Locus 1619

Sequence ID 2R_DroMel_CAF1
Location 6,072,377 – 6,072,519
Length 142
Max. P 0.818034
window2712 window2713

overview

Window 2

Location 6,072,377 – 6,072,486
Length 109
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 82.07
Mean single sequence MFE -21.67
Consensus MFE -14.76
Energy contribution -13.66
Covariance contribution -1.10
Combinations/Pair 1.20
Mean z-score -1.73
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.580179
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6072377 109 - 20766785
UUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAAAAGGGUAUCAUAGUAUGGUCACAUGUUUACAACAAAAUAAA-UGGUAUUUUCAAAUAAAACGCUCUUUUUACACUA
...((((..(((....((((((((((((((....)))))))).....((((....))))......))))))....-.))).........(((((......))))))))). ( -17.80)
>DroEre_CAF1 92734 108 - 1
UUCAGUGAAACUUCAUUUUUGUAUGCCCUUUCAA-AGGGUAUGAUAACGCGGUCACAAGUUUUCAACUAAAUGAAGUGGUAUUUACAAGUAAAACGCUCUAAAUACACU-
.........(((((((((..(((((((((.....-)))))))((.(((..(....)..))).)).)).))))))))).(((((((..(((.....))).)))))))...- ( -24.50)
>DroYak_CAF1 91573 109 - 1
UUCAGUGAAACUUCAUUUUCGCAUGCCCUUUUAA-AGGGUAUGAUAACAUAGUAACUAUUUUACAACUAAAUGAAGAGGUAUUUACAAACGAAAAGCUCUAUAUGCACUC
....((((((((((.......((((((((.....-))))))))........((((.....))))...........))))).))))).........((.......)).... ( -22.70)
>consensus
UUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAA_AGGGUAUGAUAACAUGGUCACAAGUUUACAACUAAAUGAAGUGGUAUUUACAAAUAAAACGCUCUAUAUACACU_
...((((..(((.........((((((((......)))))))).......))).....((((.....((((((......))))))......))))..........)))). (-14.76 = -13.66 +  -1.10)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,072,409 – 6,072,519
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 89.10
Mean single sequence MFE -22.92
Consensus MFE -17.82
Energy contribution -18.10
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.78
SVM decision value 0.67
SVM RNA-class probability 0.818034
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6072409 110 - 20766785
CCAGAAGGAAGAAAACCGAAACUGAAACCAGUUUUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAAAAGGGUAUCAUAGUAUGGUCACAUGUUUACAACAAAAUAAA-UG
.......((((...((.(((((((....)))))))..))....))))..((((((((((((((....)))))))).....((((....))))......))))))....-.. ( -22.60)
>DroSec_CAF1 90607 109 - 1
CCCGAAGGAAGAAAACCGAAACUAAAACCAGUUUUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAA-AGGGUAUGAUAAAAUAAUCAGAUGUUUACAACAAAAUAUA-UG
...((..((((...((.((((((......))))))..))....))))..(((((((((((((.....-))))))).))))))...))..((((((......)))))).-.. ( -18.60)
>DroSim_CAF1 95521 109 - 1
CCCGAAGGAAGAAAACCGAAACUGAAACCAGUUUUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAA-AGGGUAUGAUAAAAUAAUCAGAUGUUUACAACAAAAUAUA-UG
...((..((((...((.(((((((....)))))))..))....))))..(((((((((((((.....-))))))).))))))...))..((((((......)))))).-.. ( -21.70)
>DroEre_CAF1 92765 110 - 1
CCCGAAGGAAGAAAACCGAAACUGAAACCAGUUUUCAGUGAAACUUCAUUUUUGUAUGCCCUUUCAA-AGGGUAUGAUAACGCGGUCACAAGUUUUCAACUAAAUGAAGUG
......((.......))...(((((((.....)))))))...(((((((((..(((((((((.....-)))))))((.(((..(....)..))).)).)).))))))))). ( -25.60)
>DroYak_CAF1 91605 109 - 1
CCCGAAGGAA-AAAACCGAAACUGAAACCAGUUUUCAGUGAAACUUCAUUUUCGCAUGCCCUUUUAA-AGGGUAUGAUAACAUAGUAACUAUUUUACAACUAAAUGAAGAG
......((..-....))...(((((((.....)))))))....((((((((...((((((((.....-))))))))........((((.....))))....)))))))).. ( -26.10)
>consensus
CCCGAAGGAAGAAAACCGAAACUGAAACCAGUUUUCAGUGAAACUUCAUUUUUGUAUGCCCUUUUAA_AGGGUAUGAUAAAAUAGUCACAUGUUUACAACAAAAUAAA_UG
...((((.......((.(((((((....)))))))..))....)))).......((((((((......))))))))................................... (-17.82 = -18.10 +   0.28)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:02 2006