Locus 2410

Sequence ID 2L_DroMel_CAF1
Location 6,569,667 – 6,569,778
Length 111
Max. P 0.638514
window3878 window3879

overview

Window 8

Location 6,569,667 – 6,569,778
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 84.21
Mean single sequence MFE -39.40
Consensus MFE -23.42
Energy contribution -26.06
Covariance contribution 2.64
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.59
SVM decision value 0.06
SVM RNA-class probability 0.562997
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6569667 111 + 22407834
CGACCUUUCGGUCUAAAAAUAAGCGCCUUUGCACCGACACACAGACAGGCCGCUCCACGUGCCACGCCCCACGCCCCACUGGCCAGGUGGGCGGCGUGGAAAUGUGUGUGC
.((((....)))).........(((....)))....(((((((..((.(((((.((((.(((((.((.....)).....))).)).))))))))).))....))))))).. ( -43.30)
>DroSec_CAF1 41758 96 + 1
CGACCUUUCGGUCUAAAAAUAAGCGCCUU--------CACACAGACAGGCCGCUCCACGUGCCACG-------CCCCACUGGCCAGGUGGGCGGCGUGGACAGGUGUGUGC
.((((....))))........((((((((--------(.....)).))).)))).(((.(((((((-------(((((((.....)))))..))))))).)).)))..... ( -40.10)
>DroSim_CAF1 43739 96 + 1
CGACCUUUCGGUCUAAAAAUAAGCGCCUU--------CACACAGACAGGCCGCUCCACGUGCCACG-------CCCCACUGGCCAGGUGGGCGGCGUGGACAGGUGUGUGC
.((((....))))........((((((((--------(.....)).))).)))).(((.(((((((-------(((((((.....)))))..))))))).)).)))..... ( -40.10)
>DroEre_CAF1 42606 89 + 1
CGACCUUUCGGUCUAAAAAUAAGCGCCUU--------CACACAGACACA--GCUCC-CCUGCCACG-------C-CCACUGGCCAGGGGGGCGGCG---GCAGCUGUGUGC
.((((....))))................--------(((((((.(.(.--(((((-(((((((..-------.-....))).))))))))).).)---....))))))). ( -37.80)
>DroYak_CAF1 43047 89 + 1
CGACCUUUCGGUCUAAAAAUAAGCGCCUU--------CACACAGACACA--CGUCU-CCUGCCACG-------C-CCACUGGCCAGGUGGGCGGCA---GCAGCUGUGUGC
.((((....))))................--------........((((--((.((-.(((((..(-------(-(((((.....)))))))))))---).)).)))))). ( -35.70)
>consensus
CGACCUUUCGGUCUAAAAAUAAGCGCCUU________CACACAGACAGGCCGCUCCACGUGCCACG_______CCCCACUGGCCAGGUGGGCGGCGUGGACAGGUGUGUGC
.((((....))))........................((((((..((.(((((.((((.(((((...............))).)).))))))))).))......)))))). (-23.42 = -26.06 +   2.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,569,667 – 6,569,778
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 84.21
Mean single sequence MFE -44.78
Consensus MFE -26.20
Energy contribution -27.76
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.59
SVM decision value 0.22
SVM RNA-class probability 0.638514
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6569667 111 - 22407834
GCACACACAUUUCCACGCCGCCCACCUGGCCAGUGGGGCGUGGGGCGUGGCACGUGGAGCGGCCUGUCUGUGUGUCGGUGCAAAGGCGCUUAUUUUUAGACCGAAAGGUCG
(.(((((((...(((((((..((((.......)))))))))))((((.(((.((.....)))))))))))))))))(((((....)))))........((((....)))). ( -51.40)
>DroSec_CAF1 41758 96 - 1
GCACACACCUGUCCACGCCGCCCACCUGGCCAGUGGGG-------CGUGGCACGUGGAGCGGCCUGUCUGUGUG--------AAGGCGCUUAUUUUUAGACCGAAAGGUCG
.....(((.((.(((((((..((((.......))))))-------))))))).)))(((((.(((.((.....)--------))))))))).......((((....)))). ( -43.40)
>DroSim_CAF1 43739 96 - 1
GCACACACCUGUCCACGCCGCCCACCUGGCCAGUGGGG-------CGUGGCACGUGGAGCGGCCUGUCUGUGUG--------AAGGCGCUUAUUUUUAGACCGAAAGGUCG
.....(((.((.(((((((..((((.......))))))-------))))))).)))(((((.(((.((.....)--------))))))))).......((((....)))). ( -43.40)
>DroEre_CAF1 42606 89 - 1
GCACACAGCUGC---CGCCGCCCCCCUGGCCAGUGG-G-------CGUGGCAGG-GGAGC--UGUGUCUGUGUG--------AAGGCGCUUAUUUUUAGACCGAAAGGUCG
..((((((((.(---(((((((((.((....)).))-)-------.)))))..)-).)))--)))))..((((.--------...)))).........((((....)))). ( -43.20)
>DroYak_CAF1 43047 89 - 1
GCACACAGCUGC---UGCCGCCCACCUGGCCAGUGG-G-------CGUGGCAGG-AGACG--UGUGUCUGUGUG--------AAGGCGCUUAUUUUUAGACCGAAAGGUCG
((((((..((.(---((((((((((.......))))-)-------)..))))).-))..)--)))))..((((.--------...)))).........((((....)))). ( -42.50)
>consensus
GCACACACCUGUCCACGCCGCCCACCUGGCCAGUGGGG_______CGUGGCACGUGGAGCGGCCUGUCUGUGUG________AAGGCGCUUAUUUUUAGACCGAAAGGUCG
.((((((.........(((((((((...((((.((..........))))))..)))).))))).....))))))........................((((....)))). (-26.20 = -27.76 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:22 2006