Locus 5421

Sequence ID 3L_DroMel_CAF1
Location 14,854,441 – 14,854,575
Length 134
Max. P 0.823448
window8580 window8581 window8582

overview

Window 0

Location 14,854,441 – 14,854,551
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.70
Mean single sequence MFE -26.02
Consensus MFE -11.55
Energy contribution -12.30
Covariance contribution 0.75
Combinations/Pair 1.08
Mean z-score -2.38
Structure conservation index 0.44
SVM decision value 0.69
SVM RNA-class probability 0.823448
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14854441 110 - 23771897
UCCUCG------UUGUCGU----ACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCACUUUUAAUAAAUAAAGUUGAAAGGUUGUCCGGGUAUGUGG
.((.((------(..(((.----((((.(((((((((((.....(((......)))))))))))))).............((((((((.......)))))))).)))).)))..))).)) ( -27.80)
>DroVir_CAF1 49277 101 - 1
-------------AGUCGU----ACGAAAAUACUUGAGAAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAUGUAAUAAGCACUUUUAAUAAAUAAAGGUGAACUUUUA--AGCGAAUGAAG
-------------..((((----(((..((((((((((.....((((......))))))))))))))..)))......((((((((.....))))))))........--.))))...... ( -24.50)
>DroGri_CAF1 45123 103 - 1
-------------AGUCGU----UCGAAAAUGCUUGAGAAAAUCGUGUUAAAUCGCGCUCAAGUGCUAAAGUAAUAAGCACUUUUAAUAAAUAAAGGUGAAUUGUUGUCGGAGAGUCAAA
-------------..((.(----((((....(((((((.....((((......))))))))))).......((((((.((((((((.....))))))))..)))))))))))))...... ( -23.40)
>DroWil_CAF1 285711 117 - 1
UCCUCAAUGCUUUUGUCGUGAGAACGAAAAU-CGUGAGAAAAUCGUGUUAAGUGGCGCGCAAGUGUUAAAAUAAUAAGCACUUUUAAUAAAUAAAGUUGAAAGGCUGUAUGAGCGA-AA-
((((((.((((((((((....).)))))).(-(....))......(((((..((((((....))))))...)))))(((.((((((((.......)))))))))))))))))).))-..- ( -31.90)
>DroMoj_CAF1 56186 100 - 1
-------------AGUCGU----AUAAAAAUACUUGAGAAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAUGUAAUAAGCAGUUUUAAUAAAUAAAGGUGA-CAUUUA--AGCGAAUGUUG
-------------..((((----.((((((((((((((.....((((......))))))))))))))..........(((.(((((.....))))).)).-).))))--.))))...... ( -21.60)
>DroPer_CAF1 83790 110 - 1
UCCUCG------UUGUCGU----ACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCACUUUUAAUAAAUAAAGUUGAGAGGUUUCUUGGGUGUGAAA
.(((((------((....(----((...(((((((((((.....(((......))))))))))))))...)))...)))(((((........)))))...))))((((........)))) ( -26.90)
>consensus
_____________AGUCGU____ACGAAAAUACUUGAGAAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCACUUUUAAUAAAUAAAGGUGAAAGGUUGU_AGAGAAUGAAG
...............(((......))).((((((((((.....((((......))))))))))))))...........((.(((((.....))))).))..................... (-11.55 = -12.30 +   0.75)

