Locus 5200

Sequence ID 3R_DroMel_CAF1
Location 13,621,407 – 13,621,567
Length 160
Max. P 0.985343
window8487 window8488

overview

Window 7

Location 13,621,407 – 13,621,503
Length 96
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 72.39
Mean single sequence MFE -28.25
Consensus MFE -19.02
Energy contribution -19.17
Covariance contribution 0.14
Combinations/Pair 1.38
Mean z-score -1.96
Structure conservation index 0.67
SVM decision value 2.00
SVM RNA-class probability 0.985343
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13621407 96 + 27905053
-----------------GCAUCUGUUUCUCAGCACUCGAGGAUGGCUGCUACCCUGGCUGGGUCUAAUUGGACUAGCCAUUCUCUUCCAGUUUAGCUGGAGCCUUUGGCUUAU
-----------------....(((.....))).....(((((((((((((.....)))..(((((....))))))))))))))).(((((.....)))))(((...))).... ( -32.50)
>DroSec_CAF1 1 80 + 1
---------------------------------ACUCGUGGAUGGCUACUGCCCUGGCUGGGUCUAAUUGGACUGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAU
---------------------------------....(.((((((((.(.((....)).)(((((....))))))))))))).).(((((.....)))))(((...))).... ( -28.20)
>DroSim_CAF1 1 83 + 1
------------------------------AGCACUCGCGGAUGGCUACUGCCCUGGCUGGGUCUAAUUGGACUGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAU
------------------------------(((....((((((((((.(.((....)).)(((((....)))))))))))))...(((((.....))))))).....)))... ( -29.50)
>DroEre_CAF1 1 80 + 1
---------------------------------ACUCGAGGAUGGCUACUGCCUUGGUUGGGUCUCAUUGGUCUGGCAAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAU
---------------------------------....(((((((((....)))...((..(..(.....)..)..)).)))))).(((((.....)))))(((...))).... ( -27.70)
>DroMoj_CAF1 8719 113 + 1
UUGUGGACUUAAUUAAUUAAUCUAUUUUAUAGCACGCGUGGCUGGCUCUUGCCCUGGCUAUUUUUGAUUGGACUUGCGAUUCUGUUUCAAUUCUGCUGGAGCCUUUGGUUAAU
..(((((.((((....)))))))))....((((.((...(((((((....)))(..((.....((((.((((........))))..))))....))..)))))..)))))).. ( -22.40)
>DroAna_CAF1 1 80 + 1
---------------------------------ACUCGAGGAUGGCUACUGCCUUGGCUGGGACUCAUCGGUCUGGCUAUUCUGUUCCAGUUUGGCUGGAGCUUGUGGCUUAU
---------------------------------..........((((((.(((..((((((......)))))).)))......(((((((.....)))))))..))))))... ( -29.20)
>consensus
_________________________________ACUCGAGGAUGGCUACUGCCCUGGCUGGGUCUAAUUGGACUGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAU
.......................................((((((((.(.((....)).)(((((....)))))))))))))...(((((.....)))))(((...))).... (-19.02 = -19.17 +   0.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,621,463 – 13,621,567
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 79.05
Mean single sequence MFE -25.65
Consensus MFE -14.25
Energy contribution -14.62
Covariance contribution 0.36
Combinations/Pair 1.31
Mean z-score -1.76
Structure conservation index 0.56
SVM decision value 0.08
SVM RNA-class probability 0.571522
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13621463 104 + 27905053
UAGCCAUUCUCUUCCAGUUUAGCUGGAGCCUUUGGCUUAUUGGAGGCUACUAUAUUUAUGUGAGUAGCGAUUAUCUUUUCCAUUAAC-----UAAAGCUAAUGAAUUCG
((((.......((((((.....))))))..(((((.(((.(((((((((((.(((....)))))))))(.....)..))))).))))-----))))))))......... ( -25.60)
>DroSec_CAF1 41 104 + 1
UGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAUUGGAGGCUACUAUAUUUAUGUGAGUAACGAUUAUCUUUUCCAUGAGU-----UAUAUCUAAUGGAUUCG
...(((((....(((((.....)))))(((((..(....)..)))))...((((((((((.(((.............))))))))).-----))))...)))))..... ( -23.82)
>DroSim_CAF1 44 104 + 1
UGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAUUGGAGGCUACUAUAUUUAUGUGAGUAGCGAUUAUAUUUUGCGUGAGU-----UAUAUCUAAUGGUUCCG
.(((((.....((((((.....))))))....)))))....((((((((((.(((....))))))))).((((.((...((....))-----...)).))))..)))). ( -29.40)
>DroEre_CAF1 41 104 + 1
UGGCAAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAUCGGAGGCUACUAUAUUUAUGUAAGUACCGACUAAUUUUUCCAUGAAU-----UAAAGCUAAUGGAUUAU
...........((((((.....))))))((.(((((((.((((..(((((.........)).))).)))).((((((......))))-----))))))))).))..... ( -24.20)
>DroYak_CAF1 44 104 + 1
UGGCCAUUCUCUUUCAGUUUUGCUGGAGCCUGUGGCUUAUUGGAGGCUACUAUAUUUAUGUGAGUGCCAACUACUUUUUGCAUGAAU-----UGAAGCUAAUAAAUUAA
.((((((....((((((.....))))))...))))))..(((..((((.(...(((((((((((((.....)))))...))))))))-----.).))))..)))..... ( -25.40)
>DroMoj_CAF1 8792 105 + 1
UUGCGAUUCUGUUUCAAUUCUGCUGGAGCCUUUGGUUAAUUGGCGGCUACUACAUAUACGUGAGUAUAUAUUAUAA---AUAUGAAUUGCAUUGCAACUAAAUACC-AA
.(((((((((((((.....((((..(((((...))))..)..)))).......((((((....)))))).....))---))).))))))))...............-.. ( -25.50)
>consensus
UGGCCAUUCUCUUCCAGUUUUGCUGGAGCCUUUGGCUUAUUGGAGGCUACUAUAUUUAUGUGAGUACCGAUUAUAUUUUCCAUGAAU_____UAAAGCUAAUGAAUUAG
..((((.....((((((.....))))))....))))(((((((..........(((((((..((............))..)))))))..........)))))))..... (-14.25 = -14.62 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:55 2006