Locus 6336

Sequence ID 3L_DroMel_CAF1
Location 16,962,828 – 16,962,918
Length 90
Max. P 0.809215
window10157 window10158

overview

Window 7

Location 16,962,828 – 16,962,918
Length 90
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 82.37
Mean single sequence MFE -24.88
Consensus MFE -15.55
Energy contribution -17.44
Covariance contribution 1.89
Combinations/Pair 1.11
Mean z-score -2.72
Structure conservation index 0.62
SVM decision value 0.64
SVM RNA-class probability 0.809215
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16962828 90 + 23771897
AUCUCAUUCUUUUUCAGAGUCUGCAUGCCAUCGCU--------GGCG-UCCAGGGACCCAGAGUCCAAACCAUCUGGGUCCCCAUCCUCGUUGUCCCUA
................(((..((.((((((....)--------))))-).))((((((((((..........))))))))))....))).......... ( -30.40)
>DroSec_CAF1 1894 90 + 1
AUCUCAUUCUUUUUCAGAGUCUGCAUGCCAUCGCU--------GGCG-UCUAGGGACCCAGAGUCCAAUCCAUCUGGGUCCCCAUCCUCGUUGUCCCUA
................(((..((.((((((....)--------))))-)...((((((((((..........))))))))))))..))).......... ( -30.20)
>DroSim_CAF1 1881 90 + 1
AUCUCAUUCUUUUUCAGAGUCUGCAUGCCAUCGCU--------GGCG-UCCAGGGACCCAGAGUCCAAUCCAUCUGGGUCCCCAUCCUCGUUGUCCCUA
................(((..((.((((((....)--------))))-).))((((((((((..........))))))))))....))).......... ( -30.40)
>DroEre_CAF1 1891 90 + 1
AUCUCAUUCUUCUUCAGAGUCUGCAUGCCAUCGCU--------GGCG-UCCAGGGACCCUGAGUCCAAUUCAUCUGGGUCCCCAUCCUCGUUCUCCCUA
................(((..((.((((((....)--------))))-).))((((((((((((...)))))...)))))))....))).......... ( -25.80)
>DroYak_CAF1 1882 90 + 1
AUCUCAUUCUUUUUUAGUGUCUGCAUGCCAUCGCU--------GGCG-UCCAGGGACCCUAGGUCCAAUCCAGCUGGGUCCCCAUCCUCGUUCUCCCUA
.....................((.((((((....)--------))))-).))(((((((..((......))....)))))))................. ( -23.60)
>DroPer_CAF1 1939 87 + 1
AUCUCGUUCUUUUUCAGCGUCUGCAUGCCGUCCUGAUCUGCCUGAUCUUCAAG--CCCCAG------AUCCCUCUC-GUCCUCAUCCUCGU---CUCCG
..................(((((...((......((((.....)))).....)--)..)))------)).......-..............---..... (  -8.90)
>consensus
AUCUCAUUCUUUUUCAGAGUCUGCAUGCCAUCGCU________GGCG_UCCAGGGACCCAGAGUCCAAUCCAUCUGGGUCCCCAUCCUCGUUGUCCCUA
................(((..((...(((..............)))......((((((((((..........))))))))))))..))).......... (-15.55 = -17.44 +   1.89)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,962,828 – 16,962,918
Length 90
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 82.37
Mean single sequence MFE -29.87
Consensus MFE -16.98
Energy contribution -18.87
Covariance contribution 1.89
Combinations/Pair 1.11
Mean z-score -2.55
Structure conservation index 0.57
SVM decision value 0.28
SVM RNA-class probability 0.664294
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16962828 90 - 23771897
UAGGGACAACGAGGAUGGGGACCCAGAUGGUUUGGACUCUGGGUCCCUGGA-CGCC--------AGCGAUGGCAUGCAGACUCUGAAAAAGAAUGAGAU
(((((.......(..((((((((((((.(.......)))))))))))))..-)(((--------(....)))).......))))).............. ( -34.30)
>DroSec_CAF1 1894 90 - 1
UAGGGACAACGAGGAUGGGGACCCAGAUGGAUUGGACUCUGGGUCCCUAGA-CGCC--------AGCGAUGGCAUGCAGACUCUGAAAAAGAAUGAGAU
(((((.......(..((((((((((((.(.......)))))))))))))..-)(((--------(....)))).......))))).............. ( -35.60)
>DroSim_CAF1 1881 90 - 1
UAGGGACAACGAGGAUGGGGACCCAGAUGGAUUGGACUCUGGGUCCCUGGA-CGCC--------AGCGAUGGCAUGCAGACUCUGAAAAAGAAUGAGAU
(((((.......(..((((((((((((.(.......)))))))))))))..-)(((--------(....)))).......))))).............. ( -34.30)
>DroEre_CAF1 1891 90 - 1
UAGGGAGAACGAGGAUGGGGACCCAGAUGAAUUGGACUCAGGGUCCCUGGA-CGCC--------AGCGAUGGCAUGCAGACUCUGAAGAAGAAUGAGAU
...((((.....(..(((((((((...(((.......))))))))))))..-)(((--------(....)))).......))))............... ( -28.50)
>DroYak_CAF1 1882 90 - 1
UAGGGAGAACGAGGAUGGGGACCCAGCUGGAUUGGACCUAGGGUCCCUGGA-CGCC--------AGCGAUGGCAUGCAGACACUAAAAAAGAAUGAGAU
(((.........(..(((((((((....((......))..)))))))))..-)(((--------(....)))).........))).............. ( -26.50)
>DroPer_CAF1 1939 87 - 1
CGGAG---ACGAGGAUGAGGAC-GAGAGGGAU------CUGGGG--CUUGAAGAUCAGGCAGAUCAGGACGGCAUGCAGACGCUGAAAAAGAACGAGAU
((...---.))..........(-(.......(------((((.(--((((.....)))))...))))).((((........))))........)).... ( -20.00)
>consensus
UAGGGACAACGAGGAUGGGGACCCAGAUGGAUUGGACUCUGGGUCCCUGGA_CGCC________AGCGAUGGCAUGCAGACUCUGAAAAAGAAUGAGAU
..........(((..((((((((((((..........))))))))))......(((..............)))...))..)))................ (-16.98 = -18.87 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:57 2006