alignment

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secondary structure

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Window 1

Location 14,854,481 – 14,854,575
Length 94
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -20.85
Consensus MFE -14.39
Energy contribution -14.75
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value -0.02
SVM RNA-class probability 0.523261
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14854481 94 + 23771897
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAAGUAUUUUCGUACGACAACGAGGACACAUUCCGGCGUUCUCGUUCUCG----------------
.......(((...((.(((((((((.((((......))))))))))))).))...)))(((.(((((((((.(......).))))))))).)))---------------- ( -27.60)
>DroPse_CAF1 86349 85 + 1
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAAGUAUUUUCGUACGACAACGAGGACACAUUCCUCCUUGA-------------------------
.......(((...((.(((((((((.((((......))))))))))))).))...)))...(((.(((((.....))))).))).------------------------- ( -20.90)
>DroSim_CAF1 31668 85 + 1
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAGGUAUUUUCGUACGACAACGAGGACACAUUCCGGCGUUC-------------------------
.(((............(((((((((.((((......))))))))))))).(((((((......)))))))........)))....------------------------- ( -19.20)
>DroEre_CAF1 33081 97 + 1
UGCUUAUUACUUUAACACUUAAACGCGAUUUAACACGAUUUGCUCAAGCAUUUUCGUACGACAACGAGGACACAUUCCGGCGCUCCCCUUCUCCUCC-------------
........................(((.......((((..(((....)))...))))..........(((.....)))..)))..............------------- ( -13.00)
>DroYak_CAF1 27661 110 + 1
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAAGUAUUUUCGUACGACAACGAGGACACAUUCCGGCGUUCUCCUUCUCGUCCCCGUCCCCGUUCU
.............((((((((((((.((((......)))))))))))))......(.((((.((.((((((.(......).)))))).)).)))).)........))).. ( -23.50)
>DroPer_CAF1 83830 85 + 1
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAAGUAUUUUCGUACGACAACGAGGACACAUUCCUCCUUGA-------------------------
.......(((...((.(((((((((.((((......))))))))))))).))...)))...(((.(((((.....))))).))).------------------------- ( -20.90)
>consensus
UGCUUAUUACUUUAACACUUGAGCGCGAUUUAACACGAUUUGCUCAAGUAUUUUCGUACGACAACGAGGACACAUUCCGGCGUUC_________________________
................(((((((((.((((......))))))))))))).(((((((......)))))))........................................ (-14.39 = -14.75 +   0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,854,481 – 14,854,575
Length 94
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -27.50
Consensus MFE -20.28
Energy contribution -20.03
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -2.61
Structure conservation index 0.74
SVM decision value 0.64
SVM RNA-class probability 0.807301
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14854481 94 - 23771897
----------------CGAGAACGAGAACGCCGGAAUGUGUCCUCGUUGUCGUACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
----------------(((.((((((.((((......)))).)))))).)))(((...(((((((((((.....(((......))))))))))))))...)))....... ( -33.10)
>DroPse_CAF1 86349 85 - 1
-------------------------UCAAGGAGGAAUGUGUCCUCGUUGUCGUACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
-------------------------.(((.(((((.....))))).)))...(((...(((((((((((.....(((......))))))))))))))...)))....... ( -26.50)
>DroSim_CAF1 31668 85 - 1
-------------------------GAACGCCGGAAUGUGUCCUCGUUGUCGUACGAAAAUACCUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
-------------------------.((((..(((.....))).))))((..(((...(((((.(((((.....(((......)))))))).)))))...)))....)). ( -17.50)
>DroEre_CAF1 33081 97 - 1
-------------GGAGGAGAAGGGGAGCGCCGGAAUGUGUCCUCGUUGUCGUACGAAAAUGCUUGAGCAAAUCGUGUUAAAUCGCGUUUAAGUGUUAAAGUAAUAAGCA
-------------.........(((((.(((......))))))))(((....(((...(((((((((((.....(((......))))))))))))))...)))...))). ( -22.90)
>DroYak_CAF1 27661 110 - 1
AGAACGGGGACGGGGACGAGAAGGAGAACGCCGGAAUGUGUCCUCGUUGUCGUACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
...((((.((((((((((....((......))......)))))))))).))))((...(((((((((((.....(((......))))))))))))))...))........ ( -38.50)
>DroPer_CAF1 83830 85 - 1
-------------------------UCAAGGAGGAAUGUGUCCUCGUUGUCGUACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
-------------------------.(((.(((((.....))))).)))...(((...(((((((((((.....(((......))))))))))))))...)))....... ( -26.50)
>consensus
_________________________GAACGCCGGAAUGUGUCCUCGUUGUCGUACGAAAAUACUUGAGCAAAUCGUGUUAAAUCGCGCUCAAGUGUUAAAGUAAUAAGCA
................................(((.....)))..(((....(((...(((((((((((.....(((......))))))))))))))...)))...))). (-20.28 = -20.03 +  -0.25)

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 11:49:59 2006