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
9	0.0008717	0.07962	ct_743	hctA	-7.87	0.092034	214 -- 220	82 -- 88	histone H1-like protein	_____________213_____221\n_____________\|_______\|\n5'-GUU...AAAAG_______AAAAA...AAA-3'\n______________AUACGGC\n______________\|\|\|\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	214 -- 220	82 -- 88	-10.5788 kcal/mol	1.61458 kcal/mol	1.09753 kcal/mol	213 221@LB@ \| \|@LB@5'-GUU...AAAAG AAAAA...AAA-3'@LB@ AUACGGC@LB@ \|\|\|\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -10.5788 kcal/mol@LB@Unfolding Energy - mRNA 1.61458 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 82 -- 88@LB@
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@
173	0.07335	0.3448	ct_543	hisS	-6.45	0.189015	1 -- 7	82 -- 88	histidine--tRNA ligase	______________1______8\n______________\|______\|\n___________5'-_______GUAUU...AGC-3'\n______________AUGCGGC\n______________\|\|:\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	1 -- 7	82 -- 88	-9.9342 kcal/mol	2.38776 kcal/mol	1.09753 kcal/mol	1 8@LB@ \| \|@LB@ 5'- GUAUU...AGC-3'@LB@ AUGCGGC@LB@ \|\|:\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -6.45 kcal/mol@LB@Hybridization Energy -9.9342 kcal/mol@LB@Unfolding Energy - mRNA 2.38776 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 1 -- 7@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 82 -- 88@LB@
123	0.04914	0.3262	ct_754	icc	-7.18	0.131374	254 -- 264	47 -- 57		_____________253_________265\n_____________\|___________\|\n5'-AUU...AUUCA___________UCCCU...GCU-3'\n______________CUUCUGUGUAC\n______________\|::\|\|\|\|\|\|\|\|\n______________GGGGACACAUG\n3'-UUU...GAAGG___________UUUGU...GAA-5'\n_____________\|___________\|\n_____________58__________46\n	258 -- 264	47 -- 53	-16.923 kcal/mol	2.45356 kcal/mol	7.2877 kcal/mol	253 265@LB@ \| \|@LB@5'-AUU...AUUCA UCCCU...GCU-3'@LB@ CUUCUGUGUAC@LB@ \|::\|\|\|\|\|\|\|\|@LB@ GGGGACACAUG@LB@3'-UUU...GAAGG UUUGU...GAA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.923 kcal/mol@LB@Unfolding Energy - mRNA 2.45356 kcal/mol@LB@Unfolding Energy - sRNA 7.2877 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 47 -- 53@LB@
26	0.006621	0.2093	ct_267	ihfA	-8.59	0.062448	193 -- 205	17 -- 31	DNA-binding protein HU	_____________192_____________206\n_____________\|_______________\|\n5'-UAA...GCAAC_______________AACGA...AUA-3'\n______________AAGCUA__CCAUGGC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UUCGAU__GGUACCG\n3'-UUU...CAGUC______AA_______CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	199 -- 205	17 -- 23	-17.4173 kcal/mol	3.97125 kcal/mol	4.86101 kcal/mol	192 206@LB@ \| \|@LB@5'-UAA...GCAAC AACGA...AUA-3'@LB@ AAGCUA CCAUGGC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCGAU GGUACCG@LB@3'-UUU...CAGUC AA CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -17.4173 kcal/mol@LB@Unfolding Energy - mRNA 3.97125 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
54	0.02089	0.29	ct_119	incA	-7.14	0.134009	237 -- 243	52 -- 58	inclusion membrane protein A	_____________236_____244\n_____________\|_______\|\n5'-UCC...CAUCU_______CACCU...AGA-3'\n______________CCCCCUG\n______________\|\|\|\|\|\|\|\n______________GGGGGAC\n3'-UUU...UGAAG_______ACAUG...GAA-5'\n_____________\|_______\|\n_____________59______51\n	237 -- 243	52 -- 58	-14.4133 kcal/mol	0.279731 kcal/mol	6.99083 kcal/mol	236 244@LB@ \| \|@LB@5'-UCC...CAUCU CACCU...AGA-3'@LB@ CCCCCUG@LB@ \|\|\|\|\|\|\|@LB@ GGGGGAC@LB@3'-UUU...UGAAG ACAUG...GAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -14.4133 kcal/mol@LB@Unfolding Energy - mRNA 0.279731 kcal/mol@LB@Unfolding Energy - sRNA 6.99083 kcal/mol@LB@@LB@Position - mRNA 237 -- 243@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 52 -- 58@LB@
