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
11	0.002752	0.1836	ct_015	phoH	-12.12	0.007844	167 -- 186	33 -- 60	ATPase	_____________166__________________________187\n_____________\|____________________________\|\n5'-CCA...CUAUC_____________________U______UUUAG...UAA-3'\n______________UCCCCCUU________ACACU_GAGUCA\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|_\|\|\|\|\|\|\n______________AGGGGGGA________UGUGA_CUCAGU\n3'-UUU...ACUGA________CACAUGUU_____U______CUUCG...GAA-5'\n_____________\|____________________________\|\n_____________61___________________________32\n	168 -- 174	53 -- 59	-26.4608 kcal/mol	2.95889 kcal/mol	11.3851 kcal/mol	166 187@LB@ \| \|@LB@5'-CCA...CUAUC U UUUAG...UAA-3'@LB@ UCCCCCUU ACACU GAGUCA@LB@ \|\|\|\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA UGUGA CUCAGU@LB@3'-UUU...ACUGA CACAUGUU U CUUCG...GAA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -26.4608 kcal/mol@LB@Unfolding Energy - mRNA 2.95889 kcal/mol@LB@Unfolding Energy - sRNA 11.3851 kcal/mol@LB@@LB@Position - mRNA 167 -- 186@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 53 -- 59@LB@
12	0.002873	0.1836	ct_040	ruvB	-8.58	0.062725	112 -- 136	36 -- 60	Holliday junction DNA helicase RuvB	_____________111_______________________137\n_____________\|_________________________\|\n5'-CAG...GGGAA_________ACUU___C________GAUGU...AAG-3'\n______________UCCCUCUUG____CAG_CGCUGGAG\n______________\|\|\|\|:\|:\|\|____\|\|:_\|:\|\|:\|\|\|\n______________AGGGGGGAC____GUU_GUGAUCUC\n3'-UUU...ACUGA_________ACAU___U________AGUCU...GAA-5'\n_____________\|_________________________\|\n_____________61________________________35\n	113 -- 119	53 -- 59	-26.2752 kcal/mol	7.75429 kcal/mol	9.944 kcal/mol	111 137@LB@ \| \|@LB@5'-CAG...GGGAA ACUU C GAUGU...AAG-3'@LB@ UCCCUCUUG CAG CGCUGGAG@LB@ \|\|\|\|:\|:\|\| \|\|: \|:\|\|:\|\|\|@LB@ AGGGGGGAC GUU GUGAUCUC@LB@3'-UUU...ACUGA ACAU U AGUCU...GAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -26.2752 kcal/mol@LB@Unfolding Energy - mRNA 7.75429 kcal/mol@LB@Unfolding Energy - sRNA 9.944 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 53 -- 59@LB@
13	0.003406	0.1836	ct_744	N/A	-10.55	0.020316	225 -- 240	17 -- 33		_____________224_______________241\n_____________\|_________________\|\n5'-AAA...UCUCU_________________UUCUG...AAU-3'\n______________GGAAGCUGUU_CAUGGU\n______________:\|\|\|\|\|\|:\|\|_\|\|\|\|\|:\n______________UCUUCGAUAA_GUACCG\n3'-UUU...CUCAG__________G______CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	225 -- 231	27 -- 33	-21.2225 kcal/mol	5.69382 kcal/mol	4.97804 kcal/mol	224 241@LB@ \| \|@LB@5'-AAA...UCUCU UUCUG...AAU-3'@LB@ GGAAGCUGUU CAUGGU@LB@ :\|\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ UCUUCGAUAA GUACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -21.2225 kcal/mol@LB@Unfolding Energy - mRNA 5.69382 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
14	0.003406	0.1836	ct_744	N/A	-10.55	0.020316	225 -- 240	17 -- 33		_____________224_______________241\n_____________\|_________________\|\n5'-AAA...UCUCU_________________UUCUG...AAU-3'\n______________GGAAGCUGUU_CAUGGU\n______________:\|\|\|\|\|\|:\|\|_\|\|\|\|\|:\n______________UCUUCGAUAA_GUACCG\n3'-UUU...CUCAG__________G______CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	225 -- 231	27 -- 33	-21.2225 kcal/mol	5.69382 kcal/mol	4.97804 kcal/mol	224 241@LB@ \| \|@LB@5'-AAA...UCUCU UUCUG...AAU-3'@LB@ GGAAGCUGUU CAUGGU@LB@ :\|\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ UCUUCGAUAA GUACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -21.2225 kcal/mol@LB@Unfolding Energy - mRNA 5.69382 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
15	0.003628	0.1836	ct_134	N/A	-6.77	0.161910	221 -- 229	80 -- 88		_____________220_______230\n_____________\|_________\|\n5'-CAA...UGUGU_________CGAUG...UUC-3'\n______________AUACGGUUA\n______________\|\|\|\|\|\|:\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	223 -- 229	80 -- 86	-9.99522 kcal/mol	2.13198 kcal/mol	1.09753 kcal/mol	220 230@LB@ \| \|@LB@5'-CAA...UGUGU CGAUG...UUC-3'@LB@ AUACGGUUA@LB@ \|\|\|\|\|\|:\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -9.99522 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 221 -- 229@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 80 -- 86@LB@
