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
69	0.02639	0.29	ct_745	hemG	-5.84	0.251832	282 -- 296	21 -- 34	protoporphyrinogen oxidase	_____________281_____________297\n_____________\|_______________\|\n5'-UUU...AUGUG___CU_U________GAAA-3'\n______________CAG__G_CUAUUCUA\n______________\|\|\|__\|_\|\|\|\|\|\|:\|\n______________GUC__C_GAUAAGGU\n3'-UUU...UCUCA___UU__________ACCGC...GAA-5'\n_____________\|_______________\|\n_____________35______________20\n	290 -- 296	21 -- 27	-11.5957 kcal/mol	1.02702 kcal/mol	4.73132 kcal/mol	281 297@LB@ \| \|@LB@5'-UUU...AUGUG CU U GAAA-3'@LB@ CAG G CUAUUCUA@LB@ \|\|\| \| \|\|\|\|\|\|:\|@LB@ GUC C GAUAAGGU@LB@3'-UUU...UCUCA UU ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -11.5957 kcal/mol@LB@Unfolding Energy - mRNA 1.02702 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 282 -- 296@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 21 -- 27@LB@
134	0.05433	0.3262	ct_581	thrS	-7.17	0.132364	52 -- 64	21 -- 33	threonine--tRNA ligase	_____________51___________65\n_____________\|____________\|\n5'-AAA...CUAAA_______CC___GAACU...CAG-3'\n______________AGAAGCU__UCC\n______________\|\|\|\|\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________20\n	52 -- 58	27 -- 33	-13.855 kcal/mol	1.83194 kcal/mol	4.72509 kcal/mol	51 65@LB@ \| \|@LB@5'-AAA...CUAAA CC GAACU...CAG-3'@LB@ AGAAGCU UCC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -13.855 kcal/mol@LB@Unfolding Energy - mRNA 1.83194 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 52 -- 64@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 27 -- 33@LB@
161	0.06753	0.3424	ct_656	N/A	-5.22	0.330968	193 -- 236	21 -- 57		_____________192_____________________________________________237\n_____________\|_______________________________________________\|\n5'-AUG...GGGAG_________________GCAAUUCAUAGC_______U________G_AACCA...UGA-3'\n______________UCUCU_UGUAUGGACAC____________GAGUCAG___CUGUUC_A\n______________:\|:\|\|_\|\|\|\|:::\|\|\|\|____________\|\|\|\|\|\|\|___\|\|:\|\|\|_\|\n______________GGGGA_ACAUGUUUGUG____________CUCAGUC___GAUAAG_U\n3'-UUU...GAAGG_____C___________AU_________________UUC______G_ACCGC...GAA-5'\n_____________\|_______________________________________________\|\n_____________58______________________________________________20\n	221 -- 227	32 -- 38	-30.4155 kcal/mol	12.5085 kcal/mol	12.6912 kcal/mol	192 237@LB@ \| \|@LB@5'-AUG...GGGAG GCAAUUCAUAGC U G AACCA...UGA-3'@LB@ UCUCU UGUAUGGACAC GAGUCAG CUGUUC A@LB@ :\|:\|\| \|\|\|\|:::\|\|\|\| \|\|\|\|\|\|\| \|\|:\|\|\| \|@LB@ GGGGA ACAUGUUUGUG CUCAGUC GAUAAG U@LB@3'-UUU...GAAGG C AU UUC G ACCGC...GAA-5'@LB@ \| \|@LB@ 58 20@LB@@LB@@LB@Energy -5.22 kcal/mol@LB@Hybridization Energy -30.4155 kcal/mol@LB@Unfolding Energy - mRNA 12.5085 kcal/mol@LB@Unfolding Energy - sRNA 12.6912 kcal/mol@LB@@LB@Position - mRNA 193 -- 236@LB@Position - sRNA 21 -- 57@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 32 -- 38@LB@
163	0.06794	0.3424	ct_661	N/A	-2.85	0.735752	184 -- 191	21 -- 28	DNA topoisomerase IV subunit B	_____________183______192\n_____________\|________\|\n5'-AAA...UUGCC________CACAC...GCG-3'\n______________UUAUUCCA\n______________:\|\|\|\|\|\|\|\n______________GAUAAGGU\n3'-UUU...UCUUC________ACCGC...GAA-5'\n_____________\|________\|\n_____________29_______20\n	185 -- 191	21 -- 27	-7.6538 kcal/mol	0.450062 kcal/mol	4.35509 kcal/mol	183 192@LB@ \| \|@LB@5'-AAA...UUGCC CACAC...GCG-3'@LB@ UUAUUCCA@LB@ :\|\|\|\|\|\|\|@LB@ GAUAAGGU@LB@3'-UUU...UCUUC ACCGC...GAA-5'@LB@ \| \|@LB@ 29 20@LB@@LB@@LB@Energy -2.85 kcal/mol@LB@Hybridization Energy -7.6538 kcal/mol@LB@Unfolding Energy - mRNA 0.450062 kcal/mol@LB@Unfolding Energy - sRNA 4.35509 kcal/mol@LB@@LB@Position - mRNA 184 -- 191@LB@Position - sRNA 21 -- 28@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 21 -- 27@LB@
