Locus 6539

Sequence ID 3L_DroMel_CAF1
Location 17,284,465 – 17,284,741
Length 276
Max. P 0.992039
window10630 window10631 window10632 window10633

overview

Window 0

Location 17,284,465 – 17,284,568
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.99
Mean single sequence MFE -37.74
Consensus MFE -27.64
Energy contribution -28.24
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.73
SVM decision value 0.61
SVM RNA-class probability 0.797177
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17284465 103 - 23771897
AAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----------CUUACCAUCGCUGGAGG------AGCAGGUCCUU
.((((((((((.(.(((((((((......((((((((....)))))))).....))))))))).).))))..)))-----------))).(((....)))(((------(.....)))). ( -36.30)
>DroSec_CAF1 168148 103 - 1
AAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----------CUUACCAUCGCUGGAGG------AGCAGGUCCUU
.((((((((((.(.(((((((((......((((((((....)))))))).....))))))))).).))))..)))-----------))).(((....)))(((------(.....)))). ( -36.30)
>DroSim_CAF1 164373 103 - 1
AAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----------CUUACCAUCGCUGGAGG------AGCAGGUCCUU
.((((((((((.(.(((((((((......((((((((....)))))))).....))))))))).).))))..)))-----------))).(((....)))(((------(.....)))). ( -36.30)
>DroEre_CAF1 171155 103 - 1
AAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCCCAGCAG-----------CUUUCCAUCGCUGGAGG------AGCAGGUCCUU
...(((((.((.(.(((((((((......((((((((....)))))))).....))))))))).).))))))).(-----------(((((((....)))).)------)))........ ( -38.40)
>DroYak_CAF1 176321 120 - 1
AAAGCUGGCGGCGAUGGCAACCACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCCCAGCAGCUCCGCAGCUGCUUUCCAUCGCUGGAGGUCCUUUGGCAGGUCCUU
..((((((((((((((....).....((.((((((((....)))))))).)).)))))))))))))....(((((((....))))))).((((....))))((.(((.....))).)).. ( -41.40)
>consensus
AAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG___________CUUACCAUCGCUGGAGG______AGCAGGUCCUU
...((((.(((.(.(((((((((......((((((((....)))))))).....))))))))).).))))))).............(((.(((....))))))................. (-27.64 = -28.24 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,284,493 – 17,284,608
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.91
Mean single sequence MFE -36.43
Consensus MFE -32.64
Energy contribution -33.24
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.90
SVM decision value 2.30
SVM RNA-class probability 0.992039
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17284493 115 - 23771897
AACAACCCGCGCAACGAGCAGCAAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----
..........((......((((.....((.(....).))....))))((((.(.(((((((((......((((((((....)))))))).....))))))))).).)))).))..----- ( -36.00)
>DroSec_CAF1 168176 115 - 1
AACAACCCGCGCAACGAGCAGCAAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----
..........((......((((.....((.(....).))....))))((((.(.(((((((((......((((((((....)))))))).....))))))))).).)))).))..----- ( -36.00)
>DroSim_CAF1 164401 115 - 1
AACAACCCGCGCAACGAGCAGCAAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG-----
..........((......((((.....((.(....).))....))))((((.(.(((((((((......((((((((....)))))))).....))))))))).).)))).))..----- ( -36.00)
>DroEre_CAF1 171183 106 - 1
A---------GCAGCGAGCAGCGAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCCCAGCAG-----
.---------((((....(((.......)))....))))....(((((.((.(.(((((((((......((((((((....)))))))).....))))))))).).)))))))..----- ( -34.70)
>DroYak_CAF1 176361 120 - 1
AAGAGCGCGCGCAACGAGCAGCAAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACCACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCCCAGCAGCUCCG
