Locus 1789

Sequence ID 3L_DroMel_CAF1
Location 5,070,487 – 5,070,679
Length 192
Max. P 0.999891
window2772 window2773 window2774 window2775

overview

Window 2

Location 5,070,487 – 5,070,607
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.75
Mean single sequence MFE -31.81
Consensus MFE -28.76
Energy contribution -28.36
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.41
Structure conservation index 0.90
SVM decision value 0.91
SVM RNA-class probability 0.879126
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5070487 120 - 23771897
ACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGACUUCGCCCUCGGCUUUUUACCCAAAAGUGGAUUCAAUUAA
....((((((((.((((....).))).))))))))((((((.((..((.....(((((((((.......)))))))))......))..)).))))))...(((....))).......... ( -32.20)
>DroSec_CAF1 277008 120 - 1
GCUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAAUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGAUUUCGCCCUCGGCUUUUUACCCAAAAGUGGAUUCAAUUAA
((..((((((((.((((....).))).))))))))((((.(((((.((((((..........))))))....)))))...))))))..((.((((((.....)))))).))......... ( -31.50)
>DroSim_CAF1 298288 120 - 1
ACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGACUUCGCCCUCGGCUUUUUACCCAAAAGUGGAUUCAAUUAA
....((((((((.((((....).))).))))))))((((((.((..((.....(((((((((.......)))))))))......))..)).))))))...(((....))).......... ( -32.20)
>DroEre_CAF1 283914 120 - 1
ACUGAAUGCAUUGCCCUUUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCGUUUUUCCAGGUCUUCGCCCUCGACUUUUUACCCAAAAGUGGAUUCAAUUAA
..(((((.((((.......((((((.((..((...((...((((((((((((..........))))))))...))))..))...))..)).))))))........)))).)))))..... ( -32.56)
>DroYak_CAF1 287818 120 - 1
ACUGAAUGCAUUGCCGUGUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGUCUUCGCCCUCGACUUUUUACCCAAAAGUGGAUUCAAUUAA
..((((.(((..(((..(((((((((...(((.......)))...)))))))))((((((((.......)))))))))))..).))..((.((((((.....)))))).))))))..... ( -30.60)
>consensus
ACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGACUUCGCCCUCGGCUUUUUACCCAAAAGUGGAUUCAAUUAA
..(((((.(...((....((((((((...(.(((.....))).).))))))))(((((((((.......)))))))))......)).....((((((.....))))))).)))))..... (-28.76 = -28.36 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,070,527 – 5,070,647
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.92
Mean single sequence MFE -27.82
Consensus MFE -24.10
Energy contribution -24.46
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -2.44
Structure conservation index 0.87
SVM decision value 3.00
SVM RNA-class probability 0.998080
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5070527 120 + 23771897
UCCUGGAAAAAUGCUCUUUUCUUCCAGUAAGAGCGUUCCACUUUCAAUGCAUUCCACUCUUAUGGCGCAAUGCAUUCAGUUUACUCUUUCGCUCUCUUUUGGCCUUCGAACUGGGCUUUC
..(((((((((......))).))))))..((((((..........(((((((((((......)))...)))))))).............)))))).....(((((.......)))))... ( -27.30)
>DroSec_CAF1 277048 120 + 1
UCCUGGAAAAAUGCUCUUUUCUUCCAGUAAGAGCGUUCCAUUUUCAAUGCAUUCCACUCUUAUGGCGCAAUGCAUUCAGCUUACUCUUUCGCUCUCUUUUGGCCUUCGAACAGGGCUUUC
..(((((((((......))).))))))..((((((..........(((((((((((......)))...)))))))).............)))))).....((((((.....))))))... ( -27.50)
>DroSim_CAF1 298328 120 + 1
UCCUGGAAAAAUGCUCUUUUCUUCCAGUAAGAGCGUUCCACUUUCAAUGCAUUCCACUCUUAUGGCGCAAUGCAUUCAGUUUACUCUUUCGCUCUCUUUUGGCCUUCGAACAGGGCUUUC
..(((((((((......))).))))))..((((((..........(((((((((((......)))...)))))))).............)))))).....((((((.....))))))... ( -27.50)
>DroEre_CAF1 283954 120 + 1
ACCUGGAAAAACGCUCUUUUCUUCCAGUAAGAGCGUUCCACUUUCAAUGCAUUCCACUCUUAAAGGGCAAUGCAUUCAGUUUACUCUUUCGCUCUCUUUUGGCCUUCAAACUGGGGAUUC
.((((((...((((((((..........)))))))))))......((((((((((.((.....)))).))))))))((((((........(((.......)))....))))))))).... ( -29.00)
>DroYak_CAF1 287858 120 + 1
ACCUGGAAAAAUGCUCUUUUCUUCCAGUAAGAGCGUUCCACUUUCAAUGCAUUCCACUCUUACACGGCAAUGCAUUCAGUUUACUCUUUCGCUCUCUUUUGGCCUUCAAACUGGGCUUUC
..(((((((((......))).))))))..((((((..........((((((((((..........)).)))))))).............)))))).....(((((.......)))))... ( -27.80)
>consensus
UCCUGGAAAAAUGCUCUUUUCUUCCAGUAAGAGCGUUCCACUUUCAAUGCAUUCCACUCUUAUGGCGCAAUGCAUUCAGUUUACUCUUUCGCUCUCUUUUGGCCUUCGAACUGGGCUUUC
..(((((((((......))).))))))..((((((..........((((((((.(.((.....)).).)))))))).............)))))).....(((((.......)))))... (-24.10 = -24.46 +   0.36)

