Locus 6261

Sequence ID 2R_DroMel_CAF1
Location 19,650,120 – 19,650,308
Length 188
Max. P 0.904300
window10017 window10018

overview

Window 7

Location 19,650,120 – 19,650,237
Length 117
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 86.88
Mean single sequence MFE -41.38
Consensus MFE -32.50
Energy contribution -34.25
Covariance contribution 1.75
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.79
SVM decision value 1.04
SVM RNA-class probability 0.904300
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19650120 117 - 20766785
GCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCGCAAACCUAGCGAAA--AGGAUUCAAAGGAUCUGCUGUUGUUGCAAGCAACAGUGAACAAUAAGCUUUGGCCUCAUCCUCCAA
((((((((((((((...)))))))...(((((((.......)))))))...--.(((((.....)))))((((((((.....)))))))).........)).)))))............ ( -41.70)
>DroSec_CAF1 6887 117 - 1
GCCAGGCGGCGGAUAAUGCCUGCCAUCUGCUGGGGCGCAAACCCAGCGAAA--AGGAUUCAAAGGAUAUGCUGUUGUUGCAAGCAACAGUGAACAAUAAGCUCUGGCCUCCUCCUCCAA
((((((((((((.......)))))((((((((((.......))))))(((.--....)))...))))..((((((((.....)))))))).........)).)))))............ ( -43.50)
>DroEre_CAF1 6943 115 - 1
GCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCACAAACCGGGCGAAAAGAGGAUUCCCAGGAUCUGCUGUUGUUGCAAGCAACAGUGAACAAUGAGCUCCAGCCCC----UUCCA
...(((.(((((((...)))))))....((((((((.((..((.((.(((.......))))).)).((.((((((((.....))))))))))....)).)))))))).))----).... ( -42.60)
>DroYak_CAF1 7155 116 - 1
GCCAGCCAGCGGAUAAUGUCUGCCAUCUGCUGGGACAGAAGACGGGCGAAAAAAGGAUUCAAAGGAUCUGCUGUUGUUGCAAGCAACAGUGAACAAUGAGCUCUGGCCUCC---UCCUA
((((.(((((((((..........)))))))))..........((((.......(((((.....)))))((((((((.....)))))))).........))))))))....---..... ( -37.70)
>consensus
GCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCACAAACCGAGCGAAA__AGGAUUCAAAGGAUCUGCUGUUGUUGCAAGCAACAGUGAACAAUAAGCUCUGGCCUCC___UCCAA
(((((((((((((.....))))))...(((((((.......)))))))......(((((.....)))))((((((((.....)))))))).........)).)))))............ (-32.50 = -34.25 +   1.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,650,197 – 19,650,308
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.89
Mean single sequence MFE -35.33
Consensus MFE -26.33
Energy contribution -27.45
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.66
Structure conservation index 0.75
SVM decision value 0.31
SVM RNA-class probability 0.684154
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19650197 111 - 20766785
CACCGCUGAAA-GGAUGUCUGAAAUCCCGACCAAUUCAAUCCGGGCUAGUUAC-------CAUUGAAAUGCAA-AUCCCAGCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCGCAA
...(((.....-((((.......))))....((.((((((..((........)-------))))))).))...-..((((((.((..(((((((...)))))))..)))))))))))... ( -35.70)
>DroSec_CAF1 6964 100 - 1
------------GGAUGUCUGAAAUCCCGACCAAUUCAAUCCGGGCUAGUUAC-------CAUUGAAAUGCAA-AUCCCAGCCAGGCGGCGGAUAAUGCCUGCCAUCUGCUGGGGCGCAA
------------((((.......)))).......((((((..((........)-------))))))).(((..-.(((((((.((..(((((.......)))))..))))))))).))). ( -33.10)
>DroEre_CAF1 7018 120 - 1
CGCCGCUGAAAGGGAUGUCUGAAAUCCCGACCAAUUCAAACCGGGCUAGUUACUGAAAUGCAUUGAAAUGCAAAAUCCCAGCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCACAA
.(((((.....(((((.......)))))...((((.((...(((........)))...)).))))....))......(((((.((..(((((((...)))))))..)))))))))).... ( -40.70)
>DroYak_CAF1 7231 110 - 1
---CGCUGAAAGGGAUGUCUGAAAUCCCGACCAAUUCAAUCCGGGCUAGUUAC-------CAUUGAAAUGCAAAAUUCCAGCCAGCCAGCGGAUAAUGUCUGCCAUCUGCUGGGACAGAA
---..(((...(((((.......)))))...((.((((((..((........)-------))))))).)).....(((((((.((...((((((...))))))...)))))))))))).. ( -31.80)
>consensus
___CGCUGAAA_GGAUGUCUGAAAUCCCGACCAAUUCAAUCCGGGCUAGUUAC_______CAUUGAAAUGCAA_AUCCCAGCCAGGCGGCGGAUAAUGUCUGCCAUCUGCUGGGGCACAA
...........(((((.......)))))...((.((((((.....................)))))).)).....(((((((.(((.((((((.....)))))).))))))))))..... (-26.33 = -27.45 +   1.12)

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 12:06:52 2006