Locus 4526

Sequence ID 2L_DroMel_CAF1
Location 12,969,236 – 12,969,391
Length 155
Max. P 0.989756
window7121 window7122 window7123 window7124

overview

Window 1

Location 12,969,236 – 12,969,356
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.71
Mean single sequence MFE -36.30
Consensus MFE -27.12
Energy contribution -27.56
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.96
Structure conservation index 0.75
SVM decision value 1.37
SVM RNA-class probability 0.947157
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12969236 120 + 22407834
AUUCCGGGGAUGAGUUAUGCUGCAAUCUGUGGGAAGCAGGGUACAAAAAAAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCUCAACAACAACUGCAAGGACCAAUAACAA
.(((((.((((..((......)).)))).))))).((((((((((........)))))..(((((((....)))))))...)))))..(((............))).............. ( -34.10)
>DroSec_CAF1 13943 119 + 1
UUUCCGCGGAUGAGUUAUGCUGCAAUCUGUGGCAAGCAGGGUAUAAAA-AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAAUUGCAAGGACCAAUAACAA
..((((((.........)))((((((.(((((((.((((((((((...-......)))))(((((((....)))))))...)))))..)))).....))))))))).))).......... ( -35.40)
>DroSim_CAF1 14761 119 + 1
UUUCCGCGGAUGAGUUAUGCUGCAAUCUGUGGCAAGCAGGGUAUAAAA-AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAACUGCAAGGACCAAUAACAA
..(((((((.((.....(((..(.....)..))).((((((((((...-......)))))(((((((....)))))))...)))))............)).))))..))).......... ( -35.50)
>DroEre_CAF1 2654 118 + 1
UUUCCAGGAAUGAGUUAUGCUGCAAUCUGUGGGAAGCAGGGUAUAAAA--AAAUGUAUGCCAGAUCCAUAGGGAUCUGGAUCCUGCAAAGCGCCACAACAACUGCAAGGACCAAUAACAA
..(((.(((.((((.....)).)).)))(((((..((((((((((...--...))))).((((((((....))))))))..)))))....).))))...........))).......... ( -34.90)
>DroYak_CAF1 15533 118 + 1
UUACCGGGGAUGAGUUAUGCUGCAAUCUGUGGGAAGCAGGGUAUAAAA--AAAAGUAUGCCAGAUCCAUAGGGAUCUGGAUGCUGCAAUGCCCCACAACAAUUGCAAGGACCCAUAACAA
......(..(((.(((....((((((.((((((..(((..((......--...(((((.((((((((....)))))))))))))))..)))))))))...))))))..))).)))..).. ( -41.60)
>consensus
UUUCCGGGGAUGAGUUAUGCUGCAAUCUGUGGGAAGCAGGGUAUAAAA_AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAACUGCAAGGACCAAUAACAA
.............(((((.(((((...(((((...((((((((((........)))))..(((((((....)))))))...)))))......))))).....)))..))....))))).. (-27.12 = -27.56 +   0.44)