alignment

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secondary structure

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Window 4

Location 5,070,527 – 5,070,647
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.92
Mean single sequence MFE -33.92
Consensus MFE -31.16
Energy contribution -31.96
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.92
SVM decision value 4.41
SVM RNA-class probability 0.999891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5070527 120 - 23771897
GAAAGCCCAGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGA
....(((.........))).....(((((((....((....)).((((((((.((((....).))).))))))))..........))))))).(((((((((.......))))))))).. ( -34.80)
>DroSec_CAF1 277048 120 - 1
GAAAGCCCUGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAGCUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAAUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGA
....(.(((......))).)....(((((((....((....)).((((((((.((((....).))).))))))))..........))))))).(((((((((.......))))))))).. ( -35.70)
>DroSim_CAF1 298328 120 - 1
GAAAGCCCUGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGA
....(.(((......))).)....(((((((....((....)).((((((((.((((....).))).))))))))..........))))))).(((((((((.......))))))))).. ( -35.40)
>DroEre_CAF1 283954 120 - 1
GAAUCCCCAGUUUGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCCCUUUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCGUUUUUCCAGGU
..........((((.....)))).(((((((....((....)).((((((((.(((((...))).))))))))))..........))))))).(((((((((.......))))))))).. ( -31.10)
>DroYak_CAF1 287858 120 - 1
GAAAGCCCAGUUUGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCCGUGUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGU
....(((.........))).....(((((((....((....)).((((((((.(((........)))))))))))..........))))))).(((((((((.......))))))))).. ( -32.60)
>consensus
GAAAGCCCAGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAGUGGAACGCUCUUACUGGAAGAAAAGAGCAUUUUUCCAGGA
....(((.........))).....(((((((....((....)).((((((((.(((.......))).))))))))..........))))))).(((((((((.......))))))))).. (-31.16 = -31.96 +   0.80)

alignment

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secondary structure

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Window 5

Location 5,070,567 – 5,070,679
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.89
Mean single sequence MFE -32.38
Consensus MFE -24.43
Energy contribution -24.67
Covariance contribution 0.24
Combinations/Pair 1.11
Mean z-score -2.35
Structure conservation index 0.75
SVM decision value 1.10
SVM RNA-class probability 0.915714
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5070567 112 - 23771897
UGCGUUUCAUUCAAUGCAGCUAAAAGCUGGU--------UGAAAGCCCAGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAG
((((((((((((............((((((.--------(....).))))))....((((((.......(....).(((.......))).))).)))....))))))))))))....... ( -30.30)
>DroSec_CAF1 277088 112 - 1
UGCGUCUCAUUCAAUGCAGCUAAAAGCUGGU--------UGAAAGCCCUGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAGCUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAA
.((.((((.((((((.((((.....))))))--------)))).(.(((......))).)....))))))............(.((((((((.((((....).))).)))))))).)... ( -32.90)
>DroSim_CAF1 298368 112 - 1
UGCGUUUCAUUCAAUGCAGCUAAAAGCUGGU--------UGAAAGCCCUGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAG
.((.((((.((((((.((((.....))))))--------)))).(.(((......))).)....))))))............(.((((((((.((((....).))).)))))))).)... ( -30.30)
>DroEre_CAF1 283994 112 - 1
UGCGUUUCAUUCAAUGCAGCCAAAAGCUGGU--------UGAAUCCCCAGUUUGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCCCUUUAAGAGUGGAAUGCAUUGAAAG
((((((((((((......(((..(((((((.--------.......)))))))...)))....((((.((((....(((.......))).)))).))))..))))))))))))....... ( -32.80)
>DroYak_CAF1 287898 120 - 1
UGCAUUUCGUUCAAUGCAGCCAAAUGCUGGUUGACUGGUUGAAAGCCCAGUUUGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCCGUGUAAGAGUGGAAUGCAUUGAAAG
(((.((((((((...(((......)))(((((((((((.(....).))))))....))))).....))))))))..)))...(.((((((((.(((........))))))))))).)... ( -35.60)
>consensus
UGCGUUUCAUUCAAUGCAGCUAAAAGCUGGU________UGAAAGCCCAGUUCGAAGGCCAAAAGAGAGCGAAAGAGUAAACUGAAUGCAUUGCGCCAUAAGAGUGGAAUGCAUUGAAAG
(((((((((((((((((((((...((((((................))))))....)))..........(....)...........)))))).........))))))))))))....... (-24.43 = -24.67 +   0.24)

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 10:16:29 2006