Locus 2820

Sequence ID 3L_DroMel_CAF1
Location 8,041,524 – 8,041,656
Length 132
Max. P 0.949402
window4403 window4404 window4405

overview

Window 3

Location 8,041,524 – 8,041,632
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -25.18
Consensus MFE -19.76
Energy contribution -20.24
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.78
SVM decision value 0.08
SVM RNA-class probability 0.572699
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8041524 108 - 23771897
CAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUUGGAAUCAGAAUCCA-----AUCCAACUGUGUCAGCUGCGACUUGCUUUGUUUACAAACAAAUAAGGCAAA
((..(((((((((..(((......)))..)))...(((((.(((((.......))))-----))))))..))))))..))....(((((((((((......))))))))))). ( -30.70)
>DroSec_CAF1 12653 108 - 1
CAAAUGGCAUUGAGCUCCUGCCCUGCAAAUCAGAAUUGGAAUCGAAAUCAGAAUCCA-----AUCCAACUGUGUCAGCUGCGACUUGCUUUGUUUACAAACAAAUAAGGCAAA
((..((((((.(.((.........))......(.((((((.((.......)).))))-----)).)..).))))))..))....(((((((((((......))))))))))). ( -24.60)
>DroSim_CAF1 12669 108 - 1
CAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUCGAAAUCAGAAUUCA-----AUCCAACUGUGUCAGCUGCGACUUGCUUUGUUUACAAACAAAUAAGGCAAA
((..(((((((((..(((......)))..)))(.((((((.((.......)).))))-----)).)....))))))..))....(((((((((((......))))))))))). ( -26.00)
>DroEre_CAF1 12490 108 - 1
CAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUCAGAGUCGAAAUCAGAAUCCA-----AUCCAACUGUGUCAGCUUCGACUUGCGUUGUUUACAAACAAAUAAGGCAAA
....(((..((((..(((......)))..))))..)))((((((((....((...((-----.......))..))...))))))))((.((((((......)))))).))... ( -21.80)
>DroYak_CAF1 12972 113 - 1
CAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGACUCAGAAUCGAAAUCAGAAUCCAAUCCAAUCCAACUGUGUCAGCUUCGACUUGCUUUGUUUACAAACAAAUAAGGCAAA
.....(((..(((..(((......)))..)))(((.(((....(....).((......))........))).))).))).....(((((((((((......))))))))))). ( -22.80)
>consensus
CAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUCGAAAUCAGAAUCCA_____AUCCAACUGUGUCAGCUGCGACUUGCUUUGUUUACAAACAAAUAAGGCAAA
....(((((((((..(((......)))..))).....(((.((.......)).)))..............))))))........(((((((((((......))))))))))). (-19.76 = -20.24 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,041,558 – 8,041,656
Length 98
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -32.06
Consensus MFE -26.22
Energy contribution -25.90
Covariance contribution -0.32
Combinations/Pair 1.14
Mean z-score -1.94
Structure conservation index 0.82
SVM decision value 1.39
SVM RNA-class probability 0.949402
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8041558 98 + 23771897
AGCUGACACAGUUGGAU-----UGGAUUCUGAUUCCAAUUCCAAUUCUGAUUUCCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGCGGUUACUA----
(((((((.(((((((((-----((((.......))))).)))))..)))....(((((((....))))...(((....)))))))))))))............---- ( -32.50)
>DroSec_CAF1 12687 98 + 1
AGCUGACACAGUUGGAU-----UGGAUUCUGAUUUCGAUUCCAAUUCUGAUUUGCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGCGGUUACUA----
((.((((......((((-----((((.((.......)).)))))))).....((((((((..((.((((..(((....))))))))).)))))))))))))).---- ( -31.30)
>DroSim_CAF1 12703 98 + 1
AGCUGACACAGUUGGAU-----UGAAUUCUGAUUUCGAUUCCAAUUCUGAUUUCCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGCGGUUACUA----
(((((((.(((((((((-----((((.......))))).)))))..)))....(((((((....))))...(((....)))))))))))))............---- ( -29.80)
>DroEre_CAF1 12524 98 + 1
AGCUGACACAGUUGGAU-----UGGAUUCUGAUUUCGACUCUGAUUCUGAUUUCCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGUGGUUACUA----
(((((((.((((..(((-----.((....(((((((..(((((...........)))))..)))).)))...)))))..)))).)))))))............---- ( -31.00)
>DroYak_CAF1 13006 107 + 1
AGCUGACACAGUUGGAUUGGAUUGGAUUCUGAUUUCGAUUCUGAGUCUGAUUUCCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGUGGUUACUAUGUA
(((((((.((((..((((((((..(((((.((.......)).)))))..)..)))))((((.........)))).))..)))).)))))))................ ( -35.70)
>consensus
AGCUGACACAGUUGGAU_____UGGAUUCUGAUUUCGAUUCCAAUUCUGAUUUCCAGGGCAGGAGCUCAAUGCCAUUUGGCUGGGUCAGUUCUGCGGUUACUA____
(((((((.((((..(((......(((.......)))((((((..(((((.....)))))..)))).))......)))..)))).)))))))................ (-26.22 = -25.90 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,041,558 – 8,041,656
Length 98
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 92.32
Mean single sequence MFE -23.24
Consensus MFE -18.70
Energy contribution -18.74
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -1.44
Structure conservation index 0.80
SVM decision value 0.16
SVM RNA-class probability 0.614328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8041558 98 - 23771897
----UAGUAACCGCAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUUGGAAUCAGAAUCCA-----AUCCAACUGUGUCAGCU
----.(((...(((((..((((.((((((....))).....((....))..)))...))))..(((((.(((((.......))))-----)))))))))))...))) ( -27.70)
>DroSec_CAF1 12687 98 - 1
----UAGUAACCGCAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGCAAAUCAGAAUUGGAAUCGAAAUCAGAAUCCA-----AUCCAACUGUGUCAGCU
----.(((...(((((..((((....(((....))).(((.((....))....))).)))).((((((.((.......)).))))-----))....)))))...))) ( -23.30)
>DroSim_CAF1 12703 98 - 1
----UAGUAACCGCAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUCGAAAUCAGAAUUCA-----AUCCAACUGUGUCAGCU
----..............(((((.(((((....)))..(((..(((......)))..)))(.((((((.((.......)).))))-----)).)...)).))))).. ( -22.10)
>DroEre_CAF1 12524 98 - 1
----UAGUAACCACAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUCAGAGUCGAAAUCAGAAUCCA-----AUCCAACUGUGUCAGCU
----.(((...(((((..((((....(((....))).((((..(((......)))..))))..))))..((.......)).....-----......)))))...))) ( -21.60)
>DroYak_CAF1 13006 107 - 1
UACAUAGUAACCACAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGACUCAGAAUCGAAAUCAGAAUCCAAUCCAAUCCAACUGUGUCAGCU
.....(((...(((((..((((....(((....))).((((..(((......)))..))))..))))..((.......))................)))))...))) ( -21.50)
>consensus
____UAGUAACCGCAGAACUGACCCAGCCAAAUGGCAUUGAGCUCCUGCCCUGGAAAUCAGAAUUGGAAUCGAAAUCAGAAUCCA_____AUCCAACUGUGUCAGCU
.....(((...(((((..((((.((((((....))).....((....))..)))...))))....(((.((.......)).)))............)))))...))) (-18.70 = -18.74 +   0.04)

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 10:42:31 2006