Locus 8340

Sequence ID 3L_DroMel_CAF1
Location 21,852,138 – 21,852,243
Length 105
Max. P 0.626567
window13650 window13651

overview

Window 0

Location 21,852,138 – 21,852,243
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.39
Mean single sequence MFE -24.75
Consensus MFE -18.44
Energy contribution -17.72
Covariance contribution -0.72
Combinations/Pair 1.24
Mean z-score -0.90
Structure conservation index 0.74
SVM decision value 0.19
SVM RNA-class probability 0.626567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21852138 105 + 23771897
-----------CACACAACCGUAAUGAUCAAUCA----AUCAAUCGAACAUAGACCUGUCCAGUAUUUCCACUUGCCCUGGCUACCGGCGGCCUACAUGCUGGUAUCUCAGGCUUGGCGG
-----------.......((((..((((......----))))......((.((.((((.(((((((........(((((((...)))).)))....))))))).....)))))))))))) ( -27.30)
>DroPse_CAF1 71803 107 + 1
-----------CACACAAA--UACAAAUGAAAAAAUACAACAAUAAAACGUAGACCUGUCCAGUAUUUCCACUUGCCCUGGCUACCGGCGGCCUACAUGCUGGUAUUUCAGGCUUAGCGG
-----------........--...........................(((.((((((.(((((((........(((((((...)))).)))....))))))).....)))).)).))). ( -23.60)
>DroSim_CAF1 31717 109 + 1
-----------CACACAACCGUAAUGAUCAAUCAAUCAAUCAAUCGAACAUAGACCUGUCCAGUAUUUCCACUUGCCCUGGCUACCGGCGGCCUACAUGCUGGUAUCUCAGGCUUGGCGG
-----------.......((((..((((......))))..........((.((.((((.(((((((........(((((((...)))).)))....))))))).....)))))))))))) ( -27.30)
>DroEre_CAF1 32563 105 + 1
-----------CACAAAACCGAAAUGAUCAAUCA----AUCGAACGAACAUAGACCUGUCCAGUAUUUCCACUUGCCCUGGCUACCGGCGGCCUACAUGCUGGUAUCUCAGGCUUGGCGG
-----------.......(((...((((......----))))......((.((.((((.(((((((........(((((((...)))).)))....))))))).....)))))))).))) ( -24.80)
>DroWil_CAF1 18288 118 + 1
AUCUUCAAAAAAAAAAAAACAAAAAAAACAAAUAAUU-ACCAAUCAUA-UUAGACCUGCCCAGUAUUUCCACUGGCUUUGGCUACCGGUGGCCUACAUGCUGGUAUUUCAGGCCUUACGG
.....................................-..........-..((.((((.(((((((..(((((((.........))))))).....))))))).....)))).))..... ( -21.80)
>DroMoj_CAF1 87836 113 + 1
AUAUCGAAAAAAAAAAAAUCGAAUUAAAAAA---AUG---UAAUACUA-UUAGACCUGUCCAGUAUUUCCACUUGCUUUGGCUACCGGUGGUCUACAUGCUGGUAUUUCAGGCUUAGCGG
...((((...........)))).........---...---.....(..-(((..((((.(((((((..(((((.((....))....))))).....))))))).....))))..)))..) ( -23.70)
>consensus
___________CACAAAACCGAAAUAAUCAAUCAAU__AUCAAUCGAACAUAGACCUGUCCAGUAUUUCCACUUGCCCUGGCUACCGGCGGCCUACAUGCUGGUAUCUCAGGCUUGGCGG
..................................................(((.((((.(((((((........(((((((...)))).)))....))))))).....)))).))).... (-18.44 = -17.72 +  -0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,852,138 – 21,852,243
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.39
Mean single sequence MFE -30.65
Consensus MFE -22.09
Energy contribution -22.53
Covariance contribution 0.45
Combinations/Pair 1.09
Mean z-score -0.87
Structure conservation index 0.72
SVM decision value -0.01
SVM RNA-class probability 0.526347
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21852138 105 - 23771897
CCGCCAAGCCUGAGAUACCAGCAUGUAGGCCGCCGGUAGCCAGGGCAAGUGGAAAUACUGGACAGGUCUAUGUUCGAUUGAU----UGAUUGAUCAUUACGGUUGUGUG-----------
.(((..((((..........(.(((((((((.((((((.(((.......)))...))))))...))))))))).)(((..(.----...)..))).....))))..)))----------- ( -30.90)
>DroPse_CAF1 71803 107 - 1
CCGCUAAGCCUGAAAUACCAGCAUGUAGGCCGCCGGUAGCCAGGGCAAGUGGAAAUACUGGACAGGUCUACGUUUUAUUGUUGUAUUUUUUCAUUUGUA--UUUGUGUG-----------
..((.((....(((((((.((((((((((((.((((((.(((.......)))...))))))...))))))))......)))))))))))....)).)).--........----------- ( -29.30)
>DroSim_CAF1 31717 109 - 1
CCGCCAAGCCUGAGAUACCAGCAUGUAGGCCGCCGGUAGCCAGGGCAAGUGGAAAUACUGGACAGGUCUAUGUUCGAUUGAUUGAUUGAUUGAUCAUUACGGUUGUGUG-----------
.(((..((((..........(.(((((((((.((((((.(((.......)))...))))))...))))))))).)(((..(((....)))..))).....))))..)))----------- ( -33.70)
>DroEre_CAF1 32563 105 - 1
CCGCCAAGCCUGAGAUACCAGCAUGUAGGCCGCCGGUAGCCAGGGCAAGUGGAAAUACUGGACAGGUCUAUGUUCGUUCGAU----UGAUUGAUCAUUUCGGUUUUGUG-----------
.(((.(((((.(((((....(.(((((((((.((((((.(((.......)))...))))))...))))))))).)....(((----(....)))))))))))))).)))----------- ( -34.50)
>DroWil_CAF1 18288 118 - 1
CCGUAAGGCCUGAAAUACCAGCAUGUAGGCCACCGGUAGCCAAAGCCAGUGGAAAUACUGGGCAGGUCUAA-UAUGAUUGGU-AAUUAUUUGUUUUUUUUGUUUUUUUUUUUUUGAAGAU
((....)).......((((((((((((((((.((((((.(((.......)))...))))))...))))).)-)))).)))))-)................((((((........)))))) ( -31.30)
>DroMoj_CAF1 87836 113 - 1
CCGCUAAGCCUGAAAUACCAGCAUGUAGACCACCGGUAGCCAAAGCAAGUGGAAAUACUGGACAGGUCUAA-UAGUAUUA---CAU---UUUUUUAAUUCGAUUUUUUUUUUUUCGAUAU
..((((.((.((......))))...((((((.((((((.(((.......)))...))))))...)))))).-))))....---...---.........((((...........))))... ( -24.20)
>consensus
CCGCCAAGCCUGAAAUACCAGCAUGUAGGCCGCCGGUAGCCAGGGCAAGUGGAAAUACUGGACAGGUCUAUGUUCGAUUGAU__AUUGAUUGAUCAUUACGGUUGUGUG___________
.......((.((......))))(((((((((.((((((.(((.......)))...))))))...)))))))))............................................... (-22.09 = -22.53 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:02 2006