Locus 4019

Sequence ID 2L_DroMel_CAF1
Location 11,668,478 – 11,668,626
Length 148
Max. P 0.999949
window6334 window6335 window6336

overview

Window 4

Location 11,668,478 – 11,668,588
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 97.45
Mean single sequence MFE -25.70
Consensus MFE -23.94
Energy contribution -24.14
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.31
Structure conservation index 0.93
SVM decision value 4.38
SVM RNA-class probability 0.999885
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11668478 110 + 22407834
CAUGAAGUAUUUAUCUCUCGACCAUCGGGCCAUACAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUGCAGGCACUAUUAGAAAUGUAAAUUUGACA
......((((......((((.....))))..))))....(((((((((((((.((((((...(.((....((......))...)))...)))))).))))))))))).)) ( -21.90)
>DroSec_CAF1 129724 110 + 1
CAUGAAGUAUUUAUCUCUCGGCCAUCGGGCCGUACAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUCCAGGCACUAUUAGAAAUGUAAAUUUGACA
......((..........(((((....))))).........(((((((((((.((((((...(.((....((......))...)))...)))))).))))))))))))). ( -25.70)
>DroSim_CAF1 127624 110 + 1
CAUGAAGUAUUUAUCUCUCGGCCAUCGGGCCAUACAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUGCAGGCACUAUUAGAAAUGUAAAUUUGACA
......((...........((((....))))..........(((((((((((.((((((...(.((....((......))...)))...)))))).))))))))))))). ( -25.70)
>DroEre_CAF1 151214 110 + 1
CAUGAAGUAUUUAUCUAUCGGCCAUCGGGCCAUGCAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUGUAGGCACUAUUAGAAAUGUAAAUUUGACA
......((...........((((....))))..........(((((((((((.((((((...(.(((((..........))).)))...)))))).))))))))))))). ( -26.10)
>DroYak_CAF1 125533 110 + 1
CAUGAAGUAUUUAUCUCUCGGCCAUCGGGCCAUACAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUGCAGGCGCUAUUAGAAAUGUAAAUUUGACA
......((...........((((....))))..........(((((((((((.((((((..((.((....((......))...))))..)))))).))))))))))))). ( -29.10)
>consensus
CAUGAAGUAUUUAUCUCUCGGCCAUCGGGCCAUACAAAUUGCAAAUUUACAUAUCUAAUUACGACCACAAACAAUAUCGUGCAGGCACUAUUAGAAAUGUAAAUUUGACA
......((...........((((....))))..........(((((((((((.((((((...(.((....((......))...)))...)))))).))))))))))))). (-23.94 = -24.14 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,668,478 – 11,668,588
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 97.45
Mean single sequence MFE -31.44
Consensus MFE -30.50
Energy contribution -30.22
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -3.05
Structure conservation index 0.97
SVM decision value 4.78
SVM RNA-class probability 0.999949
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11668478 110 - 22407834
UGUCAAAUUUACAUUUCUAAUAGUGCCUGCACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGUAUGGCCCGAUGGUCGAGAGAUAAAUACUUCAUG
((.(((((((((((.((((((..(((...(((((......)))))...))))))))).)))))))))))))((((((.(((((....)))))....))))))........ ( -28.30)
>DroSec_CAF1 129724 110 - 1
UGUCAAAUUUACAUUUCUAAUAGUGCCUGGACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGUACGGCCCGAUGGCCGAGAGAUAAAUACUUCAUG
((.(((((((((((.((((((..(((((..(((....)))..).)).))..)))))).)))))))))))))((((((.(((((....)))))....))))))........ ( -33.50)
>DroSim_CAF1 127624 110 - 1
UGUCAAAUUUACAUUUCUAAUAGUGCCUGCACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGUAUGGCCCGAUGGCCGAGAGAUAAAUACUUCAUG
((.(((((((((((.((((((..(((...(((((......)))))...))))))))).)))))))))))))((((((.(((((....)))))....))))))........ ( -31.00)
