Locus 5843

Sequence ID 2R_DroMel_CAF1
Location 18,497,109 – 18,497,269
Length 160
Max. P 0.957612
window9371 window9372 window9373

overview

Window 1

Location 18,497,109 – 18,497,229
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.75
Mean single sequence MFE -39.38
Consensus MFE -38.51
Energy contribution -38.33
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -3.13
Structure conservation index 0.98
SVM decision value 1.48
SVM RNA-class probability 0.957612
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497109 120 + 20766785
UUAAAAAGCGCCUACACGCCUGACACGCCCCCUCAAGUGUUGGCAGUCGCUGCUGUUGACAAACAAACAGCAAAAGGCCACAAAAGACACAAAGGGGGCUGUGUUCCAACACUUGAGUUC
.......(((......)))..((((((((((((...(((((.(..(((..(((((((........)))))))...)))..)....)))))..))))))).)))))............... ( -40.10)
>DroSec_CAF1 15739 119 + 1
UUAAAAAGCGCCUACACGCCUGACACGCC-CCUCAAGUGUUGGCAGUCGCUGCUGUUGACAAACAAACAGCAAAAGGCCACAAAAGACACAAAGGGGGCUGCGUUCCAACACUUGAGUUC
.......(((......)))..........-.((((((((((((.((.((((((((((........)))))))...((((.(............)..)))))))))))))))))))))... ( -38.80)
>DroSim_CAF1 4889 120 + 1
UUAAAAAGCGCCUACACGCCUGACACGCCCCCUCAAGUGUUGGCAGUCGCUGCUGUUGACAAACAAACAGCAAAAGGCCACAAAAGACACAAAGGGGGCUGCGUUCCAACACUUGAGUUC
.......(((......)))............((((((((((((.((.((((((((((........)))))))...((((.(............)..)))))))))))))))))))))... ( -38.80)
>DroEre_CAF1 21305 120 + 1
UUAAAAAGCGCCUACACGCCUGACACGCCCCCUCAAGUGUUGGCAGCCGCUGCUGUUGACAAACAAACAGCAAAAGGCCACAAAAGACACAAAGGGGGCUGCGUUCCAACACUUGAGUUC
.......(((......)))............(((((((((((((((((.((((((((........))))))....(....)............)).))))))....)))))))))))... ( -39.80)
>consensus
UUAAAAAGCGCCUACACGCCUGACACGCCCCCUCAAGUGUUGGCAGUCGCUGCUGUUGACAAACAAACAGCAAAAGGCCACAAAAGACACAAAGGGGGCUGCGUUCCAACACUUGAGUUC
.......(((......)))............((((((((((((.((.((((((((((........)))))))...((((.(............)..)))))))))))))))))))))... (-38.51 = -38.33 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,497,109 – 18,497,229
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -46.73
Consensus MFE -44.09
Energy contribution -44.40
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.84
Structure conservation index 0.94
SVM decision value 1.17
SVM RNA-class probability 0.925162
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497109 120 - 20766785
GAACUCAAGUGUUGGAACACAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCAACACUUGAGGGGGCGUGUCAGGCGUGUAGGCGCUUUUUAA
......(((((((...((((.((((((((.((((......((((...((((((((.(((....)))))))))))..))))))))..))))))))((.....)))))).)))))))..... ( -46.00)
>DroSec_CAF1 15739 119 - 1
GAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCAACACUUGAGG-GGCGUGUCAGGCGUGUAGGCGCUUUUUAA
......(((((((...((((.((((((((.((((......((((...((((((((.(((....)))))))))))..))))))))..))))-)).)).....))))...)))))))..... ( -43.60)
>DroSim_CAF1 4889 120 - 1
GAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCAACACUUGAGGGGGCGUGUCAGGCGUGUAGGCGCUUUUUAA
......(((((((...((((.((((((((.((((......((((...((((((((.(((....)))))))))))..))))))))..)))))))).......))))...)))))))..... ( -47.70)
>DroEre_CAF1 21305 120 - 1
GAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGGCUGCCAACACUUGAGGGGGCGUGUCAGGCGUGUAGGCGCUUUUUAA
......(((((((...((((.((((((((.((((.....(..(((..((((((((........)))))))).)))..)..))))..)))))))).......))))...)))))))..... ( -49.60)
>consensus
GAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCAACACUUGAGGGGGCGUGUCAGGCGUGUAGGCGCUUUUUAA
......(((((((...((((.((((((((.((((......((((...((((((((.(((....)))))))))))..))))))))..)))))))).......))))...)))))))..... (-44.09 = -44.40 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,497,149 – 18,497,269
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -41.86
Consensus MFE -41.71
Energy contribution -41.59
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 1.00
SVM decision value 0.62
SVM RNA-class probability 0.801616
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18497149 120 - 20766785
GAGCAAAAGAGACGCGACUGUGGCCGACUGCUAAAAAACAGAACUCAAGUGUUGGAACACAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCA
..((((..((((((((((((((.(((((.(((...............))))))))..)))))......)))))))))))))(((...((((((((.(((....)))))))))))..))). ( -37.36)
>DroSec_CAF1 15778 120 - 1
GAGCAAAAGAGACGCGGCUGUGGCCGACUGCUAAAAAACAGAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCA
..((((((((.(((.(((((((.(((((.(((...............))))))))..))))))).....))).))))))))(((...((((((((.(((....)))))))))))..))). ( -43.36)
>DroSim_CAF1 4929 120 - 1
GAGCAAAAGAGACGCGGCUGUGGCCGACUGCUAAAAAACAGAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCA
..((((((((.(((.(((((((.(((((.(((...............))))))))..))))))).....))).))))))))(((...((((((((.(((....)))))))))))..))). ( -43.36)
>DroEre_CAF1 21345 120 - 1
GAGCAAAAGAGACGCGGCUGUGGCCGACUGCUAAAAAACAGAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGGCUGCCA
......((((((((((((((((.(((((.(((...............))))))))..)))))))......)))))))))(..(((..((((((((........)))))))).)))..).. ( -43.36)
>consensus
GAGCAAAAGAGACGCGGCUGUGGCCGACUGCUAAAAAACAGAACUCAAGUGUUGGAACGCAGCCCCCUUUGUGUCUUUUGUGGCCUUUUGCUGUUUGUUUGUCAACAGCAGCGACUGCCA
..((((((((.(((.(((((((.(((((.(((...............))))))))..))))))).....))).))))))))(((...((((((((.(((....)))))))))))..))). (-41.71 = -41.59 +  -0.12)

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 11:56:04 2006