Locus 4402

Sequence ID X_DroMel_CAF1
Location 11,595,673 – 11,595,858
Length 185
Max. P 0.993883
window7226 window7227 window7228 window7229

overview

Window 6

Location 11,595,673 – 11,595,786
Length 113
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.43
Mean single sequence MFE -34.19
Consensus MFE -21.89
Energy contribution -22.17
Covariance contribution 0.28
Combinations/Pair 1.17
Mean z-score -2.01
Structure conservation index 0.64
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11595673 113 + 22224390
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCGG--GCAGCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCG-GGCAAUUUUCGGCCGAUCCAUUUGGCCA--UUUGGCC
.................((((.......((((((((((--((.......)))).......)))))))).......))))(-(.(((.....((((((.....)))))).--.))).)) ( -33.35)
>DroSec_CAF1 27900 109 + 1
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCG------GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCG-GGCAAUUUUCGGCCGAUCCAUUUGGCCA--UUUGGCC
.................((((......(((((....(------(((((((........))))))))...))))).))))(-(.(((.....((((((.....)))))).--.))).)) ( -35.60)
>DroSim_CAF1 27289 109 + 1
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCG------GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCG-GGCAAUUUUCGGCCGAUCCAUUUGGCCA--UUUGGCC
.................((((......(((((....(------(((((((........))))))))...))))).))))(-(.(((.....((((((.....)))))).--.))).)) ( -35.60)
>DroEre_CAF1 27934 114 + 1
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCGGUCGCGGUCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCG-GGCAAUUUUCGGCCGAUC-AUUUGGCCG--UUUGGCC
.................((((......(((((..((....))((((((((........))))))))...))))).))))(-(.(((....(((((((..-..)))))))--.))).)) ( -38.60)
>DroYak_CAF1 28458 105 + 1
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCGC--AGCUCCACAGCCUCACAUUUGCGGCCAUUUCACGUAGUUG-GGCAAUUUUCGGCCGAUC--------CA--UUUGGCC
...((((((((((..((((((.......((((..((..--.)).)))).((.........))))))))...))).)))))-))........((((((..--------..--.)))))) ( -26.40)
>DroAna_CAF1 38687 96 + 1
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGCCG------------------CACAUUUGCGGCCAUUUGACGGGGUCUUGCCAAUUUUCGGUCAGUU----UCCCCCCCGGGGGCC
.................(((((((....(((((((------------------((....))))))))).....((((.((.(((.......))).))..----.))))...))))))) ( -35.60)
>consensus
AAUUUCAAUUUGUUUAUGGCUUCUUUUCGUGGUCGCG______GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCG_GGCAAUUUUCGGCCGAUC_AUUUGGCCA__UUUGGCC
.........(((((...((((.......(((((((((......................))))))))).......))))..))))).....((((((...............)))))) (-21.89 = -22.17 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,595,711 – 11,595,826
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 87.44
Mean single sequence MFE -41.06
Consensus MFE -34.18
Energy contribution -34.74
Covariance contribution 0.56
Combinations/Pair 1.16
Mean z-score -2.00
Structure conservation index 0.83
SVM decision value 1.36
SVM RNA-class probability 0.946525
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11595711 115 + 22224390
--GCAGCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAAUGGUCCAAUGGCAUACUGGUCCAAUGGUCCAGUGGUCC
--((.(((((((........)))))))((((.......(((((.(.......).)))))(((((.((((....)))))))))...)))))).((((((.((...)).)))))).... ( -43.30)
>DroSec_CAF1 27937 112 + 1
-----GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAGUGGUUCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCC
-----(((((((........)))))))...........(((((.(.......).)))))(((((.(((((((.(((((.((((......)).)).))))).))))))).)))))... ( -41.80)
>DroSim_CAF1 27326 112 + 1
-----GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAGUGGUCCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCC
-----(((((((........)))))))...........(((((.(.......).)))))(((((.(((((((.(((((.(((((....))).)).))))).))))))).)))))... ( -43.30)
>DroEre_CAF1 27972 116 + 1
UCGCGGUCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCGGGCAAUUUUCGGCCGAUC-AUUUGGCCGUUUGGCCAAUGGUCCAAUGGCAUAGUGGUCCAGUGGUCCAUUGGUCC
..((((((((((........))))))))......((....)).))......(((((((..-..)))))))...(((((((((.(((.((((......).))).))).))))))))). ( -49.30)
>DroYak_CAF1 28496 99 + 1
--AGCUCCACAGCCUCACAUUUGCGGCCAUUUCACGUAGUUGGGCAAUUUUCGGCCGAUC--------CAUUUGGCCAAUGGUUCAAU--------GGUCCAAUGGUCCAAUGGUCC
