Locus 5584

Sequence ID	3R_DroMel_CAF1
Location	14,762,463 – 14,762,555
Length	92
Max. P	0.996255

overview

Window 3

Location	14,762,463 – 14,762,555
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-21.71
Consensus MFE	-17.72
Energy contribution	-18.12
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.72
Structure conservation index	0.82
SVM decision value	2.67
SVM RNA-class probability	0.996255
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14762463 92 + 27905053
GUCGCAAUUUACAUAGUCAUAGGCCAAUUAUGGCCAUCUAUGCACACACACACACACACAAUCAAACACUUGUACGUGAGUGGCAUAAUUGC
...(((((.............(((((....)))))...(((((.(((.(((..(((..............)))..))).))))))))))))) ( -23.04)
>DroSec_CAF1 21374 90 + 1
GUCGCAAUUUACAUAGUCAUAGGCCAAUUAUGGCCAUCUAUGCACACACA--CACACACAAUCAAACACUCGUACGUGAGUGGCAUAAUUGC
...(((((.............(((((....)))))...(((((.(((.((--(..((..............))..))).))))))))))))) ( -22.24)
>DroSim_CAF1 22534 92 + 1
GUCGCAAUUUACAUAGUCAUAGGCCAAUUAUGGCCAUCUAUGCACACACACACACACACAAUCAAACACUCGUACGUGAGUGGCAUAAUUGC
...(((((.............(((((....)))))...(((((.(((.(((..((................))..))).))))))))))))) ( -22.09)
>DroEre_CAF1 21628 83 + 1
GUCGCAAUUUACAUAGUCAUAG-CCAAUUAUGGCCAUCUAUGCACAC--------ACACAAUCAAACACCCGUACGUGAGUGGCAUAAUUGC
...(((((.......(((((((-....)))))))....(((((.(((--------.(((...(........)...))).))))))))))))) ( -18.30)
>DroYak_CAF1 22045 84 + 1
GUCGCCAUUUACAUAGUCAUAGGCCAAUUAUGGCCAUCUCUGCACAC--------CCACAAUCAAACACGCGUACGUGAGUGGCAUAAUUGC
...(((((((((.........(((((....)))))......((....--------..............))....)))))))))........ ( -22.87)
>consensus
GUCGCAAUUUACAUAGUCAUAGGCCAAUUAUGGCCAUCUAUGCACACACA__CACACACAAUCAAACACUCGUACGUGAGUGGCAUAAUUGC
(((((......(((((.....(((((....)))))..)))))........................(((......))).)))))........ (-17.72 = -18.12 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	14,762,463 – 14,762,555
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	91.74
Mean single sequence MFE	-30.96
Consensus MFE	-22.64
Energy contribution	-23.32
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-3.31
Structure conservation index	0.73
SVM decision value	1.47
SVM RNA-class probability	0.956534
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14762463 92 - 27905053
GCAAUUAUGCCACUCACGUACAAGUGUUUGAUUGUGUGUGUGUGUGUGUGCAUAGAUGGCCAUAAUUGGCCUAUGACUAUGUAAAUUGCGAC
((((((..(((((.(((((((((........))))))))).))).)).(((((((..(((((....))))).....)))))))))))))... ( -34.30)
>DroSec_CAF1 21374 90 - 1
GCAAUUAUGCCACUCACGUACGAGUGUUUGAUUGUGUGUG--UGUGUGUGCAUAGAUGGCCAUAAUUGGCCUAUGACUAUGUAAAUUGCGAC
((((((..(((((.(((((((((........)))))))))--.))).))((((((..(((((....))))).....)))))).))))))... ( -32.90)
>DroSim_CAF1 22534 92 - 1
GCAAUUAUGCCACUCACGUACGAGUGUUUGAUUGUGUGUGUGUGUGUGUGCAUAGAUGGCCAUAAUUGGCCUAUGACUAUGUAAAUUGCGAC
((((((..(((((.(((((((((........))))))))).))).)).(((((((..(((((....))))).....)))))))))))))... ( -34.00)
>DroEre_CAF1 21628 83 - 1
GCAAUUAUGCCACUCACGUACGGGUGUUUGAUUGUGU--------GUGUGCAUAGAUGGCCAUAAUUGG-CUAUGACUAUGUAAAUUGCGAC
(((((((...(((((......)))))..)))))))((--------(..((((((((((((((....)))-))))..)))))))...)))... ( -28.10)
>DroYak_CAF1 22045 84 - 1
GCAAUUAUGCCACUCACGUACGCGUGUUUGAUUGUGG--------GUGUGCAGAGAUGGCCAUAAUUGGCCUAUGACUAUGUAAAUGGCGAC
.((((((((((((((..((((((.((........)).--------)))))).))).))).))))))))(((....((...))....)))... ( -25.50)
>consensus
GCAAUUAUGCCACUCACGUACGAGUGUUUGAUUGUGUGUG__UGUGUGUGCAUAGAUGGCCAUAAUUGGCCUAUGACUAUGUAAAUUGCGAC
(((((((...(((((......)))))..)))))))..........((.(((((((..(((((....))))).....)))))))....))... (-22.64 = -23.32 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:43 2006