Locus 1120

Sequence ID 3L_DroMel_CAF1
Location 3,281,560 – 3,281,759
Length 199
Max. P 0.957472
window1738 window1739 window1740

overview

Window 8

Location 3,281,560 – 3,281,680
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.58
Mean single sequence MFE -32.39
Consensus MFE -23.11
Energy contribution -23.54
Covariance contribution 0.43
Combinations/Pair 1.23
Mean z-score -1.67
Structure conservation index 0.71
SVM decision value 0.18
SVM RNA-class probability 0.623752
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3281560 120 - 23771897
UAGGGGAUUCCUGAAUCUCUACAUUAGGAAUUUGUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAAUGGAUUCUUUAGCUUCUUCUGCAGCACUUUCCUUGGCCUCCUCUA
(((((((..((..............(((((..((((....(((((.(((((.(((....))).)))))..)))))...........((.......))))))..))))).))..))))))) ( -28.56)
>DroSec_CAF1 11534 120 - 1
UAGGGGAUUCCUGGACUUCUACACUAGGAAUCUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAACGGAUUCCUUAGCUUCUUCUGGAGCACUUUCCUCGGUCUCCUCUA
(((((((..((.(((..........((((((((.......(((((.(((((.(((....))).)))))..))))).))))))))..(((((....)))))....)))..))..))))))) ( -38.80)
>DroSim_CAF1 12385 120 - 1
UAGGGGUUUCCUGAAUUUCUACACUGGGAAUCUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCCUCGGGAACGGAUUCCUUAGCUUCUUCUGGAGCACUUUCCUUGGUCUCCUCUA
((((((...((.(((..........((((((((.......(((((.(((((.(((....))).).)))).))))).))))))))..(((((....)))))...)))...))...)))))) ( -34.80)
>DroEre_CAF1 11733 105 - 1
CAGGUGAUUCC---------------GGAACUGCCUUAACUUUCUCAGGAGAUGUAUCGACAACUUCUUGGGGUACGGUUUCUUCAGCUACUUGUGGAGCACUUUCCUUGGUCUCCUCAU
.((.(((....---------------((((((((((((........(((((.(((....))).)))))))))))..)))))).))).))...((.((((.(((......))))))).)). ( -26.70)
>DroYak_CAF1 12170 120 - 1
CAGGGGAUUCCUGGAUUUCUGCACUAGGAAUUUGUUUGACUUCCUCAGGAGAUGUAUCGACAAGUUCUUCGGGAACGGUUUCUUUAGCUUCUUCUGGAGCACUUUCCUCGACCUUCUCAA
..((((((((((((.........)))))))...........)))))..((((....((((.((((.((((((((..((((.....))))..)))))))).))))...))))...)))).. ( -33.10)
>consensus
UAGGGGAUUCCUGAAUUUCUACACUAGGAAUUUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAACGGAUUCUUUAGCUUCUUCUGGAGCACUUUCCUUGGUCUCCUCUA
.(((((((((((((.........)))))))))))))....(((((.(((((.(((....)))..))))).)))))...........(((((....))))).................... (-23.11 = -23.54 +   0.43)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,281,600 – 3,281,720
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.58
Mean single sequence MFE -33.37
Consensus MFE -25.59
Energy contribution -25.62
Covariance contribution 0.03
Combinations/Pair 1.25
Mean z-score -1.61
Structure conservation index 0.77
SVM decision value 0.16
SVM RNA-class probability 0.612876
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3281600 120 - 23771897
UCCUUGAUUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGAUUCCUGAAUCUCUACAUUAGGAAUUUGUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAAUGGAU
(((((((.....)))(((((((..((....(((((((.....(((((((....))))))).....(((((.((....)).))))).))))))).....))...)))))))))))...... ( -33.10)
>DroSec_CAF1 11574 120 - 1
UCCUUGACUUCUUCAGGAGAAGAUUCUUUAGUCUCCUCCAUAGGGGAUUCCUGGACUUCUACACUAGGAAUCUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAACGGAU
(((.........(((((((.((((......)))).))))..(((((((((((((.........)))))))))))))))).(((((.(((((.(((....))).)))))..))))).))). ( -39.70)
