Locus 3988

Sequence ID	2R_DroMel_CAF1
Location	13,187,747 – 13,187,853
Length	106
Max. P	0.588618

overview

Window 8

Location	13,187,747 – 13,187,853
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.60
Mean single sequence MFE	-20.39
Consensus MFE	-11.94
Energy contribution	-13.55
Covariance contribution	1.61
Combinations/Pair	1.12
Mean z-score	-1.68
Structure conservation index	0.59
SVM decision value	0.11
SVM RNA-class probability	0.588618
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13187747 106 + 20766785
UCGGAUGUAUACAACAAUAUACACAUUACAAGGACAUACACAGUAAUAAAAACU-----AAACACCAUGAAGGGUUUUCU-----CUGGUUC-UUGAUCCUCCG---AGUGGAAGACCCA
(((((((((((......)))))).....(((((((......(((.......)))-----((((.((.....))))))...-----...))))-)))....))))---).(((.....))) ( -21.10)
>DroPse_CAF1 1832 116 + 1
CCGGGUGUAUACAACAAUAUACAAAAUACAA-GACACACACAAUAAUAAAAAUCUUUUGAAUUCCCAUCGUGGAAUUGCUUCCAUCUUGUGAUCUGAUCCUCCA---AUCGGAAGAUCCU
....((((((......))))))....(((((-((......(((.............)))((((((......)))))).......)))))))....((((.(((.---...))).)))).. ( -21.52)
>DroSec_CAF1 1060 105 + 1
UCGGAUGUAUACAACAAUAUACACAUUACAA-GACAUACAUAGUAAUAAAAACU-----AAACACCAUGAUGGGUUUUCU-----CUGGUUC-UUGAUCCUCCG---AGCGGAAGACCCU
..((.((((((......)))))).(((((..-..........))))).......-----.....)).....(((((((((-----...((((-..........)---)))))))))))). ( -20.10)
>DroEre_CAF1 1029 103 + 1
UCGGAUGUAUACAACAAUAUACACAUUACAA-GACAUACACUGUAAUAAAAACU-----AAACACCAUGGUGGGU--UCU-----CUGGUUC-UUGAUCCUCCA---AGCGGAAGACCCU
..((.((((((......)))))).((((((.-.........)))))).......-----.....)).....((((--..(-----(((...(-(((......))---))))))..)))). ( -21.50)
>DroYak_CAF1 990 103 + 1
UCGGAUGUAUACAACAAUAUACACAUUACAA-GACAUACACAGUAAUAAAAACU-----AAACACCAUGAUGGGU--UCU-----CUGGUUC-UUGAUCCUCCA---AGCGGAAGACCCU
..((.((((((......)))))).(((((..-..........))))).......-----.....)).....((((--..(-----(((...(-(((......))---))))))..)))). ( -20.20)
>DroAna_CAF1 986 107 + 1
UUGGAUGUAUACAACAAUAUAGACAGUAUCA-GACAUACACAAUUAUAAAAAAU-----A--UUCCAUAUUGGGUUUUCU-----UUUUUUUUCUAAUCUUCCACUCAAAGGAAGACCCU
.(((((((((......)))))....((((..-...))))...............-----.--.))))....(((((((((-----(((...................)))))))))))). ( -17.91)
>consensus
UCGGAUGUAUACAACAAUAUACACAUUACAA_GACAUACACAGUAAUAAAAACU_____AAACACCAUGAUGGGUUUUCU_____CUGGUUC_UUGAUCCUCCA___AGCGGAAGACCCU
..((.((((((......)))))).(((((.............))))).................)).....(((((((((......(((............)))......))))))))). (-11.94 = -13.55 +   1.61)

alignment

secondary structure

dotplot

Window 9

Location	13,187,747 – 13,187,853
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.60
Mean single sequence MFE	-25.78
Consensus MFE	-16.80
Energy contribution	-16.72
Covariance contribution	-0.08
Combinations/Pair	1.25
Mean z-score	-1.26
Structure conservation index	0.65
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13187747 106 - 20766785
UGGGUCUUCCACU---CGGAGGAUCAA-GAACCAG-----AGAAAACCCUUCAUGGUGUUU-----AGUUUUUAUUACUGUGUAUGUCCUUGUAAUGUGUAUAUUGUUGUAUACAUCCGA
.(((((((((...---.)))))))(((-(.((((.-----.(((.....))).))))...(-----(((.......))))........))))..(((((((((....))))))))))).. ( -24.00)
>DroPse_CAF1 1832 116 - 1
AGGAUCUUCCGAU---UGGAGGAUCAGAUCACAAGAUGGAAGCAAUUCCACGAUGGGAAUUCAAAAGAUUUUUAUUAUUGUGUGUGUC-UUGUAUUUUGUAUAUUGUUGUAUACACCCGG
..((((((((...---.)))))))).....(((((((((((....))))..((((((((((.....)))))))))).........)))-))))....(((((((....)))))))..... ( -33.10)
>DroSec_CAF1 1060 105 - 1
AGGGUCUUCCGCU---CGGAGGAUCAA-GAACCAG-----AGAAAACCCAUCAUGGUGUUU-----AGUUUUUAUUACUAUGUAUGUC-UUGUAAUGUGUAUAUUGUUGUAUACAUCCGA
..((((((((...---.))))))))..-......(-----(((.....((((((((((...-----.........))))))).)))))-))...(((((((((....))))))))).... ( -26.20)
>DroEre_CAF1 1029 103 - 1
AGGGUCUUCCGCU---UGGAGGAUCAA-GAACCAG-----AGA--ACCCACCAUGGUGUUU-----AGUUUUUAUUACAGUGUAUGUC-UUGUAAUGUGUAUAUUGUUGUAUACAUCCGA
..((((((((...---.))))))))((-((((.((-----(..--(((......))).)))-----.))))))(((((((........-)))))))((((((((....)))))))).... ( -25.80)
>DroYak_CAF1 990 103 - 1
AGGGUCUUCCGCU---UGGAGGAUCAA-GAACCAG-----AGA--ACCCAUCAUGGUGUUU-----AGUUUUUAUUACUGUGUAUGUC-UUGUAAUGUGUAUAUUGUUGUAUACAUCCGA
..((((((((...---.))))))))..-......(-----(((--...((((((((((...-----.........))))))).)))))-))...(((((((((....))))))))).... ( -25.10)
>DroAna_CAF1 986 107 - 1
AGGGUCUUCCUUUGAGUGGAAGAUUAGAAAAAAAA-----AGAAAACCCAAUAUGGAA--U-----AUUUUUUAUAAUUGUGUAUGUC-UGAUACUGUCUAUAUUGUUGUAUACAUCCAA
.(((((((((.......)))))))...........-----........(((((((((.--(-----(((...((((......))))..-.))))...)))))))))..........)).. ( -20.50)
>consensus
AGGGUCUUCCGCU___UGGAGGAUCAA_GAACCAG_____AGAAAACCCAUCAUGGUGUUU_____AGUUUUUAUUACUGUGUAUGUC_UUGUAAUGUGUAUAUUGUUGUAUACAUCCGA
..((((((((.......))))))))............................(((................((((((.............))))))(((((((....))))))).))). (-16.80 = -16.72 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:05 2006