61	0.02387	0.29	ct_628	ispA	-7.51	0.111028	11 -- 52	17 -- 56	farnesyl diphosphate synthase	_____________10__________________________________________53\n_____________\|___________________________________________\|\n5'-UUC...GAGAG_G____AA___A_____GAAAA________________UA___AGAGG...UAG-3'\n______________C_UUGU__UAC_AAACG_____AGUUAGGAGCU_UUCC__GGU\n______________\|_:\|\|\|__\|\|\|_\|\|\|\|:_____\|\|\|:\|\|:\|\|\|\|_\|\|\|\|__\|\|:\n______________G_GACA__AUG_UUUGU_____UCAGUCUUCGA_AAGG__CCG\n3'-UUU...AAGGG_G____C__________GAUC____________U____UA___CAAUC...GAA-5'\n_____________\|___________________________________________\|\n_____________57__________________________________________16\n	36 -- 42	28 -- 34	-30.6817 kcal/mol	10.2369 kcal/mol	12.9359 kcal/mol	10 53@LB@ \| \|@LB@5'-UUC...GAGAG G AA A GAAAA UA AGAGG...UAG-3'@LB@ C UUGU UAC AAACG AGUUAGGAGCU UUCC GGU@LB@ \| :\|\|\| \|\|\| \|\|\|\|: \|\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|:@LB@ G GACA AUG UUUGU UCAGUCUUCGA AAGG CCG@LB@3'-UUU...AAGGG G C GAUC U UA CAAUC...GAA-5'@LB@ \| \|@LB@ 57 16@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -30.6817 kcal/mol@LB@Unfolding Energy - mRNA 10.2369 kcal/mol@LB@Unfolding Energy - sRNA 12.9359 kcal/mol@LB@@LB@Position - mRNA 11 -- 52@LB@Position - sRNA 17 -- 56@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 28 -- 34@LB@
146	0.05858	0.3298	ct_655	kdsA	-5.70	0.267824	236 -- 245	48 -- 57	2-dehydro-3-deoxyphosphooctonate aldolase	_____________235________246\n_____________\|__________\|\n5'-GCU...GCAGG__________AUUGA...CUC-3'\n______________CCCUUGUGUA\n______________\|\|\|:\|\|\|\|\|\|\n______________GGGGACACAU\n3'-UUU...GAAGG__________GUUUG...GAA-5'\n_____________\|__________\|\n_____________58_________47\n	237 -- 243	50 -- 56	-16.3498 kcal/mol	3.37377 kcal/mol	7.27486 kcal/mol	235 246@LB@ \| \|@LB@5'-GCU...GCAGG AUUGA...CUC-3'@LB@ CCCUUGUGUA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GGGGACACAU@LB@3'-UUU...GAAGG GUUUG...GAA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -5.70 kcal/mol@LB@Hybridization Energy -16.3498 kcal/mol@LB@Unfolding Energy - mRNA 3.37377 kcal/mol@LB@Unfolding Energy - sRNA 7.27486 kcal/mol@LB@@LB@Position - mRNA 236 -- 245@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 50 -- 56@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@
112	0.04461	0.3262	ct_089	lcrE	-7.82	0.094118	129 -- 157	3 -- 33	low calcium response protein E	_____________128_____________________________158\n_____________\|_______________________________\|\n5'-CGG...UACCA_______UUA_____AAA_____________CUUUG...UUA-3'\n______________AGAAGUU___CC_UG___UUAGAAU_CCAGC\n______________\|\|\|\|\|:\|___\|\|_\|\|___\|\|\|\|\|\|\|_\|\|\|:\|\n______________UCUUCGA___GG_AC___AAUCUUA_GGUUG\n3'-UUU...CUCAG_______UAA__U__CGC_______U_____AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	129 -- 135	27 -- 33	-21.9416 kcal/mol	5.52555 kcal/mol	8.59196 kcal/mol	128 158@LB@ \| \|@LB@5'-CGG...UACCA UUA AAA CUUUG...UUA-3'@LB@ AGAAGUU CC UG UUAGAAU CCAGC@LB@ \|\|\|\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ UCUUCGA GG AC AAUCUUA GGUUG@LB@3'-UUU...CUCAG UAA U CGC U AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -21.9416 kcal/mol@LB@Unfolding Energy - mRNA 5.52555 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 129 -- 157@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 27 -- 33@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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