|\|\|\|_:\|\|\|_\|\|\n______________UGACC__CG_UACACUC_UUAC_GC\n3'-UUU...CAUUA_____UU__U_______G____A__ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	185 -- 191	45 -- 51	-22.2356 kcal/mol	5.51256 kcal/mol	3.30158 kcal/mol	177 198@LB@ \| \|@LB@5'-AUU...GAGAA ACUAU...GGG-3'@LB@ ACUGG GC AUGUGAG GAUG CG@LB@ \|\|\|\|\| \|\| \|\|\|\|\|\|\| :\|\|\| \|\|@LB@ UGACC CG UACACUC UUAC GC@LB@3'-UUU...CAUUA UU U G A ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -22.2356 kcal/mol@LB@Unfolding Energy - mRNA 5.51256 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 178 -- 197@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 45 -- 51@LB@
127	0.01387	0.3627	b1224	narG	-12.01	0.089072	151 -- 160	37 -- 46	nitrate reductase 1 alpha subunit	_____________150________161\n_____________\|__________\|\n5'-UAA...ACAUU__________AUUUA...AGG-3'\n______________AGCAAUGUCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGUUACAGC\n3'-UUU...UACAC__________ACGAA...GCG-5'\n_____________\|__________\|\n_____________47_________36\n	154 -- 160	37 -- 43	-14.8133 kcal/mol	1.65076 kcal/mol	1.15554 kcal/mol	150 161@LB@ \| \|@LB@5'-UAA...ACAUU AUUUA...AGG-3'@LB@ AGCAAUGUCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGUUACAGC@LB@3'-UUU...UACAC ACGAA...GCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -14.8133 kcal/mol@LB@Unfolding Energy - mRNA 1.65076 kcal/mol@LB@Unfolding Energy - sRNA 1.15554 kcal/mol@LB@@LB@Position - mRNA 151 -- 160@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 37 -- 43@LB@
132	0.01454	0.37	b1083	flgL	-7.54	0.428067	272 -- 293	37 -- 57	flagellar hook-filament junction protein	_____________271____________________294\n_____________\|______________________\|\n5'-UUG...UGGAU______CG_C__ACA_______ACGGGUA-3'\n______________GAAGUA__G_GA___GAUGUCG\n______________\|\|\|\|:\|__\|_\|\|___:\|\|\|\|\|\|\n______________CUUCGU__C_CU___UUACAGC\n3'-UUU...AUGAC______UA_A__CG________ACGAA...GCG-5'\n_____________\|______________________\|\n_____________58_____________________36\n	287 -- 293	37 -- 43	-16.4529 kcal/mol	5.68525 kcal/mol	3.2267 kcal/mol	271 294@LB@ \| \|@LB@5'-UUG...UGGAU CG C ACA ACGGGUA-3'@LB@ GAAGUA G GA GAUGUCG@LB@ \|\|\|\|:\| \| \|\| :\|\|\|\|\|\|@LB@ CUUCGU C CU UUACAGC@LB@3'-UUU...AUGAC UA A CG ACGAA...GCG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -7.54 kcal/mol@LB@Hybridization Energy -16.4529 kcal/mol@LB@Unfolding Energy - mRNA 5.68525 kcal/mol@LB@Unfolding Energy - sRNA 3.2267 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
137	0.01545	0.379	b0881	clpS	-11.92	0.091960	57 -- 82	37 -- 62	regulatory protein for ClpA substrate specificity	_____________56_________________________83\n_____________\|__________________________\|\n5'-GCA...AACGC_____AC__G_______CA_______CUGAU...UCA-3'\n______________UAUUG__AG_AAUGUGA__GAUGUCG\n______________\|\|:\|\|__\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________AUGAC__UC_UUACACU__UUACAGC\n3'-UUU...UCAUU_____CU__G_______CG_______ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	76 -- 82	37 -- 43	-23.3317 kcal/mol	8.10565 kcal/mol	3.3026 kcal/mol	56 83@LB@ \| \|@LB@5'-GCA...AACGC AC G CA CUGAU...UCA-3'@LB@ UAUUG AG AAUGUGA GAUGUCG@LB@ \|\|:\|\| \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ AUGAC UC UUACACU UUACAGC@LB@3'-UUU...UCAUU CU G CG ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -23.3317 kcal/mol@LB@Unfolding Energy - mRNA 8.10565 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 57 -- 82@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 37 -- 43@LB@
