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
5	0.0004969	0.07439	ct_056	N/A	-17.69	0.000175	196 -- 255	6 -- 56		_____________195________________________________________________________________256\n_____________\|__________________________________________________________________\|\n5'-GUG...AGGAU_____AU__________CCCU__C______UUACGUAAACAGACAU_______A____________UUCCU...AAG-3'\n______________CCCUG______GACACU____UC_GAAGCU________________UUCC_UG__GUUAGAAUACC\n______________\|\|\|\|\|______:\|\|\|\|\|____\|\|_\|\|\|\|\|\|________________\|\|\|\|_\|\|__\|\|\|\|\|\|\|\|\|\|\|\n______________GGGAC______UUGUGA____AG_CUUCGA________________AAGG_AC__CAAUCUUAUGG\n3'-UUU...AAGGG_____ACAUGU______UCUC__U______U___________________U__CG___________UUGAA-5'\n_____________\|__________________________________________________________________\|\n_____________57_________________________________________________________________5\n	249 -- 255	6 -- 12	-39.697 kcal/mol	5.45688 kcal/mol	16.5497 kcal/mol	195 256@LB@ \| \|@LB@5'-GUG...AGGAU AU CCCU C UUACGUAAACAGACAU A UUCCU...AAG-3'@LB@ CCCUG GACACU UC GAAGCU UUCC UG GUUAGAAUACC@LB@ \|\|\|\|\| :\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ GGGAC UUGUGA AG CUUCGA AAGG AC CAAUCUUAUGG@LB@3'-UUU...AAGGG ACAUGU UCUC U U U CG UUGAA-5'@LB@ \| \|@LB@ 57 5@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -39.697 kcal/mol@LB@Unfolding Energy - mRNA 5.45688 kcal/mol@LB@Unfolding Energy - sRNA 16.5497 kcal/mol@LB@@LB@Position - mRNA 196 -- 255@LB@Position - sRNA 6 -- 56@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 6 -- 12@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@
133	0.05414	0.3262	ct_059	fer	-7.78	0.096344	200 -- 207	80 -- 87	ferredoxin	_____________199______208\n_____________\|________\|\n5'-UUC...AGUCC________AGCUC...CUU-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.7757 kcal/mol	1.8981 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-UUC...AGUCC AGCUC...CUU-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -10.7757 kcal/mol@LB@Unfolding Energy - mRNA 1.8981 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 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
8	0.0008373	0.07962	ct_066	N/A	-11.14	0.014316	190 -- 205	17 -- 33		_____________189_______________206\n_____________\|_________________\|\n5'-UUU...CACUA_________________UACGG...GUU-3'\n______________AGGAGCUAUUC_AUGGC\n______________\|\|:\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCUUCGAUAAG_UACCG\n3'-UUU...CUCAG___________G_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	194 -- 200	23 -- 29	-22.6652 kcal/mol	6.55112 kcal/mol	4.97804 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...CACUA UACGG...GUU-3'@LB@ AGGAGCUAUUC AUGGC@LB@ \|\|:\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCUUCGAUAAG UACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -22.6652 kcal/mol@LB@Unfolding Energy - mRNA 6.55112 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 23 -- 29@LB@
95	0.03456	0.2959	ct_073	N/A	-12.13	0.007785	261 -- 279	41 -- 58	contains leader (19) peptide	_____________260_________________280\n_____________\|___________________\|\n5'-GAC...CUGAU_________AUU_______UGACA...GGG-3'\n______________CCCUCUGUG___CAAACAU\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|\|:\n______________GGGGGACAC___GUUUGUG\n3'-UUU...UGAAG_________AU________AUCUC...GAA-5'\n_____________\|___________________\|\n_____________59__________________40\n	263 -- 269	50 -- 56	-22.185 kcal/mol	2.22773 kcal/mol	7.82865 kcal/mol	260 280@LB@ \| \|@LB@5'-GAC...CUGAU AUU UGACA...GGG-3'@LB@ CCCUCUGUG CAAACAU@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\|\|:@LB@ GGGGGACAC GUUUGUG@LB@3'-UUU...UGAAG AU AUCUC...GAA-5'@LB@ \| \|@LB@ 59 40@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -22.185 kcal/mol@LB@Unfolding Energy - mRNA 2.22773 kcal/mol@LB@Unfolding Energy - sRNA 7.82865 kcal/mol@LB@@LB@Position - mRNA 261 -- 279@LB@Position - sRNA 41 -- 58@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 50 -- 56@LB@