17	0.003987	0.1836	ct_843	rs15	-6.01	0.232273	282 -- 295	22 -- 34	30S ribosomal protein S15	_____________281____________296\n_____________\|______________\|\n5'-AGG...AUGUG____UU________GACUG-3'\n______________CAGA__GCUAUUCU\n______________\|\|\|\|__\|\|\|\|\|\|\|:\n______________GUCU__CGAUAAGG\n3'-UUU...UCUCA____U_________UACCG...GAA-5'\n_____________\|______________\|\n_____________35_____________21\n	288 -- 294	23 -- 29	-14.3687 kcal/mol	3.62939 kcal/mol	4.72608 kcal/mol	281 296@LB@ \| \|@LB@5'-AGG...AUGUG UU GACUG-3'@LB@ CAGA GCUAUUCU@LB@ \|\|\|\| \|\|\|\|\|\|\|:@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -6.01 kcal/mol@LB@Hybridization Energy -14.3687 kcal/mol@LB@Unfolding Energy - mRNA 3.62939 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 23 -- 29@LB@
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@LB@
119	0.04857	0.3262	ct_706	clpP_2	-8.60	0.061801	14 -- 27	22 -- 35	ATP-dependent Clp protease proteolytic subunit	_____________13_____________28\n_____________\|______________\|\n5'-CGA...AAGAU______________UUCUU...GGC-3'\n______________UUAGAGGUUGUUCC\n______________\|:\|\|\|:\|:\|:\|\|\|\|\n______________AGUCUUCGAUAAGG\n3'-UUU...AUCUC______________UACCG...GAA-5'\n_____________\|______________\|\n_____________36_____________21\n	16 -- 22	27 -- 33	-17.9181 kcal/mol	4.58788 kcal/mol	4.72627 kcal/mol	13 28@LB@ \| \|@LB@5'-CGA...AAGAU UUCUU...GGC-3'@LB@ UUAGAGGUUGUUCC@LB@ \|:\|\|\|:\|:\|:\|\|\|\|@LB@ AGUCUUCGAUAAGG@LB@3'-UUU...AUCUC UACCG...GAA-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.9181 kcal/mol@LB@Unfolding Energy - mRNA 4.58788 kcal/mol@LB@Unfolding Energy - sRNA 4.72627 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 27 -- 33@LB@
144	0.05714	0.3262	ct_392	yprS	-4.10	0.509599	238 -- 247	22 -- 33		_____________237__________248\n_____________\|____________\|\n5'-AGG...CCCUG____________CAAUU...GUC-3'\n______________AGAGGCU__UCC\n______________\|\|\|:\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	238 -- 244	27 -- 33	-11.7781 kcal/mol	2.9519 kcal/mol	4.72509 kcal/mol	237 248@LB@ \| \|@LB@5'-AGG...CCCUG CAAUU...GUC-3'@LB@ AGAGGCU UCC@LB@ \|\|\|:\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -11.7781 kcal/mol@LB@Unfolding Energy - mRNA 2.9519 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 27 -- 33@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@LB@
189	0.0841	0.363	ct_792	mutS	-5.18	0.336119	140 -- 151	22 -- 33	DNA mismatch repair protein MutS	_____________139__________152\n_____________\|____________\|\n5'-AUA...ACAUA____C_______CCUAC...AAG-3'\n______________AGAG_CUGUUCC\n______________\|\|\|:_\|\|:\|\|\|\|\n______________UCUU_GAUAAGG\n3'-UUU...CUCAG____C_______UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	145 -- 151	22 -- 28	-12.2041 kcal/mol	2.29966 kcal/mol	4.72509 kcal/mol	139 152@LB@ \| \|@LB@5'-AUA...ACAUA C CCUAC...AAG-3'@LB@ AGAG CUGUUCC@LB@ \|\|\|: \|\|:\|\|\|\|@LB@ UCUU GAUAAGG@LB@3'-UUU...CUCAG C UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -12.2041 kcal/mol@LB@Unfolding Energy - mRNA 2.29966 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 22 -- 28@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)

Job resubmission

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usability assessment

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service.

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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