Locus 9618

Sequence ID 3R_DroMel_CAF1
Location 25,404,422 – 25,404,553
Length 131
Max. P 0.969173
window15369 window15370 window15371 window15372

overview

Window 9

Location 25,404,422 – 25,404,528
Length 106
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.75
Mean single sequence MFE -30.52
Consensus MFE -22.91
Energy contribution -22.97
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -2.16
Structure conservation index 0.75
SVM decision value 1.64
SVM RNA-class probability 0.969173
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404422 106 + 27905053
AGGCCAAAUACUGGAAUGCCGAGUGUAAGCCAGGAGUCU---CUGAUCAUUCAUCAAGCUGAACGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGACACG
.(((...(((((((....)).)))))..)))....(((.---((.....((((......)))).(((((.(((.(((((......)))))))).)))))..)))))... ( -30.70)
>DroPse_CAF1 98427 99 + 1
UGUCCAGUCUCUGGGACUCUG----UU-----AGAGCUUC-UCUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUCUGACAAAGGACGGC
.((((((((.....)))).((----((-----(((.....-..(((.((((((......)))))))))..(((.(((((......)))))))))))))))..))))... ( -32.30)
>DroEre_CAF1 92385 87 + 1
AGGCCAAAUACUG-------------------AGAGCUU---CUGAUCAUUCAUCAAGCUGAACGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGACACG
.(.((........-------------------..(((((---.(((....)))..)))))....(((((.(((.(((((......)))))))).)))))...)).)... ( -24.30)
>DroWil_CAF1 112191 95 + 1
GGGCCAAAU-----GACUUUG----CU-----UGGGCUUGGGCUGAUCAUUCAUCAAGCUAACUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGGCAAA
..(((....-----.......----..-----..(((((((..(((....))))))))))...((((((.(((.(((((......)))))))).))))))...)))... ( -31.40)
>DroYak_CAF1 95785 106 + 1
AGGCCAAAUACUGGAGUGCCGAGUGUAAGCCAAGAGCUU---CUGAUCAUUCAUCAAGCUAAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGACACG
.(((...(((((((....)).)))))..)))...(((((---.(((....)))..)))))...((((((.(((.(((((......)))))))).))))))......... ( -32.50)
>DroPer_CAF1 95685 99 + 1
UGUCCAGUCUCUGGGACUCUG----UU-----AGAGCUUC-UCUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGACGGC
.((((((((.....))))...----..-----..(((((.-..(((....)))..)))))...((((((.(((.(((((......)))))))).))))))..))))... ( -31.90)
>consensus
AGGCCAAAUACUGGGACUCUG____UU_____AGAGCUU___CUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGGACACG
.(.((.............................(((((....(((....)))..)))))....(((((.(((.(((((......)))))))).)))))...)).)... (-22.91 = -22.97 +   0.06)