--.(((....)))....((((.(.(((((((..((...(((((((....((.((((((..--------...))))))))..)))))))--------.))..)))))))))))).... ( -27.60)
>consensus
_____GCCGCAGCCUCACAUUUGCGGCCAUUUCACGUAGUCGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAAUGGUCCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCC
.....(((((((........)))))))...........(((((.(.......).)))))......(((((((.(((((.(((.(((.........))).))).))))).))))))). (-34.18 = -34.74 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,595,749 – 11,595,858
Length 109
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 90.46
Mean single sequence MFE -51.00
Consensus MFE -45.25
Energy contribution -47.00
Covariance contribution 1.75
Combinations/Pair 1.10
Mean z-score -2.92
Structure conservation index 0.89
SVM decision value 2.43
SVM RNA-class probability 0.993883
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11595749 109 + 22224390
CGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAAUGGUCCAAUGGCAUACUGGUCCAAUGGUCCAGUGGUCCAAU--------GCUGUAUUGGCGCAUUGGCCGGGGGCGUC
...((.......((((((.....)))))).((((((((((((.(((((((((((((((.((...)).)))))......))--------)))..)))))).))))))))))).))... ( -45.60)
>DroSec_CAF1 27972 117 + 1
CGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAGUGGUUCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCCAAUGAUCCAUUGCUGCAUUGGCGCAUUGGCCGGGGGCGUC
...((.......((((((.....)))))).(((((((((((((.(((((.((((((((..((.(((.((...)).))).))..)))))).))))))))).))))))))))).))... ( -49.10)
>DroSim_CAF1 27361 117 + 1
CGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAGUGGUCCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCCAAUGGUCCAUUGCUGCAUUGGCGCAUUGGCCGGGGGCGUC
...((.......((((((.....)))))).((((((((((((.((((((.((((((((.(((.(((.((...)).))).))).)))))).))))))))).))))))))))).))... ( -56.00)
>DroEre_CAF1 28012 116 + 1
CGGGCAAUUUUCGGCCGAUC-AUUUGGCCGUUUGGCCAAUGGUCCAAUGGCAUAGUGGUCCAGUGGUCCAUUGGUCCAUUGGUGCACUGGUGCAUUGGUGCAUUCGCCGGGGGCGUC
.((.(((....(((((((..-..))))))).))).))....((((..((((.((((((.((((((...)))))).))))))((((((..(....)..))))))..)))).))))... ( -53.30)
>consensus
CGGGCAAUUUUCGGCCGAUCCAUUUGGCCAUUUGGCCAAUGGUCCAAUGGCAUAGUGGUCCAAUGGUCCAGUGGUCCAAUGGUCCAUUGCUGCAUUGGCGCAUUGGCCGGGGGCGUC
...((.......((((((.....)))))).(((((((((((..((((((.((((((((.(((.(((.((...)).))).))).)))))).))))))))..))))))))))).))... (-45.25 = -47.00 +   1.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,595,749 – 11,595,858
Length 109
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 90.46
Mean single sequence MFE -40.90
Consensus MFE -32.16
Energy contribution -34.60
Covariance contribution 2.44
Combinations/Pair 1.06
Mean z-score -2.43
Structure conservation index 0.79
SVM decision value 1.14
SVM RNA-class probability 0.921729
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11595749 109 - 22224390
GACGCCCCCGGCCAAUGCGCCAAUACAGC--------AUUGGACCACUGGACCAUUGGACCAGUAUGCCAUUGGACCAUUGGCCAAAUGGCCAAAUGGAUCGGCCGAAAAUUGCCCG
...(((.(((((((((((.........))--------))))).))(((((.((...)).)))))........)).(((((((((....)))).)))))...)))............. ( -40.20)
>DroSec_CAF1 27972 117 - 1
GACGCCCCCGGCCAAUGCGCCAAUGCAGCAAUGGAUCAUUGGACCACUGGACCAUUGGACCACUAUGCCAUUGAACCACUGGCCAAAUGGCCAAAUGGAUCGGCCGAAAAUUGCCCG
........(((((.......(((((((....(((.(((.(((.((...)).))).))).)))...)).)))))..(((.(((((....)))))..)))...)))))........... ( -37.90)
>DroSim_CAF1 27361 117 - 1
GACGCCCCCGGCCAAUGCGCCAAUGCAGCAAUGGACCAUUGGACCACUGGACCAUUGGACCACUAUGCCAUUGGACCACUGGCCAAAUGGCCAAAUGGAUCGGCCGAAAAUUGCCCG
........(((((......((((((((....(((.(((.(((.((...)).))).))).)))...)).)))))).(((.(((((....)))))..)))...)))))........... ( -43.20)
>DroEre_CAF1 28012 116 - 1
GACGCCCCCGGCGAAUGCACCAAUGCACCAGUGCACCAAUGGACCAAUGGACCACUGGACCACUAUGCCAUUGGACCAUUGGCCAAACGGCCAAAU-GAUCGGCCGAAAAUUGCCCG
.........(((((.(((((..........)))))....(((.(((((((.(((.(((.(......)))).))).))))))))))..(((((....-....)))))....))))).. ( -42.30)
>consensus
GACGCCCCCGGCCAAUGCGCCAAUGCAGCAAUGGACCAUUGGACCACUGGACCAUUGGACCACUAUGCCAUUGGACCACUGGCCAAAUGGCCAAAUGGAUCGGCCGAAAAUUGCCCG
...((....((((((((..((((((((....(((.(((.(((.((...)).))).))).)))...)).))))))..))))))))...(((((.........)))))......))... (-32.16 = -34.60 +   2.44)

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 11:24:06 2006