Locus 68

Sequence ID X_DroMel_CAF1
Location 315,008 – 315,161
Length 153
Max. P 0.999768
window82 window83 window84

overview

Window 2

Location 315,008 – 315,122
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.64
Mean single sequence MFE -34.41
Consensus MFE -30.21
Energy contribution -30.13
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -2.91
Structure conservation index 0.88
SVM decision value 4.04
SVM RNA-class probability 0.999768
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 315008 114 + 22224390
GCACAAGGCACGUGCGCGAUCUGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGUUUUUAAAUAGAAACUCGCUAUUUCCCCAUG
((((((..(((((....((((.((..............)------).)))).)))))..))))(((((((..(((((((.(.......).)))))))..)))))))))............ ( -27.04)
>DroSec_CAF1 57978 114 + 1
GCACAAGGCACGUGCGAGAUCUGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUU
((((((..(((((....((((.((..............)------).)))).)))))..))))(((((((..(((((((((.......)))))))))..)))))))))............ ( -34.84)
>DroSim_CAF1 78591 114 + 1
GCACAAGGCACGUGCGCGAUCUGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUU
((((((..(((((....((((.((..............)------).)))).)))))..))))(((((((..(((((((((.......)))))))))..)))))))))............ ( -34.84)
>DroEre_CAF1 58724 120 + 1
GCACAAGGCACGUGCGCGAUCUGAAAACAAUUUACCACUGCGAUCCCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAACGCAGACUUUGAAGGGAAACUCGCCAUUUCCCCAUU
((.....(((.(((.(..(..((....))..)..)))))))(((....))).))(..(((.(((((((((.((((((((((.......)))))))))).))))))))).)))..)..... ( -37.30)
>DroYak_CAF1 79482 114 + 1
GCACAAGGCACGUGCGCGAUCUGAAAACAAUUUACCACU------CCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAGAGGGAAACUCGCCAUUUCCCCAUU
((((.......))))((((((.((..............)------).)))).))(..(((.(((((((((.((((((((((.......)))))))))).))))))))).)))..)..... ( -38.04)
>consensus
GCACAAGGCACGUGCGCGAUCUGAAAACAAUUUACCACU______CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUU
((((.......))))((((((..........................)))).))(..(((.(((((((((..(((((((((.......)))))))))..))))))))).)))..)..... (-30.21 = -30.13 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 315,008 – 315,122
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.64
Mean single sequence MFE -34.10
Consensus MFE -27.72
Energy contribution -28.52
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.81
SVM decision value 0.72
SVM RNA-class probability 0.831243
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 315008 114 - 22224390
CAUGGGGAAAUAGCGAGUUUCUAUUUAAAAACUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCAGAUCGCGCACGUGCCUUGUGC
((..(((.....(((((((((..((((((.............))))))..))))))).........((.((((.(------((............))).)))))))).....)))..)). ( -26.42)
>DroSec_CAF1 57978 114 - 1
AAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCAGAUCUCGCACGUGCCUUGUGC
....((((......(((((((..(((((((((.......)))))))))..)))))))((((((..((((......------))))...)))))).......))))(((((.....))))) ( -33.30)
>DroSim_CAF1 78591 114 - 1
AAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCAGAUCGCGCACGUGCCUUGUGC
.(..(((.....(((((((((..(((((((((.......)))))))))..))))))).........((.((((.(------((............))).)))))))).....)))..).. ( -32.90)
>DroEre_CAF1 58724 120 - 1
AAUGGGGAAAUGGCGAGUUUCCCUUCAAAGUCUGCGUUCGACUUUAAAGUGAAACUCACAAUUCUCGCUGAUCGGGAUCGCAGUGGUAAAUUGUUUUCAGAUCGCGCACGUGCCUUGUGC
....(((((.((..(((((((.(((.((((((.......)))))).))).))))))).)).)))))((.((((..((..(((((.....)))))..)).))))))(((((.....))))) ( -41.60)
>DroYak_CAF1 79482 114 - 1
AAUGGGGAAAUGGCGAGUUUCCCUCUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCUCGCUGAUCGG------AGUGGUAAAUUGUUUUCAGAUCGCGCACGUGCCUUGUGC
....(((((.((..(((((((.((.(((((((.......))))))).)).))))))).)).)))))((.((((.(------((............))).))))))(((((.....))))) ( -36.30)
>consensus
AAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG______AGUGGUAAAUUGUUUUCAGAUCGCGCACGUGCCUUGUGC
.(..(((.....(((((((((..(((((((((.......)))))))))..)))))))((((((..((((............))))...))))))...........)).....)))..).. (-27.72 = -28.52 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 315,047 – 315,161
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.72
Mean single sequence MFE -28.44
Consensus MFE -23.10
Energy contribution -22.82
Covariance contribution -0.28
Combinations/Pair 1.13
Mean z-score -2.22
Structure conservation index 0.81
SVM decision value 1.95
SVM RNA-class probability 0.983630
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 315047 114 + 22224390
-----CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGUUUUUAAAUAGAAACUCGCUAUUUCCCCAUGU-AUUGUUUAAAAGAGGUAUUAAAACAGCCCGCACCCGCU
-----......((((.(((..(((((((((..(((((((.(.......).)))))))..)))))))))...))).....(.-.((((((.............))))))..).....)))) ( -21.22)
>DroSec_CAF1 58017 102 + 1
-----CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUC-A---UUUCAAAGCGGCAUUACAACUG---------GCU
-----......((((..(((.(((((((((..(((((((((.......)))))))))..))))))))).)))..)......-.---........(((........)))---------))) ( -26.80)
>DroSim_CAF1 78630 102 + 1
-----CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUC-A---UUUCAAAGCGGCAUUACAACUG---------GCU
-----......((((..(((.(((((((((..(((((((((.......)))))))))..))))))))).)))..)......-.---........(((........)))---------))) ( -26.80)
>DroEre_CAF1 58764 120 + 1
CGAUCCCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAACGCAGACUUUGAAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUUAAAACGGCAUUAGAACUGGUCGCAGCCACU
.(((....))).((((((((.(((((((((.((((((((((.......)))))))))).))))))))).))))..(((.(((..((((.......))))...))).)))))))....... ( -38.60)
>DroYak_CAF1 79521 91 + 1
-----CCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAGAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUCAAAGCG------------------------
-----.......(((..(((.(((((((((.((((((((((.......)))))))))).))))))))).)))..).((......)).......)).------------------------ ( -28.80)
>consensus
_____CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUU_AUUGUUUCAAAGCGGCAUUACAACUG_________GCU
............(.(..(((.(((((((((..(((((((((.......)))))))))..))))))))).)))..).)........................................... (-23.10 = -22.82 +  -0.28)

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 09:32:55 2006