Locus 1832

Sequence ID 3R_DroMel_CAF1
Location 5,239,133 – 5,239,279
Length 146
Max. P 0.610000
window3013 window3014

overview

Window 3

Location 5,239,133 – 5,239,239
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 79.08
Mean single sequence MFE -23.20
Consensus MFE -13.58
Energy contribution -15.62
Covariance contribution 2.04
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.59
SVM decision value 0.16
SVM RNA-class probability 0.610000
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5239133 106 - 27905053
ACUGCUGCACAUAACAACUGUGUAAGGUUUAUGGAAUGCAAUAGCAAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACUACCGUUAUUCAUUAUUGUAUCAAUACU
(((..((((((.......)))))).))).....((.((((((((...((((((....(((........)))(((.....)))))))))..))))))))))...... ( -21.30)
>DroSec_CAF1 12903 94 - 1
ACUGCUGCACAAAACAACUGUGUAAAGUUUAUGGAGUGCAAUAGCGAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACUACCGAUUU------------UAAUACU
.......((((((((((((......))))...((((((((((.((......))))))))))))))))))))(((.....))).....------------....... ( -27.40)
>DroSim_CAF1 12967 93 - 1
ACUGCUGCACAUAACAACUGUGUAAAGUUUAUGGAGUGCAAUAGCGAAAUGGCAUUGCACUUUGU-UUGUGGGUUAACUACCGAUUU------------UAAUACU
(((..((((((.......)))))).)))..(..(((((((((.((......)))))))))))..)-..((((.....))))......------------....... ( -24.40)
>DroEre_CAF1 15165 105 - 1
-UUGCUACACAAAACACCUGUGUAAAGUUUAAAGCAUACAAUAGCGAAAAGCCUAUGCACUUUGUUUUGUAGAUAAACUACCGGUUUUCAUAAUUGUAUCAAUAUA
-(((.(((((((((((...(((((..((((...((........))...))))...)))))..)))))))).((.((((.....))))))......))).))).... ( -20.20)
>DroYak_CAF1 12939 105 - 1
-UUGCUGCACAAAACAACUGUGUAAAGUUUAAACCAUACAAUAGCGAAAAGGCUUUGCACUUUGUUUUGUUGGUAAACUACCGGGUUUCAUAAUUGUAUUAUUAUU
-((((((.(((((((((..(((((((((((...................))))))))))).))))))))))))))).............................. ( -22.71)
>consensus
ACUGCUGCACAAAACAACUGUGUAAAGUUUAUGGAAUGCAAUAGCGAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACUACCGAUUUUCAU_AUUGUAUUAAUACU
.......((((((((((..((((((.(((.......(((....)))....))).)))))).))))))))))(((.....)))........................ (-13.58 = -15.62 +   2.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,239,160 – 5,239,279
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -27.72
Consensus MFE -15.76
Energy contribution -17.20
Covariance contribution 1.44
Combinations/Pair 1.13
Mean z-score -2.11
Structure conservation index 0.57
SVM decision value 0.04
SVM RNA-class probability 0.554642
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5239160 119 - 27905053
AUCUAAACGCUUUUGACGCAAUAACGAAGUAAAAUAUUUCACUGCUGCACAUAACAACUGUGUAAGGUUUAUGGAAUGCAAUAGCAAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACU
............(((((.((..((((((((.....((((((..(((..(((((.....)))))..)))...))))))(((((.((......)))))))))))))))...)).))))).. ( -30.10)
>DroSec_CAF1 12918 119 - 1
AUCUAAACGGUUUUGAAGCAAUAACGUAGUAAAAUAUAUCACUGCUGCACAAAACAACUGUGUAAAGUUUAUGGAGUGCAAUAGCGAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACU
.....................(((((((((..........)))))..((((((((((((......))))...((((((((((.((......)))))))))))))))))))).))))... ( -30.20)
>DroSim_CAF1 12982 118 - 1
AUCUAAACGGUUUUGGAGCAAUAACGUAGUAAAAUAUAUCACUGCUGCACAUAACAACUGUGUAAAGUUUAUGGAGUGCAAUAGCGAAAUGGCAUUGCACUUUGU-UUGUGGGUUAACU
.((((((....))))))....((((((((((...........)))))).(((((.((((......)))).(..(((((((((.((......)))))))))))..)-))))).))))... ( -28.90)
>DroEre_CAF1 15192 110 - 1
AUCUAAACGGUUUUAGCGCAAUAACGUAGUAA---------UUGCUACACAAAACACCUGUGUAAAGUUUAAAGCAUACAAUAGCGAAAAGCCUAUGCACUUUGUUUUGUAGAUAAACU
........(((((...(........(((((..---------..)))))((((((((...(((((..((((...((........))...))))...)))))..)))))))).)..))))) ( -23.00)
>DroYak_CAF1 12966 110 - 1
AUCUAAACAGUUUCAGCGCAAUAACGUAGUAA---------UUGCUGCACAAAACAACUGUGUAAAGUUUAAACCAUACAAUAGCGAAAAGGCUUUGCACUUUGUUUUGUUGGUAAACU
........((((((.(((((((.((...)).)---------)))).))(((((((((..(((((((((((...................))))))))))).)))))))))..).))))) ( -26.41)
>consensus
AUCUAAACGGUUUUGGCGCAAUAACGUAGUAAAAUAU_UCACUGCUGCACAAAACAACUGUGUAAAGUUUAUGGAAUGCAAUAGCGAAAUGGCAUUGCACUUUGUUUUGUGGGUUAACU
((((.....................((((((...........))))))(((((((((..((((((.(((.......(((....)))....))).)))))).)))))))))))))..... (-15.76 = -17.20 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:36 2006