Locus 4040

Sequence ID 2L_DroMel_CAF1
Location 11,704,465 – 11,704,555
Length 90
Max. P 0.959222
window6364 window6365

overview

Window 4

Location 11,704,465 – 11,704,555
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.19
Mean single sequence MFE -31.25
Consensus MFE -21.85
Energy contribution -21.47
Covariance contribution -0.39
Combinations/Pair 1.08
Mean z-score -2.79
Structure conservation index 0.70
SVM decision value 0.94
SVM RNA-class probability 0.886749
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11704465 90 + 22407834
------------GUGCUGGUGUG----UGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGAAUGCU--------------
------------((((((((((.----.....))))))(((((((((((((((((.(..(((....)))..)..))))))...))))))).)))))))).......-------------- ( -29.00)
>DroPse_CAF1 158665 102 + 1
------------G--UGUGUGU----GUGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGACUGCCGCUAUGGCUAUGUC
------------(--((((((.----(((....))))))...(((((((((((((.(..(((....)))..)..))))))...))))))).....))))(((.(((.....)))...))) ( -30.20)
>DroSim_CAF1 163469 94 + 1
------------GUGCUGGUGUGUGUGUGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGAAUGCU--------------
------------((((..(((((.((((....))))))))..(((((((((((((.(..(((....)))..)..))))))...)))))))..)..)))).......-------------- ( -30.00)
>DroYak_CAF1 162749 102 + 1
GUGCUGGUGUUAGUGCUGGUGU----GUGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGAAUGCU--------------
((((((((((..(..(......----)..)..))))))(((((((((((((((((.(..(((....)))..)..))))))...))))))).)))))))).......-------------- ( -33.50)
>DroAna_CAF1 170051 96 + 1
------------GUGGGUGUGU----GUAUGGGUGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGAAUGCCACU--------GCC
------------...((((((.----((((..((((((....(((((((((((((.(..(((....)))..)..))))))...)))))))...))))))..))))))).--------))) ( -34.60)
>DroPer_CAF1 159730 104 + 1
------------CUGUGUGUGU----GUGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGACUGCCGCUAUGGCUAUGUC
------------..(((((((.----(((....))))))...(((((((((((((.(..(((....)))..)..))))))...))))))).....))))(((.(((.....)))...))) ( -30.20)
>consensus
____________GUGCGGGUGU____GUGUGGGCGCCACAAAAAUGAAAACAAAUUUUGGCAUGAUUGCUGAUUGUUUGUCUUUUUCAUUGUUUGGCACGAAUGCC______________
...............................(((((((....(((((((((((((.(..(((....)))..)..))))))...)))))))...))))......))).............. (-21.85 = -21.47 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,704,465 – 11,704,555
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.19
Mean single sequence MFE -20.70
Consensus MFE -18.00
Energy contribution -17.87
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -2.60
Structure conservation index 0.87
SVM decision value 1.50
SVM RNA-class probability 0.959222
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11704465 90 - 22407834
--------------AGCAUUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACA----CACACCAGCAC------------
--------------.......((((((...((((((...((((((......(((....))).....))))))))))))....)))))).....----...........------------ ( -17.80)
>DroPse_CAF1 158665 102 - 1
GACAUAGCCAUAGCGGCAGUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACAC----ACACACA--C------------
(((...(((.....))).)))((((((...((((((...((((((......(((....))).....))))))))))))....))))))......----.......--.------------ ( -24.00)
>DroSim_CAF1 163469 94 - 1
--------------AGCAUUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACACACACACACCAGCAC------------
--------------.......((((((...((((((...((((((......(((....))).....))))))))))))....))))))....................------------ ( -17.80)
>DroYak_CAF1 162749 102 - 1
--------------AGCAUUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACAC----ACACCAGCACUAACACCAGCAC
--------------.......((((((...((((((...((((((......(((....))).....))))))))))))....))))))......----......((..........)).. ( -18.10)
>DroAna_CAF1 170051 96 - 1
GGC--------AGUGGCAUUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCACCCAUAC----ACACACCCAC------------
((.--------.(((......((((((...((((((...((((((......(((....))).....))))))))))))....))))))......----.)))..))..------------ ( -22.52)
>DroPer_CAF1 159730 104 - 1
GACAUAGCCAUAGCGGCAGUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACAC----ACACACACAG------------
(((...(((.....))).)))((((((...((((((...((((((......(((....))).....))))))))))))....))))))......----..........------------ ( -24.00)
>consensus
______________AGCAUUCGUGCCAAACAAUGAAAAAGACAAACAAUCAGCAAUCAUGCCAAAAUUUGUUUUCAUUUUUGUGGCGCCCACAC____ACACAAGCAC____________
.....................((((((...((((((...((((((......(((....))).....))))))))))))....))))))................................ (-18.00 = -17.87 +  -0.14)

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 11:07:47 2006