Locus 2180

Sequence ID X_DroMel_CAF1
Location 5,902,828 – 5,903,040
Length 212
Max. P 0.968170
window3537 window3538 window3539 window3540

overview

Window 7

Location 5,902,828 – 5,902,934
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 95.75
Mean single sequence MFE -28.65
Consensus MFE -28.06
Energy contribution -27.75
Covariance contribution -0.31
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.98
SVM decision value 0.88
SVM RNA-class probability 0.873534
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902828 106 - 22224390
CAAACAACUGCAGCGGCGGCAAGAAAGCGGCAGCCAAAACAAAAGCAAAAAGGCCAACAUCUCUGACGGCCUUUCACCUGUUGGAUGUCGAGAAAAGCAACUGCCU
.........((((..((.((......))((((.((((......((...(((((((..((....))..)))))))...)).)))).)))).......))..)))).. ( -29.90)
>DroSec_CAF1 19480 106 - 1
CAAACAACUGCAGCGGCGGCAAGAAAGCGGCAGCCAAAACAAAAGCAAAAAGGCCAACAUCUCUGACGGCCUUUCACCUGUUGGAUGUCGGGAAAAGCAACUGCCU
.........((((..((.((......))((((.((((......((...(((((((..((....))..)))))))...)).)))).)))).......))..)))).. ( -29.90)
>DroSim_CAF1 16848 106 - 1
CAAACAACUGCAGCGGCGGCAAGAAAGCGGCAGCCAAAACAAAAGCAAAAAGGCCAACAUCUCUGACGGCCUUUCACCUGUUGGAUGUCGAGAAAAGCAACUGCCU
.........((((..((.((......))((((.((((......((...(((((((..((....))..)))))))...)).)))).)))).......))..)))).. ( -29.90)
>DroEre_CAF1 19498 105 - 1
CAAACAACUGCAGCAGCGGCAAGAAAGUGGCAGCCAAAACAAAAGCGAAGAGGCCAACGUCUCUGACGGCCUUUCACCUGUUGAAUGUCGAAA-AAGCAACUGCCU
............((((..((.......(((((.....((((...(.((.((((((...(((...))))))))))).).))))...)))))...-..))..)))).. ( -24.90)
>consensus
CAAACAACUGCAGCGGCGGCAAGAAAGCGGCAGCCAAAACAAAAGCAAAAAGGCCAACAUCUCUGACGGCCUUUCACCUGUUGGAUGUCGAGAAAAGCAACUGCCU
.........((((..((.((......))((((.((((......((...(((((((..((....))..)))))))...)).)))).)))).......))..)))).. (-28.06 = -27.75 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,902,903 – 5,903,005
Length 102
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 96.59
Mean single sequence MFE -27.20
Consensus MFE -27.09
Energy contribution -27.15
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.24
Structure conservation index 1.00
SVM decision value 1.62
SVM RNA-class probability 0.968170
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902903 102 + 22224390
GCCGCUUUCUUGCCGCCGCUGCAGUUGUUUGUCGAAACUUAAUUGUAACUGCCAAAUAAUUCGUGGCGGCCACAGAAAGAGAUUAUCAUUAUUAUUACUAUU-
..(.((((((.((((((((.(.(((((((((.((..((......))...)).))))))))))))))))))...)))))).).....................- ( -28.70)
>DroSec_CAF1 19555 102 + 1
GCCGCUUUCUUGCCGCCGCUGCAGUUGUUUGUCGAAACUUAAUUGUAACUGCCAAAUAAUUCGUGGCGGCCACAGAAAGAGAUUAUCAUUAUUAUUACUAUU-
..(.((((((.((((((((.(.(((((((((.((..((......))...)).))))))))))))))))))...)))))).).....................- ( -28.70)
>DroSim_CAF1 16923 102 + 1
GCCGCUUUCUUGCCGCCGCUGCAGUUGUUUGUCGAAACUUAAUUGUAACUGCCAAAUAAUUCGUGGCGGCCACAGAAAGAGAUUAUCAUUAUUAUUACUAUU-
..(.((((((.((((((((.(.(((((((((.((..((......))...)).))))))))))))))))))...)))))).).....................- ( -28.70)
>DroEre_CAF1 19572 103 + 1
GCCACUUUCUUGCCGCUGCUGCAGUUGUUUGUCGAAACUUAAUUGUAACUGCCAAAUAAUUCGUGGCGGCCACAGAAACAGAUUAUCAUUAUCAUUGUUAUUA
.....(((((.(((((..(.(.(((((((((.((..((......))...)).)))))))))))..)))))...)))))..(((.......))).......... ( -22.70)
>consensus
GCCGCUUUCUUGCCGCCGCUGCAGUUGUUUGUCGAAACUUAAUUGUAACUGCCAAAUAAUUCGUGGCGGCCACAGAAAGAGAUUAUCAUUAUUAUUACUAUU_
