Locus 288

Sequence ID 2R_DroMel_CAF1
Location 1,698,456 – 1,698,546
Length 90
Max. P 0.686664
window602 window603

overview

Window 2

Location 1,698,456 – 1,698,546
Length 90
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 82.34
Mean single sequence MFE -22.63
Consensus MFE -15.64
Energy contribution -16.17
Covariance contribution 0.53
Combinations/Pair 1.17
Mean z-score -1.88
Structure conservation index 0.69
SVM decision value 0.32
SVM RNA-class probability 0.686664
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1698456 90 + 20766785
GACUCCAACGCCGACUUUAGGCACCUGGCCCUCCGUUGACAUAACGGUUCAUUAUGUCAAAAUGAUUUAAUAAACCGCCCGGCCAAC-------CUC---
.........(((.......)))...(((((....((((...))))((((.((((.(((.....))).)))).))))....)))))..-------...--- ( -22.20)
>DroSec_CAF1 84283 97 + 1
GACUCCAACGCCGACUUCAGGCACCUGGCCCUCCGUUGACAUAACGGUUCAUUAUGUCAAAAUGAUUUAAUAAACCGCCCGGCCAACCGCCAGCCUC---
.........(((.......)))..(((((.....((((.(....(((((.((((.(((.....))).)))).)))))....).)))).)))))....--- ( -24.90)
>DroSim_CAF1 81760 97 + 1
GACUCCAACGCCGACUUCAGGCACCUGGCCCUCCGUUGACAUAACGGUUCAUUAUGUCAAAAUGAUUUAAUAAACCGCCCGGCCAACCGCCAGCCUC---
.........(((.......)))..(((((.....((((.(....(((((.((((.(((.....))).)))).)))))....).)))).)))))....--- ( -24.90)
>DroEre_CAF1 89748 91 + 1
GACUCCACUGCCGACUUCAGGCACCUGGCCCUCCGUUGACAUAACGGAUCAUUAUGUCAAAAUGAUUUAAUAAUCCGCCCGGCCAACC-----UUU----
........((((.......))))..(((((....((((...))))((((.((((.(((.....))).)))).))))....)))))...-----...---- ( -22.80)
>DroYak_CAF1 9891 92 + 1
GACUCCAACGCCGACUUCGAGCACCUGGCCCUCCGUUGACAUAACGGUUCAUUAUGUCAAAAUCAUUUAAUAAGCCGCGCGGGCAACA-----UUUC---
.........((((....)).)).....((((....(((((((((.......))))))))).............((...))))))....-----....--- ( -19.70)
>DroAna_CAF1 10815 96 + 1
-ACUCCAACAACUACUUUGC---UCUGGCCGUGUGUUGACAUAACGGUUCAUUGUGUCAAAGUGAUUUAAUAAACAGCACGGUCACUCUCUCACCUACCA
-...................---..(((((((((.(((((((((.......))))))))).((..........)).)))))))))............... ( -21.30)
>consensus
GACUCCAACGCCGACUUCAGGCACCUGGCCCUCCGUUGACAUAACGGUUCAUUAUGUCAAAAUGAUUUAAUAAACCGCCCGGCCAACC_____CCUC___
.........(((.......)))...(((((....((((...))))((((.((((.(((.....))).)))).))))....)))))............... (-15.64 = -16.17 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,698,456 – 1,698,546
Length 90
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 82.34
Mean single sequence MFE -30.09
Consensus MFE -20.48
Energy contribution -22.15
Covariance contribution 1.67
Combinations/Pair 1.18
Mean z-score -1.48
Structure conservation index 0.68
SVM decision value -0.03
SVM RNA-class probability 0.519596
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1698456 90 - 20766785
---GAG-------GUUGGCCGGGCGGUUUAUUAAAUCAUUUUGACAUAAUGAACCGUUAUGUCAACGGAGGGCCAGGUGCCUAAAGUCGGCGUUGGAGUC
---...-------((((((..((((((((((((..((.....))..))))))))))))..))))))......(((...(((.......)))..))).... ( -28.30)
>DroSec_CAF1 84283 97 - 1
---GAGGCUGGCGGUUGGCCGGGCGGUUUAUUAAAUCAUUUUGACAUAAUGAACCGUUAUGUCAACGGAGGGCCAGGUGCCUGAAGUCGGCGUUGGAGUC
---((.((((((.((((((..((((((((((((..((.....))..))))))))))))..))))))...((((.....))))...)))))).))...... ( -37.60)
>DroSim_CAF1 81760 97 - 1
---GAGGCUGGCGGUUGGCCGGGCGGUUUAUUAAAUCAUUUUGACAUAAUGAACCGUUAUGUCAACGGAGGGCCAGGUGCCUGAAGUCGGCGUUGGAGUC
---((.((((((.((((((..((((((((((((..((.....))..))))))))))))..))))))...((((.....))))...)))))).))...... ( -37.60)
>DroEre_CAF1 89748 91 - 1
----AAA-----GGUUGGCCGGGCGGAUUAUUAAAUCAUUUUGACAUAAUGAUCCGUUAUGUCAACGGAGGGCCAGGUGCCUGAAGUCGGCAGUGGAGUC
----...-----.((((((..((((((((((((..((.....))..))))))))))))..))))))......(((..((((.......)))).))).... ( -30.10)
>DroYak_CAF1 9891 92 - 1
---GAAA-----UGUUGCCCGCGCGGCUUAUUAAAUGAUUUUGACAUAAUGAACCGUUAUGUCAACGGAGGGCCAGGUGCUCGAAGUCGGCGUUGGAGUC
---....-----.....((.(((((((((...........(((((((((((...)))))))))))....((((.....)))).))))).)))).)).... ( -27.80)
>DroAna_CAF1 10815 96 - 1
UGGUAGGUGAGAGAGUGACCGUGCUGUUUAUUAAAUCACUUUGACACAAUGAACCGUUAUGUCAACACACGGCCAGA---GCAAAGUAGUUGUUGGAGU-
((((..(((..(((((((.................)))))))((((.((((...)))).))))..)))...)))).(---((((.....))))).....- ( -19.13)
>consensus
___GAGG_____GGUUGGCCGGGCGGUUUAUUAAAUCAUUUUGACAUAAUGAACCGUUAUGUCAACGGAGGGCCAGGUGCCUGAAGUCGGCGUUGGAGUC
.............((((((..((((((((((((..((.....))..))))))))))))..))))))......(((.(((((.......)))))))).... (-20.48 = -22.15 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:38 2006