..((((((..((.....)).))...((...(....)..))...(((((.((.(.(((((((........((((((((....)))))))).......))))))).).))))))).)))).. ( -39.46)
>consensus
AACAACCCGCGCAACGAGCAGCAAACAACUGGCAACUGUGAAAGCUGGCGGCGAUGGCAACAACCCGAUAUUGUUUUGGCCAAAAUAGUUUUAAUUGUUGCCAGCUCCGCAGCAG_____
..........((......((((.....((.(....).))....))))((((.(.(((((((((......((((((((....)))))))).....))))))))).).)))).))....... (-32.64 = -33.24 +   0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,284,608 – 17,284,703
Length 95
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 91.46
Mean single sequence MFE -42.17
Consensus MFE -32.53
Energy contribution -33.65
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -2.05
Structure conservation index 0.77
SVM decision value 0.53
SVM RNA-class probability 0.771943
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17284608 95 + 23771897
CGCUGUUGGCAACAUUUUAUUAGAAUGCAGGCCGGGUCC------GGGUCAAACCGCAAGGG-G-GGUCGGUGUCAAGGAGCGCUGGCCACCGGGAGUGGCAA
.((..(((((..(((((.....)))))...)))...(((------((......((....)).-.-(((((((((......))))))))).)))))))..)).. ( -39.30)
>DroSec_CAF1 168291 96 + 1
CGCUGCUGGCAACAUUUUAUUAGAAUGCAGGCCGGGUCC------GGGUCAAACCGCAAGGGGG-GGUCGGUGUCAGGGGGCGCUGGCCACCGGGAGUGGCAA
.((..(((((..(((((.....)))))...)))...(((------((......((....))...-((((((((((....)))))))))).)))))))..)).. ( -44.60)
>DroSim_CAF1 164516 96 + 1
CGCUGCUGGCAACAUUUUAUUAGAAUGCAGGCCGGGUCC------GGGUCAAACCGCAAGGGGG-GGUCGGUGUCAGGGGGCGCUGGCCACCGGGAGUGGCAA
.((..(((((..(((((.....)))))...)))...(((------((......((....))...-((((((((((....)))))))))).)))))))..)).. ( -44.60)
>DroYak_CAF1 176481 103 + 1
CGCUGCUGGCAACAUUUUAUUAGAAUGCAGGCCGAGUCCGGGUACGGGUCAAACCGCAAGGGGGGAUUCGGUGUCAGGGGGGAGUGGCCACCGGGAGUGGCAA
((((.((((...(((((.....)))))..(((((..(((.(..(((((((...((....))...))))).))..)....)))..))))).)))).)))).... ( -40.20)
>consensus
CGCUGCUGGCAACAUUUUAUUAGAAUGCAGGCCGGGUCC______GGGUCAAACCGCAAGGGGG_GGUCGGUGUCAGGGGGCGCUGGCCACCGGGAGUGGCAA
.((..(((((..(((((.....)))))...)))...(((..............((....)).((.((((((((((....)))))))))).)))))))..)).. (-32.53 = -33.65 +   1.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,284,647 – 17,284,741
Length 94
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -21.24
Consensus MFE -20.05
Energy contribution -20.11
Covariance contribution 0.06
Combinations/Pair 1.13
Mean z-score -1.25
Structure conservation index 0.94
SVM decision value 0.60
SVM RNA-class probability 0.794611
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17284647 94 - 23771897
CCCUAACCCCUCGCCCAACACCCGCUGGCCACUCCCACUUGCCACUCCCGGUGGCCAGCGCUCCUUGACACCGACC-C-CCCUUGCGGUUUGACCC-----
...............(((....(((((((((((................)))))))))))....)))..((((...-.-......)))).......----- ( -23.49)
>DroSec_CAF1 168330 95 - 1
CCUUCGCCCCUCGCCCACCACCCGCUGGCCGCUCCCACUUGCCACUCCCGGUGGCCAGCGCCCCCUGACACCGACC-CCCCCUUGCGGUUUGACCC-----
......................(((((((((((................))))))))))).........((((.(.-.......))))).......----- ( -22.39)
>DroSim_CAF1 164555 95 - 1
CCUUCGCCCCUCGCCCACCACCCGCUGGCCGCUCCCACUUGCCACUCCCGGUGGCCAGCGCCCCCUGACACCGACC-CCCCCUUGCGGUUUGACCC-----
......................(((((((((((................))))))))))).........((((.(.-.......))))).......----- ( -22.39)
>DroYak_CAF1 176521 83 - 1
--CU----------------CCUGCUGGCCACUCCCACUUGCCACUCCCGGUGGCCACUCCCCCCUGACACCGAAUCCCCCCUUGCGGUUUGACCCGUACC
--..----------------.....((((((((................))))))))..........................(((((......))))).. ( -16.69)
>consensus
CCCUCGCCCCUCGCCCACCACCCGCUGGCCACUCCCACUUGCCACUCCCGGUGGCCAGCGCCCCCUGACACCGACC_CCCCCUUGCGGUUUGACCC_____
......................(((((((((((................))))))))))).........((((............))))............ (-20.05 = -20.11 +   0.06)

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 12:23:37 2006