>DroSim_CAF1 12425 120 - 1
UCCUUGACUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGUUUCCUGAAUUUCUACACUGGGAAUCUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCCUCGGGAACGGAU
.(((.((..(((((....))))).))...))).(((..((.((((((((((..............)))))))))).))..(((((.(((((.(((....))).).)))).))))).))). ( -34.14)
>DroEre_CAF1 11773 105 - 1
UCCUUGAUCUCUUCAGGAGAAGUUUCUUUGGGCUCCUCUACAGGUGAUUCC---------------GGAACUGCCUUAACUUUCUCAGGAGAUGUAUCGACAACUUCUUGGGGUACGGUU
.((...((((((....((((((((.....((((...(((...((.....))---------------)))...)))).))).))))).))))))(((((..(((....))).))))))).. ( -25.60)
>DroYak_CAF1 12210 120 - 1
UCCUUAAUUUCUUCAGGAGCAGUUUCUUUGGGCUCCUCUACAGGGGAUUCCUGGAUUUCUGCACUAGGAAUUUGUUUGACUUCCUCAGGAGAUGUAUCGACAAGUUCUUCGGGAACGGUU
((((.((....)).))))((((..(((..((..(((((....)))))..)).)))...))))...(((((((((((..((((((...))))..))...)))))))))))((....))... ( -34.30)
>consensus
UCCUUGAUUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGAUUCCUGAAUUUCUACACUAGGAAUUUCUUUGACUUCCUCAGGAGCUGUAUCGACAACUUCUUCGGGAACGGAU
.((............((((.((((......)))).))))..(((((((((((((.........)))))))))))))....(((((.(((((.(((....)))..))))).))))).)).. (-25.59 = -25.62 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,281,640 – 3,281,759
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -35.11
Consensus MFE -28.25
Energy contribution -28.64
Covariance contribution 0.39
Combinations/Pair 1.23
Mean z-score -2.24
Structure conservation index 0.80
SVM decision value 1.48
SVM RNA-class probability 0.957472
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3281640 119 - 23771897
GUCUCUGGAGCAGUCUCUUUGAUUUCCUCGGGAGUGCUUUCCUUGAUUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGAUUCCUGAAUCUCUACAUUAGGAAUUUGUUUGAC
(((...(((((((((.....))))..((..(((((.(((..(((((.....)))))..))))))))..))))))).....((.((((((((((.........)))))))))).)).))) ( -34.80)
>DroSec_CAF1 11614 119 - 1
GUCUCUGGAGCAGUCUCUUUGAUUUCCUCGGGAGUGCUUUCCUUGACUUCUUCAGGAGAAGAUUCUUUAGUCUCCUCCAUAGGGGAUUCCUGGACUUCUACACUAGGAAUCUCUUUGAC
(((...((((((.((((............)))).)))..)))..)))....(((((((.((((......)))).))))..(((((((((((((.........)))))))))))))))). ( -40.30)
>DroSim_CAF1 12465 119 - 1
GUCUCUGGAGCAGUCUCUUUGAUUUCCUCGGGAGUGCUUUCCUUGACUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGUUUCCUGAAUUUCUACACUGGGAAUCUCUUUGAC
......(((((((((.....))))..((..(((((.(((..(((((.....)))))..))))))))..)))))))..((.((((((((((..............)))))))))).)).. ( -36.84)
>DroEre_CAF1 11813 100 - 1
----CUGAAGCAGCCUCUUUGAUUUCCUCGGGAGUGGUCUCCUUGAUCUCUUCAGGAGAAGUUUCUUUGGGCUCCUCUACAGGUGAUUCC---------------GGAACUGCCUUAAC
----.(((.((((..(((..((((.(((..((((..((((....((...((((....))))..))...))))..))))..))).))))..---------------))).)))).))).. ( -27.70)
>DroYak_CAF1 12250 119 - 1
GACUCUGGAGCAGUCUCUUUGAUUUCCUCGGGAGUGCUUUCCUUAAUUUCUUCAGGAGCAGUUUCUUUGGGCUCCUCUACAGGGGAUUCCUGGAUUUCUGCACUAGGAAUUUGUUUGAC
.(((((.(((.((((.....))))..))).)))))........(((.(((((.((..((((..(((..((..(((((....)))))..)).)))...)))).))))))).)))...... ( -35.90)
>consensus
GUCUCUGGAGCAGUCUCUUUGAUUUCCUCGGGAGUGCUUUCCUUGAUUUCUUCAGGAGAAGAUUCUUUAGGCUCCUCCAUAGGGGAUUCCUGAAUUUCUACACUAGGAAUUUCUUUGAC
.....(((((.(((((....(((((.((((((((....)))))(((.....))).))).)))))....))))).))))).(((((((((((((.........))))))))))))).... (-28.25 = -28.64 +   0.39)

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 09:59:36 2006