Locus 3423

Sequence ID 3R_DroMel_CAF1
Location 9,300,328 – 9,300,450
Length 122
Max. P 0.778938
window5491 window5492

overview

Window 1

Location 9,300,328 – 9,300,422
Length 94
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.73
Mean single sequence MFE -32.60
Consensus MFE -22.33
Energy contribution -22.13
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.68
SVM decision value 0.55
SVM RNA-class probability 0.778938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9300328 94 + 27905053
----------------------GGCCAACUUCCCUCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCACAGAU
----------------------.(((.....(((((.((..(((((((((((...((((((((.....))))))))....))))...)))))))..)).)).)))..)))...... ( -28.90)
>DroPse_CAF1 69638 114 + 1
CCAUCUCCGUUGCAGUUGCCGUUGCC--GUUGCCCCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAGCAUAAUUUUUCGGCAAUUUAUUGCGUGUUUGUAUGGGCGGGCCCGGAU
.....(((...(((((....((((((--((((((.((((((....)))))).)))))((((((.....))))))....)))))))..)))))..........(((....)))))). ( -37.70)
>DroSec_CAF1 71475 94 + 1
----------------------GGCCAACUUCCCUCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGUGGGCACAGAU
----------------------.(((.....(((((.((..(((((((((((...((((((((.....))))))))....))))...)))))))..)).)).)))..)))...... ( -29.60)
>DroEre_CAF1 72386 94 + 1
----------------------UGCCAACUUCCCUCGAAUUGCGCAAUUUGUGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCUCGAAU
----------------------.(((.....(((((.((..(((((((..((.((((((((((.....))))))))....)).))..)))))))..)).)).)))..)))...... ( -28.10)
>DroAna_CAF1 70354 100 + 1
GCA---------CAG-------UGGCAAGUUGCCUCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGUGCAAUUUAUUGCGUGUUUGGAUGGGUGGGCACAGAU
(((---------(((-------(.((((((((((.......).))))))))).))((((((((.....)))))))).)))))..........((((..(......)..)))).... ( -33.00)
>DroPer_CAF1 72713 114 + 1
CCAGCGCCAUCUCCGUUGCCGUUGCC--GUUGCCCCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAGCAUAAUUUUUCGGCAAUUUAUUGCGUGUUUGUAUGGGCGGGCCCGGAU
.(((((.......)))))(((..(((--..((((((((((.(((((((((((((.((((((((.....)))))))).)).))))...))))))))))))...)))))))).))).. ( -38.30)
>consensus
______________________UGCCAACUUCCCUCGAAUUGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCACAGAU
.......................(((......((((((((.(((((((((((...((((((((.....))))))))....))))...))))))))))))...)))..)))...... (-22.33 = -22.13 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,300,346 – 9,300,450
Length 104
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 82.11
Mean single sequence MFE -28.17
Consensus MFE -20.35
Energy contribution -20.10
Covariance contribution -0.25
Combinations/Pair 1.14
Mean z-score -1.37
Structure conservation index 0.72
SVM decision value 0.02
SVM RNA-class probability 0.546042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9300346 104 + 27905053
UGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCACAGAUUGUGGGUAAAGUGGGCGUGGCAAUGGG----C
..((((((((((((.(((((((.(((((......))))).))))))).))))(((((((......))))))))))))))).((...(....)...))......----. ( -27.40)
>DroPse_CAF1 69676 87 + 1
UGCGCAAUUUGCGGCAAGUUGUGUAAAGCAUAAUUUUUCGGCAAUUUAUUGCGUGUUUGUAUGGGCGGGCCCGGAUUGUGA-----------------CUGGG----U
.(((((((((((((.((((((((.....)))))))).)).))))...)))))))((((....))))..((((((.......-----------------)))))----) ( -26.30)
>DroEre_CAF1 72404 103 + 1
UGCGCAAUUUGUGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCUCGAAUUGUGGGCAAA-UGGGCGUGGCAAUGGG----C
.(((((((..((.((((((((((.....))))))))....)).))..)))))))((..(....(.((.(((((..(((....))).-))))).)).)..)..)----) ( -27.10)
>DroYak_CAF1 72375 104 + 1
UGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCACAGAUUGUGGGUAAAGUGGGAGUGGCACUGGG----C
..((((((((((((.(((((((.(((((......))))).))))))).))))(((((((......))))))))))))))).((..((((.......))))..)----) ( -30.80)
>DroAna_CAF1 70378 105 + 1
UGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGUGCAAUUUAUUGCGUGUUUGGAUGGGUGGGCACAGAUUGUAGGCCAG---AGGGUGGCUCUGAGGCAAC
((((((((((((((.((((((..(((((......)))))..)))))).))))((((..(......)..)))))))))))....(((---((.....)))))..))).. ( -32.20)
>DroPer_CAF1 72751 87 + 1
UGCGCAAUUUGCGGCAAGUUGUGUAAAGCAUAAUUUUUCGGCAAUUUAUUGCGUGUUUGUAUGGGCGGGCCCGGAUUGUGA-----------------CUGGG----A
.(((((((((((((.((((((((.....)))))))).)).))))...)))))))((((....))))...(((((.......-----------------)))))----. ( -25.20)
>consensus
UGCGCAAUUUGCGGCAAGUUGUGUAAAACAUAAUUUUUGGGCAAUUUAUUGCGUGUUUGGAUGGGCGGGCACAGAUUGUGGG_AAA___GG_GUGGCACUGGG____C
..(((((((((.(.((((((((.(((((......))))).)))))))..(((.(((....))).)))).).)))))))))............................ (-20.35 = -20.10 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:36 2006