Locus 8834

Sequence ID 3R_DroMel_CAF1
Location 23,647,478 – 23,647,571
Length 93
Max. P 0.890051
window14183 window14184

overview

Window 3

Location 23,647,478 – 23,647,571
Length 93
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 77.67
Mean single sequence MFE -22.28
Consensus MFE -9.23
Energy contribution -9.40
Covariance contribution 0.17
Combinations/Pair 1.11
Mean z-score -2.63
Structure conservation index 0.41
SVM decision value 0.96
SVM RNA-class probability 0.890051
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23647478 93 + 27905053
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCA--CAAAACUGCAA------CACA-UUGCAGCUGGAACAGCACCAGAGGCAAACUAACU
........((((((........)))))).....((((((.(((.--.....((((((------....-))))))((((.......)))).)))...)))))) ( -24.50)
>DroVir_CAF1 148860 84 + 1
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCA--CAAAACUGUAACUGCAGCACA-CUGCUG---CAUCACAGGCC---------CA---
.((...(((((((((......((((.....))))))))))).))--.....((((...((((((...-..))))---))..))))..)---------).--- ( -24.70)
>DroPse_CAF1 111993 82 + 1
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCACACAAAAGUGUAA------CACAGCUGCAGCUGUAACAGAA--------------ACA
.(....(((((((((......((((.....))))))))))((.((((....)))).)------)(((((....))))).)))...--------------.). ( -20.30)
>DroMoj_CAF1 158276 84 + 1
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCA--CAAAACUGUAACUGCAGCACG-CUGCGG---CAUCACAGGCU---------CG---
......(((((((((......((((.....))))))))))).))--.....((((..((((((....-))))))---....))))...---------..--- ( -21.30)
>DroAna_CAF1 110420 84 + 1
GGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCA--CAAAACUGCAA------CACA-CUGCAGCUGGAACAGAAGCG---------CCACU
........((((((........)))))).....(((.(((((..--.....(((((.------....-.)))))(((...)))..)))---------))))) ( -22.60)
>DroPer_CAF1 110321 82 + 1
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCACACAAAAGUGUAA------CACAGCUGCAGCUGUAACAGAA--------------ACA
.(....(((((((((......((((.....))))))))))((.((((....)))).)------)(((((....))))).)))...--------------.). ( -20.30)
>consensus
AGGAUAUGUGCCAAUAAAAAGUUUGGCAAACAAAGUUGGCGUCA__CAAAACUGUAA______CACA_CUGCAGCUGCAACAGAAGC__________C_AC_
......(((((((((......((((.....))))))))))).)).......(((((.............)))))............................ ( -9.23 =  -9.40 +   0.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,647,478 – 23,647,571
Length 93
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 77.67
Mean single sequence MFE -23.83
Consensus MFE -7.50
Energy contribution -7.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.31
SVM decision value -0.04
SVM RNA-class probability 0.513479
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23647478 93 - 27905053
AGUUAGUUUGCCUCUGGUGCUGUUCCAGCUGCAA-UGUG------UUGCAGUUUUG--UGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
((((...((((..((((.......))))..))))-.(((------(..(......)--..)))).)))).(((.((((((........)))))).))).... ( -24.00)
>DroVir_CAF1 148860 84 - 1
---UG---------GGCCUGUGAUG---CAGCAG-UGUGCUGCAGUUACAGUUUUG--UGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
---..---------(((......((---((((..-...))))))(((((......)--))))))).....(((.((((((........)))))).))).... ( -27.30)
>DroPse_CAF1 111993 82 - 1
UGU--------------UUCUGUUACAGCUGCAGCUGUG------UUACACUUUUGUGUGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
...--------------....((((((((....)))))(------((((((....)))))))...)))..(((.((((((........)))))).))).... ( -23.10)
>DroMoj_CAF1 158276 84 - 1
---CG---------AGCCUGUGAUG---CCGCAG-CGUGCUGCAGUUACAGUUUUG--UGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
---((---------((.(((((((.---..((((-....)))).))))))).))))--............(((.((((((........)))))).))).... ( -22.50)
>DroAna_CAF1 110420 84 - 1
AGUGG---------CGCUUCUGUUCCAGCUGCAG-UGUG------UUGCAGUUUUG--UGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCC
..(((---------((..((......((((((((-....------))))))))...--.)))))))....(((.((((((........)))))).))).... ( -23.00)
>DroPer_CAF1 110321 82 - 1
UGU--------------UUCUGUUACAGCUGCAGCUGUG------UUACACUUUUGUGUGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
...--------------....((((((((....)))))(------((((((....)))))))...)))..(((.((((((........)))))).))).... ( -23.10)
>consensus
_GU_G__________GCUUCUGUUACAGCUGCAG_UGUG______UUACAGUUUUG__UGACGCCAACUUUGUUUGCCAAACUUUUUAUUGGCACAUAUCCU
......................................................................(((.((((((........)))))).))).... ( -7.50 =  -7.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:50 2006