Locus 3463

Sequence ID 2R_DroMel_CAF1
Location 11,629,397 – 11,629,487
Length 90
Max. P 0.555810
window5650 window5651

overview

Window 0

Location 11,629,397 – 11,629,487
Length 90
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 96.02
Mean single sequence MFE -9.52
Consensus MFE -9.12
Energy contribution -8.96
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.06
Structure conservation index 0.96
SVM decision value 0.02
SVM RNA-class probability 0.541672
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11629397 90 + 20766785
AACAUAUAUUCGAUCGAUCACAUAAGCUAUCGUAAUCAUAGGCCCAACACUACUUUAAGACACACGACCAA-AAACCGAUCGCUUUACACA
..........((((((((.((..........)).))).(((........)))...................-.....)))))......... (  -7.70)
>DroSec_CAF1 1950 90 + 1
AACAUACUUUCGAUCGAUCACAUAAGCUAUCGCAAUCAUAGGCCCAACACUACUUUAAGACACACGACCAA-AAACCGAUCGCUUUACACA
..........((((((.........((....)).....(((........)))...................-....))))))......... (  -9.60)
>DroSim_CAF1 1953 90 + 1
AACAUACUUUCGAUCGAUCACAUAAGCUAUCGCAAUCAUAGGCCCAACACUACUUUAAGACACACGACCAA-AAACCGAUCGCUUUACACA
..........((((((.........((....)).....(((........)))...................-....))))))......... (  -9.60)
>DroEre_CAF1 1914 90 + 1
AACAUACUUUCGAUCGAUCACAUAAGCUAUCGCUAUCAUAGGCCCAACACUACUUUAAGACACACGACAAA-AAACCGAUCGCUUUACACA
..........((((((........(((....)))....(((........)))...................-....))))))......... ( -10.30)
>DroYak_CAF1 1938 91 + 1
AACAUACUUUCGAUCGAUCACAUAAGCAAUCGCUAUCAUAGGCCCAACACUACCUUAAGACACACGACAAAAAAACCGAUCGCUUUACACA
..........((((((........(((....)))....(((........)))........................))))))......... ( -10.40)
>consensus
AACAUACUUUCGAUCGAUCACAUAAGCUAUCGCAAUCAUAGGCCCAACACUACUUUAAGACACACGACCAA_AAACCGAUCGCUUUACACA
..........((((((.........((....)).....(((........)))........................))))))......... ( -9.12 =  -8.96 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,629,397 – 11,629,487
Length 90
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 96.02
Mean single sequence MFE -21.59
Consensus MFE -20.04
Energy contribution -19.76
Covariance contribution -0.28
Combinations/Pair 1.04
Mean z-score -1.11
Structure conservation index 0.93
SVM decision value 0.04
SVM RNA-class probability 0.555810
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11629397 90 - 20766785
UGUGUAAAGCGAUCGGUUU-UUGGUCGUGUGUCUUAAAGUAGUGUUGGGCCUAUGAUUACGAUAGCUUAUGUGAUCGAUCGAAUAUAUGUU
.(((((...(((((((((.-.((((((((.((((............)))).)))))))).....((....)))))))))))..)))))... ( -21.50)
>DroSec_CAF1 1950 90 - 1
UGUGUAAAGCGAUCGGUUU-UUGGUCGUGUGUCUUAAAGUAGUGUUGGGCCUAUGAUUGCGAUAGCUUAUGUGAUCGAUCGAAAGUAUGUU
.(..((...(((((((((.-..(((((((.((((............)))).)))))))((....))......)))))))))....))..). ( -20.90)
>DroSim_CAF1 1953 90 - 1
UGUGUAAAGCGAUCGGUUU-UUGGUCGUGUGUCUUAAAGUAGUGUUGGGCCUAUGAUUGCGAUAGCUUAUGUGAUCGAUCGAAAGUAUGUU
.(..((...(((((((((.-..(((((((.((((............)))).)))))))((....))......)))))))))....))..). ( -20.90)
>DroEre_CAF1 1914 90 - 1
UGUGUAAAGCGAUCGGUUU-UUUGUCGUGUGUCUUAAAGUAGUGUUGGGCCUAUGAUAGCGAUAGCUUAUGUGAUCGAUCGAAAGUAUGUU
.(..((...(((((((((.-..(((((((.((((............)))).)))))))((....))......)))))))))....))..). ( -21.70)
>DroYak_CAF1 1938 91 - 1
UGUGUAAAGCGAUCGGUUUUUUUGUCGUGUGUCUUAAGGUAGUGUUGGGCCUAUGAUAGCGAUUGCUUAUGUGAUCGAUCGAAAGUAUGUU
.(..((...(((((((((.....(((((.((((...((((........))))..))))))))).........)))))))))....))..). ( -22.94)
>consensus
UGUGUAAAGCGAUCGGUUU_UUGGUCGUGUGUCUUAAAGUAGUGUUGGGCCUAUGAUUGCGAUAGCUUAUGUGAUCGAUCGAAAGUAUGUU
.(..((...(((((((((....(((((((.((((............)))).)))))))((....))......)))))))))....))..). (-20.04 = -19.76 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:10 2006