Locus 6984

Sequence ID 3R_DroMel_CAF1
Location 18,419,362 – 18,419,500
Length 138
Max. P 0.869084
window11323 window11324

overview

Window 3

Location 18,419,362 – 18,419,472
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.33
Mean single sequence MFE -29.66
Consensus MFE -16.18
Energy contribution -16.38
Covariance contribution 0.20
Combinations/Pair 1.19
Mean z-score -1.58
Structure conservation index 0.55
SVM decision value 0.00
SVM RNA-class probability 0.534922
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18419362 110 + 27905053
GACUACUACUACUAA--AAAAUUUGCUGUAGGUCAGUGCACA--------AGAGAAUCUCUUGAAAGUAGCCAUAGCUAUAAGCUAGCCAACUGGUCAUCACCGCCUCGGCGGCUGACUC
(((((...(((((..--.......((((.....))))...((--------((((...))))))..)))))...((((.....))))......))))).(((((((....)))).)))... ( -31.00)
>DroSec_CAF1 5114 93 + 1
GACUACUACUACUACUUGAAAUCUGCUGUAGGCCAGU---------------------------AAGUAGCCAUAGCUACAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUC
..............................(((((((---------------------------..(((((....)))))..(....)..))))))).(((((((....)))).)))... ( -27.90)
>DroSim_CAF1 5536 93 + 1
AACUACUACUAUUACUUAAAAUCUGCUGUAGUCCAGU---------------------------UAGUAGCCAUAGCUAUAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUC
..(((((((((((((............)))))..)).---------------------------))))))...((((.....))))(((....)))..(((((((....)))).)))... ( -24.40)
>DroEre_CAF1 5436 116 + 1
GACUACGACUG---CUGAAAAUCUGCUGCG-GUCAGUGGAAAUGAUGUGCAGAGCACCCCUUGAAAGUAGCCAUAGCUAGGAGCUAGCCAACUGGCCAUCACCUCCUCGGUGGCUGACUC
..(((((((((---(............)))-))).)))).......((((...))))........(((((((((....(((((...(((....)))......)))))..)))))).))). ( -34.70)
>DroYak_CAF1 5472 116 + 1
GACUACGACUG---CUGAAAAUCUGAUAUG-GUUAGUGCAAGUUAUGAACAGAGAAUCUUCUGAAAGUAAUCAUAGCUACAAGCUAGCCAACUGGCCAUCACCUCCUCGGUGGCUGACUC
...........---..............((-((((((...((((((((.(((((....))))).......))))))))....))))))))...(((((((........)))))))..... ( -30.30)
>consensus
GACUACUACUA_UACUGAAAAUCUGCUGUAGGUCAGUG_A__________AGAG_A_C___UGAAAGUAGCCAUAGCUACAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUC
........................((((.....)))).............................(((((....)))))..(((((....)))))..(((((((....)))).)))... (-16.18 = -16.38 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,419,400 – 18,419,500
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.11
Mean single sequence MFE -29.02
Consensus MFE -20.85
Energy contribution -21.13
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.72
SVM decision value 0.86
SVM RNA-class probability 0.869084
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18419400 100 + 27905053
CA--------AGAGAAUCUCUUGAAAGUAGCCAUAGCUAUAAGCUAGCCAACUGGUCAUCACCGCCUCGGCGGCUGACUCAGAU------------UCAGAUUGAGACUCAGGCAUGCAA
((--------((((...))))))...(((((....)))))..((..(((..(((((((...((((....)))).)))).))).(------------((.....))).....)))..)).. ( -31.80)
>DroSec_CAF1 5151 84 + 1
------------------------AAGUAGCCAUAGCUACAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUCAGAU------------UCAGAUUGAGACUCAGGCAUGCAA
------------------------..((((((.((((.....))))(((....)))..(((((((....)))).)))(((((..------------.....))))).....))).))).. ( -26.60)
>DroSim_CAF1 5573 84 + 1
------------------------UAGUAGCCAUAGCUAUAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUCAGAU------------UCAGAUUGAGACUCAGGCAUGCAA
------------------------..((((((.((((.....))))(((....)))..(((((((....)))).)))(((((..------------.....))))).....))).))).. ( -26.60)
>DroEre_CAF1 5472 108 + 1
AAUGAUGUGCAGAGCACCCCUUGAAAGUAGCCAUAGCUAGGAGCUAGCCAACUGGCCAUCACCUCCUCGGUGGCUGACUCAGAU------------UCAGAUUGAGACUCAGGCAUGCAA
.............(((..(((.((...(((((((....(((((...(((....)))......)))))..))))))).(((((..------------.....)))))..)))))..))).. ( -29.80)
>DroYak_CAF1 5508 120 + 1
AGUUAUGAACAGAGAAUCUUCUGAAAGUAAUCAUAGCUACAAGCUAGCCAACUGGCCAUCACCUCCUCGGUGGCUGACUCAGAUUCAGAUUCAGAUUCAGAUUGAGACUCAGGCAUGCAA
((((((((.(((((....))))).......))))))))....((..(((....(((((((........)))))))..(((((..((.((.......)).))))))).....)))..)).. ( -30.30)
>consensus
__________AGAG_A_C___UGAAAGUAGCCAUAGCUACAAGCUAGCCAACUGGCCAUCACCGCCUCGGCGGCUGACUCAGAU____________UCAGAUUGAGACUCAGGCAUGCAA
..........................((((((.((((.....))))(((....)))..(((((((....)))).)))(((((...................))))).....))).))).. (-20.85 = -21.13 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:49 2006