Locus 1440

Sequence ID 2L_DroMel_CAF1
Location 3,833,164 – 3,833,267
Length 103
Max. P 0.817726
window2344 window2345

overview

Window 4

Location 3,833,164 – 3,833,267
Length 103
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -32.43
Consensus MFE -30.38
Energy contribution -30.87
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.94
SVM decision value 0.67
SVM RNA-class probability 0.817726
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3833164 103 + 22407834
GGCUCAUCACCCCGAUGUUUGGGCAAACCAUAUGCUCU--GGCAGCAUGAACCAGUGUGUCCACGGUCCAUGGAGCAACCCCCAAAAAACGGACACCCCUUGCCC
(((........(((...((((((.........(((...--.))).((((.(((.(((....)))))).))))........))))))...))).........))). ( -27.13)
>DroSec_CAF1 22072 102 + 1
GGCUCAUCACCCCGAUGUUUGGGCAAACCAUAUGCUCU--GGCAGCAUGGACCAGUGUGUCCACGGUCCAUGGAGCAACCCCCAAAAAA-GGACACCCCUUGCCC
(((.((((.....))))((((((.........(((...--.))).((((((((.(((....)))))))))))........)))))).((-((.....))))))). ( -34.30)
>DroEre_CAF1 26532 104 + 1
GGCUCAUCACCCCGAUGUUUGGGCAAACCAUAUGCUCU-GGGCAGCACGGACCAGUGUGUCCACGGUCCAUGGAGCAACCCCCAAAAAAAGGACACCCCUGGCCC
((((((((.....))))((((((....((((..(((.(-(((((.(((......))))))))).)))..)))).......))))))...(((.....))))))). ( -33.20)
>DroYak_CAF1 23349 105 + 1
GGCUCAUCACCCCGAUGUUUGGGCAAACCAUAUGCUCUCUGGCAACAUGGACCAGUGUGUCCACGGUCCAUGGAGCAACCCCCAAAAAAAGGACACCCCCUGCCA
(((.((((.....))))((((((.........((((....)))).((((((((.(((....)))))))))))........))))))...(((......)))))). ( -35.10)
>consensus
GGCUCAUCACCCCGAUGUUUGGGCAAACCAUAUGCUCU__GGCAGCAUGGACCAGUGUGUCCACGGUCCAUGGAGCAACCCCCAAAAAAAGGACACCCCUUGCCC
(((.((((.....))))((((((.........((((....)))).((((((((.(((....)))))))))))........))))))....((.....))..))). (-30.38 = -30.87 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,833,164 – 3,833,267
Length 103
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -41.23
Consensus MFE -36.62
Energy contribution -37.38
Covariance contribution 0.75
Combinations/Pair 1.09
Mean z-score -1.49
Structure conservation index 0.89
SVM decision value 0.01
SVM RNA-class probability 0.538062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3833164 103 - 22407834
GGGCAAGGGGUGUCCGUUUUUUGGGGGUUGCUCCAUGGACCGUGGACACACUGGUUCAUGCUGCC--AGAGCAUAUGGUUUGCCCAAACAUCGGGGUGAUGAGCC
.(((...(((((.((((.((((((.((......(((((((((((....))).)))))))))).))--))))...))))..)))))...((((.....)))).))) ( -37.80)
>DroSec_CAF1 22072 102 - 1
GGGCAAGGGGUGUCC-UUUUUUGGGGGUUGCUCCAUGGACCGUGGACACACUGGUCCAUGCUGCC--AGAGCAUAUGGUUUGCCCAAACAUCGGGGUGAUGAGCC
((((((((((((.((-((.....)))).))))))((((((((((....))).)))))))...(((--(.......))))))))))...((((.....)))).... ( -41.20)
>DroEre_CAF1 26532 104 - 1
GGGCCAGGGGUGUCCUUUUUUUGGGGGUUGCUCCAUGGACCGUGGACACACUGGUCCGUGCUGCCC-AGAGCAUAUGGUUUGCCCAAACAUCGGGGUGAUGAGCC
(((((((..((((((..((..(((((....)))))..))....)))))).)))))))(((((....-..)))))..(((((((((........))))...))))) ( -43.90)
>DroYak_CAF1 23349 105 - 1
UGGCAGGGGGUGUCCUUUUUUUGGGGGUUGCUCCAUGGACCGUGGACACACUGGUCCAUGUUGCCAGAGAGCAUAUGGUUUGCCCAAACAUCGGGGUGAUGAGCC
((((((((((((.(((((....))))).))))))((((((((((....))).))))))).))))))..........(((((((((........))))...))))) ( -42.00)
>consensus
GGGCAAGGGGUGUCCUUUUUUUGGGGGUUGCUCCAUGGACCGUGGACACACUGGUCCAUGCUGCC__AGAGCAUAUGGUUUGCCCAAACAUCGGGGUGAUGAGCC
(((((.((((((.(((((....))))).))))))((((((((((....))).)))))))..)))))..........(((((((((........))))...))))) (-36.62 = -37.38 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:42 2006