Locus 1955

Sequence ID 2L_DroMel_CAF1
Location 5,275,409 – 5,275,569
Length 160
Max. P 0.791868
window3164 window3165

overview

Window 4

Location 5,275,409 – 5,275,529
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -47.79
Consensus MFE -25.18
Energy contribution -25.97
Covariance contribution 0.78
Combinations/Pair 1.30
Mean z-score -2.33
Structure conservation index 0.53
SVM decision value 0.07
SVM RNA-class probability 0.569979
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5275409 120 + 22407834
AUCCUCCAGCGACGCAUGCCGCUCAUCCACUUCCACGGCAAGCAAAGCCACCCUUUGGUUGGCCGCCUUAUUAUCGGCCCUCAGCUUGAGGUUCUCCUCAUGCUGCUGCCUAUAGGCAAG
........(((..((.(((((..............))))).))...((((((....)).)))))))(((.((((.(((...((((.(((((....))))).))))..))).))))..))) ( -39.84)
>DroPse_CAF1 55365 120 + 1
AUCCUCGAGCGUGGCAUGCCGCUCGUCCACCUCGGCGGCGAGCAAAGCCACCCUCUGGUUGGCUGCCUUAUUGUCGGAGCGCAGCUUAAGGUUCUCCUCGUGCUGCUGGCGAUAGGCUCG
.....(((((..((((.((((((((.((.(....).)))))))..(((((.....))))))))))))(((((((((....(((((...(((....)))...))))))))))))))))))) ( -53.80)
>DroGri_CAF1 3333 120 + 1
AUCCUCCAGGCUUGCAUGCCGCUCAUCAACCUCGGCGGCAAGCAUCGCCACUCGCUGAUUGGCCGCCUUAUUGUCGGCACGCAGCUUGAGGUUCUCCUCGUGCUGCUGUCGGUAUGCCUG
......(((((.(((.(((((((..........))))))).))).........((((((..((((.(.....).))))..(((((.(((((....))))).))))).))))))..))))) ( -51.60)
>DroWil_CAF1 6445 120 + 1
CUCCUCCAUGGUGGCAUGACGUUCAUCCACCUCCAAGGCCAUAAGAGCUACACGCUGAUUGGCCGCCUUAUUGUCGGCCCGCAAUUUUAGAUUCUCCUCAUGUUGCUGACGAUAGGCCAC
.........(((((.(((.....)))))))).....(((((....(((.....)))...)))))((((.(((((((((..(((.................))).)))))))))))))... ( -39.83)
>DroAna_CAF1 31182 120 + 1
CUCCUCCAAGGAGGCAUGUCGCUCGUCCACCUCCACGGCCAGGAGAGCCACCCGCUGGUUCGCCGCCUUGUUGUCGGCCCGCAGCUUCAGGUUCUCCUCGUGCUGCUGGCGAUAGGCCAG
.........(((((.(((.....)))...)))))..((((.((.((((((.....)))))).)).......(((((.((.(((((...(((....)))...))))).))))))))))).. ( -48.90)
>DroPer_CAF1 55376 120 + 1
AUCCUCGAGCGUGGCAUGCCGCUCGUCCACCUCGGCGGCCAGCAAAGCCACCCUCUGGUUGGCCGCCUUAUUAUCGGAGCGCAGCUUAAGGUUCUCCUCGUGCUGCUGGCGAUAGGCUCG
.....(((((.((...((((((((.........((((((((((..((.....))...)))))))))).........))))(((((...(((....)))...))))).)))).)).))))) ( -52.77)
>consensus
AUCCUCCAGCGUGGCAUGCCGCUCAUCCACCUCCACGGCCAGCAAAGCCACCCGCUGGUUGGCCGCCUUAUUGUCGGCCCGCAGCUUAAGGUUCUCCUCGUGCUGCUGGCGAUAGGCCAG
.................(((((............))))).......((((.((...)).)))).((((.((((((((....((((...(((....)))...))))))))))))))))... (-25.18 = -25.97 +   0.78)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,275,449 – 5,275,569
