Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
147	0.05913	0.3307	ct_243	lpxD	-5.18	0.335797	179 -- 192	18 -- 32	UDP-3-O-acylglucosamine N-acyltransferase	_____________178_____________193\n_____________\|_______________\|\n5'-UCA...CAUGC_______G____A__AGUGC...UCG-3'\n______________GAAGCUA__CCG_GG\n______________\|\|\|\|\|\|\|__\|\|:_\|\|\n______________CUUCGAU__GGU_CC\n3'-UUU...UCAGU_______AA___A__GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	179 -- 185	26 -- 32	-15.005 kcal/mol	4.85774 kcal/mol	4.96566 kcal/mol	178 193@LB@ \| \|@LB@5'-UCA...CAUGC G A AGUGC...UCG-3'@LB@ GAAGCUA CCG GG@LB@ \|\|\|\|\|\|\| \|\|: \|\|@LB@ CUUCGAU GGU CC@LB@3'-UUU...UCAGU AA A GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -15.005 kcal/mol@LB@Unfolding Energy - mRNA 4.85774 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 26 -- 32@LB@
162	0.06757	0.3424	ct_083	N/A	-6.28	0.205297	111 -- 125	18 -- 33		_____________110______________126\n_____________\|________________\|\n5'-GCU...CAAGA________CAG_____AAAUC...UUU-3'\n______________AGAAGCUG____GUGG\n______________\|\|\|\|\|\|\|:____:\|\|\|\n______________UCUUCGAU____UACC\n3'-UUU...CUCAG________AAGG____GCAAU...GAA-5'\n_____________\|________________\|\n_____________34_______________17\n	112 -- 118	26 -- 32	-15.1014 kcal/mol	3.84734 kcal/mol	4.97798 kcal/mol	110 126@LB@ \| \|@LB@5'-GCU...CAAGA CAG AAAUC...UUU-3'@LB@ AGAAGCUG GUGG@LB@ \|\|\|\|\|\|\|: :\|\|\|@LB@ UCUUCGAU UACC@LB@3'-UUU...CUCAG AAGG GCAAU...GAA-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -15.1014 kcal/mol@LB@Unfolding Energy - mRNA 3.84734 kcal/mol@LB@Unfolding Energy - sRNA 4.97798 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 26 -- 32@LB@
171	0.07267	0.3448	ct_057	gcpE	-5.03	0.358241	27 -- 78	18 -- 60	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)	_____________26____________________________________________________79\n_____________\|_____________________________________________________\|\n5'-AGA...GAACA____UCAA_______AAUU________AUUUUUAAAG_______UC_______AGACC...AAU-3'\n______________UCCC____CCC_GUG____UAUAAACA__________GGAAGUU__UCCAUGG\n______________\|\|\|\|____\|\|\|_\|\|\|____\|\|:\|\|\|\|\|__________:\|\|\|\|:\|__\|\|\|\|\|\|\|\n______________AGGG____GGG_CAC____AUGUUUGU__________UCUUCGA__AGGUACC\n3'-UUU...ACUGA___________A_______________GAUCUCAG_________UA_______GCAAU...GAA-5'\n_____________\|_____________________________________________________\|\n_____________61____________________________________________________17\n	72 -- 78	18 -- 24	-36.1086 kcal/mol	16.1769 kcal/mol	14.9054 kcal/mol	26 79@LB@ \| \|@LB@5'-AGA...GAACA UCAA AAUU AUUUUUAAAG UC AGACC...AAU-3'@LB@ UCCC CCC GUG UAUAAACA GGAAGUU UCCAUGG@LB@ \|\|\|\| \|\|\| \|\|\| \|\|:\|\|\|\|\| :\|\|\|\|:\| \|\|\|\|\|\|\|@LB@ AGGG GGG CAC AUGUUUGU UCUUCGA AGGUACC@LB@3'-UUU...ACUGA A GAUCUCAG UA GCAAU...GAA-5'@LB@ \| \|@LB@ 61 17@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -36.1086 kcal/mol@LB@Unfolding Energy - mRNA 16.1769 kcal/mol@LB@Unfolding Energy - sRNA 14.9054 kcal/mol@LB@@LB@Position - mRNA 27 -- 78@LB@Position - sRNA 18 -- 60@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 18 -- 24@LB@
