Locus 5976

Sequence ID 3R_DroMel_CAF1
Location 15,766,339 – 15,766,574
Length 235
Max. P 0.984386
window9757 window9758 window9759 window9760 window9761

overview

Window 7

Location 15,766,339 – 15,766,437
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 97.28
Mean single sequence MFE -25.87
Consensus MFE -25.07
Energy contribution -24.63
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -4.31
Structure conservation index 0.97
SVM decision value 1.97
SVM RNA-class probability 0.984386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15766339 98 - 27905053
CUGAAUUAAAUGUUAAUACUUCCGCUGUGUGUGCGCUCGAUGCGCAUGAAUUUCUAACAAAUUUAGCACAUAAUGGUUAUUAUUAUAUUAUUUCACAA
.((((.((((((.(((((...(((.(((((((((((.....)))).(((((((.....)))))))))))))).))).))))).))).))).))))... ( -24.60)
>DroSec_CAF1 23541 98 - 1
CUGAAUUAAAUAAUAAUACUUCCGCUGUGUGUGCGCUCAAUGCGCAUAAAUUUCUAACAAAUUUAGCACAUAAUGGUUAUUAUUAUAUUAUUUCACAA
.((((.((((((((((((...(((.(((((((((((.....)))).(((((((.....)))))))))))))).))).))))))))).))).))))... ( -28.50)
>DroSim_CAF1 23522 98 - 1
CUGAAUUAAAUGUUAAUACUUCCGCUGUGUGUGCGCUCAAUGCGCAUAAAUUUCUAACAAAUUUAGCACAUAAUGGUUAUUAUUAUAUUAUUUCACAA
.((((.((((((.(((((...(((.(((((((((((.....)))).(((((((.....)))))))))))))).))).))))).))).))).))))... ( -24.50)
>consensus
CUGAAUUAAAUGUUAAUACUUCCGCUGUGUGUGCGCUCAAUGCGCAUAAAUUUCUAACAAAUUUAGCACAUAAUGGUUAUUAUUAUAUUAUUUCACAA
.((((.((((((.(((((...(((.(((((((((((.....)))).(((((((.....)))))))))))))).))).))))).))).))).))))... (-25.07 = -24.63 +  -0.44)

