Locus 10218

Sequence ID 3R_DroMel_CAF1
Location 27,404,199 – 27,404,359
Length 160
Max. P 0.611103
window16276 window16277

overview

Window 6

Location 27,404,199 – 27,404,319
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.13
Mean single sequence MFE -54.55
Consensus MFE -35.21
Energy contribution -35.77
Covariance contribution 0.56
Combinations/Pair 1.52
Mean z-score -1.33
Structure conservation index 0.65
SVM decision value 0.16
SVM RNA-class probability 0.611103
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404199 120 - 27905053
CUCUGCACAGUCCGCUCGGAAACGGACCAACGGGUCAUGGCAGUCACAUGCCUGGAGGACCAAUCCCAGGACCAGGUCCUGGGCCUGGCGGCCUAGUAGGUCCCGGUGGCAUCUCCCCCG
.........(((((........)))))...((((....((((......)))).(((((.(((..((((((((...)))))))).((((.((((.....)))))))))))..))))))))) ( -50.90)
>DroVir_CAF1 7273 117 - 1
CCCUGCACAGUCCACUGGGUAAUGGGCCAACAAAUCA---CAGUCACAUGUCCGGUGGACCAGGUCCAGGCCCGGGUCCUGGGCCGGGCGGUUUAGUUGGACCCGGUGGCAUGUCGCCAG
.((((.((.(((((((((..(.(((((..........---..))).)))..)))))))))...)).)))).((((((((((((((....))))))...))))))))((((.....)))). ( -52.90)
>DroPse_CAF1 6885 120 - 1
CGUUGCACAGUCCGCUGGGCAAUGGACCGACGAAUCAUGGCAGUCAUAUGCCAGGUGGACCCGGUCCAGGUCCUGGGCCUGGGCCCGGUGGCCUCGUCGGACCAGGUGGCAUGUCUCCCG
.(((((.(((....))).)))))((.(((((((....(((((......)))))(((.(.((.(((((((((.....))))))))).))).)))))))))).)).((.((....)).)).. ( -58.90)
>DroWil_CAF1 6233 120 - 1
CUUUGCACAGUCCUCUUGGCAAUGGUCCUGCGAGUCAUGGCAAUCAUAUGCCUGGUGGGCCAGGUCCGGGACCAGGUCCUGGGCCAGGCAAUCUAGUCGGGCCUGGAGGCAUUUCUCCCG
.........(.(((((.(((..((((((.((.((.((((.......)))).)).))))))))((((((((((...)))))))))).(((......)))..))).)))))).......... ( -49.20)
>DroMoj_CAF1 6951 117 - 1
CUCUGCACAGUCCGCUGGGCAAUGGACCAACGAAUCA---CAGUCAUAUGUCCGGCGGACCAGGUCCGGGGCCAGGUCCUGGGCCGGGUGGCUUAGUCGGACCUGGUGGCAUGUCGCCGG
.((((.((.((((((((((((...(((..........---..)))...))))))))))))...)).))))(((((((((((((((....))))))...)))))))))(((.....))).. ( -57.00)
>DroAna_CAF1 6180 120 - 1
CACUGCAUAGUCCGUUGGGCAACGGUCCCACGGGUCACGGGAGUCACAUGCCCGGCGGACCUGGUCCCGGGCCUGGACCUGGGCCUGGUGGCGUCGUGGGACCUGGUGGCAUAUCCCCCG
((((.....((((...))))...(((((((((((((.((((.........))))...))))..(((((((((((......)))))))).)))..))))))))).))))............ ( -58.40)
>consensus
CUCUGCACAGUCCGCUGGGCAAUGGACCAACGAAUCAUGGCAGUCACAUGCCCGGUGGACCAGGUCCAGGACCAGGUCCUGGGCCGGGCGGCCUAGUCGGACCUGGUGGCAUGUCCCCCG
.........(.((((..(((......(((((.......((((......)))).(((.(.((.((((((((((...)))))))))).))).)))..))))))))..))))).......... (-35.21 = -35.77 +   0.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 7