16	0.003859	0.1836	ct_666	N/A	-9.59	0.035525	190 -- 206	16 -- 33		_____________189________________207\n_____________\|__________________\|\n5'-GAU...AAAAG_____G____________AGCGG...AAA-3'\n______________AGAGG_UA_UCUAUGGCG\n______________\|\|\|:\|_\|\|_\|\|:\|\|\|\|\|\|\n______________UCUUC_AU_AGGUACCGC\n3'-UUU...CUCAG_____G__A_________AAUCU...GAA-5'\n_____________\|__________________\|\n_____________34_________________15\n	200 -- 206	16 -- 22	-21.7302 kcal/mol	4.22495 kcal/mol	7.91433 kcal/mol	189 207@LB@ \| \|@LB@5'-GAU...AAAAG G AGCGG...AAA-3'@LB@ AGAGG UA UCUAUGGCG@LB@ \|\|\|:\| \|\| \|\|:\|\|\|\|\|\|@LB@ UCUUC AU AGGUACCGC@LB@3'-UUU...CUCAG G A AAUCU...GAA-5'@LB@ \| \|@LB@ 34 15@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -21.7302 kcal/mol@LB@Unfolding Energy - mRNA 4.22495 kcal/mol@LB@Unfolding Energy - sRNA 7.91433 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 16 -- 33@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 16 -- 22@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@
18	0.004135	0.1836	ct_799	N/A	-8.26	0.074627	30 -- 52	17 -- 35	50S ribosomal protein L25/general stress protein Ctc	_____________29______________________53\n_____________\|_______________________\|\n5'-AUC...AAUAA_________GCAA__A_______AGACG...GAA-3'\n______________UCAGAGGCU____GU_CCAUGGU\n______________\|\|\|\|\|:\|\|\|____:\|_\|\|\|\|\|\|:\n______________AGUCUUCGA____UA_GGUACCG\n3'-UUU...AUCUC_______________A_______CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	46 -- 52	17 -- 23	-22.1109 kcal/mol	8.8748 kcal/mol	4.9781 kcal/mol	29 53@LB@ \| \|@LB@5'-AUC...AAUAA GCAA A AGACG...GAA-3'@LB@ UCAGAGGCU GU CCAUGGU@LB@ \|\|\|\|\|:\|\|\| :\| \|\|\|\|\|\|:@LB@ AGUCUUCGA UA GGUACCG@LB@3'-UUU...AUCUC A CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -22.1109 kcal/mol@LB@Unfolding Energy - mRNA 8.8748 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 30 -- 52@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 17 -- 23@LB@
19	0.004244	0.1836	ct_583	gp6D	-9.00	0.049504	83 -- 102	18 -- 35	virulence protein GP6-D	_____________82___________________103\n_____________\|____________________\|\n5'-UAA...CUAUC________CGCUA_______GAAAC...CUC-3'\n______________UCAGAAGC_____UCCAUGG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\|\n______________AGUCUUCG_____AGGUACC\n3'-UUU...AUCUC________AUA_________GCAAU...GAA-5'\n_____________\|____________________\|\n_____________36___________________17\n	96 -- 102	18 -- 24	-22.1713 kcal/mol	8.18904 kcal/mol	4.97803 kcal/mol	82 103@LB@ \| \|@LB@5'-UAA...CUAUC CGCUA GAAAC...CUC-3'@LB@ UCAGAAGC UCCAUGG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGUCUUCG AGGUACC@LB@3'-UUU...AUCUC AUA GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -22.1713 kcal/mol@LB@Unfolding Energy - mRNA 8.18904 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 83 -- 102@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 18 -- 24@LB@
20	0.004812	0.1918	ct_026	rs16	-8.27	0.073959	26 -- 51	3 -- 33	30S ribosomal protein S16	_____________25______________________________52\n_____________\|_______________________________\|\n5'-CUG...ACGAA________________AA_________G___CGGAU...AUA-3'\n______________AGGAGUUA____GUGG__UU_GAGUAU_AGC\n______________\|\|:\|\|:\|\|____:\|\|\|__\|\|_\|\|:\|\|:_\|:\|\n______________UCUUCGAU____UACC__AA_CUUAUG_UUG\n3'-UUU...CUCAG________AAGG____GC__U______G___AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	27 -- 33	26 -- 32	-20.5759 kcal/mol	3.70935 kcal/mol	8.59196 kcal/mol	25 52@LB@ \| \|@LB@5'-CUG...ACGAA AA G CGGAU...AUA-3'@LB@ AGGAGUUA GUGG UU GAGUAU AGC@LB@ \|\|:\|\|:\|\| :\|\|\| \|\| \|\|:\|\|: \|:\|@LB@ UCUUCGAU UACC AA CUUAUG UUG@LB@3'-UUU...CUCAG AAGG GC U G AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -20.5759 kcal/mol@LB@Unfolding Energy - mRNA 3.70935 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 26 -- 51@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 26 -- 32@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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