Locus 5856

Sequence ID 2R_DroMel_CAF1
Location 18,516,316 – 18,516,451
Length 135
Max. P 0.980763
window9403 window9404

overview

Window 3

Location 18,516,316 – 18,516,425
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.29
Mean single sequence MFE -28.00
Consensus MFE -16.98
Energy contribution -17.82
Covariance contribution 0.84
Combinations/Pair 1.23
Mean z-score -2.80
Structure conservation index 0.61
SVM decision value 1.87
SVM RNA-class probability 0.980763
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18516316 109 + 20766785
-GCAACCGGCAA-CCAGC-------AACUUGCAACUUGCGACUGCUGCGACUGUUG--CGACGGGCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAGCUGCCAAACAC
-(((....((((-(((((-------(..((((.....)))).))))).....))))--)(((((....))))).....)))....................(((((....)))))..... ( -32.20)
>DroVir_CAF1 24181 91 + 1
-------AGCCACACAGC-------A---------UUGC---C--GUCAACAGCAGCCAGACGGCCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAACUGCCA-ACAC
-------.......(((.-------.---------((((---(--((....((((....(((((....))))).....)))).((......)).......)))))))..)))...-.... ( -18.90)
>DroSec_CAF1 15281 116 + 1
-GCAACCGGCAA-CCAGCAACCAGCAACCAGCAACUUGCAACUGCUGUGACUGCUG--CGACGGGCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAACUGCCAAACAC
-......((((.-.(((((.((((((....((.....))...))))).)..)))))--.(((((....))))).....))))...................(((((....)))))..... ( -31.20)
>DroEre_CAF1 18497 107 + 1
-GCAACCAGCAA-CCAGC-------AACCAGCAACUUGCAACU--UGCGACUGCUG--CGACGGGCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAACUGCCAAACAC
-(((..(((((.-...((-------((...((.....))...)--)))...)))))--.(((((....))))).....)))....................(((((....)))))..... ( -29.00)
>DroYak_CAF1 21133 108 + 1
GGCAACUUGCAA-CCAGC-------AACUUGCAACUUGCAACU--CGCAACUGCUG--CGACGGGCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAACUGCCAAACAC
.((((.((((..-...))-------)).)))).....(((...--.(((.....))--)(((((....))))).....)))....................(((((....)))))..... ( -28.70)
>consensus
_GCAACCAGCAA_CCAGC_______AACCAGCAACUUGCAACU__UGCGACUGCUG__CGACGGGCAACUGUCCAUUAUGCUCACUCACCUGUAAAAUAAAUGGCAAAACUGCCAAACAC
.......((((...................(((..(((((.....))))).))).....(((((....))))).....))))...................(((((....)))))..... (-16.98 = -17.82 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,516,347 – 18,516,451
Length 104
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.65
Mean single sequence MFE -35.18
Consensus MFE -21.92
Energy contribution -24.03
Covariance contribution 2.11
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.62
SVM decision value -0.00
SVM RNA-class probability 0.531292
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18516347 104 - 20766785
GGGGCAGC-----AGUUGUCAG------UUGGCCAAAGUGUUUGGCAGCUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGCCCGUCG--CAACAGUCGCAGCAGU
.(((((((-----...((((((------(((.((((.....))))))))).(((((((((((.....)))))))).))).....)))))))))))((.(--(.......)).))... ( -35.80)
>DroVir_CAF1 24197 109 - 1
GCGUGAGCCUCAGAGUUGUCAGCGC---GUUGCCAAAGUGU-UGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGGCCGUCUGGCUGCUGUUGAC--G--
((....)).........(((((((.---((.((((..(.((-..((.(((((((((((((((.....)))))))).)))....)))).))..)))...)))).)))))))))--.-- ( -37.30)
>DroSec_CAF1 15319 104 - 1
GGGGCAGC-----AGUUGUCAG------UUGGCCAAAGUGUUUGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGCCCGUCG--CAGCAGUCACAGCAGU
.(((((((-----...((((.(------((((((((.....))))).....(((((((((((.....)))))))).))))))).)))))))))))((.(--(....)).))...... ( -33.70)
>DroEre_CAF1 18528 102 - 1
GGGGCAGC-----AGUUGUCAG------UUGGCCAAAGUGUUUGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGCCCGUCG--CAGCAGUCGCA--AGU
.(((((((-----...((((.(------((((((((.....))))).....(((((((((((.....)))))))).))))))).)))))))))))....--..((....)).--... ( -34.00)
>DroWil_CAF1 22293 103 - 1
GGGA---------GUUUGUCAGCGCUGGCUGGGCCAAGUGU-UGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUAGACAGUUGCAAGUCU--CUUUUUUUGGG--GCC
....---------((((((((((((((((...))).)))))-)))).(((.(((((((((((.....)))))))).))).)))))))........((((--(.......)))--)). ( -32.30)
>DroYak_CAF1 21165 102 - 1
GGGGCAGC-----AGUUGUCAG------UUGGCCAAAGUGUUUGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGCCCGUCG--CAGCAGUUGCG--AGU
.(((((((-----...((((.(------((((((((.....))))).....(((((((((((.....)))))))).))))))).))))))))))).(((--(((...)))))--).. ( -38.00)
>consensus
GGGGCAGC_____AGUUGUCAG______UUGGCCAAAGUGUUUGGCAGUUUUGCCAUUUAUUUUACAGGUGAGUGAGCAUAAUGGACAGUUGCCCGUCG__CAGCAGUCGCA__AGU
.(((((((........((((...........(((((.....))))).(((.(((((((((((.....)))))))).))).))).)))))))))))...................... (-21.92 = -24.03 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:32 2006