Locus 38

Sequence ID 4_DroMel_CAF1
Location 376,815 – 376,908
Length 93
Max. P 0.999937
window61 window62

overview

Window 1

Location 376,815 – 376,908
Length 93
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 76.51
Mean single sequence MFE -25.52
Consensus MFE -20.65
Energy contribution -20.43
Covariance contribution -0.22
Combinations/Pair 1.15
Mean z-score -3.95
Structure conservation index 0.81
SVM decision value 4.67
SVM RNA-class probability 0.999937
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 376815 93 + 1281640
AUAUAUCAUAUUCUAGCAAGAAAGUUACACAAUGGUUUGACUGAGUAGUCAAUCUCGACUACACAGUCAAGCUUUUUACACCCGU--------UUCUCGUU
..............(((.(((((..........((((((((((.((((((......)))))).))))))))))...........)--------)))).))) ( -26.40)
>DroSec_CAF1 1496 97 + 1
GUAUAUCAUACUCUACCCAGAAAUGUAUACAUUGGUUUGAUUUAGUAGUCAACCCUGACUACACAGUCAAGCUAUGUAGACCAACCAAACUAGAUCU----
...........((((.........((.(((((.(((((((((..(((((((....)))))))..)))))))))))))).)).........))))...---- ( -23.77)
>DroSim_CAF1 1602 96 + 1
GUAUAUCAUACUCUACCCAGAAAUGUACACAUGGGUUUGAUUUAGUAGUCAACCCUGACUACCCAGUCAAGCUAUGUGGACCAACCA-ACUAGAUCU----
...........((((..((....))..(((((((.(((((((..(((((((....)))))))..)))))))))))))).........-..))))...---- ( -26.40)
>consensus
GUAUAUCAUACUCUACCCAGAAAUGUACACAUUGGUUUGAUUUAGUAGUCAACCCUGACUACACAGUCAAGCUAUGUAGACCAACCA_ACUAGAUCU____
...........................(((((.(((((((((..((((((......))))))..))))))))))))))....................... (-20.65 = -20.43 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 376,815 – 376,908
Length 93
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 76.51
Mean single sequence MFE -24.67
Consensus MFE -14.91
Energy contribution -14.03
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -1.76
Structure conservation index 0.60
SVM decision value 0.39
SVM RNA-class probability 0.715138
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 376815 93 - 1281640
AACGAGAA--------ACGGGUGUAAAAAGCUUGACUGUGUAGUCGAGAUUGACUACUCAGUCAAACCAUUGUGUAACUUUCUUGCUAGAAUAUGAUAUAU
..((((((--------(...(..(((...(.(((((((.(((((((....))))))).))))))).)..)))..)...)))))))................ ( -25.90)
>DroSec_CAF1 1496 97 - 1
----AGAUCUAGUUUGGUUGGUCUACAUAGCUUGACUGUGUAGUCAGGGUUGACUACUAAAUCAAACCAAUGUAUACAUUUCUGGGUAGAGUAUGAUAUAC
----.......((((((((((((..........))))..((((((......))))))..))))))))....((((((((((((....)))).))).))))) ( -21.90)
>DroSim_CAF1 1602 96 - 1
----AGAUCUAGU-UGGUUGGUCCACAUAGCUUGACUGGGUAGUCAGGGUUGACUACUAAAUCAAACCCAUGUGUACAUUUCUGGGUAGAGUAUGAUAUAC
----...((((.(-..(...((.(((((.(.((((...(((((((......)))))))...)))).)..))))).))....)..).))))........... ( -26.20)
>consensus
____AGAUCUAGU_UGGUUGGUCUACAUAGCUUGACUGUGUAGUCAGGGUUGACUACUAAAUCAAACCAAUGUGUACAUUUCUGGGUAGAGUAUGAUAUAC
...................(((........(((((((....))))))).((((........)))))))..(((((....((((....))))....))))). (-14.91 = -14.03 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:11 2006