161	0.02011	0.4072	b2820	recB	-12.55	0.072418	202 -- 213	37 -- 48	exonuclease V (RecBCD complex) beta subunit	_____________201__________214\n_____________\|____________\|\n5'-GGC...AAGAA____________CCGAG...UUG-3'\n______________UGAGUGAUGUCG\n______________\|\|\|\|::\|\|\|\|\|\|\n______________ACUCGUUACAGC\n3'-UUU...GUUAC____________ACGAA...GCG-5'\n_____________\|____________\|\n_____________49___________36\n	207 -- 213	37 -- 43	-16.4196 kcal/mol	2.71715 kcal/mol	1.1567 kcal/mol	201 214@LB@ \| \|@LB@5'-GGC...AAGAA CCGAG...UUG-3'@LB@ UGAGUGAUGUCG@LB@ \|\|\|\|::\|\|\|\|\|\|@LB@ ACUCGUUACAGC@LB@3'-UUU...GUUAC ACGAA...GCG-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.4196 kcal/mol@LB@Unfolding Energy - mRNA 2.71715 kcal/mol@LB@Unfolding Energy - sRNA 1.1567 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 37 -- 43@LB@
174	0.02116	0.4072	b3081	fadH	-11.31	0.116093	186 -- 215	37 -- 63	2 4-dienoyl-CoA reductase NADH and FMN-linked	_____________185______________________________216\n_____________\|________________________________\|\n5'-UGG...UUUAC______________UUUA_____UACCC____CUGUU...ACC-3'\n______________AUACUGGA__CAAU____UGAGC_____GUCG\n______________\|\|\|\|\|\|\|\|__\|\|\|\|____\|\|\|\|\|_____\|\|\|\|\n______________UAUGACCU__GUUA____ACUCG_____CAGC\n3'-UUU...UUCAU________UC____C________UUA______ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________64_______________________________36\n	187 -- 193	56 -- 62	-21.1868 kcal/mol	6.57497 kcal/mol	3.30267 kcal/mol	185 216@LB@ \| \|@LB@5'-UGG...UUUAC UUUA UACCC CUGUU...ACC-3'@LB@ AUACUGGA CAAU UGAGC GUCG@LB@ \|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|@LB@ UAUGACCU GUUA ACUCG CAGC@LB@3'-UUU...UUCAU UC C UUA ACGAA...GCG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -21.1868 kcal/mol@LB@Unfolding Energy - mRNA 6.57497 kcal/mol@LB@Unfolding Energy - sRNA 3.30267 kcal/mol@LB@@LB@Position - mRNA 186 -- 215@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 56 -- 62@LB@
181	0.0223	0.4113	b3770	ilvE	-12.64	0.069830	250 -- 281	37 -- 61	branched-chain amino acid aminotransferase	_____________249______________________________282\n_____________\|________________________________\|\n5'-UUU...GGUUC_______AGAC____AG___CAU_________CACGC...GCA-3'\n______________GCUGGGA____GCGA__GUG___GUGAUGUCG\n______________:\|\|\|\|:\|____\|\|:\|__\|\|\|___\|::\|\|\|\|\|\|\n______________UGACCUU____CGUU__CAC___CGUUACAGC\n3'-UUU...CAUUA_______________A____U___________ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________62_______________________________36\n	275 -- 281	37 -- 43	-25.0056 kcal/mol	9.06403 kcal/mol	3.30158 kcal/mol	249 282@LB@ \| \|@LB@5'-UUU...GGUUC AGAC AG CAU CACGC...GCA-3'@LB@ GCUGGGA GCGA GUG GUGAUGUCG@LB@ :\|\|\|\|:\| \|\|:\| \|\|\| \|::\|\|\|\|\|\|@LB@ UGACCUU CGUU CAC CGUUACAGC@LB@3'-UUU...CAUUA A U ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -12.64 kcal/mol@LB@Hybridization Energy -25.0056 kcal/mol@LB@Unfolding Energy - mRNA 9.06403 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 250 -- 281@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 275 -- 281@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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