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
200	0.0896	0.3683	ct_487	yhhF	-5.19	0.334580	14 -- 20	79 -- 85	methyltransferase	_____________13______21\n_____________\|_______\|\n5'-ACG...UCCUC_______UAAUG...UUA-3'\n______________CGGUUAG\n______________\|\|\|:\|\|:\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	14 -- 20	79 -- 85	-7.01592 kcal/mol	0.727938 kcal/mol	1.09751 kcal/mol	13 21@LB@ \| \|@LB@5'-ACG...UCCUC UAAUG...UUA-3'@LB@ CGGUUAG@LB@ \|\|\|:\|\|:@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -7.01592 kcal/mol@LB@Unfolding Energy - mRNA 0.727938 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 14 -- 20@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 79 -- 85@LB@
184	0.0822	0.363	ct_497	dnaB	-7.07	0.138978	138 -- 179	3 -- 57	replicative DNA helicase	_____________137________________________________________________________180\n_____________\|__________________________________________________________\|\n5'-ACG...AUAUU_____A_____CCU________CCG____G_________UU_________________CAUAA...GUG-3'\n______________CCCCU___UAC___AAC_CUGG____AGA_AGCU__UCC____________UACCAAC\n______________\|\|\|\|\|___\|\|\|___\|\|\|_\|\|:\|____\|\|\|_\|\|\|\|__\|\|\|____________\|\|\|\|\|\|\|\n______________GGGGA___AUG___UUG_GAUC____UCU_UCGA__AGG____________AUGGUUG\n3'-UUU...GAAGG_____CAC___U_____U____UCAG________UA___UACCGCAAUCUU_______AA-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________2\n	173 -- 179	3 -- 9	-29.7257 kcal/mol	6.10481 kcal/mol	16.5501 kcal/mol	137 180@LB@ \| \|@LB@5'-ACG...AUAUU A CCU CCG G UU CAUAA...GUG-3'@LB@ CCCCU UAC AAC CUGG AGA AGCU UCC UACCAAC@LB@ \|\|\|\|\| \|\|\| \|\|\| \|\|:\| \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ GGGGA AUG UUG GAUC UCU UCGA AGG AUGGUUG@LB@3'-UUU...GAAGG CAC U U UCAG UA UACCGCAAUCUU AA-5'@LB@ \| \|@LB@ 58 2@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -29.7257 kcal/mol@LB@Unfolding Energy - mRNA 6.10481 kcal/mol@LB@Unfolding Energy - sRNA 16.5501 kcal/mol@LB@@LB@Position - mRNA 138 -- 179@LB@Position - sRNA 3 -- 57@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 3 -- 9@LB@
190	0.08414	0.363	ct_503	N/A	-6.17	0.215667	244 -- 250	81 -- 87		_____________243_____251\n_____________\|_______\|\n5'-UGG...UUUGU_______UCGCA...CUC-3'\n______________UACGGUU\n______________\|\|\|\|\|:\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	244 -- 250	81 -- 87	-7.94334 kcal/mol	0.67364 kcal/mol	1.09752 kcal/mol	243 251@LB@ \| \|@LB@5'-UGG...UUUGU UCGCA...CUC-3'@LB@ UACGGUU@LB@ \|\|\|\|\|:\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.94334 kcal/mol@LB@Unfolding Energy - mRNA 0.67364 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 244 -- 250@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 81 -- 87@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@
76	0.02744	0.29	ct_510	secY	-5.37	0.309530	200 -- 207	80 -- 87	preprotein translocase subunit SecY	_____________199______208\n_____________\|________\|\n5'-GAU...AAGUU________CAUUG...UCC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	201 -- 207	80 -- 86	-9.93483 kcal/mol	3.46443 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GAU...AAGUU CAUUG...UCC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -5.37 kcal/mol@LB@Hybridization Energy -9.93483 kcal/mol@LB@Unfolding Energy - mRNA 3.46443 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
118	0.04846	0.3262	ct_515	rs8	-12.50	0.006183	13 -- 43	3 -- 33	30S ribosomal protein S8	_____________12_______________________________44\n_____________\|________________________________\|\n5'-GGA...GACGA___U________UU__________UG______AAAUC...UGC-3'\n______________GGA_GUUAUUCC__UGGU_UUAGA__AUCAGC\n______________:\|\|_\|:\|\|\|\|\|\|__\|\|\|:_\|\|\|\|\|__\|:\|\|:\|\n______________UCU_CGAUAAGG__ACCG_AAUCU__UGGUUG\n3'-UUU...CUCAG___U________U_____C_____UA______AA-5'\n_____________\|________________________________\|\n_____________34_______________________________2\n	18 -- 24	22 -- 28	-29.6343 kcal/mol	8.5463 kcal/mol	8.59196 kcal/mol	12 44@LB@ \| \|@LB@5'-GGA...GACGA U UU UG AAAUC...UGC-3'@LB@ GGA GUUAUUCC UGGU UUAGA AUCAGC@LB@ :\|\| \|:\|\|\|\|\|\| \|\|\|: \|\|\|\|\| \|:\|\|:\|@LB@ UCU CGAUAAGG ACCG AAUCU UGGUUG@LB@3'-UUU...CUCAG U U C UA AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -29.6343 kcal/mol@LB@Unfolding Energy - mRNA 8.5463 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 13 -- 43@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 22 -- 28@LB@
