Locus 2389

Sequence ID 2R_DroMel_CAF1
Location 8,623,459 – 8,623,599
Length 140
Max. P 0.975902
window3952 window3953

overview

Window 2

Location 8,623,459 – 8,623,572
Length 113
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 86.45
Mean single sequence MFE -38.45
Consensus MFE -30.14
Energy contribution -30.00
Covariance contribution -0.14
Combinations/Pair 1.14
Mean z-score -2.94
Structure conservation index 0.78
SVM decision value 0.78
SVM RNA-class probability 0.849500
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8623459 113 + 20766785
GCAAAUUUGAUGUUCCGCUCGAACACUUUCCAGUGGGGACCCUUCGCCCAU-----CGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC
((......((....(((((.(((....))).)))))(((((((.((.....-----)).))))))).......))((((((((((.((((.....))))))))))))))))....... ( -42.20)
>DroSec_CAF1 3135 112 + 1
GCAAAUUUGAUGUUCCGCUCGAACACUUUCCAGUGGGGACCCUUCGCCCAU-----CGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCC-
((......((....(((((.(((....))).)))))(((((((.((.....-----)).))))))).......))((((((((((.((((.....))))))))))))))))......- ( -42.20)
>DroSim_CAF1 3074 113 + 1
GCAAAUUUGAUGUUCCGCUCGAACACUUUCCAGUGGGGACCCUUCGCCCAU-----CGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC
((......((....(((((.(((....))).)))))(((((((.((.....-----)).))))))).......))((((((((((.((((.....))))))))))))))))....... ( -42.20)
>DroEre_CAF1 3739 87 + 1
GCAAAUUUGAUGUUCCGCUCGAACACU-UCCAGUGGGGACCCUU------------------------------CGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUGGCC
..............(((((.((.....-)).)))))((.((...------------------------------(((((((((((.((((.....)))))))))))))))....)))) ( -29.80)
>DroYak_CAF1 3512 113 + 1
GCAAAUUUGAUGUUCCACUCGAACACUUUCCAGUGGGGAGCCUUCGCCCAU-----CGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC
((......((....(((((.(((....))).)))))(((.(((.((.....-----)).))).))).......))((((((((((.((((.....))))))))))))))))....... ( -38.10)
>DroAna_CAF1 3305 118 + 1
GCAAAUUUGAUGUUCCGCUCGAACACUUUUUAGCGGCGACCUUUCGUCCAUCAGAUCGUCGGAUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUUGGC
....((((((((..(((((.(((....))).))))).(((.....))))))))))).((((((......)))..(((((((((((.((((.....))))))))))))))).....))) ( -36.20)
>consensus
GCAAAUUUGAUGUUCCGCUCGAACACUUUCCAGUGGGGACCCUUCGCCCAU_____CGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC
............(((((((.(((....))).))))))).......((((...........))))..........(((((((((((.((((.....)))))))))))))))........ (-30.14 = -30.00 +  -0.14)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 8,623,499 – 8,623,599
Length 100
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 96.35
Mean single sequence MFE -28.03
Consensus MFE -27.40
Energy contribution -27.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.98
SVM decision value 1.76
SVM RNA-class probability 0.975902
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8623499 100 + 20766785
CCUUCGCCCAUCGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC-CCAAAAGCAACAGCAACAACAACAAGA
.....((((......))))......((((.((((((((((.((((.....))))))))))))))(((((....-...)))))...............)))) ( -27.50)
>DroSec_CAF1 3175 99 + 1
CCUUCGCCCAUCGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCC--CCAAAAGCAGCAGCAGCAACAACAACA
.....((((......))))...........((((((((((.((((.....))))))))))))))(((((...--...))))).((....)).......... ( -28.80)
>DroSim_CAF1 3114 101 + 1
CCUUCGCCCAUCGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCCGCCAAAAGCAGCAGCAGCAACAACAACA
.....((((......))))...........((((((((((.((((.....))))))))))))))(((((........))))).((....)).......... ( -28.60)
>DroYak_CAF1 3552 100 + 1
CCUUCGCCCAUCGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC-CCAAAAGCAACAAAAGCAACAACAACA
.....((((......))))...((((....((((((((((.((((.....))))))))))))))(((((....-...)))))....))))........... ( -27.20)
>consensus
CCUUCGCCCAUCGCAGGGUCCACUUUCUUCGCUUAGUGGCUCGUUGAUUGAAUGGCCACUAAGUGCUUUCCCC_CCAAAAGCAACAGCAGCAACAACAACA
.....((((......))))...........((((((((((.((((.....))))))))))))))(((((........)))))................... (-27.40 = -27.40 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:51 2006