172	0.07285	0.3448	ct_090	lcrD	-6.84	0.155915	81 -- 102	18 -- 39	low calcium response protein D	_____________80______________________103\n_____________\|_______________________\|\n5'-AUU...GGAAA___________U________GA_ACCAC...UGU-3'\n______________AGAGUU_GAAG_UUAUUCCA__G\n______________\|\|\|\|\|:_\|\|\|\|_:\|\|\|\|\|\|\|__\|\n______________UCUCAG_CUUC_GAUAAGGU__C\n3'-UUU...UGUGA______U_____________AC_GCAAU...GAA-5'\n_____________\|_______________________\|\n_____________40______________________17\n	93 -- 99	21 -- 27	-20.344 kcal/mol	3.91171 kcal/mol	9.59078 kcal/mol	80 103@LB@ \| \|@LB@5'-AUU...GGAAA U GA ACCAC...UGU-3'@LB@ AGAGUU GAAG UUAUUCCA G@LB@ \|\|\|\|\|: \|\|\|\| :\|\|\|\|\|\|\| \|@LB@ UCUCAG CUUC GAUAAGGU C@LB@3'-UUU...UGUGA U AC GCAAU...GAA-5'@LB@ \| \|@LB@ 40 17@LB@@LB@@LB@Energy -6.84 kcal/mol@LB@Hybridization Energy -20.344 kcal/mol@LB@Unfolding Energy - mRNA 3.91171 kcal/mol@LB@Unfolding Energy - sRNA 9.59078 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 18 -- 39@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 21 -- 27@LB@
175	0.07342	0.3448	ct_738	yycJ	-7.78	0.096435	160 -- 204	18 -- 50	Zn-dependent hydrolase	_____________159____________________________________________205\n_____________\|______________________________________________\|\n5'-CAU...ACCGC_____________UCCAAUUAUCAAA______C_A___A_______AAGGU...AAC-3'\n______________GU_CAAAUACUAG_____________UCAGGA_G_UUA_UCCAUGG\n______________\|\|_\|\|\|\|:\|\|\|\|\|_____________\|\|\|\|:\|_\|_:\|\|_\|\|\|\|\|\|\|\n______________CA_GUUUGUGAUC_____________AGUCUU_C_GAU_AGGUACC\n3'-UUU...GGACA__U__________UC_______________________A_______GCAAU...GAA-5'\n_____________\|______________________________________________\|\n_____________51_____________________________________________17\n	198 -- 204	18 -- 24	-28.1471 kcal/mol	7.4527 kcal/mol	12.9164 kcal/mol	159 205@LB@ \| \|@LB@5'-CAU...ACCGC UCCAAUUAUCAAA C A A AAGGU...AAC-3'@LB@ GU CAAAUACUAG UCAGGA G UUA UCCAUGG@LB@ \|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|:\| \| :\|\| \|\|\|\|\|\|\|@LB@ CA GUUUGUGAUC AGUCUU C GAU AGGUACC@LB@3'-UUU...GGACA U UC A GCAAU...GAA-5'@LB@ \| \|@LB@ 51 17@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -28.1471 kcal/mol@LB@Unfolding Energy - mRNA 7.4527 kcal/mol@LB@Unfolding Energy - sRNA 12.9164 kcal/mol@LB@@LB@Position - mRNA 160 -- 204@LB@Position - sRNA 18 -- 50@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@LB@
176	0.07518	0.3511	ct_481	N/A	-6.18	0.214715	76 -- 94	18 -- 35		_____________75__________________95\n_____________\|___________________\|\n5'-AUA...CCAUU__U___AU___________AAACA...AUU-3'\n______________UC_GAA__CUGUUCUAUGG\n______________\|\|_\|\|\|__\|\|:\|\|\|:\|\|\|\|\n______________AG_CUU__GAUAAGGUACC\n3'-UUU...AUCUC__U___C____________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________36__________________17\n	88 -- 94	18 -- 24	-16.4052 kcal/mol	5.24588 kcal/mol	4.97803 kcal/mol	75 95@LB@ \| \|@LB@5'-AUA...CCAUU U AU AAACA...AUU-3'@LB@ UC GAA CUGUUCUAUGG@LB@ \|\| \|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ AG CUU GAUAAGGUACC@LB@3'-UUU...AUCUC U C GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -16.4052 kcal/mol@LB@Unfolding Energy - mRNA 5.24588 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 76 -- 94@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 18 -- 24@LB@
