Locus 4961

Sequence ID X_DroMel_CAF1
Location 12,953,018 – 12,953,176
Length 158
Max. P 0.999582
window8083 window8084 window8085

overview

Window 3

Location 12,953,018 – 12,953,136
Length 118
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 75.07
Mean single sequence MFE -43.17
Consensus MFE -24.91
Energy contribution -25.47
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.58
SVM decision value 1.04
SVM RNA-class probability 0.905257
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953018 118 + 22224390
UAGGGGGAUUGUGAAGGUAGAAGUCUUCGCUGGUUCAACC-AGCGUUUUUAAGUGGCCAAGACGUCGGGCCACGCUAAGGUCAAGGGACAACUAGCCCCUGACCUUCGGACACAACCCA
....(((.(((((..(((.........((((((.....))-)))).......((((((.........)))))))))(((((((.(((........))).)))))))....)))))))). ( -47.50)
>DroSec_CAF1 19379 104 + 1
---------------GGAAGAAGCCUUCGCUAGUUCAACGUCUCGUUUUUAAGUGGCCAAGACGUCGGGCCACGCUAAGGUCAAGGGACAACUAGCCGCUGACCUUCGGGCAAAAGCCA
---------------.((((.(((....(((((((....(((((..(((((.((((((.........))))))..)))))....)))))))))))).)))...)))).(((....))). ( -36.70)
>DroEre_CAF1 10556 110 + 1
CAGGGGGCCCU---------CCACCUUCGGUGGGUCAACGUCUCGUUUUUAAGUGGCCAAGACGCGGGGCCACGCUAAGGUCAAGGGACAACCGGCCCCUGACCUUCGUGGACAAGCCA
..((.(((((.---------((......)).)))))...((((.........((((((.........))))))((.(((((((.(((........))).))))))).))))))...)). ( -45.30)
>consensus
_AGGGGG________GG_AGAAGCCUUCGCUGGUUCAACGUCUCGUUUUUAAGUGGCCAAGACGUCGGGCCACGCUAAGGUCAAGGGACAACUAGCCCCUGACCUUCGGGCACAAGCCA
......................((((..........................((((((.........))))))...(((((((.(((........))).))))))).))))........ (-24.91 = -25.47 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,953,018 – 12,953,136
Length 118
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 75.07
Mean single sequence MFE -46.17
Consensus MFE -29.66
Energy contribution -31.33
Covariance contribution 1.67
Combinations/Pair 1.10
Mean z-score -2.75
Structure conservation index 0.64
SVM decision value 3.75
SVM RNA-class probability 0.999582
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953018 118 - 22224390
UGGGUUGUGUCCGAAGGUCAGGGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGCU-GGUUGAACCAGCGAAGACUUCUACCUUCACAAUCCCCCUA
.((((((((....((((((((((((.....).)))))))))))...((((((.........)))))).......((((-((.....))))))..............))))))))..... ( -50.30)
>DroSec_CAF1 19379 104 - 1
UGGCUUUUGCCCGAAGGUCAGCGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGAGACGUUGAACUAGCGAAGGCUUCUUCC---------------
.((((..(((...((((((((.(((.....).)).)))))))).))).)))).(((((((((............)))))))))(((..(((....)))..))).--------------- ( -39.20)
>DroEre_CAF1 10556 110 - 1
UGGCUUGUCCACGAAGGUCAGGGGCCGGUUGUCCCUUGACCUUAGCGUGGCCCCGCGUCUUGGCCACUUAAAAACGAGACGUUGACCCACCGAAGGUGG---------AGGGCCCCCUG
.(((((.(((((.(((((((((((.(....).))))))))))).(.((((..(.((((((((............)))))))).)..)))))....))))---------))))))..... ( -49.00)
>consensus
UGGCUUGUGCCCGAAGGUCAGGGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGAGACGUUGAACCAGCGAAGGCUUCU_CC________CCCCCU_
..((((.......((((((((((((.....).)))))))))))..(((((..((((((((((............))))))))))..))).)).))))...................... (-29.66 = -31.33 +   1.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,953,058 – 12,953,176
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.10
Mean single sequence MFE -37.12
Consensus MFE -24.24
Energy contribution -25.68
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.65
SVM decision value 0.52
SVM RNA-class probability 0.768590
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953058 118 - 22224390
UAUUGAAAACCUUUUGCAAUCUGGACGCCAACUGACAUCAUGGGUUGUGU-CCGAAGGUCAGGGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGCU-
...............((....(((((((.((((.(.....).))))))))-)))((((((((((((.....).))))))))))).))((((((.........))))))...........- ( -43.50)
>DroSec_CAF1 19404 119 - 1
UAUUGAAAACCUUUUGCAAUCUGGACGCCAACUGACAUCAUGGCUUUUGC-CCGAAGGUCAGCGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGAGA
......................(((((((..(((((.....(((....))-).....))))).))).....))))((((...((((.((((((.........))))))))))...)))). ( -32.90)
>DroEre_CAF1 10587 119 - 1
UAUUGAAAACCUUUGGCAAUCUCGACGCCAACUGACAUCAUGGCUUGUCC-ACGAAGGUCAGGGGCCGGUUGUCCCUUGACCUUAGCGUGGCCCCGCGUCUUGGCCACUUAAAAACGAGA
...................(((((..((.....((((........)))).-...(((((((((((.(....).))))))))))).))((((((.........)))))).......))))) ( -39.10)
>DroYak_CAF1 11092 93 - 1
UAUUGCGAACCUUUUGCAAUCUC------AGCUGACCUCAUGGCUCUUGGUCUGAAGGUCAGGGGUUAGUUGUCCCUUGACCUUAGC---------------------UUAAAAGCGAGC
.(((((((.....)))))))(((------.(((((((...........))))..(((((((((((........)))))))))))...---------------------.....)))))). ( -33.00)
>consensus
UAUUGAAAACCUUUUGCAAUCUCGACGCCAACUGACAUCAUGGCUUGUGC_CCGAAGGUCAGGGGCUAGUUGUCCCUUGACCUUAGCGUGGCCCGACGUCUUGGCCACUUAAAAACGAGA
...............((.........((((..((....))))))..........((((((((((((.....).))))))))))).))((((((.........))))))............ (-24.24 = -25.68 +   1.44)

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 11:36:59 2006