alignment

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secondary structure

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Window 0

Location 25,404,422 – 25,404,528
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.75
Mean single sequence MFE -28.69
Consensus MFE -19.97
Energy contribution -19.80
Covariance contribution -0.17
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.70
SVM decision value 1.36
SVM RNA-class probability 0.946456
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404422 106 - 27905053
CGUGUCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACGUUCAGCUUGAUGAAUGAUCAG---AGACUCCUGGCUUACACUCGGCAUUCCAGUAUUUGGCCU
.((((((...(((....(((((((......)))))))...((((((((((......)))))).))))---.)))....))...))))..(((.............))). ( -28.92)
>DroPse_CAF1 98427 99 - 1
GCCGUCCUUUGUCAGAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAGA-GAAGCUCU-----AA----CAGAGUCCCAGAGACUGGACA
...((((...(((....(((((((......)))))))...((((((((((......)))))).)))).-(..((((.-----..----..))))..)...))).)))). ( -32.00)
>DroEre_CAF1 92385 87 - 1
CGUGUCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACGUUCAGCUUGAUGAAUGAUCAG---AAGCUCU-------------------CAGUAUUUGGCCU
..........((((((.(((((((......)))))))...((((((((((......)))))).))))---.......-------------------.....)))))).. ( -22.60)
>DroWil_CAF1 112191 95 - 1
UUUGCCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAGUUAGCUUGAUGAAUGAUCAGCCCAAGCCCA-----AG----CAAAGUC-----AUUUGGCCC
(((((...(((((((..(((((((......))))).))..)))))))...(((((.(((....)))...)))))...-----.)----))))(((-----....))).. ( -28.10)
>DroYak_CAF1 95785 106 - 1
CGUGUCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUUAGCUUGAUGAAUGAUCAG---AAGCUCUUGGCUUACACUCGGCACUCCAGUAUUUGGCCU
.((((((..((((((..(((((((......))))).))..))))))...(((((..(((....))).---)))))...))...))))..(((.(..........)))). ( -28.50)
>DroPer_CAF1 95685 99 - 1
GCCGUCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAGA-GAAGCUCU-----AA----CAGAGUCCCAGAGACUGGACA
...((((...(((....(((((((......)))))))...((((((((((......)))))).)))).-(..((((.-----..----..))))..)...))).)))). ( -32.00)
>consensus
CGUGUCCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAG___AAGCUCU_____AA____CAGAGUCCCAGUAUUUGGCCU
...(.((..((((((..(((((((......))))).))..))))))...(((((..(((....)))....))))).............................)).). (-19.97 = -19.80 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,404,459 – 25,404,553
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.74
Mean single sequence MFE -26.62
Consensus MFE -16.75
Energy contribution -16.95
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -2.21
Structure conservation index 0.63
SVM decision value 0.48
SVM RNA-class probability 0.752149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404459 94 + 27905053
CU--CUGAUCAUUCAUCAAGCUGAACGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGG-ACACGACAAGGCGAUUGCA---GCUAUCGGAAU
.(--(((((.........(((((...(((((.(((.(((((......)))))))).))))).....-...((......))....))---))))))))).. ( -26.80)
>DroVir_CAF1 105010 84 + 1
UU--AUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGGCAGGCGUUCGCCAUUUGCCGUUUGCC--------------
..--((((....))))(((((....((((((.(((.(((((......)))))))).))))))(((....))).......)))))..-------------- ( -26.00)
>DroPse_CAF1 98455 92 + 1
UUCUCUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUCUGACAAAGG-ACGGCACAAGGCGUUUGCCC---A----AAAAU
.....(((.((((((......))))))))).((((..(((((((.....(((((((((.....)))-).))))))))))))...)))---)----..... ( -28.80)
>DroYak_CAF1 95822 97 + 1
UU--CUGAUCAUUCAUCAAGCUAAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGG-ACACGACAAGGCGAUUGCAGCAGCUAUCGGUAU
..--(((((.........((((...((((((.(((.(((((......)))))))).))))))....-..........((.......)))))))))))... ( -24.00)
>DroAna_CAF1 96392 94 + 1
UU--CUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGG-ACACGACACGGCGUUUGUU---GCUAUCGGAAU
((--(((((....((....((((..((((((.(((.(((((......)))))))).))))))..(.-...)....))))...))..---...))))))). ( -27.80)
>DroPer_CAF1 95713 92 + 1
UUCUCUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGG-ACGGCACAAGGCGUUUGCCC---A----AAAAU
.....(((.((((((......))))))))).((((..(((((((....(((.(((((....)))))-)))....)))))))...)))---)----..... ( -26.30)
>consensus
UU__CUGAUCAUUCAUCAAGCUGAAUGUCAAUGGGACACGUUUUUUCACGUGCCUUUUGACAAAGG_ACACCACAAGGCGUUUGCC____C____GGAAU
.....((((.....)))).......((((((.(((.(((((......)))))))).))))))...................................... (-16.75 = -16.95 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,404,459 – 25,404,553
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.74
Mean single sequence MFE -25.97
Consensus MFE -17.41
Energy contribution -17.13
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.67
SVM decision value 0.47
SVM RNA-class probability 0.749185
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25404459 94 - 27905053
AUUCCGAUAGC---UGCAAUCGCCUUGUCGUGU-CCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACGUUCAGCUUGAUGAAUGAUCAG--AG
....((((((.---.((....)).))))))...-.(((((((((..(((((((......))))).))..))))((((((......))))))..)))--)) ( -24.50)
>DroVir_CAF1 105010 84 - 1
--------------GGCAAACGGCAAAUGGCGAACGCCUGCCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAU--AA
--------------((.....((((...(((....)))))))....(((((((......)))))))))..(((((((((......)))))).))).--.. ( -28.70)
>DroPse_CAF1 98455 92 - 1
AUUUU----U---GGGCAAACGCCUUGUGCCGU-CCUUUGUCAGAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAGAGAA
.....----(---((((....(((((.((.((.-....)).)).)))))((((......))))).))))((((((((((......)))))).)))).... ( -28.10)
>DroYak_CAF1 95822 97 - 1
AUACCGAUAGCUGCUGCAAUCGCCUUGUCGUGU-CCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUUAGCUUGAUGAAUGAUCAG--AA
....((((.((....)).))))..(..(((.((-....((((((..(((((((......))))).))..))))))....)).)))..)........--.. ( -26.00)
>DroAna_CAF1 96392 94 - 1
AUUCCGAUAGC---AACAAACGCCGUGUCGUGU-CCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAG--AA
((((....(((---.....((((......))))-....((((((..(((((((......))))).))..))))))....)))....))))......--.. ( -22.50)
>DroPer_CAF1 95713 92 - 1
AUUUU----U---GGGCAAACGCCUUGUGCCGU-CCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAGAGAA
.....----(---((((....(((((.((.((.-....)).)).)))))((((......))))).))))((((((((((......)))))).)))).... ( -26.00)
>consensus
AUUCC____G____GGCAAACGCCUUGUCGCGU_CCUUUGUCAAAAGGCACGUGAAAAAACGUGUCCCAUUGACAUUCAGCUUGAUGAAUGAUCAG__AA
..............................................(((((((......)))))))....(((((((((......)))))).)))..... (-17.41 = -17.13 +  -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 13:38:22 2006