Locus 2972

Sequence ID 2L_DroMel_CAF1
Location 8,511,236 – 8,511,375
Length 139
Max. P 0.865595
window4719 window4720

overview

Window 9

Location 8,511,236 – 8,511,335
Length 99
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 84.34
Mean single sequence MFE -26.42
Consensus MFE -16.42
Energy contribution -16.82
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.62
SVM decision value 0.59
SVM RNA-class probability 0.791918
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8511236 99 - 22407834
AAGCCAAAAAAGAGCCAGCACCAGCAAAGAAGUCUGUGCAAGAUCCCGUACCUUCUAUUAAGAAGG------------UUCCUGCAGCUAAAAAGUCAGGACAAACUGC------UG
...............(((((...(((.((....)).)))..........(((((((....))))))------------)(((((..(((....)))))))).....)))------)) ( -23.40)
>DroSec_CAF1 20403 99 - 1
AAGCCAAAAAAGAGCAAGCACCAGCAAAGAAGUCUGUGCAAGAUCCCGUACCUUCUAUAAAGAAGG------------UUCCUGCAGCUAAAAAGUCAGGACAAACUGC------UG
............((((.((((..((......))..))))..........(((((((....))))))------------)(((((..(((....)))))))).....)))------). ( -24.20)
>DroSim_CAF1 20075 99 - 1
AAGCAAAAAAAGAGCAAGCACCAGCAAAGAAGUCUGUGCAAGAUCCCGUACCUUCUAUAAAGAAGG------------UUCCUGCAGCUAAAAAGUCAGGACAAACUGC------UG
............((((.((((..((......))..))))..........(((((((....))))))------------)(((((..(((....)))))))).....)))------). ( -24.20)
>DroEre_CAF1 19981 117 - 1
AAGCCAAAAAAGAGCAAGCACCAGCCAAGAAGUCUGUCCAACAACCCGCACCUUCUAUAAAGAAGGCUGCCCAGGUAGCUCCUGCUGCUAAGAAGUCAGGACAAACUAAAAAGACUG
..(((......).))......((((.....(((.(((((........(((((((((....)))))).)))...((((((....)))))).........))))).))).....).))) ( -30.40)
>DroYak_CAF1 20947 111 - 1
AAGCCAAAAAAGAGCAAGCACCAGCCAAGAAGUCUGUCCAAGAUCCCGCACCUUCUACUAAGAAGGCUGCCCAAGUGGCUCCUGAAGCUAAAAAGUCAGGACAAACUGC------UU
..(((......).))(((((...((((.(..((((.....))))..)(((((((((....)))))).))).....))))((((((..........)))))).....)))------)) ( -29.90)
>consensus
AAGCCAAAAAAGAGCAAGCACCAGCAAAGAAGUCUGUGCAAGAUCCCGUACCUUCUAUAAAGAAGG____________UUCCUGCAGCUAAAAAGUCAGGACAAACUGC______UG
.................((((..((......))..))))...........((((((....)))))).............(((((..(((....))))))))................ (-16.42 = -16.82 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,511,267 – 8,511,375
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.62
Mean single sequence MFE -31.04
Consensus MFE -24.11
Energy contribution -24.86
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.78
SVM decision value 0.85
SVM RNA-class probability 0.865595
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8511267 108 + 22407834
AA------------CCUUCUUAAUAGAAGGUACGGGAUCUUGCACAGACUUCUUUGCUGGUGCUGGCUCUUUUUUGGCUUUCACAGGAGCAGCUUUAGUCUUUUUCUCUUGCUUUUUCGG
.(------------((((((....))))))).((..(....(((.(((.......(((((.((((.(((((...((.....)).))))))))).))))).......))))))..)..)). ( -29.94)
>DroSec_CAF1 20434 108 + 1
AA------------CCUUCUUUAUAGAAGGUACGGGAUCUUGCACAGACUUCUUUGCUGGUGCUUGCUCUUUUUUGGCUUCCACAGGAGCAGCUUUAGUCUUUUUCACUUGCUUUUUCGG
.(------------((((((....))))))).((..(....(((.((........(((((.(((.((((((...(((...))).))))))))).)))))........)))))..)..)). ( -30.09)
>DroSim_CAF1 20106 108 + 1
AA------------CCUUCUUUAUAGAAGGUACGGGAUCUUGCACAGACUUCUUUGCUGGUGCUUGCUCUUUUUUUGCUUCCACAGGAGCAGCUUUAGUCUUUUUCACUUGCUUUUUCGG
.(------------((((((....))))))).((..(....(((.((........(((((.(((.((((((.............))))))))).)))))........)))))..)..)). ( -27.81)
>DroYak_CAF1 20978 120 + 1
AGCCACUUGGGCAGCCUUCUUAGUAGAAGGUGCGGGAUCUUGGACAGACUUCUUGGCUGGUGCUUGCUCUUUUUUGGCUUCAACAGGAGCAGCUUUAGUCUUUUUCUCUUGCUUUUUCGG
.(((.....))).(((((((....)))))))(((((((((.....)))......((((((.(((.((((((..(((....))).))))))))).))))))......))))))........ ( -36.30)
>consensus
AA____________CCUUCUUAAUAGAAGGUACGGGAUCUUGCACAGACUUCUUUGCUGGUGCUUGCUCUUUUUUGGCUUCCACAGGAGCAGCUUUAGUCUUUUUCACUUGCUUUUUCGG
..............((((((....))))))..((..(....(((.(((.......(((((.(((.((((((.............))))))))).))))).......))))))..)..)). (-24.11 = -24.86 +   0.75)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:57 2006