Location 27,404,239 – 27,404,359
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.08
Mean single sequence MFE -45.27
Consensus MFE -30.93
Energy contribution -31.63
Covariance contribution 0.70
Combinations/Pair 1.34
Mean z-score -1.26
Structure conservation index 0.68
SVM decision value 0.07
SVM RNA-class probability 0.570858
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404239 120 - 27905053
CCGCAGCCACCGAUGAACAACGGGCAGAUGGGUCCUCCUCCUCUGCACAGUCCGCUCGGAAACGGACCAACGGGUCAUGGCAGUCACAUGCCUGGAGGACCAAUCCCAGGACCAGGUCCU
(((.(((..(((........)))(((((.(((......)))))))).......))))))....(((((..((((.((((.......))))))))..((.((.......)).)).))))). ( -43.40)
>DroVir_CAF1 7313 117 - 1
CAACAGACGCACAUGAACAAUGGACAAAUGGGUCCGCCGCCCCUGCACAGUCCACUGGGUAAUGGGCCAACAAAUCA---CAGUCACAUGUCCGGUGGACCAGGUCCAGGCCCGGGUCCU
.....(((.............((((......)))).(((..((((.((.(((((((((..(.(((((..........---..))).)))..)))))))))...)).))))..)))))).. ( -39.90)
>DroPse_CAF1 6925 120 - 1
CCGCAGCCACCCAUGAACAAUGGACAGAUGGGUCCGCCCCCGUUGCACAGUCCGCUGGGCAAUGGACCGACGAAUCAUGGCAGUCAUAUGCCAGGUGGACCCGGUCCAGGUCCUGGGCCU
.........((((.((....(((((....(((((((((.(((((((.(((....))).)))))))............(((((......)))))))))))))).)))))..)).))))... ( -56.10)
>DroWil_CAF1 6273 120 - 1
CCGCAGCCACCCAUGAAUAAUGGACAAAUGGGUCCUCCUCCUUUGCACAGUCCUCUUGGCAAUGGUCCUGCGAGUCAUGGCAAUCAUAUGCCUGGUGGGCCAGGUCCGGGACCAGGUCCU
.(((((..((((((.............))))))......((.((((.(((.....))))))).))..)))))..(((.((((......))))))).(((((.((((...)))).))))). ( -39.02)
>DroMoj_CAF1 6991 117 - 1
CAACAGACGCACAUGAAUAAUGGACAAAUGGGUCCGCCGCCUCUGCACAGUCCGCUGGGCAAUGGACCAACGAAUCA---CAGUCAUAUGUCCGGCGGACCAGGUCCGGGGCCAGGUCCU
.....................((((...(((.((((((((....))...((((((((((((...(((..........---..)))...))))))))))))..))..)))).))).)))). ( -44.80)
>DroAna_CAF1 6220 120 - 1
CCGCAGCCACCGAUGAACAAUGGACAGAUGGGUCCGCCGCCACUGCAUAGUCCGUUGGGCAACGGUCCCACGGGUCACGGGAGUCACAUGCCCGGCGGACCUGGUCCCGGGCCUGGACCU
(((..(((((((.((..((((((((.....((....))((....))...))))))))..)).))))......)))..)))..(((.((.((((((..(((...))))))))).))))).. ( -48.40)
>consensus
CCGCAGCCACCCAUGAACAAUGGACAAAUGGGUCCGCCGCCUCUGCACAGUCCGCUGGGCAAUGGACCAACGAAUCAUGGCAGUCACAUGCCCGGUGGACCAGGUCCAGGACCAGGUCCU
.....................((((.....((((((((.((..(((.(((....))).)))..)).............((((......)))).))))))))..))))(((((...))))) (-30.93 = -31.63 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:45 2006