>DroEre_CAF1 151214 110 - 1
UGUCAAAUUUACAUUUCUAAUAGUGCCUACACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGCAUGGCCCGAUGGCCGAUAGAUAAAUACUUCAUG
((.(((((((((((.((((((..(((...(((((......)))))...))))))))).)))))))))))))(((((..(((((....))))).)))))............ ( -30.80)
>DroYak_CAF1 125533 110 - 1
UGUCAAAUUUACAUUUCUAAUAGCGCCUGCACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGUAUGGCCCGAUGGCCGAGAGAUAAAUACUUCAUG
((.(((((((((((.((((((.(((((...((((......)))))).))).)))))).)))))))))))))((((((.(((((....)))))....))))))........ ( -33.60)
>consensus
UGUCAAAUUUACAUUUCUAAUAGUGCCUGCACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUUUGCAAUUUGUAUGGCCCGAUGGCCGAGAGAUAAAUACUUCAUG
((.(((((((((((.((((((..((((...((((......)))))).))..)))))).)))))))))))))((((((.(((((....)))))....))))))........ (-30.50 = -30.22 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,668,517 – 11,668,626
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.52
Mean single sequence MFE -26.85
Consensus MFE -17.06
Energy contribution -16.34
Covariance contribution -0.72
Combinations/Pair 1.18
Mean z-score -3.19
Structure conservation index 0.64
SVM decision value -0.05
SVM RNA-class probability 0.505822
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11668517 109 - 22407834
UAAAUUAUUUUUCGCAAUUUAUUGUCUUUGGAUUUAUU--UGUCA-AAUUUACAUUUCUAAUAGUGCCUG-----CACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUU---UGCA
((((((.......((((....)))).....))))))..--((.((-(((((((((.((((((..(((...-----(((((......)))))...))))))))).)))))))))---)))) ( -23.40)
>DroPse_CAF1 119304 120 - 1
ACUAUUAUUUUUAGCAAUUUAUUUUCUUUAGAUUUAUUUUUGUCGCAAUUUGCAUUUCUAAUGGCCACCGAUACACCCGAUAUUGUUUGCGGUUGUAAUUAGAAAUGUAAAUGCAGUGCC
.............(((..............(((........)))(((.((((((((((((((.((.((((..(((........)))...)))).)).)))))))))))))))))..))). ( -31.50)
>DroSec_CAF1 129763 109 - 1
UAAAUUAUUUUUCGCAAUUUAUUGUCUUUGGAUUUAUU--UGUCA-AAUUUACAUUUCUAAUAGUGCCUG-----GACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUU---UGCA
((((((.......((((....)))).....))))))..--((.((-(((((((((.((((((..(((((.-----.(((....)))..).)).))..)))))).)))))))))---)))) ( -24.20)
>DroEre_CAF1 151253 109 - 1
UAAAUUAUUUUUCGCAAUUUAUUGUCUUUGGAUUUAUU--UGUCA-AAUUUACAUUUCUAAUAGUGCCUA-----CACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUU---UGCA
((((((.......((((....)))).....))))))..--((.((-(((((((((.((((((..(((...-----(((((......)))))...))))))))).)))))))))---)))) ( -24.50)
>DroYak_CAF1 125572 109 - 1
UAAAUUAUUUUUCGCAAUUUAUUGUCUUUGGAUUUAUU--UGUCA-AAUUUACAUUUCUAAUAGCGCCUG-----CACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUU---UGCA
((((((.......((((....)))).....))))))..--((.((-(((((((((.((((((.(((((..-----.((((......)))))).))).)))))).)))))))))---)))) ( -26.00)
>DroPer_CAF1 120857 120 - 1
ACUAUUAUUUUUAGCAAUUUAUUUUCUUUAGAUUUAUUUUUGUCGCAAUUUGCAUUUCUAAUGGCCACCGAUACACCCGAUAUUGUUUGCGGUUGUAAUUAGAAAUGUAAAUGCAGUGCC
.............(((..............(((........)))(((.((((((((((((((.((.((((..(((........)))...)))).)).)))))))))))))))))..))). ( -31.50)
>consensus
UAAAUUAUUUUUCGCAAUUUAUUGUCUUUGGAUUUAUU__UGUCA_AAUUUACAUUUCUAAUAGCGCCUG_____CACGAUAUUGUUUGUGGUCGUAAUUAGAUAUGUAAAUU___UGCA
.............(((..............(((........)))...((((((((.((((((..((.(((.......(((......)))))).))..)))))).))))))))....))). (-17.06 = -16.34 +  -0.72)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:18 2006