Locus 6987

Sequence ID 3L_DroMel_CAF1
Location 18,861,297 – 18,861,388
Length 91
Max. P 0.998539
window11336 window11337

overview

Window 6

Location 18,861,297 – 18,861,388
Length 91
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 72.15
Mean single sequence MFE -19.42
Consensus MFE -5.86
Energy contribution -5.56
Covariance contribution -0.30
Combinations/Pair 1.50
Mean z-score -2.32
Structure conservation index 0.30
SVM decision value 2.08
SVM RNA-class probability 0.987382
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861297 91 + 23771897
UUAGAAUUAUUUGUAUGUAACACACAUACAUAUGUACAUAUG----------UAUAUAUAU--------GGGAAGCCAUAUAGAUUGAGUCCAGUUGAGGGACUGAUAA
...........(((((((.....)))))))..(((((....)----------))))(((((--------((....)))))))...(.(((((.......))))).)... ( -22.80)
>DroSec_CAF1 26253 78 + 1
UUAGAAUUAUUUGUAUAUAACAAACAUACAUAC-----------------------UAUAU--------GGGAAGCCAUAUAGAUUGAGACCAAUUGAGCAAUUGAUAA
.....((((.((((..................(-----------------------(((((--------((....))))))))((((....))))...)))).)))).. ( -15.30)
>DroSim_CAF1 26805 78 + 1
UUAGAAUUAUUUGUAUAUAACACACAUACAUAC-----------------------UAUAU--------GGGAAGCCAUAUAGAUUGAGACCAAUUGAGCAAUUGAUAA
.....((((.((((..................(-----------------------(((((--------((....))))))))((((....))))...)))).)))).. ( -15.30)
>DroEre_CAF1 26773 109 + 1
UUGGAAUUAUUUGUAUAUAACGCACAUAUGUACAUACAUGCGAGUAUAUGUAUGUAUGUACAUAAGCAUUGAAAGCCAUAUAGAUUGAGACCAAUUGAGUGAUUGAUAA
.(((..((((((((((..........((((((((((((((((......)))))))))))))))).((.......)).))))))).)))..)))((..(....)..)).. ( -28.70)
>DroYak_CAF1 27312 97 + 1
UUAGAAAUUUUUGUAUAUAACGCACAUAUGUACAUA----CGAGUAUAAAAAUGUAUGUAU--------GCCAAGCCAUAUAGAUUGAGACCAGUUGAGAGAUUGAUAA
.......((..(.(((((...((.(((((((((((.----...........))))))))))--------)....)).))))).)..))...(((((....))))).... ( -15.00)
>consensus
UUAGAAUUAUUUGUAUAUAACACACAUACAUAC_UA_____G__________U_UAUAUAU________GGGAAGCCAUAUAGAUUGAGACCAAUUGAGCGAUUGAUAA
............(((((((.......)))))))..........................................................(((((....))))).... ( -5.86 =  -5.56 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,861,297 – 18,861,388
Length 91
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 72.15
Mean single sequence MFE -17.17
Consensus MFE -4.74
Energy contribution -5.10
Covariance contribution 0.36
Combinations/Pair 1.23
Mean z-score -2.76
Structure conservation index 0.28
SVM decision value 3.13
SVM RNA-class probability 0.998539
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861297 91 - 23771897
UUAUCAGUCCCUCAACUGGACUCAAUCUAUAUGGCUUCCC--------AUAUAUAUA----------CAUAUGUACAUAUGUAUGUGUGUUACAUACAAAUAAUUCUAA
.....(((((.......))))).....(((((((....))--------))))).(((----------(((((....))))))))(((((...)))))............ ( -19.20)
>DroSec_CAF1 26253 78 - 1
UUAUCAAUUGCUCAAUUGGUCUCAAUCUAUAUGGCUUCCC--------AUAUA-----------------------GUAUGUAUGUUUGUUAUAUACAAAUAAUUCUAA
..(((((((....)))))))......((((((((....))--------)))))-----------------------)..(((((((.....)))))))........... ( -16.30)
>DroSim_CAF1 26805 78 - 1
UUAUCAAUUGCUCAAUUGGUCUCAAUCUAUAUGGCUUCCC--------AUAUA-----------------------GUAUGUAUGUGUGUUAUAUACAAAUAAUUCUAA
..(((((((....)))))))......((((((((....))--------)))))-----------------------)..((((((((...))))))))........... ( -15.90)
>DroEre_CAF1 26773 109 - 1
UUAUCAAUCACUCAAUUGGUCUCAAUCUAUAUGGCUUUCAAUGCUUAUGUACAUACAUACAUAUACUCGCAUGUAUGUACAUAUGUGCGUUAUAUACAAAUAAUUCCAA
...............((((........((((((((.......((.(((((((((((((.(........).)))))))))))))...)))))))))).........)))) ( -23.04)
>DroYak_CAF1 27312 97 - 1
UUAUCAAUCUCUCAACUGGUCUCAAUCUAUAUGGCUUGGC--------AUACAUACAUUUUUAUACUCG----UAUGUACAUAUGUGCGUUAUAUACAAAAAUUUCUAA
...........................((((((((...((--------(((..(((((...........----.)))))..)))))..))))))))............. ( -11.40)
>consensus
UUAUCAAUCGCUCAAUUGGUCUCAAUCUAUAUGGCUUCCC________AUAUAUA_A__________C_____UA_GUAUGUAUGUGUGUUAUAUACAAAUAAUUCUAA
..((((((......))))))........................................................(((((((.......)))))))............ ( -4.74 =  -5.10 +   0.36)

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 12:34:55 2006