Locus 2327

Sequence ID X_DroMel_CAF1
Location 6,259,067 – 6,259,252
Length 185
Max. P 0.945432
window3771 window3772 window3773

overview

Window 1

Location 6,259,067 – 6,259,176
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -19.93
Consensus MFE -19.70
Energy contribution -19.95
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.99
SVM decision value 0.45
SVM RNA-class probability 0.740968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259067 109 - 22224390
ACGCGUAUCAAGUUACAACUUGCAACAAAUAUUAAAUCAGUAAAAUGUCCUUUAGGGCGCACUCCACUGUAAUUGUUGUUGCAGCCACCCGUAUUCCUUCCUUUUUUUC-----------
..(((((......)))....((((((((..((((...((((....(((((....)))))......))))))))..))))))))))........................----------- ( -20.60)
>DroSec_CAF1 720 107 - 1
ACGCGUAUCAAGUUACAACUUGCAACAAAUAUUAAAUCAGUAAAAUGUCCUUUAGGGCGCACUCCACUGUAAUUGUUGUUGCAGCCACCCGUACUCCCUUCUU--UUCC-----------
..(((((......)))....((((((((..((((...((((....(((((....)))))......))))))))..))))))))))..................--....----------- ( -20.60)
>DroSim_CAF1 728 107 - 1
ACGCGUAUCAAGUUACAAUUUGCAACAAAUAUUAAAUCAGUAAAAUGUCCUUUAGGGCGCACUCCACUGUAAUUGUUGUUGCAGCCACCCAUACUCCUUCCUU--UUCC-----------
..(((((......)))....((((((((..((((...((((....(((((....)))))......))))))))..))))))))))..................--....----------- ( -20.60)
>DroYak_CAF1 238 118 - 1
ACGCGUAUCAAGUUACAACUUGCAACAAAUAUUAAAUCAGUAAAAUGUCCUUUAGGGCGCACUCCACUAUAAUUGUUGUUGCAGCCACCCGUACUCCUUCCUU--UUCUCCGCCUCUCCC
..(((((......)))...(((((((((..((((...........(((((....)))))..........))))..)))))))))...................--......))....... ( -17.90)
>consensus
ACGCGUAUCAAGUUACAACUUGCAACAAAUAUUAAAUCAGUAAAAUGUCCUUUAGGGCGCACUCCACUGUAAUUGUUGUUGCAGCCACCCGUACUCCUUCCUU__UUCC___________
..(((((......)))....((((((((..((((...((((....(((((....)))))......))))))))..))))))))))................................... (-19.70 = -19.95 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,259,096 – 6,259,212
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.79
Mean single sequence MFE -36.00
Consensus MFE -33.19
Energy contribution -33.00
Covariance contribution -0.19
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.92
SVM decision value 1.35
SVM RNA-class probability 0.945432
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259096 116 + 22224390
AACAACAAUUACAGUGGAGUGCGCCCUAAAGGACAUUUUACUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUUGCAAGGAGCAGC----GCUGUGGGACG
...........((((((((((..((.....)).))))))))))...........(((.((...(((((((((((....)))))))))))((((((.....)))))----)...)).))). ( -36.20)
>DroSec_CAF1 747 120 + 1
AACAACAAUUACAGUGGAGUGCGCCCUAAAGGACAUUUUACUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCAAGUUGCACGUCGCAAGGAGGGACGCAGGAUGUGGGACG
...........((((((((((..((.....)).))))))))))...........(((.((.(((((((((((((....)))))))))).((((.(.....).))))...))).)).))). ( -34.70)
>DroSim_CAF1 755 116 + 1
AACAACAAUUACAGUGGAGUGCGCCCUAAAGGACAUUUUACUGAUUUAAUAUUUGUUGCAAAUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAAGAAGCAGC----GUUGUGGGACG
.(((((.....((((((((((..((.....)).))))))))))...........(((((....(((((((((((....)))))))))))..((....)).)))))----)))))...... ( -39.60)
>DroYak_CAF1 276 116 + 1
AACAACAAUUAUAGUGGAGUGCGCCCUAAAGGACAUUUUACUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAACGAGCAGC----GCUGUGGGACG
..((((((.((((((((((((..((.....)).)))))))))......))).)))))).....(((((((((((....)))))))))))((((.((...(((...----))).)).)))) ( -33.50)
>consensus
AACAACAAUUACAGUGGAGUGCGCCCUAAAGGACAUUUUACUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAAGGAGCAGC____GCUGUGGGACG
..((((((.((((((((((((..((.....)).))))))))))......)).)))))).....(((((((((((....)))))))))))((((.((...(((.......))).)).)))) (-33.19 = -33.00 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,259,136 – 6,259,252
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.79
Mean single sequence MFE -39.98
Consensus MFE -37.88
Energy contribution -37.88
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.54
Structure conservation index 0.95
SVM decision value 0.55
SVM RNA-class probability 0.776685
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6259136 116 + 22224390
CUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUUGCAAGGAGCAGC----GCUGUGGGACGCAGGAUGAGCCCAAGGAUCUGCCGGCUGCUUCUUGUGAGA
.....................((.((((((((((....)))))))))))).(..(((((((((((----....((((...(.....)..)))).((.....)).)))))))))))..).. ( -41.00)
>DroSec_CAF1 787 120 + 1
CUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCAAGUUGCACGUCGCAAGGAGGGACGCAGGAUGUGGGACGCAGGAUGAGCCCAAGGAUAUGCCGGCUGCUUCUUGUGAGA
....((..(((((..((((..((.((((((((((....))))))))))))(((.(.....).))))))))))))..))(((((((.(((((...((.....)))))).).)))))))... ( -37.00)
>DroSim_CAF1 795 116 + 1
CUGAUUUAAUAUUUGUUGCAAAUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAAGAAGCAGC----GUUGUGGGACGCAGGAUGAGCCCAAGGAUCUGCCGGCUGCUUCUUGUGAGA
.......................(((((((((((....)))))))))))..((((((((((((((----....((((...(.....)..)))).((.....)).)))))))))))))).. ( -43.80)
>DroYak_CAF1 316 116 + 1
CUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAACGAGCAGC----GCUGUGGGACGCAGGAUGAGCCCAAGGAUCUGCCGGCUGCUUCUUGUGAGA
.....................((.((((((((((....)))))))))))).((((((.(((((((----....((((...(.....)..)))).((.....)).))))))).)))))).. ( -38.10)
>consensus
CUGAUUUAAUAUUUGUUGCAAGUUGUAACUUGAUACGCGUCGAGUUGCACGUCGCAAGGAGCAGC____GCUGUGGGACGCAGGAUGAGCCCAAGGAUCUGCCGGCUGCUUCUUGUGAGA
.......................(((((((((((....)))))))))))..((((((((((((((........((((...(.....)..)))).((.....)).)))))))))))))).. (-37.88 = -37.88 +   0.00)

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 10:31:40 2006