Locus 5416

Sequence ID 3L_DroMel_CAF1
Location 14,837,307 – 14,837,412
Length 105
Max. P 0.676469
window8572 window8573

overview

Window 2

Location 14,837,307 – 14,837,412
Length 105
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -18.32
Consensus MFE -12.48
Energy contribution -12.90
Covariance contribution 0.42
Combinations/Pair 1.07
Mean z-score -1.42
Structure conservation index 0.68
SVM decision value 0.30
SVM RNA-class probability 0.676469
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14837307 105 + 23771897
UACAAAAAUAGAUGAAGAAAAAU---CCCCAAAAA-----AAGAGUAACCAAAACCAGACAACGGACCAAACUUGGCUCUGGCUUUGCCAUUGGCACUGUUGUAAUUUUCUAU
...............((((((..---.........-----..(.((.......)))..(((((((.((((...((((.........))))))))..)))))))..)))))).. ( -17.80)
>DroPse_CAF1 70268 89 + 1
---GAAACUACAAAAAACAAAAA----CGAG--UA-----AAGAGUAACCAA-ACCAAACAACGGACCAAAGUUGGCUCGAGCUUUGCCAUUGGCAUUGUUC---------AU
---....................----.(((--(.-----..(.((......-)))...((((........))))))))((((..((((...))))..))))---------.. ( -17.80)
>DroSec_CAF1 14031 103 + 1
UACAAAAAUAGAUGAAGAAAAAU---CCCCA--AA-----AAGAGUAACCAAAACCAGACAACGGACCAAAGUUGGCUCUGGCUUUGCCAUUGGCAUUGUUGUAAUUUUCUAU
...............((((((..---.....--..-----..............(((((((((........))))..)))))(..((((...))))..)......)))))).. ( -16.80)
>DroSim_CAF1 14586 103 + 1
UACAAAAAUAGAUGAAGAAAAAU---CCCAA--AA-----AAGAGUAACCAAAACCAGACAACGGACCAAAGUUGGCUCUGGCUUUGCCAUUGGCACUGUUGUAAUUUUCUAU
...............((((((.(---(....--..-----..))..............(((((((.((((...((((.........))))))))..)))))))..)))))).. ( -18.00)
>DroYak_CAF1 10197 109 + 1
UACAAAAAUAGAUGAAGAAAACAAAGCC--A--AAAAAAGAAGAGUAACCAAAACCAGACAACGGACCAAAGUUGGCUCUGGCUUUGCCAUUGGCACUGUUGUAAUUUUCGAU
............((((((.((((..(((--(--(..((((.(((((...(.......).((((........)))))))))..))))....)))))..))))....)))))).. ( -21.70)
>DroPer_CAF1 67715 89 + 1
---GAAACUACAAAAAACAAAAA----CGAG--UA-----AAGAGUAACCAA-ACCAAACAACGGACCAAAGUUGGCUCGAGCUUUGCCAUUGGCAUUGUUC---------AU
---....................----.(((--(.-----..(.((......-)))...((((........))))))))((((..((((...))))..))))---------.. ( -17.80)
>consensus
UACAAAAAUAGAUGAAGAAAAAA___CCCAA__AA_____AAGAGUAACCAAAACCAGACAACGGACCAAAGUUGGCUCUGGCUUUGCCAUUGGCACUGUUGUAAUUUUCUAU
..........................................................(((((((.((((...((((.........))))))))..))))))).......... (-12.48 = -12.90 +   0.42)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,837,307 – 14,837,412
Length 105
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -21.56
Consensus MFE -16.81
Energy contribution -16.62
Covariance contribution -0.19
Combinations/Pair 1.16
Mean z-score -1.03
Structure conservation index 0.78
SVM decision value 0.03
SVM RNA-class probability 0.547723
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14837307 105 - 23771897
AUAGAAAAUUACAACAGUGCCAAUGGCAAAGCCAGAGCCAAGUUUGGUCCGUUGUCUGGUUUUGGUUACUCUU-----UUUUUGGGG---AUUUUUCUUCAUCUAUUUUUGUA
(((((............((((...)))).(((((((((((..(..........)..)))))))))))......-----....(((((---(....)))))))))))....... ( -23.60)
>DroPse_CAF1 70268 89 - 1
AU---------GAACAAUGCCAAUGGCAAAGCUCGAGCCAACUUUGGUCCGUUGUUUGGU-UUGGUUACUCUU-----UA--CUCG----UUUUUGUUUUUUGUAGUUUC---
..---------((((((((((...)))).(((.(((((((((..((...))..).)))))-))))))......-----..--....----...))))))...........--- ( -15.80)
>DroSec_CAF1 14031 103 - 1
AUAGAAAAUUACAACAAUGCCAAUGGCAAAGCCAGAGCCAACUUUGGUCCGUUGUCUGGUUUUGGUUACUCUU-----UU--UGGGG---AUUUUUCUUCAUCUAUUUUUGUA
(((((.........(((.((((..(((((.(((((((....)))))))...))))))))).))).........-----..--(((((---(....)))))))))))....... ( -26.00)
>DroSim_CAF1 14586 103 - 1
AUAGAAAAUUACAACAGUGCCAAUGGCAAAGCCAGAGCCAACUUUGGUCCGUUGUCUGGUUUUGGUUACUCUU-----UU--UUGGG---AUUUUUCUUCAUCUAUUUUUGUA
..((((((......(((.((((..(((((.(((((((....)))))))...))))))))).)))....(((..-----..--..)))---..))))))............... ( -23.30)
>DroYak_CAF1 10197 109 - 1
AUCGAAAAUUACAACAGUGCCAAUGGCAAAGCCAGAGCCAACUUUGGUCCGUUGUCUGGUUUUGGUUACUCUUCUUUUUU--U--GGCUUUGUUUUCUUCAUCUAUUUUUGUA
..(((((((...(((((.(((((.(.((((((((((..((((........)))))))))))))).).............)--)--))).)))))..........))))))).. ( -24.86)
>DroPer_CAF1 67715 89 - 1
AU---------GAACAAUGCCAAUGGCAAAGCUCGAGCCAACUUUGGUCCGUUGUUUGGU-UUGGUUACUCUU-----UA--CUCG----UUUUUGUUUUUUGUAGUUUC---
..---------((((((((((...)))).(((.(((((((((..((...))..).)))))-))))))......-----..--....----...))))))...........--- ( -15.80)
>consensus
AUAGAAAAUUACAACAAUGCCAAUGGCAAAGCCAGAGCCAACUUUGGUCCGUUGUCUGGUUUUGGUUACUCUU_____UU__UUGGG___AUUUUUCUUCAUCUAUUUUUGUA
..............(((.((((..(((((.(((((((....)))))))...))))))))).)))................................................. (-16.81 = -16.62 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:51 2006