Locus 3610

Sequence ID X_DroMel_CAF1
Location 9,668,295 – 9,668,454
Length 159
Max. P 0.971610
window5907 window5908 window5909

overview

Window 7

Location 9,668,295 – 9,668,414
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 90.91
Mean single sequence MFE -33.68
Consensus MFE -25.30
Energy contribution -26.58
Covariance contribution 1.28
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.75
SVM decision value 0.64
SVM RNA-class probability 0.809161
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9668295 119 - 22224390
AUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGUGGGGUUUUUUAAGGGGAGACCUUGAAUAUCUCCCAACGGGAGUCCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUCGA
...((((..((..((((((((((.............((((((...(((((((.....)))))))...(((((...)))))))))))...(....).))..))))))))..))..)))). ( -31.90)
>DroSec_CAF1 3906 119 - 1
AUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGGGGAGUUUUUUGAGGGGAGACCUUGAAUAUCUCCCAACGGGAGACCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUCGA
.((..(((..(((((((.((((...............(((((....((.((((....)))).))...)))))...((....))))))..))))).)).....)))..)).......... ( -35.50)
>DroSim_CAF1 17490 117 - 1
AUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGAGGGGUU-UUUGAAGGGAGACCUUGAAUAUCUCCCAACGGGAGACCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUC-A
.((..(((..(((((((.(((((.....................-.((.((((....)))).))..((((((...)))))).)))))..))))).)).....)))..))........-. ( -32.30)
>DroEre_CAF1 10792 118 - 1
AUGUGAAUAAACAGCGAGUGUGGAAUGGAUGAAAAAGGGG-GUUUUUUGCGGGGAGACCUUGAAUAUCUCCCAACGGGAGACCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUCGA
...((((..((..((((((((....(((..((...((.((-((((((((..((((((.........))))))..)))))))))).....)).))..))).))))))))..))..)))). ( -38.30)
>DroYak_CAF1 15022 104 - 1
AUGUGAAUAAACAGCGGGUGUGGAAUGAAUGAAAAAGGGG---------------AACCUUGAAUAUCUCCCAACGGGAGACCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUCGA
.((..(((...((((((.(((((...........((((..---------------..)))).....((((((...)))))).)))))..)))))).......)))..)).......... ( -30.40)
>consensus
AUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGGGG_GUUUUUUGAGGGGAGACCUUGAAUAUCUCCCAACGGGAGACCCACAAACUGUUGGCCAAACAUUUGCAAUUCUUUCGA
.((..(((...((((((.(((((..........................((((....)))).....((((((...)))))).)))))..)))))).......)))..)).......... (-25.30 = -26.58 +   1.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,668,334 – 9,668,454
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.27
Mean single sequence MFE -30.33
Consensus MFE -22.21
Energy contribution -23.13
Covariance contribution 0.92
Combinations/Pair 1.16
Mean z-score -2.85
Structure conservation index 0.73
SVM decision value 1.68
SVM RNA-class probability 0.971610
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9668334 120 + 22224390
CUCCCGUUGGGAGAUAUUCAAGGUCUCCCCUUAAAAAACCCCACUUUUUCAUUCAUUCCACACCCGCUGCUUAUUCACAUUCGUUUUUAUUUUUUGUUACUGAAUGUGGGGGAGAUGAAA
(((((...(((((((.......))))))).............................................(((((((((.(..((.....))..).))))))))))))))...... ( -27.90)
>DroSec_CAF1 3945 118 + 1
CUCCCGUUGGGAGAUAUUCAAGGUCUCCCCUCAAAAAACUCCCCUUUUUCAUUCAUUCCACACCCGCUGCUUAUUCACAUUCGUUUUUAUUUUUUGUUACUGGGUGUGGGGG--AUGAAA
.....(..(((((((.......)))))))..)..............((((((((...(((((((((..((.........................))...))))))))).))--)))))) ( -33.61)
