Locus 5804

Sequence ID	2R_DroMel_CAF1
Location	18,378,749 – 18,378,844
Length	95
Max. P	0.945355

overview

Window 8

Location	18,378,749 – 18,378,844
Length	95
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	78.25
Mean single sequence MFE	-20.60
Consensus MFE	-12.14
Energy contribution	-11.87
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-2.33
Structure conservation index	0.59
SVM decision value	1.35
SVM RNA-class probability	0.945355
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18378749 95 + 20766785
AGUGUUAAAACAUGAAAAGCUGCGCCUGGCAGCGGGACAACAGUGUGCCGCCGAAGAUACCAACACCAACUAUUGGUAUCCGCCAGCAGA----------ACU--------CA
.((((....))))((....((((...((((.((((.(((....))).))))....((((((((.........)))))))).)))))))).----------..)--------). ( -30.90)
>DroPse_CAF1 22742 93 + 1
AGUGUUAAAACAUUAAAAGCUGCG-CUGGAAAAAGGACAACAGUUA--AAUAGAAGAUACCAACA----CUAUUGGUAUC---CAGCAGA----------ACAUAGUACACCA
.((((......((((....(((((-(((............))))..--.......((((((((..----...))))))))---..)))).----------...)))))))).. ( -19.50)
>DroGri_CAF1 22733 86 + 1
AGUGUUAAAACAUUAAAAGCUAGG-CUGGAAAAAGGACAACAGUUA--AAUAGAAGAUACCAACA----CUAUUGGUAUCC---AGCGGU----------ACGGAG-------
(((((....)))))....(((..(-(((((.....(((....))).--.........((((((..----...)))))))))---))))))----------......------- ( -17.00)
>DroWil_CAF1 27460 98 + 1
AGUGUUAAAACAUGAAAAGCUACG-CUGGAAAAAGGACAACGGUUA--AAUAGAAGAUACCAACA----CUAUUGGUAUCCAGCGGCAUACGAAAAAACAACU--------CU
.((((....)))).....((..((-(((((.....(((....))).--.........((((((..----...)))))))))))))))................--------.. ( -19.70)
>DroMoj_CAF1 18813 86 + 1
AGUGUUAAAACAUUAAAAGCUAGG-CUGGAAAAAGGACAACAGUUA--AAUAGAAGAUACCAACA----CUAUUGGUAUCC---AGCAGU----------ACGGAG-------
(((((....)))))....(((..(-(((((.....(((....))).--.........((((((..----...)))))))))---))))))----------......------- ( -17.00)
>DroPer_CAF1 23354 93 + 1
AGUGUUAAAACAUUAAAAGCUGCG-CUGGAAAAAGGACAACAGUUA--AAUAGAAGAUACCAACA----CUAUUGGUAUC---CAGCAGA----------ACAUAGUACACCA
.((((......((((....(((((-(((............))))..--.......((((((((..----...))))))))---..)))).----------...)))))))).. ( -19.50)
>consensus
AGUGUUAAAACAUUAAAAGCUACG_CUGGAAAAAGGACAACAGUUA__AAUAGAAGAUACCAACA____CUAUUGGUAUCC__CAGCAGA__________ACA_AG_____CA
.((((....)))).....(((....(((............)))............((((((((.........))))))))....))).......................... (-12.14 = -11.87 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	18,378,749 – 18,378,844
Length	95
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.25
Mean single sequence MFE	-21.67
Consensus MFE	-13.50
Energy contribution	-14.08
Covariance contribution	0.58
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.62
SVM decision value	1.21
SVM RNA-class probability	0.931423
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18378749 95 - 20766785
UG--------AGU----------UCUGCUGGCGGAUACCAAUAGUUGGUGUUGGUAUCUUCGGCGGCACACUGUUGUCCCGCUGCCAGGCGCAGCUUUUCAUGUUUUAACACU
.(--------(((----------(.((((((((((((((((((.....)))))))))))..(((((.(((....))).))))))))).))).)))))................ ( -35.40)
>DroPse_CAF1 22742 93 - 1
UGGUGUACUAUGU----------UCUGCUG---GAUACCAAUAG----UGUUGGUAUCUUCUAUU--UAACUGUUGUCCUUUUUCCAG-CGCAGCUUUUAAUGUUUUAACACU
.(((((.....((----------(.(((((---((...((((((----(..(((......)))..--..))))))).......)))))-)).)))...(((....)))))))) ( -21.50)
>DroGri_CAF1 22733 86 - 1
-------CUCCGU----------ACCGCU---GGAUACCAAUAG----UGUUGGUAUCUUCUAUU--UAACUGUUGUCCUUUUUCCAG-CCUAGCUUUUAAUGUUUUAACACU
-------....((----------...(((---(((...((((((----(..(((......)))..--..))))))).......)))))-)...)).................. ( -16.40)
>DroWil_CAF1 27460 98 - 1
AG--------AGUUGUUUUUUCGUAUGCCGCUGGAUACCAAUAG----UGUUGGUAUCUUCUAUU--UAACCGUUGUCCUUUUUCCAG-CGUAGCUUUUCAUGUUUUAACACU
..--------(((.(((....(((.....(((((((((((((..----.))))))))).......--....(((((.........)))-)))))).....)))....)))))) ( -18.80)
>DroMoj_CAF1 18813 86 - 1
-------CUCCGU----------ACUGCU---GGAUACCAAUAG----UGUUGGUAUCUUCUAUU--UAACUGUUGUCCUUUUUCCAG-CCUAGCUUUUAAUGUUUUAACACU
-------....((----------...(((---(((...((((((----(..(((......)))..--..))))))).......)))))-)...)).................. ( -16.40)
>DroPer_CAF1 23354 93 - 1
UGGUGUACUAUGU----------UCUGCUG---GAUACCAAUAG----UGUUGGUAUCUUCUAUU--UAACUGUUGUCCUUUUUCCAG-CGCAGCUUUUAAUGUUUUAACACU
.(((((.....((----------(.(((((---((...((((((----(..(((......)))..--..))))))).......)))))-)).)))...(((....)))))))) ( -21.50)
>consensus
UG_____CU_AGU__________UCUGCUG__GGAUACCAAUAG____UGUUGGUAUCUUCUAUU__UAACUGUUGUCCUUUUUCCAG_CGCAGCUUUUAAUGUUUUAACACU
..........................((((...((((((((((.....))))))))))............(((..(......)..)))...)))).................. (-13.50 = -14.08 +   0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:52 2006