Locus 8396

Sequence ID X_DroMel_CAF1
Location 20,834,238 – 20,834,353
Length 115
Max. P 0.999961
window13786 window13787 window13788 window13789

overview

Window 6

Location 20,834,238 – 20,834,328
Length 90
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.66
Mean single sequence MFE -27.07
Consensus MFE -15.14
Energy contribution -16.14
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.56
SVM decision value 0.69
SVM RNA-class probability 0.822815
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20834238 90 + 22224390
UGGCU-----------------GACACUUGGCCCGACCAAAGGCAACAGUUCGAAUAGAAGGCACUGCCU-------------AUGUGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGC
(((.(-----------------(..(((..(((........)))...))).......(((((((.(((..-------------....))).))))))))).)))....(((......))) ( -26.10)
>DroSim_CAF1 6671 102 + 1
--GCCACACAAUCCGCACACAAUACACUUGGCC--ACCAAAGGCAACGGUUCGAAUAGAAGGCACUGCC--------------AUGAGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGC
--(((.........................(((--......)))..((((..((((.(((((((.(((.--------------....))).))))))).))....)).)))).....))) ( -26.80)
>DroYak_CAF1 797 107 + 1
UAACU---UGGU----------AACACUUGACCUGACCAAAGCCAACGGUUCGAAUAGAAGGCACUGCCUAUAGGCGACGCCUAUAAACACUGCCUUCCAUCCAAUCCGCCGACUUAGUG
(((.(---((((----------.....((((.(((...........))).))))...(((((((.((..(((((((...)))))))..)).)))))))..........))))).)))... ( -28.30)
>consensus
U_GCU______U__________AACACUUGGCC_GACCAAAGGCAACGGUUCGAAUAGAAGGCACUGCCU_____________AUGAGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGC
...........................(((((.........(....)((((.((...(((((((.(((...................))).)))))))..)).)))).)))))....... (-15.14 = -16.14 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,834,238 – 20,834,328
Length 90
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.66
Mean single sequence MFE -48.43
Consensus MFE -36.52
Energy contribution -36.74
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -5.34
Structure conservation index 0.75
SVM decision value 4.90
SVM RNA-class probability 0.999961
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20834238 90 - 22224390
GCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCACAU-------------AGGCAGUGCCUUCUAUUCGAACUGUUGCCUUUGGUCGGGCCAAGUGUC-----------------AGCCA
(((.(((.((((((.((((((((((((((.(((....-------------..))).)))))))))))))).)))))).))).)))..(((........-----------------.))). ( -42.50)
>DroSim_CAF1 6671 102 - 1
GCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCUCAU--------------GGCAGUGCCUUCUAUUCGAACCGUUGCCUUUGGU--GGCCAAGUGUAUUGUGUGCGGAUUGUGUGGC--
(((.(((.((((((.((((((((((((((.(((....--------------.))).)))))))))))))).)))))).))).)))--.((((......(((....)))......))))-- ( -46.80)
>DroYak_CAF1 797 107 - 1
CACUAAGUCGGCGGAUUGGAUGGAAGGCAGUGUUUAUAGGCGUCGCCUAUAGGCAGUGCCUUCUAUUCGAACCGUUGGCUUUGGUCAGGUCAAGUGUU----------ACCA---AGUUA
.(((((((((((((.((((((((((((((.(((((((((((...))))))))))).)))))))))))))).)))))))).)))))..(((........----------))).---..... ( -56.00)
>consensus
GCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCUCAU_____________AGGCAGUGCCUUCUAUUCGAACCGUUGCCUUUGGUC_GGCCAAGUGUA__________A______AGC_A
(((.(((.((((((.((((((((((((((.(((...................))).)))))))))))))).)))))).))).)))................................... (-36.52 = -36.74 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,834,261 – 20,834,353
Length 92
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 79.47
Mean single sequence MFE -30.20
Consensus MFE -21.42
Energy contribution -22.31
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -2.96
Structure conservation index 0.71
SVM decision value 2.85
SVM RNA-class probability 0.997373
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20834261 92 + 22224390
AGGCAACAGUUCGAAUAGAAGGCACUGCCU-------------AUGUGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGCGGCCAAAUGACCAUACUCUUCCUUU
.(((.............(((((((.(((..-------------....))).))))))).........((((......)))))))..................... ( -27.60)
>DroSim_CAF1 6707 91 + 1
AGGCAACGGUUCGAAUAGAAGGCACUGCC--------------AUGAGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGCGGCCAAAUGGCCAUACUCGUCCUUC
.(....)((..(((...(((((((.(((.--------------....))).)))))))..........(((......)))((((....))))....))).))... ( -33.10)
>DroYak_CAF1 824 105 + 1
AGCCAACGGUUCGAAUAGAAGGCACUGCCUAUAGGCGACGCCUAUAAACACUGCCUUCCAUCCAAUCCGCCGACUUAGUGGGGCCCCUAACCAUCCACUUCCUUU
......((((..((((.(((((((.((..(((((((...)))))))..)).))))))).))....)).))))....((((((...........))))))...... ( -29.90)
>consensus
AGGCAACGGUUCGAAUAGAAGGCACUGCCU_____________AUGAGCACUGCCUUCCAUCCAAUCCGCCGACUUAGGCGGCCAAAUGACCAUACUCUUCCUUU
.(((...((((.((...(((((((.(((...................))).)))))))..)).))))((((......)))))))..................... (-21.42 = -22.31 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 20,834,261 – 20,834,353
Length 92
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -49.07
Consensus MFE -37.85
Energy contribution -37.41
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -6.14
Structure conservation index 0.77
SVM decision value 1.71
SVM RNA-class probability 0.973491
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20834261 92 - 22224390
AAAGGAAGAGUAUGGUCAUUUGGCCGCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCACAU-------------AGGCAGUGCCUUCUAUUCGAACUGUUGCCU
..(((((.(((............(((((......))))).((((((((((((((.(((....-------------..))).))))))))))))))))).)).))) ( -41.40)
>DroSim_CAF1 6707 91 - 1
GAAGGACGAGUAUGGCCAUUUGGCCGCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCUCAU--------------GGCAGUGCCUUCUAUUCGAACCGUUGCCU
....(((.....(((((....))))).....)))(((((.((((((((((((((.(((....--------------.))).)))))))))))))).))))).... ( -45.90)
>DroYak_CAF1 824 105 - 1
AAAGGAAGUGGAUGGUUAGGGGCCCCACUAAGUCGGCGGAUUGGAUGGAAGGCAGUGUUUAUAGGCGUCGCCUAUAGGCAGUGCCUUCUAUUCGAACCGUUGGCU
......(((((..(((.....)))))))).(((((((((.((((((((((((((.(((((((((((...))))))))))).)))))))))))))).))))))))) ( -59.90)
>consensus
AAAGGAAGAGUAUGGUCAUUUGGCCGCCUAAGUCGGCGGAUUGGAUGGAAGGCAGUGCUCAU_____________AGGCAGUGCCUUCUAUUCGAACCGUUGCCU
.............((((....)))).....((.((((((.((((((((((((((.(((...................))).)))))))))))))).)))))).)) (-37.85 = -37.41 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:55 2006