Locus 868

Sequence ID 3R_DroMel_CAF1
Location 2,927,954 – 2,928,133
Length 179
Max. P 0.929185
window1380 window1381

overview

Window 0

Location 2,927,954 – 2,928,066
Length 112
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 74.78
Mean single sequence MFE -23.73
Consensus MFE -10.86
Energy contribution -14.78
Covariance contribution 3.92
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.46
SVM decision value 1.20
SVM RNA-class probability 0.929185
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2927954 112 - 27905053
----UUUGUAAUCAGAGAACGGAAGUUUCUGAUGCAAAACCAUAACAACCCUCAACUGUUUCAUAAAGUCCCCCUUUCGUCGUGUAUUACGAAACACAAAUAGGGCUAACAAAUUC
----((((((.(((((((.(....))))))))))))))..........((((....((((((..((((.....))))....(((...))))))))).....))))........... ( -23.20)
>DroSec_CAF1 7335 116 - 1
UGUGUUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAACCAUAACAACCCUCAACUGUUUUAUAAAGUCCCCCUUUCGUUGUGUAUUACGAAACACAACUAGGGCUAACAAGUUC
((..(((((.((((((((.(....))))))))))))))..)).........................((..((((...(((((((........))))))).))))...))...... ( -28.80)
>DroSim_CAF1 6750 116 - 1
UGUGUUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAACCAUAACAACCCUCAACUGUUUUAUAAAAUCCCCCUUUCGUUGUGUAUUACGAAACACAACUAGGGCUAACAAGUUC
((..(((((.((((((((.(....))))))))))))))..))...........(((((((...........((((...(((((((........))))))).))))..))).)))). ( -28.42)
>DroEre_CAF1 8262 100 - 1
AGUAUUUGUGAUCAGCGAACGUAGGUUUCUGACGCAAAACCAUUACAACCCUCGACUGUU---------------UUCGUUGUGUAUUACGAG-UACAACUAGAACUAACAAAUUA
.((((((((((((((((((.((((((((........)))))..)))(((........)))---------------)))))))...))))))))-)))................... ( -20.80)
>DroYak_CAF1 8182 96 - 1
------------------ACGUAGUUUUUUGAUGCACAACCAUAAUAACCUUCACCUCUUUUAUA--GUCUCCCUUUCGUUGUGCAUUACGAAUUACAACUAAGGAAAUAGAAUUU
------------------..(((((((..(((((((((((.........................--...........))))))))))).)))))))................... ( -17.42)
>consensus
_GU_UUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAACCAUAACAACCCUCAACUGUUUUAUAAAGUCCCCCUUUCGUUGUGUAUUACGAAACACAACUAGGGCUAACAAAUUC
....((((((.((((.((((....)))))))))))))).................................((((...(((((((........))))))).))))........... (-10.86 = -14.78 +   3.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,928,030 – 2,928,133
Length 103
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 83.48
Mean single sequence MFE -23.53
Consensus MFE -17.44
Energy contribution -17.00
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.74
SVM decision value 0.06
SVM RNA-class probability 0.565465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2928030 103 - 27905053
ACCAACUAAAACAUUUUUAUUUGCGUCAUAAGUACUUGUCGUGAGCAAGCUUUAAAGUUUUCAAA-----------UA----UUUGUAAUCAGAGAACGGAAGUUUCUGAUGCAAAAC
...................(((((((((......((((.(....)))))((((...((((((...-----------..----..........)))))).))))....))))))))).. ( -21.86)
>DroSec_CAF1 7411 106 - 1
ACCAACUAUAACGUUUAUAUUUGCGUCAUAAGUACUUGUCGUGAGCAAGCUUUAAAGUU-UAAAA-----------UAUGUGUUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAAC
...................((((((((((((((((.(((..(((((..........)))-))..)-----------)).))))))))))(((((((.(....)))))))))))))).. ( -25.60)
>DroSim_CAF1 6826 106 - 1
ACCAACUAUAACGUUUAUAUUUGCGUCAUAAGUACUUGUCGUGAGCAAGCUUUAAAGUU-UCAAA-----------UAUGUGUUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAAC
...............((((((((...........((((.(....)))))..........-.))))-----------))))..(((((.((((((((.(....)))))))))))))).. ( -23.75)
>DroEre_CAF1 8322 117 - 1
ACCAACUAUGACGUUUAUAUUUCCCUCAUGAGUACUUAUCGUGAGUAAUCUUAAAAGUU-UCUAAAAGUUAGAACUCAAGUAUUUGUGAUCAGCGAACGUAGGUUUCUGACGCAAAAC
....(((.(((.............(((((((.......))))))).............(-((((.....))))).)))))).((((((.((((.((((....)))))))))))))).. ( -22.90)
>consensus
ACCAACUAUAACGUUUAUAUUUGCGUCAUAAGUACUUGUCGUGAGCAAGCUUUAAAGUU_UCAAA___________UAUGUGUUUGUGAUCAGAGAACGCAAGUUUCUGAUGCAAAAC
...((((..........((((((.....))))))((((.(....)))))......)))).......................((((((.((((.((((....)))))))))))))).. (-17.44 = -17.00 +  -0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:11 2006