Locus 753

Sequence ID 2R_DroMel_CAF1
Location 3,665,734 – 3,665,878
Length 144
Max. P 0.985951
window1311 window1312

overview

Window 1

Location 3,665,734 – 3,665,842
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.70
Mean single sequence MFE -28.88
Consensus MFE -17.84
Energy contribution -18.65
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -2.00
Structure conservation index 0.62
SVM decision value 0.51
SVM RNA-class probability 0.764140
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3665734 108 + 20766785
GAUGGAAAACAUGCAGAUUCAUUC---ACACCAGUUCCGAGUACAUCUG---AUACUGAUUGCAAAAACGUUAGUGCAGUAAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA------
..........((((((((..((((---...........))))..))))(---.((((.(((((....((((..(((((((...)))))))))))...))))).)))))))))..------ ( -26.80)
>DroEre_CAF1 13476 108 + 1
GAUGGGAAACAUGCAGAUUCAUUC---GCACCAGUUCCGAGUACAUCUA---ACACUGAUUGGAAAAACGUUAGUGCAGUGAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA------
....(....)((((..((((((((---((((...((((((...((....---....)).))))))........(((((((...)))))))..))))))..))))))..))))..------ ( -30.30)
>DroYak_CAF1 14244 108 + 1
GAUGGAAAACAUGCAGAUUCAUUC---GCACCAGUUGCGAGUACAUCUG---AUACUGAUUGGAAAAACAUUAGUGCAGUGAUAUUGCACAUGUGAUGCAAUGAGUGCGCAUAA------
..........((((((((..((((---(((.....)))))))..))))(---.((((.((((.(...((((..(((((((...)))))))))))..).)))).)))))))))..------ ( -31.00)
>DroAna_CAF1 11991 116 + 1
----GACUAUCUGCAGAUUCAUUCUGAGCACUAAUUCAAAGUAUAUCAAGACAUACUUAUUGUAAAAACGCUAUUGCAAUGAUAUUGCACAUGUGCGCCCGUGAGUGCGCAUAAAAAAAA
----.......(((((..((((((..(((.........((((((........))))))...((....)))))...).)))))..)))))..(((((((.(....).)))))))....... ( -27.40)
>consensus
GAUGGAAAACAUGCAGAUUCAUUC___GCACCAGUUCCGAGUACAUCUA___AUACUGAUUGGAAAAACGUUAGUGCAGUGAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA______
..........((((((((..((((...((....))...))))..)))).....((((.((((.....((((..(((((((...)))))))))))....)))).)))).))))........ (-17.84 = -18.65 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,665,771 – 3,665,878
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.46
Mean single sequence MFE -28.80
Consensus MFE -21.24
Energy contribution -20.86
Covariance contribution -0.37
Combinations/Pair 1.23
Mean z-score -3.05
Structure conservation index 0.74
SVM decision value 2.02
SVM RNA-class probability 0.985951
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3665771 107 + 20766785
GUACAUCUG---AUACUGAUUGCAAAAACGUUAGUGCAGUAAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA---------AAAGCGCAAAGUACGGCCAUAAA-AAGCACAGUUAAA
((((.....---..(((.(((((....((((..(((((((...)))))))))))...))))).)))((((....---------...))))...)))).((......-..))......... ( -30.40)
>DroEre_CAF1 13513 107 + 1
GUACAUCUA---ACACUGAUUGGAAAAACGUUAGUGCAGUGAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA---------AAAGCGCAAAGUAUGGCCAUAAA-AAGCACAGUUAAA
(((((((((---(......))))).........(((((((...))))))).)))))(((.(((..(((((....---------...)))))...))).))).....-............. ( -29.60)
>DroYak_CAF1 14281 107 + 1
GUACAUCUG---AUACUGAUUGGAAAAACAUUAGUGCAGUGAUAUUGCACAUGUGAUGCAAUGAGUGCGCAUAA---------AAAGCGCAAAGUACGGCCAUAAA-AAGCACAGUUAAA
((((.....---..(((.((((.(...((((..(((((((...)))))))))))..).)))).)))((((....---------...))))...)))).((......-..))......... ( -27.00)
>DroAna_CAF1 12027 120 + 1
GUAUAUCAAGACAUACUUAUUGUAAAAACGCUAUUGCAAUGAUAUUGCACAUGUGCGCCCGUGAGUGCGCAUAAAAAAAAAAAAAAGCGCAAAGUGCGGCCAUAAAAAAGCACAGUUAAG
.........(((.(((.....)))....((((..((((((...))))))..(((((((.(....).)))))))............))))....((((............)))).)))... ( -28.20)
>consensus
GUACAUCUA___AUACUGAUUGGAAAAACGUUAGUGCAGUGAUAUUGCACAUGUGCGGCAAUGAGUGCGCAUAA_________AAAGCGCAAAGUACGGCCAUAAA_AAGCACAGUUAAA
((((..........(((.((((.....((((..(((((((...)))))))))))....)))).)))((((................))))...))))....................... (-21.24 = -20.86 +  -0.37)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:17 2006