Locus 388

Sequence ID 2L_DroMel_CAF1
Location 1,205,989 – 1,206,091
Length 102
Max. P 0.978031
window614 window615

overview

Window 4

Location 1,205,989 – 1,206,091
Length 102
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 88.22
Mean single sequence MFE -27.64
Consensus MFE -18.76
Energy contribution -21.20
Covariance contribution 2.44
Combinations/Pair 1.04
Mean z-score -3.09
Structure conservation index 0.68
SVM decision value 1.06
SVM RNA-class probability 0.908167
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1205989 102 + 22407834
UUUCUUCCUUUUCCAGGACCUCCUCCUC-------------GCCUUCCAUAAUAGCAAUCACAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAAAAGCAAACAGAGGAGGA
.....((((.....))))(((((((...-------------((.(((((((.(((.((.((((....)))))))))...((......))..)))))))..)).....))))))). ( -26.10)
>DroSec_CAF1 1694 115 + 1
UUUCUUCCCUUUCCAGGACCUCCUCCUCCUCGCCCUACUCCGCCUUCCAUAAUAGCAAUCACAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAAAAGCAAACAGAGGAGGA
.......(((....)))......((((((((((........))...........((...((((....)))).............((((....))))....)).....)))))))) ( -25.90)
>DroSim_CAF1 1689 112 + 1
UUUCCUCCCUUUCCAGGACCUCCUCCUCCUC---CCACUCUGCCUUCCAUAAUAGCAAUCACAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAAAAGCAAACAGAGGAGGA
..((((........)))).....((((((((---......(((.(((((((.(((.((.((((....)))))))))...((......))..)))))))..)))....)))))))) ( -27.70)
>DroEre_CAF1 1641 108 + 1
-UUCGUCCUUUUCCAGGACCUCCUGCUCCU------CCGCCUCCUGCCAUAAUAGCAAUCGCAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAAAAGCAAACAGAGGCGGA
-...(((((.....)))))..........(------(((((((.(((.....(((.((.((((....)))))))))........((((....))))....)))....)))))))) ( -30.50)
>DroYak_CAF1 1753 115 + 1
UUUCUUCCUUUGCCAGGACCUCCUCCUCCUUCUCAUCCGCCUCCUGCCAUAAUAGCAAUCACAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAGAAGCAAACAGAGGCGGA
.....((((.....)))).................((((((((.(((.....(((.((.((((....)))))))))........((((....))))....)))....)))))))) ( -28.00)
>consensus
UUUCUUCCUUUUCCAGGACCUCCUCCUCCU______ACGCCGCCUUCCAUAAUAGCAAUCACAGAAAUGUGUUCUAAUUUAAAGCCAUAUAUAUGGAAAAGCAAACAGAGGAGGA
.....(((.......)))..((((((((........................(((.((.((((....)))))))))........((((....))))...........)))))))) (-18.76 = -21.20 +   2.44) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,205,989 – 1,206,091
Length 102
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 88.22
Mean single sequence MFE -37.44
Consensus MFE -26.78
Energy contribution -28.42
Covariance contribution 1.64
Combinations/Pair 1.06
Mean z-score -3.35
Structure conservation index 0.72
SVM decision value 1.80
SVM RNA-class probability 0.978031
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1205989 102 - 22407834
UCCUCCUCUGUUUGCUUUUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGUGAUUGCUAUUAUGGAAGGC-------------GAGGAGGAGGUCCUGGAAAAGGAAGAAA
.((((((((..(((((((.(((((...(((((..(....(((((.....)))))..)..)))))))))))))))-------------))))))))))((((.....))))..... ( -36.50)
>DroSec_CAF1 1694 115 - 1
UCCUCCUCUGUUUGCUUUUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGUGAUUGCUAUUAUGGAAGGCGGAGUAGGGCGAGGAGGAGGAGGUCCUGGAAAGGGAAGAAA
(((((((((.((((((((.(((((...(((((..(....(((((.....)))))..)..))))))))))))))))))(.....)..)))))))))..((((....))))...... ( -38.30)
>DroSim_CAF1 1689 112 - 1
UCCUCCUCUGUUUGCUUUUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGUGAUUGCUAUUAUGGAAGGCAGAGUGG---GAGGAGGAGGAGGUCCUGGAAAGGGAGGAAA
(((((((((.((((((((.(((((...(((((..(....(((((.....)))))..)..))))))))))))))))))...)---)))))))).....((((....))))...... ( -40.10)
>DroEre_CAF1 1641 108 - 1
UCCGCCUCUGUUUGCUUUUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGCGAUUGCUAUUAUGGCAGGAGGCGG------AGGAGCAGGAGGUCCUGGAAAAGGACGAA-
(((.(((((((((.((...(((((...(((((..(....(((((.....)))))..)..)))))))))).)).))))))------)))....))).(((((.....)))))...- ( -35.80)
>DroYak_CAF1 1753 115 - 1
UCCGCCUCUGUUUGCUUCUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGUGAUUGCUAUUAUGGCAGGAGGCGGAUGAGAAGGAGGAGGAGGUCCUGGCAAAGGAAGAAA
(((.((((((((((((((((((((...(((((..(....(((((.....)))))..)..))))))))))..)))))))))).....))))).)))..((((.....))))..... ( -36.50)
>consensus
UCCUCCUCUGUUUGCUUUUCCAUAUAUAUGGCUUUAAAUUAGAACACAUUUCUGUGAUUGCUAUUAUGGAAGGCGGAGG______AGGAGGAGGAGGUCCUGGAAAAGGAAGAAA
(((((((((..(((((((.(((((...(((((..(....(((((.....)))))..)..)))))))))))))))))..........)))))))))..((((.....))))..... (-26.78 = -28.42 +   1.64) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:42 2006