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
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@
2	8.171e-05	0.03358	ct_802	rs18	-7.95	0.088258	66 -- 79	21 -- 34	30S ribosomal protein S18	_____________65_____________80\n_____________\|______________\|\n5'-GUU...AGCCC__________CG__GAGUU...UUA-3'\n______________CAGAAGCUAU__CA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GUCUUCGAUA__GU\n3'-UUU...UCUCA__________AG__ACCGC...GAA-5'\n_____________\|______________\|\n_____________35_____________20\n	68 -- 74	26 -- 32	-17.0234 kcal/mol	4.34679 kcal/mol	4.73132 kcal/mol	65 80@LB@ \| \|@LB@5'-GUU...AGCCC CG GAGUU...UUA-3'@LB@ CAGAAGCUAU CA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GUCUUCGAUA GU@LB@3'-UUU...UCUCA AG ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -17.0234 kcal/mol@LB@Unfolding Energy - mRNA 4.34679 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 66 -- 79@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 26 -- 32@LB@
82	0.02927	0.29	ct_342	rs21	-5.39	0.307662	118 -- 125	14 -- 21	30S ribosomal protein S21	_____________117______126\n_____________\|________\|\n5'-UUA...UAAAA________ACAAU...AGU-3'\n______________GUGGUGUU\n______________:\|\|\|:\|\|\|\n______________UACCGCAA\n3'-UUU...UAAGG________UCUUA...GAA-5'\n_____________\|________\|\n_____________22_______13\n	119 -- 125	14 -- 20	-8.72589 kcal/mol	2.15057 kcal/mol	1.18847 kcal/mol	117 126@LB@ \| \|@LB@5'-UUA...UAAAA ACAAU...AGU-3'@LB@ GUGGUGUU@LB@ :\|\|\|:\|\|\|@LB@ UACCGCAA@LB@3'-UUU...UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -8.72589 kcal/mol@LB@Unfolding Energy - mRNA 2.15057 kcal/mol@LB@Unfolding Energy - sRNA 1.18847 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 14 -- 20@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@
44	0.01666	0.29	ct_438	rs7	-6.33	0.200160	214 -- 223	79 -- 88	30S ribosomal protein S7	_____________213________224\n_____________\|__________\|\n5'-GCA...ACGAC__________GAAGA...ACG-3'\n______________AUGCGGCUGA\n______________\|\|:\|\|\|\|\|:\|\n______________UAUGCCGAUU\n3'-UUU...GCCUC__________GAGGU...GAA-5'\n_____________\|__________\|\n_____________89_________78\n	217 -- 223	79 -- 85	-13.0034 kcal/mol	5.57631 kcal/mol	1.09753 kcal/mol	213 224@LB@ \| \|@LB@5'-GCA...ACGAC GAAGA...ACG-3'@LB@ AUGCGGCUGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ UAUGCCGAUU@LB@3'-UUU...GCCUC GAGGU...GAA-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -13.0034 kcal/mol@LB@Unfolding Energy - mRNA 5.57631 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 214 -- 223@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 79 -- 85@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@
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@
165	0.06872	0.3424	ct_859	lytB	-7.21	0.129268	10 -- 22	19 -- 31	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	_____________9_____________23\n_____________\|_____________\|\n5'-UCG...UAUAA___________A_UAUCU...CUA-3'\n______________AGGCUAUUCCG_G\n______________\|:\|\|\|\|\|\|\|\|:_\|\n______________UUCGAUAAGGU_C\n3'-UUU...CAGUC___________A_CGCAA...GAA-5'\n_____________\|_____________\|\n_____________32____________18\n	14 -- 20	21 -- 27	-14.969 kcal/mol	2.89565 kcal/mol	4.85984 kcal/mol	9 23@LB@ \| \|@LB@5'-UCG...UAUAA A UAUCU...CUA-3'@LB@ AGGCUAUUCCG G@LB@ \|:\|\|\|\|\|\|\|\|: \|@LB@ UUCGAUAAGGU C@LB@3'-UUU...CAGUC A CGCAA...GAA-5'@LB@ \| \|@LB@ 32 18@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -14.969 kcal/mol@LB@Unfolding Energy - mRNA 2.89565 kcal/mol@LB@Unfolding Energy - sRNA 4.85984 kcal/mol@LB@@LB@Position - mRNA 10 -- 22@LB@Position - sRNA 19 -- 31@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 21 -- 27@LB@
32	0.009822	0.2518	ct_649	ygfA	-6.64	0.172247	22 -- 28	80 -- 86	5-formyltetrahydrofolate cyclo-ligase	_____________21______29\n_____________\|_______\|\n5'-UAC...AAGUG_______CCGAG...AGC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	22 -- 28	80 -- 86	-8.81528 kcal/mol	1.11082 kcal/mol	1.06449 kcal/mol	21 29@LB@ \| \|@LB@5'-UAC...AAGUG CCGAG...AGC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -8.81528 kcal/mol@LB@Unfolding Energy - mRNA 1.11082 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 22 -- 28@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 80 -- 86@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@

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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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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