Locus 2315

Sequence ID X_DroMel_CAF1
Location 6,248,355 – 6,248,497
Length 142
Max. P 0.997404
window3749 window3750 window3751 window3752

overview

Window 9

Location 6,248,355 – 6,248,467
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.46
Mean single sequence MFE -33.93
Consensus MFE -29.15
Energy contribution -28.93
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.86
SVM decision value 1.22
SVM RNA-class probability 0.932741
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6248355 112 + 22224390
UGGGUGUGUAGGAUGUGUAG--------GAUGUGUAGGUGUGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCACGGGGAAAUCUCCUUUGUUUU
(((((((((...........--------......(((.(.(((.(.((....)).).))).).)))....(((((((.....))))))))))))).))).((((....))))........ ( -32.00)
>DroEre_CAF1 9839 91 + 1
----------------------------GGUGUGUGGG-AUGUGGAUGUGGGCAGCGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCGCGGGGAAAUCUCCUGUUUUUU
----------------------------.....((((.-.((((........((((......))))....(((((((.....))))))).))))..))))((((....))))........ ( -34.50)
>DroYak_CAF1 22256 113 + 1
UAGGUGUGU-----GUGCAGGAGUAUAGGAUGUGUAGG-AUGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCUCACGCUCCGCGGGGAAAUCUCCUUUGUUU-
......(.(-----((((....))))).).........-..((((((((((((.......(((((....)))))(((.....)))..))))))).)))))((((....)))).......- ( -35.30)
>consensus
U_GGUGUGU_____GUG_AG________GAUGUGUAGG_AUGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCGCGGGGAAAUCUCCUUUGUUUU
.........................................((((((((((((.........))).....(((((((.....))))))).)))).)))))((((....))))........ (-29.15 = -28.93 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,248,355 – 6,248,467
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.46
Mean single sequence MFE -21.62
Consensus MFE -18.33
Energy contribution -18.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.85
SVM decision value 2.82
SVM RNA-class probability 0.997206
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6248355 112 - 22224390
AAAACAAAGGAGAUUUCCCCGUGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACACACCUACACAUC--------CUACACAUCCUACACACCCA
........(((........((((((((.((.(((.(((.....))).)))....)))))))).)).........)))...............--------.................... ( -21.83)
>DroEre_CAF1 9839 91 - 1
AAAAAACAGGAGAUUUCCCCGCGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGCUGCCCACAUCCACAU-CCCACACACC----------------------------
........(((........((.(((((.((.(((.(((.....))).)))....)))))))..)).........)))....-..........---------------------------- ( -19.13)
>DroYak_CAF1 22256 113 - 1
-AAACAAAGGAGAUUUCCCCGCGGAGCGUGAGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACAU-CCUACACAUCCUAUACUCCUGCAC-----ACACACCUA
-......(((((..........(((((.((((((.(((.....))).)))...))))))))...((.....))........-...............)))))....-----......... ( -23.90)
>consensus
AAAACAAAGGAGAUUUCCCCGCGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACAU_CCUACACAUC________CU_CAC_____ACACACC_A
........(((........((.(((((..(.(((.(((.....))).)))).....)))))..)).........)))........................................... (-18.33 = -18.33 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,248,387 – 6,248,497
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.72
Mean single sequence MFE -45.58
Consensus MFE -41.79
Energy contribution -41.60
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -3.59
Structure conservation index 0.92
SVM decision value 2.85
SVM RNA-class probability 0.997404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6248387 110 + 22224390
UGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCACGGGGAAAUCUCCUUUGUUUU----------UUUCCACCUCGCGCCCACUUUUUACGCGCA
.(((((.((((((..(((((((((((....(((((((.....))))))).)).)))))).(((((((.............----------))))).))))).))))))..)))))..... ( -44.52)
>DroSec_CAF1 15199 110 + 1
UGUGCAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCACGGGGAAAUCUCCUUUGUUUU----------UUUCCACUUCGCGCCCACUUUUUACGCGCA
.((((..((((((..((.((((((((....(((((((.....))))))).)).))))))))((((((.(......)...)----------))))).......)))))).......)))). ( -44.30)
>DroEre_CAF1 9850 120 + 1
UGUGGAUGUGGGCAGCGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCGCGGGGAAAUCUCCUGUUUUUUUUUUUUUUUGUUUCCACCUCGCGCCCACUUUUUACGCGCA
.(((((.((((((.((((.(((((((....(((((((.....))))))).)).)))))..((((((((.....................)))))).))))))))))))..)))))..... ( -47.90)
>DroYak_CAF1 22290 109 + 1
UGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCUCACGCUCCGCGGGGAAAUCUCCUUUGUUU-----------UUUCCACCUUGCGCCCACUUUUUGCGAGCA
.(..((.((((((......((((((((...(((((((.....)))))))))).)))))(((((((((.(......)...-----------))))).))..))))))))..))..)..... ( -45.60)
>consensus
UGUGGAUGUGGGCAACGAUGGAGCUGAAAGGCUUAGCAGUUUGCUGAGCACACGCUCCACGGGGAAAUCUCCUUUGUUUU__________UUUCCACCUCGCGCCCACUUUUUACGCGCA
.(((((.((((((..((.((((((((....(((((((.....))))))).)).))))))))((((....)))).............................))))))..)))))..... (-41.79 = -41.60 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,248,387 – 6,248,497
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.72
Mean single sequence MFE -39.01
Consensus MFE -35.64
Energy contribution -35.95
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.74
Structure conservation index 0.91
SVM decision value 2.50
SVM RNA-class probability 0.994657
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6248387 110 - 22224390
UGCGCGUAAAAAGUGGGCGCGAGGUGGAAA----------AAAACAAAGGAGAUUUCCCCGUGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACA
............((((((((((((.(((((----------.............))))))).((((((.((.(((.(((.....))).)))....))))))))))).)))))))....... ( -39.72)
>DroSec_CAF1 15199 110 - 1
UGCGCGUAAAAAGUGGGCGCGAAGUGGAAA----------AAAACAAAGGAGAUUUCCCCGUGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUGCACA
.(.((((.....((((((((((.(.(((((----------.............))))).).((((((.((.(((.(((.....))).)))....))))))))))).))))))))))).). ( -38.32)
>DroEre_CAF1 9850 120 - 1
UGCGCGUAAAAAGUGGGCGCGAGGUGGAAACAAAAAAAAAAAAAAACAGGAGAUUUCCCCGCGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGCUGCCCACAUCCACA
............((((((((((((.(((((.......................)))))))..(((((.((.(((.(((.....))).)))....))))))).)))).))))))....... ( -40.40)
>DroYak_CAF1 22290 109 - 1
UGCUCGCAAAAAGUGGGCGCAAGGUGGAAA-----------AAACAAAGGAGAUUUCCCCGCGGAGCGUGAGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACA
............((((((((..((.(((((-----------............)))))))))(((((.((((((.(((.....))).)))...))))))))......))))))....... ( -37.60)
>consensus
UGCGCGUAAAAAGUGGGCGCGAGGUGGAAA__________AAAACAAAGGAGAUUUCCCCGCGGAGCGUGUGCUCAGCAAACUGCUAAGCCUUUCAGCUCCAUCGUUGCCCACAUCCACA
............((((((((((((.(((((.......................)))))))..(((((.((.(((.(((.....))).)))....))))))).)))).))))))....... (-35.64 = -35.95 +   0.31)

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 10:31:22 2006