alignment

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secondary structure

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Window 2

Location 12,969,236 – 12,969,356
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.71
Mean single sequence MFE -33.62
Consensus MFE -28.86
Energy contribution -28.62
Covariance contribution -0.24
Combinations/Pair 1.09
Mean z-score -2.02
Structure conservation index 0.86
SVM decision value 2.18
SVM RNA-class probability 0.989756
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12969236 120 - 22407834
UUGUUAUUGGUCCUUGCAGUUGUUGUUGAGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUUUUUUUGUACCCUGCUUCCCACAGAUUGCAGCAUAACUCAUCCCCGGAAU
......((((....((.((((((.((((......(((((..((((((((....))))))))..((((........)))).))))).((.....))...))))))))))))...))))... ( -30.30)
>DroSec_CAF1 13943 119 - 1
UUGUUAUUGGUCCUUGCAAUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU-UUUUAUACCCUGCUUGCCACAGAUUGCAGCAUAACUCAUCCGCGGAAA
..........(((.(((((((..(((..((((..(((((...(((((((....)))))))(....).....-........))))).))))))))))))))((...........))))).. ( -33.60)
>DroSim_CAF1 14761 119 - 1
UUGUUAUUGGUCCUUGCAGUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU-UUUUAUACCCUGCUUGCCACAGAUUGCAGCAUAACUCAUCCGCGGAAA
..........(((.(((((((..(((..((((..(((((...(((((((....)))))))(....).....-........))))).))))))))))))))((...........))))).. ( -33.60)
>DroEre_CAF1 2654 118 - 1
UUGUUAUUGGUCCUUGCAGUUGUUGUGGCGCUUUGCAGGAUCCAGAUCCCUAUGGAUCUGGCAUACAUUU--UUUUAUACCCUGCUUCCCACAGAUUGCAGCAUAACUCAUUCCUGGAAA
..(((((..((...(((((((..(((((.(....(((((..((((((((....)))))))).(((.....--...)))..)))))..))))))))))))))))))))............. ( -33.30)
>DroYak_CAF1 15533 118 - 1
UUGUUAUGGGUCCUUGCAAUUGUUGUGGGGCAUUGCAGCAUCCAGAUCCCUAUGGAUCUGGCAUACUUUU--UUUUAUACCCUGCUUCCCACAGAUUGCAGCAUAACUCAUCCCCGGUAA
..(..((((((..((((((((..(((((((....((((...((((((((....)))))))).(((.....--...)))...)))).)))))))))))))))....))))))..)...... ( -37.30)
>consensus
UUGUUAUUGGUCCUUGCAGUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU_UUUUAUACCCUGCUUCCCACAGAUUGCAGCAUAACUCAUCCCCGGAAA
..(((((..((...(((((((..(((((......(((((..((((((((....)))))))).(((..........)))..)))))...)))))))))))))))))))............. (-28.86 = -28.62 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,969,276 – 12,969,391
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.83
Mean single sequence MFE -24.73
Consensus MFE -19.90
Energy contribution -19.94
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.00
Structure conservation index 0.80
SVM decision value 1.31
SVM RNA-class probability 0.940936
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12969276 115 + 22407834
GUACAAAAAAAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCUCAACAACAACUGCAAGGACCAAUAACAAUGGCAUGAAUAUAACAAAAGCUUCAGUCCCAGA-----CC
...............((((((((((((....))))))...(((((((.((........))..))).))))...........))))))..........................-----.. ( -21.90)
>DroSec_CAF1 13983 114 + 1
GUAUAAAA-AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAAUUGCAAGGACCAAUAACAAUGGUAUGAAUAUAACAAAAGCUUCAGUCCCAGA-----CC
........-....(((....(((((((....)))))))..(((((((((...........))))).))))......))).(((..((((............))))...)))..-----.. ( -23.20)
>DroSim_CAF1 14801 114 + 1
GUAUAAAA-AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAACUGCAAGGACCAAUAACAAUGGCAUGAAUAUAACAAAAGCUUCAGUCCCAGA-----CC
........-......((((((((((((....))))))...(((((((.((........))..))).))))...........))))))..........................-----.. ( -21.90)
>DroEre_CAF1 2694 113 + 1
GUAUAAAA--AAAUGUAUGCCAGAUCCAUAGGGAUCUGGAUCCUGCAAAGCGCCACAACAACUGCAAGGACCAAUAACAAUGGCAUGAAUAUAACAAUAGCUUCAGUCCCAGA-----CC
........--.....((((((((((((....)))))(((.(((((((...............))).))))))).......)))))))..........................-----.. ( -25.26)
>DroYak_CAF1 15573 118 + 1
GUAUAAAA--AAAAGUAUGCCAGAUCCAUAGGGAUCUGGAUGCUGCAAUGCCCCACAACAAUUGCAAGGACCCAUAACAAUGGCAUGAAUAUAACAAAAGCUGCAGUCCCAUAAGCAGCC
........--...(((((.((((((((....)))))))))))))(((((...........)))))......((((....))))................(((((..........))))). ( -31.40)
>consensus
GUAUAAAA_AAAAUGUAUGCCAGAUCCAUGGGGAUCUGAAUCCUGCAAUGCCCCACAACAACUGCAAGGACCAAUAACAAUGGCAUGAAUAUAACAAAAGCUUCAGUCCCAGA_____CC
...............((((((((((((....))))))...(((((((...............))).))))...........))))))................................. (-19.90 = -19.94 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,969,276 – 12,969,391
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.83
Mean single sequence MFE -30.86
Consensus MFE -25.46
Energy contribution -25.42
Covariance contribution -0.04
Combinations/Pair 1.09
Mean z-score -1.49
Structure conservation index 0.83
SVM decision value 0.48
SVM RNA-class probability 0.752156
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12969276 115 - 22407834
GG-----UCUGGGACUGAAGCUUUUGUUAUAUUCAUGCCAUUGUUAUUGGUCCUUGCAGUUGUUGUUGAGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUUUUUUUGUAC
((-----((((((((((((.................((((.......)))).((((((((.(((....))))))))))).))))).))))...))))).....((((........)))). ( -30.30)
>DroSec_CAF1 13983 114 - 1
GG-----UCUGGGACUGAAGCUUUUGUUAUAUUCAUACCAUUGUUAUUGGUCCUUGCAAUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU-UUUUAUAC
.(-----((((((((..((((...((.(((....))).))..))).)..)))))((((((.((......))))))))))))((((((((....))))))))..........-........ ( -28.20)
>DroSim_CAF1 14801 114 - 1
GG-----UCUGGGACUGAAGCUUUUGUUAUAUUCAUGCCAUUGUUAUUGGUCCUUGCAGUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU-UUUUAUAC
((-----((((((((((((.................((((.......)))).((((((((.((......)))))))))).))))).))))...))))).............-........ ( -28.40)
>DroEre_CAF1 2694 113 - 1
GG-----UCUGGGACUGAAGCUAUUGUUAUAUUCAUGCCAUUGUUAUUGGUCCUUGCAGUUGUUGUGGCGCUUUGCAGGAUCCAGAUCCCUAUGGAUCUGGCAUACAUUU--UUUUAUAC
((-----((((((((..((((...((.(((....))).))..))).)..)))))(((((.(((....)))..))))))))))(((((((....)))))))..........--........ ( -28.80)
>DroYak_CAF1 15573 118 - 1
GGCUGCUUAUGGGACUGCAGCUUUUGUUAUAUUCAUGCCAUUGUUAUGGGUCCUUGCAAUUGUUGUGGGGCAUUGCAGCAUCCAGAUCCCUAUGGAUCUGGCAUACUUUU--UUUUAUAC
.(((((..(((...(..((((..((((...(((((((.......)))))))....))))..))))..)..))).)))))..((((((((....)))))))).........--........ ( -38.60)
>consensus
GG_____UCUGGGACUGAAGCUUUUGUUAUAUUCAUGCCAUUGUUAUUGGUCCUUGCAGUUGUUGUGGGGCAUUGCAGGAUUCAGAUCCCCAUGGAUCUGGCAUACAUUUU_UUUUAUAC
..........(((((((((((...((.(((....))).))..))).))))))))((((((.((......))))))))....((((((((....))))))))................... (-25.46 = -25.42 +  -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 11:20:03 2006