7	0.0007305	0.07962	ct_505	gapA	-11.17	0.013986	23 -- 47	19 -- 39	glyceraldehyde-3-phosphate dehydrogenase	_____________22________________________48\n_____________\|_________________________\|\n5'-GUC...AUAGA______AUUG___________G___UGUUA...AUU-3'\n______________AGAGUC____GGAAGUUAUUU_AUG\n______________\|\|\|\|\|\|____:\|\|\|\|:\|\|\|\|:_\|\|\|\n______________UCUCAG____UCUUCGAUAAG_UAC\n3'-UUU...UGUGA_____________________G___CGCAA...GAA-5'\n_____________\|_________________________\|\n_____________40________________________18\n	34 -- 40	26 -- 32	-23.0041 kcal/mol	2.2627 kcal/mol	9.5668 kcal/mol	22 48@LB@ \| \|@LB@5'-GUC...AUAGA AUUG G UGUUA...AUU-3'@LB@ AGAGUC GGAAGUUAUUU AUG@LB@ \|\|\|\|\|\| :\|\|\|\|:\|\|\|\|: \|\|\|@LB@ UCUCAG UCUUCGAUAAG UAC@LB@3'-UUU...UGUGA G CGCAA...GAA-5'@LB@ \| \|@LB@ 40 18@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.0041 kcal/mol@LB@Unfolding Energy - mRNA 2.2627 kcal/mol@LB@Unfolding Energy - sRNA 9.5668 kcal/mol@LB@@LB@Position - mRNA 23 -- 47@LB@Position - sRNA 19 -- 39@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 26 -- 32@LB@
67	0.02533	0.29	ct_395	grpE	-6.02	0.231793	191 -- 203	19 -- 33	stress response protein GrpE	_____________190_____________204\n_____________\|_______________\|\n5'-CCU...CGCUA_______________ACAGA...UAA-3'\n______________AGGAGCUAU__CAUG\n______________\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________UCUUCGAUA__GUAC\n3'-UUU...CUCAG_________AG____CGCAA...GAA-5'\n_____________\|_______________\|\n_____________34______________18\n	192 -- 198	26 -- 32	-14.6636 kcal/mol	3.66894 kcal/mol	4.97702 kcal/mol	190 204@LB@ \| \|@LB@5'-CCU...CGCUA ACAGA...UAA-3'@LB@ AGGAGCUAU CAUG@LB@ \|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UCUUCGAUA GUAC@LB@3'-UUU...CUCAG AG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -14.6636 kcal/mol@LB@Unfolding Energy - mRNA 3.66894 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 26 -- 32@LB@
138	0.05554	0.3262	ct_806	ptr	-4.69	0.410459	54 -- 70	19 -- 33	insulinase/protease	_____________53________________71\n_____________\|_________________\|\n5'-GUU...UCCGA________AUAUA____AUAAA...UAA-3'\n______________AGAAGCUG_____CAUG\n______________\|\|\|\|\|\|\|:_____\|\|\|\|\n______________UCUUCGAU_____GUAC\n3'-UUU...CUCAG________AAG______CGCAA...GAA-5'\n_____________\|_________________\|\n_____________34________________18\n	55 -- 61	26 -- 32	-13.627 kcal/mol	3.96302 kcal/mol	4.97702 kcal/mol	53 71@LB@ \| \|@LB@5'-GUU...UCCGA AUAUA AUAAA...UAA-3'@LB@ AGAAGCUG CAUG@LB@ \|\|\|\|\|\|\|: \|\|\|\|@LB@ UCUUCGAU GUAC@LB@3'-UUU...CUCAG AAG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -13.627 kcal/mol@LB@Unfolding Energy - mRNA 3.96302 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 54 -- 70@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 26 -- 32@LB@
150	0.06394	0.3424	ct_208	gseA	-4.42	0.454874	290 -- 300	19 -- 29	3-deoxy-D-manno-octulosonic acid transferase	_____________289________300\n_____________\|__________\|\n5'-UUG...AAAGU___U_______-3'\n______________GUU_UUCCAUG\n______________\|:\|_\|\|\|\|\|\|\|\n______________CGA_AAGGUAC\n3'-UUU...GUCUU___U_______CGCAA...GAA-5'\n_____________\|___________\|\n_____________30__________18\n	294 -- 300	19 -- 25	-10.2082 kcal/mol	1.1238 kcal/mol	4.66719 kcal/mol	289 300@LB@ \| \|@LB@5'-UUG...AAAGU U -3'@LB@ GUU UUCCAUG@LB@ \|:\| \|\|\|\|\|\|\|@LB@ CGA AAGGUAC@LB@3'-UUU...GUCUU U CGCAA...GAA-5'@LB@ \| \|@LB@ 30 18@LB@@LB@@LB@Energy -4.42 kcal/mol@LB@Hybridization Energy -10.2082 kcal/mol@LB@Unfolding Energy - mRNA 1.1238 kcal/mol@LB@Unfolding Energy - sRNA 4.66719 kcal/mol@LB@@LB@Position - mRNA 290 -- 300@LB@Position - sRNA 19 -- 29@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 19 -- 25@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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