154	0.06467	0.3424	ct_517	rl24	-3.21	0.671117	143 -- 150	27 -- 34	50S ribosomal protein L24	_____________142______151\n_____________\|________\|\n5'-UAA...CGAGA________UUGUU...AGG-3'\n______________CAGAGGCU\n______________\|\|\|\|:\|\|\|\n______________GUCUUCGA\n3'-UUU...UCUCA________UAAGG...GAA-5'\n_____________\|________\|\n_____________35_______26\n	144 -- 150	27 -- 33	-11.3134 kcal/mol	3.50051 kcal/mol	4.59929 kcal/mol	142 151@LB@ \| \|@LB@5'-UAA...CGAGA UUGUU...AGG-3'@LB@ CAGAGGCU@LB@ \|\|\|\|:\|\|\|@LB@ GUCUUCGA@LB@3'-UUU...UCUCA UAAGG...GAA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -3.21 kcal/mol@LB@Hybridization Energy -11.3134 kcal/mol@LB@Unfolding Energy - mRNA 3.50051 kcal/mol@LB@Unfolding Energy - sRNA 4.59929 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 27 -- 33@LB@
85	0.03073	0.29	ct_522	rs3	-5.11	0.345416	189 -- 204	18 -- 34	30S ribosomal protein S3	_____________188_______________205\n_____________\|_________________\|\n5'-UGU...GGCAG_______AAGG______GUCAA...UCA-3'\n______________UAGGAGU_____UAUGG\n______________:\|\|:\|\|:_____:\|\|\|\|\n______________GUCUUCG_____GUACC\n3'-UUU...UCUCA_______AUAAG_____GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	189 -- 195	28 -- 34	-12.0284 kcal/mol	1.93617 kcal/mol	4.97803 kcal/mol	188 205@LB@ \| \|@LB@5'-UGU...GGCAG AAGG GUCAA...UCA-3'@LB@ UAGGAGU UAUGG@LB@ :\|\|:\|\|: :\|\|\|\|@LB@ GUCUUCG GUACC@LB@3'-UUU...UCUCA AUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -12.0284 kcal/mol@LB@Unfolding Energy - mRNA 1.93617 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
72	0.02709	0.29	ct_530	fmt	-6.32	0.201483	239 -- 246	80 -- 87	methionyl-tRNA formyltransferase	_____________238______247\n_____________\|________\|\n5'-UAA...CAAUU________CUGUU...CGC-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	240 -- 246	80 -- 86	-12.3749 kcal/mol	4.96164 kcal/mol	1.09752 kcal/mol	238 247@LB@ \| \|@LB@5'-UAA...CAAUU CUGUU...CGC-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -12.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.96164 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 80 -- 86@LB@
21	0.0049	0.1918	ct_531	lpxA	-7.30	0.123824	16 -- 37	17 -- 34	acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase	_____________15_____________________38\n_____________\|______________________\|\n5'-UUG...GUAUC___A____AAA_______CA__CUGUU...CGC-3'\n______________CAG_AAGC___AUUCCGU__GC\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|:\|__\|\|\n______________GUC_UUCG___UAAGGUA__CG\n3'-UUU...UCUCA________A_________C___CAAUC...GAA-5'\n_____________\|______________________\|\n_____________35_____________________16\n	27 -- 33	20 -- 26	-14.3796 kcal/mol	2.10386 kcal/mol	4.97809 kcal/mol	15 38@LB@ \| \|@LB@5'-UUG...GUAUC A AAA CA CUGUU...CGC-3'@LB@ CAG AAGC AUUCCGU GC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|@LB@ GUC UUCG UAAGGUA CG@LB@3'-UUU...UCUCA A C CAAUC...GAA-5'@LB@ \| \|@LB@ 35 16@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.3796 kcal/mol@LB@Unfolding Energy - mRNA 2.10386 kcal/mol@LB@Unfolding Energy - sRNA 4.97809 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 17 -- 34@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 20 -- 26@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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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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