>DroSim_CAF1 17528 117 + 1
CUCCCGUUGGGAGAUAUUCAAGGUCUCCCUUCAAA-AACCCCUCUUUUUCAUUCAUUCCACACCCGCUGCUUAUUCACAUUCGUUUUUAUUUUUUGUUACUGGGUGUGGGGG--AUGAAA
.....(..(((((((.......)))))))..)...-..........((((((((...(((((((((..((.........................))...))))))))).))--)))))) ( -33.21)
>DroEre_CAF1 10831 117 + 1
CUCCCGUUGGGAGAUAUUCAAGGUCUCCCCGCAAAAAAC-CCCCUUUUUCAUCCAUUCCACACUCGCUGUUUAUUCACAUUCGUUUUUAUUUUUCGCUUCUGGGUGUGAGGA--AUGAAA
.....((.(((((((.......))))))).)).......-.............(((((((((.....)))....(((((((((.................))))))))))))--)))... ( -27.63)
>DroYak_CAF1 15061 103 + 1
CUCCCGUUGGGAGAUAUUCAAGGUU---------------CCCCUUUUUCAUUCAUUCCACACCCGCUGUUUAUUCACAUUCGGUUUUAUUUUUGGUUUCUGGGUGUGAGGG--AUGAAU
(((((...)))))......((((..---------------..))))....((((((((((((.....)))....((((((((((..(((....)))...)))))))))))))--)))))) ( -29.30)
>consensus
CUCCCGUUGGGAGAUAUUCAAGGUCUCCCCUCAAAAAAC_CCCCUUUUUCAUUCAUUCCACACCCGCUGCUUAUUCACAUUCGUUUUUAUUUUUUGUUACUGGGUGUGGGGG__AUGAAA
........(((((((.......)))))))..................(((((...(((((((((((..((.........................))...)))))))))))...))))). (-22.21 = -23.13 +   0.92)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,668,334 – 9,668,454
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.27
Mean single sequence MFE -32.64
Consensus MFE -23.07
Energy contribution -23.59
Covariance contribution 0.52
Combinations/Pair 1.19
Mean z-score -2.95
Structure conservation index 0.71
SVM decision value 1.47
SVM RNA-class probability 0.956873
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9668334 120 - 22224390
UUUCAUCUCCCCCACAUUCAGUAACAAAAAAUAAAAACGAAUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGUGGGGUUUUUUAAGGGGAGACCUUGAAUAUCUCCCAACGGGAG
......(((((((((((((.((..............))...(((......)))..))))))))..............(((((...(((((((.....)))))))...).))))..))))) ( -31.64)
>DroSec_CAF1 3945 118 - 1
UUUCAU--CCCCCACACCCAGUAACAAAAAAUAAAAACGAAUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGGGGAGUUUUUUGAGGGGAGACCUUGAAUAUCUCCCAACGGGAG
.....(--(((((((((((.((..............))...(((......)))..))))))))..............(((((....((.((((....)))).))...)))))...)))). ( -39.64)
>DroSim_CAF1 17528 117 - 1
UUUCAU--CCCCCACACCCAGUAACAAAAAAUAAAAACGAAUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGAGGGGUU-UUUGAAGGGAGACCUUGAAUAUCUCCCAACGGGAG
.....(--(((((((((((.((..............))...(((......)))..)))))))).............(.((((..-.((.((((....)))).))...)))))...)))). ( -36.14)
>DroEre_CAF1 10831 117 - 1
UUUCAU--UCCUCACACCCAGAAGCGAAAAAUAAAAACGAAUGUGAAUAAACAGCGAGUGUGGAAUGGAUGAAAAAGGGG-GUUUUUUGCGGGGAGACCUUGAAUAUCUCCCAACGGGAG
.(((((--(((.(((...(......)...........((..(((......))).)).))).)))))))).......((((-(...((((.(((....)))))))...)))))........ ( -28.70)
>DroYak_CAF1 15061 103 - 1
AUUCAU--CCCUCACACCCAGAAACCAAAAAUAAAACCGAAUGUGAAUAAACAGCGGGUGUGGAAUGAAUGAAAAAGGGG---------------AACCUUGAAUAUCUCCCAACGGGAG
((((((--...((((((((.(....)...............(((......)))..)))))))).))))))....((((..---------------..))))......(((((...))))) ( -27.10)
>consensus
UUUCAU__CCCCCACACCCAGUAACAAAAAAUAAAAACGAAUGUGAAUAAGCAGCGGGUGUGGAAUGAAUGAAAAAGGGG_GUUUUUUGAGGGGAGACCUUGAAUAUCUCCCAACGGGAG
((((((.....((((((((.(................)...(((......)))..)))))))).....))))))...............((((....))))......(((((...))))) (-23.07 = -23.59 +   0.52)

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 11:03:41 2006