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.72
Mean single sequence MFE -49.43
Consensus MFE -23.82
Energy contribution -24.93
Covariance contribution 1.12
Combinations/Pair 1.37
Mean z-score -2.19
Structure conservation index 0.48
SVM decision value 0.59
SVM RNA-class probability 0.791868
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5275449 120 - 22407834
UCUGGCUGCUCUGCAGGCCACCGAGUUGGGCAACUACAGACUUGCCUAUAGGCAGCAGCAUGAGGAGAACCUCAAGCUGAGGGCCGAUAAUAAGGCGGCCAACCAAAGGGUGGCUUUGCU
...(((..((((...((((.((....(((((((........)))))))..(((..((((.(((((....))))).))))...)))........)).))))......))))..)))..... ( -51.00)
>DroPse_CAF1 55405 120 - 1
CUUAGUGGCCCUGCAGUCGUCGGAGCUGGCCAACUAUCGGCGAGCCUAUCGCCAGCAGCACGAGGAGAACCUUAAGCUGCGCUCCGACAAUAAGGCAGCCAACCAGAGGGUGGCUUUGCU
(..(((.(((((......((((((((............(((((.....))))).(((((..((((....))))..))))))))))))).....((.......))..))))).)))..).. ( -51.90)
>DroGri_CAF1 3373 120 - 1
CUUGGUCGCGCUCCAAUCUGUGGAGCUGGGCACGUUGCGACAGGCAUACCGACAGCAGCACGAGGAGAACCUCAAGCUGCGUGCCGACAAUAAGGCGGCCAAUCAGCGAGUGGCGAUGCU
..(((((((((((((.....))))))..((((((((((.....))).)).....(((((..((((....))))..)))))))))).........)))))))(((.((.....)))))... ( -50.90)
>DroWil_CAF1 6485 120 - 1
UCUGGCAACUCUUCAAUCGUCCGAAUUGGCCAACUAUCGUGUGGCCUAUCGUCAGCAACAUGAGGAGAAUCUAAAAUUGCGGGCCGACAAUAAGGCGGCCAAUCAGCGUGUAGCUCUUAU
...(((..(((((((...((.(((...(((((((....)).)))))..)))...))....)))))))...........((.(((((.(......)))))).....)).....)))..... ( -32.60)
>DroAna_CAF1 31222 120 - 1
GUUGGCUGCCCUCCAGGCCACCGAGUUGGGCAACUACCGGCUGGCCUAUCGCCAGCAGCACGAGGAGAACCUGAAGCUGCGGGCCGACAACAAGGCGGCGAACCAGCGGGUGGCUCUCCU
(..(((..(((...(((((((((.((.((....))))))).)))))).(((((.(((((...(((....)))...)))))..(((........))))))))......)))..)))..).. ( -58.10)
>DroPer_CAF1 55416 120 - 1
CUUGGUGACCCUGCAGUCGUCGGAGCUGGCCAACUAUCGGCGAGCCUAUCGCCAGCAGCACGAGGAGAACCUUAAGCUGCGCUCCGAUAAUAAGGCGGCCAACCAGAGGGUGGCUUUGCU
(..(((.(((((((.((..(((((((............(((((.....))))).(((((..((((....))))..))))))))))))..))...))((....))..))))).)))..).. ( -52.10)
>consensus
CUUGGCGGCCCUGCAGUCGUCCGAGCUGGCCAACUAUCGGCUGGCCUAUCGCCAGCAGCACGAGGAGAACCUCAAGCUGCGGGCCGACAAUAAGGCGGCCAACCAGAGGGUGGCUUUGCU
...(((.((((.............(((((.......)))))..(((........(((((..((((....))))..)))))..(((........))))))........)))).)))..... (-23.82 = -24.93 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:54 2006