..(.((((((.((((((((.(.(((((((((.((..((......))...)).))))))))))))))))))...)))))).)...................... (-27.09 = -27.15 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,902,903 – 5,903,005
Length 102
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 96.59
Mean single sequence MFE -25.18
Consensus MFE -24.35
Energy contribution -24.85
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.97
SVM decision value 0.12
SVM RNA-class probability 0.595514
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902903 102 - 22224390
-AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGACAAACAACUGCAGCGGCGGCAAGAAAGCGGC
-....................((.((((((...((((((.(((.....)))((((((........((((....))))))))))...)))))).)))))).)). ( -27.10)
>DroSec_CAF1 19555 102 - 1
-AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGACAAACAACUGCAGCGGCGGCAAGAAAGCGGC
-....................((.((((((...((((((.(((.....)))((((((........((((....))))))))))...)))))).)))))).)). ( -27.10)
>DroSim_CAF1 16923 102 - 1
-AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGACAAACAACUGCAGCGGCGGCAAGAAAGCGGC
-....................((.((((((...((((((.(((.....)))((((((........((((....))))))))))...)))))).)))))).)). ( -27.10)
>DroEre_CAF1 19572 103 - 1
UAAUAACAAUGAUAAUGAUAAUCUGUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGACAAACAACUGCAGCAGCGGCAAGAAAGUGGC
.........................(((((...(((((..(((.....)))((((((........((((....))))))))))....))))).)))))..... ( -19.40)
>consensus
_AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGACAAACAACUGCAGCGGCGGCAAGAAAGCGGC
.....................((.((((((...((((((.(((.....)))((((((........((((....))))))))))...)))))).)))))).)). (-24.35 = -24.85 +   0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,902,934 – 5,903,040
Length 106
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 94.04
Mean single sequence MFE -23.73
Consensus MFE -23.51
Energy contribution -23.82
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.99
SVM decision value 1.50
SVM RNA-class probability 0.959236
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902934 106 - 22224390
UUCCUUUCGACAGUUAAUAACAAUAGAAAGAGAGU------AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGA
......((((.(.(((((......(((((((((..------.....((....)).......)))))))))(((((.((((.........)))).))))).))))).).)))) ( -25.44)
>DroSec_CAF1 19586 106 - 1
UUCCUUUCGACAGUUAAUAACAAUAGAAAGAGAGU------AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGA
......((((.(.(((((......(((((((((..------.....((....)).......)))))))))(((((.((((.........)))).))))).))))).).)))) ( -25.44)
>DroSim_CAF1 16954 106 - 1
UUCCUUUCGACAGUUAAUAACAAUAGAAAGAGAGU------AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGA
......((((.(.(((((......(((((((((..------.....((....)).......)))))))))(((((.((((.........)))).))))).))))).).)))) ( -25.44)
>DroEre_CAF1 19603 112 - 1
UUCCUUUCGACAGUUAAUGACAAUAGAAAGAGCGACAUAAUAAUAACAAUGAUAAUGAUAAUCUGUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGA
......((((.(.(((((......(((((.((...(((.((.((....)).)).))).....)).)))))(((((.((((.........)))).))))).))))).).)))) ( -18.60)
>consensus
UUCCUUUCGACAGUUAAUAACAAUAGAAAGAGAGU______AAUAGUAAUAAUAAUGAUAAUCUCUUUCUGUGGCCGCCACGAAUUAUUUGGCAGUUACAAUUAAGUUUCGA
......((((.(.(((((......(((((((((..........((....))..........)))))))))(((((.((((.........)))).))))).))))).).)))) (-23.51 = -23.82 +   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 10:28:08 2006