Locus 902

Sequence ID 3R_DroMel_CAF1
Location 3,042,612 – 3,042,704
Length 92
Max. P 0.830311
window1433 window1434

overview

Window 3

Location 3,042,612 – 3,042,704
Length 92
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 71.46
Mean single sequence MFE -22.69
Consensus MFE -7.76
Energy contribution -8.32
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.15
Structure conservation index 0.34
SVM decision value 0.71
SVM RNA-class probability 0.830311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3042612 92 + 27905053
---UCAACUU--UU-AUUAAAUGCUCUACUGUGGCUCCUU--CCUUCUAUUUUCACCCACCAGUCAUGGUGGCAAUAAAUUGCCAUCGGUACCGCACACU
---.......--..-......(((..(((((((((.....--......((((....((((((....))))))....)))).)))).)))))..))).... ( -22.30)
>DroPse_CAF1 30315 96 + 1
UAGUUAGUUA--UU-GAUUAGUGCGUGUUU-CAGAUGGACAACCGAAUUGAUUUACCCACCCGUCAUUGUGGCAAUAAGCUGCCAUCGAUAGCGCGCACU
..........--..-....(((((((((((-(.(((((......................)))))...((((((......)))))).)).)))))))))) ( -27.55)
>DroSec_CAF1 29663 95 + 1
---UCAACUUUUUU-AUUAAAUGCUCUACUGUGGUUCCUU-GUCUUGUAUUUUCACCCACCAGUCAUGGUGGCAAUAAAUUGCCAUCGGUACCGCGCACU
---...........-...............(((((.((.(-(.((.((..........)).)).)).((((((((....)))))))))).)))))..... ( -21.40)
>DroSim_CAF1 29901 92 + 1
---UCAACUU--UU-AUUAAAUGCUCUACUGUGGUUCCUU--CCUUGUAUUUUCACCCACCAGUCAUGGUGGCAAUAAAUUGCCAUCGGUACCGCGCACU
---.......--..-.......((..(((((((((.....--......((((....((((((....))))))....)))).)))).)))))..))..... ( -20.00)
>DroAna_CAF1 32289 89 + 1
---UAUGCUU--UUAAAUAAAUGUAUU----UAGGUCAUC--CACUGAAUCUUCACCCACCCGUCAUAGUGGCAAUAAUUUGCCAACGGUAUCGCGCACU
---..(((..--............(((----(((......--..))))))..........((((.....((((((....))))))))))......))).. ( -16.80)
>DroPer_CAF1 30371 96 + 1
UAGUUAGUUA--UU-GAUUAGUGCGUGUUU-UUGAUGGACAACCGAAUAGAUUUACCCACCCGUCAUUGUGGCAAUAAGCUGCCAUCGAUAGCGCGCACU
..........--..-....((((((((((.-(((((((.((................(((........)))((.....))))))))))).)))))))))) ( -28.10)
>consensus
___UCAACUU__UU_AAUAAAUGCUCUACU_UGGAUCCUC__CCUUGUAUUUUCACCCACCAGUCAUGGUGGCAAUAAAUUGCCAUCGGUACCGCGCACU
.....................(((............................................(((((((....)))))))((....)).))).. ( -7.76 =  -8.32 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,042,612 – 3,042,704
Length 92
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 71.46
Mean single sequence MFE -23.18
Consensus MFE -11.92
Energy contribution -11.78
Covariance contribution -0.14
Combinations/Pair 1.27
Mean z-score -1.47
Structure conservation index 0.51
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3042612 92 - 27905053
AGUGUGCGGUACCGAUGGCAAUUUAUUGCCACCAUGACUGGUGGGUGAAAAUAGAAGG--AAGGAGCCACAGUAGAGCAUUUAAU-AA--AAGUUGA---
...((((..(((.(.((((.........((((((....))))))((....))......--.....))))).)))..)))).....-..--.......--- ( -22.50)
>DroPse_CAF1 30315 96 - 1
AGUGCGCGCUAUCGAUGGCAGCUUAUUGCCACAAUGACGGGUGGGUAAAUCAAUUCGGUUGUCCAUCUG-AAACACGCACUAAUC-AA--UAACUAACUA
((((((.(.....(.((((((....))))))).....(((((((..((.((.....))))..)))))))-...).))))))....-..--.......... ( -27.00)
>DroSec_CAF1 29663 95 - 1
AGUGCGCGGUACCGAUGGCAAUUUAUUGCCACCAUGACUGGUGGGUGAAAAUACAAGAC-AAGGAACCACAGUAGAGCAUUUAAU-AAAAAAGUUGA---
(((((((.((....)).))..(((((((((((((....))))))((....)).......-.........))))))))))))....-...........--- ( -19.90)
>DroSim_CAF1 29901 92 - 1
AGUGCGCGGUACCGAUGGCAAUUUAUUGCCACCAUGACUGGUGGGUGAAAAUACAAGG--AAGGAACCACAGUAGAGCAUUUAAU-AA--AAGUUGA---
(((((((.((....)).))..(((((((((((((....))))))............((--......)).))))))))))))....-..--.......--- ( -21.50)
>DroAna_CAF1 32289 89 - 1
AGUGCGCGAUACCGUUGGCAAAUUAUUGCCACUAUGACGGGUGGGUGAAGAUUCAGUG--GAUGACCUA----AAUACAUUUAUUUAA--AAGCAUA---
.((((......((((((((((....)))))).....)))).((((((((........(--(....))..----......)))))))).--..)))).--- ( -19.89)
>DroPer_CAF1 30371 96 - 1
AGUGCGCGCUAUCGAUGGCAGCUUAUUGCCACAAUGACGGGUGGGUAAAUCUAUUCGGUUGUCCAUCAA-AAACACGCACUAAUC-AA--UAACUAACUA
((((((.(.....(((((((((((((((...))))))((((((((....)))))))))))).)))))..-...).))))))....-..--.......... ( -28.30)
>consensus
AGUGCGCGGUACCGAUGGCAAUUUAUUGCCACCAUGACGGGUGGGUGAAAAUACAAGG__AAGGAACCA_AGUAAAGCAUUUAAU_AA__AAGCUGA___
(((((..........((((((....))))))((((.....))))................................)))))................... (-11.92 = -11.78 +  -0.14)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:02 2006