Locus 4733

Sequence ID 3R_DroMel_CAF1
Location 12,421,262 – 12,421,421
Length 159
Max. P 0.575191
window7773 window7774

overview

Window 3

Location 12,421,262 – 12,421,382
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.99
Mean single sequence MFE -20.15
Consensus MFE -13.62
Energy contribution -14.36
Covariance contribution 0.74
Combinations/Pair 1.04
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value -0.06
SVM RNA-class probability 0.505317
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12421262 120 + 27905053
GAAGUAUGCUCAUAAAAAAAAAGGAAAAUCGUAAACUACAAUAGAUUGAUCGAUCACCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCA
(.(((.(((.....................))).))).)....((((((((((.......)))..(((((.(((((..(((...(((....))))))..))))).)))))..))))))). ( -17.70)
>DroSec_CAF1 20157 114 + 1
GAAGUAUGCUCAUAAAAAUAAA-UAAAAUCGUAAACU-----AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCA
..(((.(((.............-.......))).)))-----.((((((((((.......)))..(((((.(((((..(((...(((....))))))..))))).)))))..))))))). ( -17.65)
>DroSim_CAF1 19904 104 + 1
GAAG----CUCAUAAAA-------AAAAUCGUAAACU-----AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCCCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCA
....----.........-------.............-----.((((((((((.......)))..(((((.((((........((((....)))).....)))).)))))..))))))). ( -14.82)
>DroEre_CAF1 20498 102 + 1
AAAGUAUGCUAAUAAGCGCAGU-UAAAAGCGUAAACU-----AGAUUGAUA-----------GUAUUUCAACACCUCGUAACUAAGUUAUUACU-UGAAAGGUGAUGAAACUAUCAAUCA
...............((((...-.....)))).....-----.((((((((-----------((..((((.(((((..(((.(((....))).)-))..))))).)))))))))))))). ( -29.20)
>DroYak_CAF1 20840 114 + 1
AAGGUAUGCUAAUAAGCGAAGC-UAAAAGCGUAAACU-----AGAUUGAUCGAUCUCCAUUCGCAUUUCAACACCUCGUAACUAAGCCAUUACUUUGAAAGGUGAUGAAACAAUUAAUCA
..(((..........(((((((-.....)).......-----(((((....)))))...))))).(((((.(((((..(((.(((....)))..)))..))))).)))))......))). ( -21.40)
>consensus
GAAGUAUGCUCAUAAAAAAAAA_UAAAAUCGUAAACU_____AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCA
...........................................((((((((((.......)))..(((((.(((((..(((...(((....))))))..))))).)))))..))))))). (-13.62 = -14.36 +   0.74)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,421,302 – 12,421,421
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.73
Mean single sequence MFE -24.76
Consensus MFE -13.62
Energy contribution -14.36
Covariance contribution 0.74
Combinations/Pair 1.04
Mean z-score -2.45
Structure conservation index 0.55
SVM decision value 0.08
SVM RNA-class probability 0.575191
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12421302 119 + 27905053
AUAGAUUGAUCGAUCACCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCAACUUUUU-AGUAGUGUACUCGUACGAGCCAAAUAAACCUG
...((((....))))....(((((((((((.(((((..(((...(((....))))))..))))).))))((((((((........))-))))))......)))))))............. ( -24.60)
>DroSec_CAF1 20193 117 + 1
--AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCACCUUUUU-AGUAGUCUACUCGUACGAGCCAAAUAAACCUG
--...((((.(((.......)))....))))...((((((....(((.((((((..((((((((((..........)))))))))).-))))))..)))..))))))............. ( -28.50)
>DroSim_CAF1 19930 117 + 1
--AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCCCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCACCUUUUU-AGUAGUCUACUCGUACGAGCCAAAUAAACCUG
--...((((.(((.......)))....)))).....((((....(((.((((((..((((((((((..........)))))))))).-))))))..)))..))))............... ( -24.70)
>DroEre_CAF1 20534 98 + 1
--AGAUUGAUA-----------GUAUUUCAACACCUCGUAACUAAGUUAUUACU-UGAAAGGUGAUGAAACUAUCAAUCAAGUUUUUAAGU--------ACUACGAGCCAAAUAAAGCUG
--.((((((((-----------((..((((.(((((..(((.(((....))).)-))..))))).))))))))))))))............--------......(((........))). ( -26.00)
>DroYak_CAF1 20876 117 + 1
--AGAUUGAUCGAUCUCCAUUCGCAUUUCAACACCUCGUAACUAAGCCAUUACUUUGAAAGGUGAUGAAACAAUUAAUCAAGUGCUUCAGUAUUGUACUACUACGAUCCAAAUAA-CCCG
--.....(((((.............(((((.(((((..(((.(((....)))..)))..))))).)))))..........(((((.........)))))....))))).......-.... ( -20.00)
>consensus
__AGAUUGAUCGAUCUCCAUUCGUAUUUCAACACCUCGUAACUAAGUUAUUACUUUGAAAGGUGAUGAAACUAUUAAUCAACUUUUU_AGUAGUCUACUCGUACGAGCCAAAUAAACCUG
...((((((((((.......)))..(((((.(((((..(((...(((....))))))..))))).)))))..)))))))......................................... (-13.62 = -14.36 +   0.74)

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 11:37:40 2006