alignment

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secondary structure

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Window 8

Location 15,766,437 – 15,766,534
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -25.46
Consensus MFE -19.95
Energy contribution -20.20
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -3.02
Structure conservation index 0.78
SVM decision value 1.08
SVM RNA-class probability 0.911724
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15766437 97 + 27905053
CUUAGCGGAAAUGCAAAAUGAUGUGUGCACUUUUUUUUUUUUGCAUUUCCGCUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUA
((((((((((((((((((.((.((....))...))...))))))))))))))))))..((((..(((((((..........)))))))....)))). ( -29.30)
>DroSec_CAF1 23639 94 + 1
CUUAGCGGAAAUGCAAAAUGAUGUGUGCACUUUUU---UUCAGCAUUUCCGUUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUA
((((((((((((((((((....((....))...))---))..))))))))))))))..((((..(((((((..........)))))))....)))). ( -22.90)
>DroSim_CAF1 23620 94 + 1
CUUAGCGGAAAUGCAAAAUGAUGUGUGCACUUUUU---UUCGGCAUUUCCGUUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUA
((((((((((((((........((....)).....---....))))))))))))))..((((..(((((((..........)))))))....)))). ( -23.73)
>DroEre_CAF1 25746 92 + 1
CUUAGCGGAAAUGCAAAACGAUGUGUGCACUUUUU-----UGGCAUUUCCGCUGGGAAAUCAAAUGGCGAGCCAAUAGAAAUUUACAAAACAUGCUA
((((((((((((((.(((.((.((....)))).))-----).))))))))))))))........(((....)))....................... ( -25.90)
>consensus
CUUAGCGGAAAUGCAAAAUGAUGUGUGCACUUUUU___UUCGGCAUUUCCGCUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUA
((((((((((((((.....((.((....))...)).......))))))))))))))........(((((((..........)))))))......... (-19.95 = -20.20 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,766,437 – 15,766,534
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -20.24
Consensus MFE -15.14
Energy contribution -15.70
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.27
Structure conservation index 0.75
SVM decision value 0.34
SVM RNA-class probability 0.694729
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15766437 97 - 27905053
UAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAGCGGAAAUGCAAAAAAAAAAAAGUGCACACAUCAUUUUGCAUUUCCGCUAAG
.............(((((...((((.....))))..)))))...(((((((((((((((....................)))))))))))))))... ( -22.95)
>DroSec_CAF1 23639 94 - 1
UAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCUGAA---AAAAAGUGCACACAUCAUUUUGCAUUUCCGCUAAG
.........(((..((.((..((((.....))))..)).))..)))(((((((((...(---(((..(((....)))..)))))))))))))..... ( -16.20)
>DroSim_CAF1 23620 94 - 1
UAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCCGAA---AAAAAGUGCACACAUCAUUUUGCAUUUCCGCUAAG
.........(((..((.((..((((.....))))..)).))..)))(((((((((...(---(((..(((....)))..)))))))))))))..... ( -16.20)
>DroEre_CAF1 25746 92 - 1
UAGCAUGUUUUGUAAAUUUCUAUUGGCUCGCCAUUUGAUUUCCCAGCGGAAAUGCCA-----AAAAAGUGCACACAUCGUUUUGCAUUUCCGCUAAG
..(((.....))).....((...(((....)))...))......(((((((((((.(-----(((..(((....)))..)))))))))))))))... ( -25.60)
>consensus
UAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCCAAA___AAAAAGUGCACACAUCAUUUUGCAUUUCCGCUAAG
.............(((((...((((.....))))..)))))...(((((((((((.........((((((.......)))))))))))))))))... (-15.14 = -15.70 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,766,474 – 15,766,574
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 89.63
Mean single sequence MFE -20.07
Consensus MFE -14.35
Energy contribution -15.35
Covariance contribution 1.00
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.71
SVM decision value 0.07
SVM RNA-class probability 0.568031
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15766474 100 + 27905053
UUUUUGCAUUUCCGCUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUAAAUAAUUGAUGGACACAGACACAUUGCCGAAAUAUUCACU
..((((.((((((....))))))))))(((((..(((.(((..(((((((.....)).)))))..))).))).)))))...................... ( -15.30)
>DroSec_CAF1 23674 95 + 1
-UUCAGCAUUUCCGUUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUAAAUAAUUGAUGGACACGG---CAAUGCCGAAA-AUUCACU
-(((.(((((.((((.(....(((((.(((((((..........)))))))..(((.....))).)))))...)))))---.))))).))).-....... ( -18.20)
>DroSim_CAF1 23655 96 + 1
-UUCGGCAUUUCCGUUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUAAAUAAUUGAUGGACACGG---CAAUGCCGAAAUAUUCACU
-(((((((((.((((.(....(((((.(((((((..........)))))))..(((.....))).)))))...)))))---.)))))))))......... ( -24.30)
>DroEre_CAF1 25781 94 + 1
---UGGCAUUUCCGCUGGGAAAUCAAAUGGCGAGCCAAUAGAAAUUUACAAAACAUGCUAAAUAAUUGAUGGACACGG---ACAUGCCGAAAUAUUCAUU
---.(((((.((((.((....(((((.(((....)))......(((((((.....)).)))))..)))))...)))))---).)))))............ ( -22.50)
>consensus
_UUCGGCAUUUCCGCUGGGAAAUCAAAUUGUGAGCCAAUAGAAAUUUACAAAAUAUGAUAAAUAAUUGAUGGACACGG___CAAUGCCGAAAUAUUCACU
.((((((((((((....))))).......(((..(((.(((..(((((((.....)).)))))..))).))).)))........)))))))......... (-14.35 = -15.35 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,766,474 – 15,766,574
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 89.63
Mean single sequence MFE -20.80
Consensus MFE -16.41
Energy contribution -17.35
Covariance contribution 0.94
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.79
SVM decision value 0.46
SVM RNA-class probability 0.745056
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15766474 100 - 27905053
AGUGAAUAUUUCGGCAAUGUGUCUGUGUCCAUCAAUUAUUUAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAGCGGAAAUGCAAAAA
............(((.....)))((((.(((......(((((.((.....)))))))......)))..)))).((((((((((....)))))).)))).. ( -17.10)
>DroSec_CAF1 23674 95 - 1
AGUGAAU-UUUCGGCAUUG---CCGUGUCCAUCAAUUAUUUAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCUGAA-
.......-.(((((((((.---(((((.(((......(((((.((.....)))))))......)))..)))...(((......))).)).)))))))))- ( -20.80)
>DroSim_CAF1 23655 96 - 1
AGUGAAUAUUUCGGCAUUG---CCGUGUCCAUCAAUUAUUUAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCCGAA-
.........(((((((((.---(((((.(((......(((((.((.....)))))))......)))..)))...(((......))).)).)))))))))- ( -23.00)
>DroEre_CAF1 25781 94 - 1
AAUGAAUAUUUCGGCAUGU---CCGUGUCCAUCAAUUAUUUAGCAUGUUUUGUAAAUUUCUAUUGGCUCGCCAUUUGAUUUCCCAGCGGAAAUGCCA---
............(((((.(---((((....(((((.......(((.....)))..........(((....))).)))))......))))).))))).--- ( -22.30)
>consensus
AGUGAAUAUUUCGGCAUUG___CCGUGUCCAUCAAUUAUUUAUCAUAUUUUGUAAAUUUCUAUUGGCUCACAAUUUGAUUUCCCAACGGAAAUGCCAAA_
.........((((((.........(((.(((......(((((.((.....)))))))......)))..)))......((((((....)))))))))))). (-16.41 = -17.35 +   0.94)

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 12:09:36 2006