Locus 5886

Sequence ID 2R_DroMel_CAF1
Location 18,595,606 – 18,595,766
Length 160
Max. P 0.997163
window9450 window9451 window9452

overview

Window 0

Location 18,595,606 – 18,595,726
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -37.17
Consensus MFE -30.01
Energy contribution -29.80
Covariance contribution -0.21
Combinations/Pair 1.18
Mean z-score -4.84
Structure conservation index 0.81
SVM decision value 2.81
SVM RNA-class probability 0.997163
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18595606 120 - 20766785
GGAAAUUUUCCGAUGAUUUGGAAGCGAUUUCUCCAGAUGACAUAGAAAUUGUUUCUAGAUCUCGCAAAAUUUCAAAUUACAACUCAAGCGAAGCGUGUCAGAACGACAUGUUCGAUUUGG
.((((((((.(((.((((((((((((((((((...........))))))))))))))))))))).))))))))...........((((((((.((((((.....)))))))))).)))). ( -43.30)
>DroEre_CAF1 5469 105 - 1
GGAAAUUUUCCGAUGAUUUAGAAACGAUUACUCUAGAUGCGAUAGAAAUCGUUUUUAGAUCUCGCAAAAUUUCAAAUUACAACUUGGGCGAA---------------CUGUUCAAUUUGG
.((((((((.(((.(((((((((((((((..((((.......)))))))))))))))))))))).))))))))......(((.((((((...---------------..)))))).))). ( -34.40)
>DroYak_CAF1 5387 120 - 1
GGAAAUUUUCCGAUGAUUUAGAAACGAUUUCUCUAGAAGCUAUAGAAAUUGUUUUUAGAUCUCGCAAAAUUUCUAAUUACAACUCAGGCGAAACCGAUCAGAGCGACCUCUUUAAUUUGA
(((((((((.(((.((((((((((((((((((.(((...))).))))))))))))))))))))).)))))))))........(((.((((....)).)).)))................. ( -33.80)
>consensus
GGAAAUUUUCCGAUGAUUUAGAAACGAUUUCUCUAGAUGCCAUAGAAAUUGUUUUUAGAUCUCGCAAAAUUUCAAAUUACAACUCAGGCGAA_C___UCAGA_CGACCUGUUCAAUUUGG
.((((((((.(((.((((((((((((((((((...........))))))))))))))))))))).))))))))......(((.(((((((..................))))))).))). (-30.01 = -29.80 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,595,646 – 18,595,766
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -24.50
Consensus MFE -17.55
Energy contribution -18.33
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.72
SVM decision value -0.03
SVM RNA-class probability 0.517997
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18595646 120 + 20766785
GUAAUUUGAAAUUUUGCGAGAUCUAGAAACAAUUUCUAUGUCAUCUGGAGAAAUCGCUUCCAAAUCAUCGGAAAAUUUCCAAUGACAGCUGAAAUAAAAAUUAUAUGUCUGUAAUUACUA
((((((.((((((((.((((((.(((((.....))))).)))...(((((.......))))).....))).))))))))....((((..(((........)))..))))...)))))).. ( -24.90)
>DroEre_CAF1 5494 118 + 1
GUAAUUUGAAAUUUUGCGAGAUCUAAAAACGAUUUCUAUCGCAUCUAGAGUAAUCGUUUCUAAAUCAUCGGAAAAUUUCCAGUGACAGCCGAAAUAAAAAUUGUAGGUC--UAACUUUUC
((.(((.((((((((.((((((.((.((((((((((((.......))))..)))))))).)).))).))).)))))))).))).)).(((..(((....)))...))).--......... ( -25.60)
>DroYak_CAF1 5427 117 + 1
GUAAUUAGAAAUUUUGCGAGAUCUAAAAACAAUUUCUAUAGCUUCUAGAGAAAUCGUUUCUAAAUCAUCGGAAAAUUUCCAGUGACAGCCGAAAUAAAAAUUGUGUAUCCGUAAC---UC
((.(((.((((((((.((((((.((.((((.((((((.(((...))).)))))).)))).)).))).))).)))))))).))).)).((.((.(((.......))).)).))...---.. ( -23.00)
>consensus
GUAAUUUGAAAUUUUGCGAGAUCUAAAAACAAUUUCUAUAGCAUCUAGAGAAAUCGUUUCUAAAUCAUCGGAAAAUUUCCAGUGACAGCCGAAAUAAAAAUUGUAUGUC_GUAACU__UC
((.(((.((((((((.((((((.((.((((.((((((...........)))))).)))).)).))).))).)))))))).))).)).................................. (-17.55 = -18.33 +   0.78)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,595,646 – 18,595,766
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.11
Mean single sequence MFE -32.87
Consensus MFE -28.99
Energy contribution -28.00
Covariance contribution -0.99
Combinations/Pair 1.19
Mean z-score -4.17
Structure conservation index 0.88
SVM decision value 1.97
SVM RNA-class probability 0.984376
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18595646 120 - 20766785
UAGUAAUUACAGACAUAUAAUUUUUAUUUCAGCUGUCAUUGGAAAUUUUCCGAUGAUUUGGAAGCGAUUUCUCCAGAUGACAUAGAAAUUGUUUCUAGAUCUCGCAAAAUUUCAAAUUAC
..((((((...((((...(((....))).....))))....((((((((.(((.((((((((((((((((((...........))))))))))))))))))))).)))))))).)))))) ( -34.40)
>DroEre_CAF1 5494 118 - 1
GAAAAGUUA--GACCUACAAUUUUUAUUUCGGCUGUCACUGGAAAUUUUCCGAUGAUUUAGAAACGAUUACUCUAGAUGCGAUAGAAAUCGUUUUUAGAUCUCGCAAAAUUUCAAAUUAC
.(((((((.--.......)))))))....(((......)))((((((((.(((.(((((((((((((((..((((.......)))))))))))))))))))))).))))))))....... ( -29.80)
>DroYak_CAF1 5427 117 - 1
GA---GUUACGGAUACACAAUUUUUAUUUCGGCUGUCACUGGAAAUUUUCCGAUGAUUUAGAAACGAUUUCUCUAGAAGCUAUAGAAAUUGUUUUUAGAUCUCGCAAAAUUUCUAAUUAC
.(---((.((((...(..(((....)))..).)))).)))(((((((((.(((.((((((((((((((((((.(((...))).))))))))))))))))))))).)))))))))...... ( -34.40)
>consensus
GA__AGUUAC_GACAUACAAUUUUUAUUUCGGCUGUCACUGGAAAUUUUCCGAUGAUUUAGAAACGAUUUCUCUAGAUGCCAUAGAAAUUGUUUUUAGAUCUCGCAAAAUUUCAAAUUAC
.............................(((......)))((((((((.(((.((((((((((((((((((...........))))))))))))))))))))).))))))))....... (-28.99 = -28.00 +  -0.99)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:19 2006