162	0.06757	0.3424	ct_083	N/A	-6.28	0.205297	111 -- 125	18 -- 33		_____________110______________126\n_____________\|________________\|\n5'-GCU...CAAGA________CAG_____AAAUC...UUU-3'\n______________AGAAGCUG____GUGG\n______________\|\|\|\|\|\|\|:____:\|\|\|\n______________UCUUCGAU____UACC\n3'-UUU...CUCAG________AAGG____GCAAU...GAA-5'\n_____________\|________________\|\n_____________34_______________17\n	112 -- 118	26 -- 32	-15.1014 kcal/mol	3.84734 kcal/mol	4.97798 kcal/mol	110 126@LB@ \| \|@LB@5'-GCU...CAAGA CAG AAAUC...UUU-3'@LB@ AGAAGCUG GUGG@LB@ \|\|\|\|\|\|\|: :\|\|\|@LB@ UCUUCGAU UACC@LB@3'-UUU...CUCAG AAGG GCAAU...GAA-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -15.1014 kcal/mol@LB@Unfolding Energy - mRNA 3.84734 kcal/mol@LB@Unfolding Energy - sRNA 4.97798 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 26 -- 32@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@
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@
56	0.02215	0.29	ct_104	fabI	-6.34	0.199539	263 -- 271	80 -- 88	enoyl-(acyl carrier protein) reductase	_____________262_______272\n_____________\|_________\|\n5'-UUU...AACGG_________GGGCA...CAG-3'\n______________GUAUGGCUG\n______________:\|\|:\|\|\|\|:\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	265 -- 271	80 -- 86	-10.7973 kcal/mol	3.36368 kcal/mol	1.09753 kcal/mol	262 272@LB@ \| \|@LB@5'-UUU...AACGG GGGCA...CAG-3'@LB@ GUAUGGCUG@LB@ :\|\|:\|\|\|\|:@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.7973 kcal/mol@LB@Unfolding Energy - mRNA 3.36368 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 80 -- 86@LB@
59	0.02324	0.29	ct_106	yceC	-7.97	0.086897	139 -- 180	3 -- 31	tRNA pseudouridine synthase A	_____________138__________________________________________181\n_____________\|____________________________________________\|\n5'-CUC...GAAAA__________UAUCA______AAUUCUCGUAAAAUC________ACACU...CCG-3'\n______________AAGCUGUUCU_______UAGA_______________GUACCAAC\n______________\|\|\|\|\|:\|\|\|:_______\|\|\|\|_______________:\|\|\|\|\|\|\|\n______________UUCGAUAAGG_______AUCU_______________UAUGGUUG\n3'-UUU...CAGUC__________UACCGCA___________________________AA-5'\n_____________\|____________________________________________\|\n_____________32___________________________________________2\n	174 -- 180	3 -- 9	-21.8491 kcal/mol	5.39956 kcal/mol	8.47511 kcal/mol	138 181@LB@ \| \|@LB@5'-CUC...GAAAA UAUCA AAUUCUCGUAAAAUC ACACU...CCG-3'@LB@ AAGCUGUUCU UAGA GUACCAAC@LB@ \|\|\|\|\|:\|\|\|: \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUCGAUAAGG AUCU UAUGGUUG@LB@3'-UUU...CAGUC UACCGCA AA-5'@LB@ \| \|@LB@ 32 2@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -21.8491 kcal/mol@LB@Unfolding Energy - mRNA 5.39956 kcal/mol@LB@Unfolding Energy - sRNA 8.47511 kcal/mol@LB@@LB@Position - mRNA 139 -- 180@LB@Position - sRNA 3 -- 31@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 3 -- 9@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)

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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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