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
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@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@
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@
33	0.01042	0.2518	ct_780	N/A	-7.85	0.092931	30 -- 50	15 -- 34		_____________29____________________51\n_____________\|_____________________\|\n5'-UGU...AAAAA___C____GAA_G________GUCAA...UCA-3'\n______________CAG_AAGU___U_CAUGGCGU\n______________\|\|\|_\|\|\|:___\|_\|\|\|\|\|\|\|\|\n______________GUC_UUCG___A_GUACCGCA\n3'-UUU...UCUCA________AUA_G________AUCUU...GAA-5'\n_____________\|_____________________\|\n_____________35____________________14\n	44 -- 50	15 -- 21	-20.7959 kcal/mol	4.71518 kcal/mol	8.23265 kcal/mol	29 51@LB@ \| \|@LB@5'-UGU...AAAAA C GAA G GUCAA...UCA-3'@LB@ CAG AAGU U CAUGGCGU@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|\|@LB@ GUC UUCG A GUACCGCA@LB@3'-UUU...UCUCA AUA G AUCUU...GAA-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -20.7959 kcal/mol@LB@Unfolding Energy - mRNA 4.71518 kcal/mol@LB@Unfolding Energy - sRNA 8.23265 kcal/mol@LB@@LB@Position - mRNA 30 -- 50@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 15 -- 21@LB@
102	0.03801	0.3036	ct_001	N/A	-7.82	0.094515	254 -- 277	28 -- 49		_____________253______________________278\n_____________\|________________________\|\n5'-CUU...GGAGC_____________AUU________AACAG...UAC-3'\n______________UAUAAACACUGGA___UUAGGAGU\n______________\|\|:\|\|\|\|\|\|\|:\|\|___\|:\|\|:\|\|:\n______________AUGUUUGUGAUCU___AGUCUUCG\n3'-UUU...GACAC_____________C__________AUAAG...GAA-5'\n_____________\|________________________\|\n_____________50_______________________27\n	271 -- 277	28 -- 34	-23.2003 kcal/mol	3.96195 kcal/mol	11.4222 kcal/mol	253 278@LB@ \| \|@LB@5'-CUU...GGAGC AUU AACAG...UAC-3'@LB@ UAUAAACACUGGA UUAGGAGU@LB@ \|\|:\|\|\|\|\|\|\|:\|\| \|:\|\|:\|\|:@LB@ AUGUUUGUGAUCU AGUCUUCG@LB@3'-UUU...GACAC C AUAAG...GAA-5'@LB@ \| \|@LB@ 50 27@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -23.2003 kcal/mol@LB@Unfolding Energy - mRNA 3.96195 kcal/mol@LB@Unfolding Energy - sRNA 11.4222 kcal/mol@LB@@LB@Position - mRNA 254 -- 277@LB@Position - sRNA 28 -- 49@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 28 -- 34@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@
39	0.01357	0.2859	ct_401	gltT	-7.80	0.095127	36 -- 47	44 -- 55	sodium:dicarboxylate symport protein	_____________35___________48\n_____________\|____________\|\n5'-UGU...GGUAU____________AAAGG...AUA-3'\n______________CCUGUGUACAGA\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________GGACACAUGUUU\n3'-UUU...AGGGG____________GUGAU...GAA-5'\n_____________\|____________\|\n_____________56___________43\n	41 -- 47	44 -- 50	-17.8988 kcal/mol	2.58215 kcal/mol	7.51272 kcal/mol	35 48@LB@ \| \|@LB@5'-UGU...GGUAU AAAGG...AUA-3'@LB@ CCUGUGUACAGA@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ GGACACAUGUUU@LB@3'-UUU...AGGGG GUGAU...GAA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.8988 kcal/mol@LB@Unfolding Energy - mRNA 2.58215 kcal/mol@LB@Unfolding Energy - sRNA 7.51272 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 44 -- 50@LB@
127	0.0509	0.3262	ct_808	cafE	-7.80	0.095102	169 -- 204	18 -- 57	ribonuclease E	_____________168_________________________________________205\n_____________\|___________________________________________\|\n5'-GUU...GAGGA_______A______________CAU______ACG_________AAAAC...AAA-3'\n______________CUCCUGU____GAGCGC_AGAG___UUAGGA______CCAUGG\n______________\|:\|\|\|\|\|____:\|:\|:\|_\|\|\|\|___\|:\|\|:\|______\|\|\|\|\|\|\n______________GGGGACA____UUUGUG_UCUC___AGUCUU______GGUACC\n3'-UUU...GAAGG_______CAUG______A_____________CGAUAA______GCAAU...GAA-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________17\n	169 -- 175	51 -- 57	-30.1775 kcal/mol	9.43695 kcal/mol	12.9362 kcal/mol	168 205@LB@ \| \|@LB@5'-GUU...GAGGA A CAU ACG AAAAC...AAA-3'@LB@ CUCCUGU GAGCGC AGAG UUAGGA CCAUGG@LB@ \|:\|\|\|\|\| :\|:\|:\| \|\|\|\| \|:\|\|:\| \|\|\|\|\|\|@LB@ GGGGACA UUUGUG UCUC AGUCUU GGUACC@LB@3'-UUU...GAAGG CAUG A CGAUAA GCAAU...GAA-5'@LB@ \| \|@LB@ 58 17@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -30.1775 kcal/mol@LB@Unfolding Energy - mRNA 9.43695 kcal/mol@LB@Unfolding Energy - sRNA 12.9362 kcal/mol@LB@@LB@Position - mRNA 169 -- 204@LB@Position - sRNA 18 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 51 -- 57@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@
175	0.07342	0.3448	ct_738	yycJ	-7.78	0.096435	160 -- 204	18 -- 50	Zn-dependent hydrolase	_____________159____________________________________________205\n_____________\|______________________________________________\|\n5'-CAU...ACCGC_____________UCCAAUUAUCAAA______C_A___A_______AAGGU...AAC-3'\n______________GU_CAAAUACUAG_____________UCAGGA_G_UUA_UCCAUGG\n______________\|\|_\|\|\|\|:\|\|\|\|\|_____________\|\|\|\|:\|_\|_:\|\|_\|\|\|\|\|\|\|\n______________CA_GUUUGUGAUC_____________AGUCUU_C_GAU_AGGUACC\n3'-UUU...GGACA__U__________UC_______________________A_______GCAAU...GAA-5'\n_____________\|______________________________________________\|\n_____________51_____________________________________________17\n	198 -- 204	18 -- 24	-28.1471 kcal/mol	7.4527 kcal/mol	12.9164 kcal/mol	159 205@LB@ \| \|@LB@5'-CAU...ACCGC UCCAAUUAUCAAA C A A AAGGU...AAC-3'@LB@ GU CAAAUACUAG UCAGGA G UUA UCCAUGG@LB@ \|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|:\| \| :\|\| \|\|\|\|\|\|\|@LB@ CA GUUUGUGAUC AGUCUU C GAU AGGUACC@LB@3'-UUU...GGACA U UC A GCAAU...GAA-5'@LB@ \| \|@LB@ 51 17@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -28.1471 kcal/mol@LB@Unfolding Energy - mRNA 7.4527 kcal/mol@LB@Unfolding Energy - sRNA 12.9164 kcal/mol@LB@@LB@Position - mRNA 160 -- 204@LB@Position - sRNA 18 -- 50@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@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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