Locus 9544

Sequence ID 3R_DroMel_CAF1
Location 25,220,200 – 25,220,332
Length 132
Max. P 0.871783
window15265 window15266

overview

Window 5

Location 25,220,200 – 25,220,305
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 95.63
Mean single sequence MFE -31.63
Consensus MFE -28.47
Energy contribution -29.83
Covariance contribution 1.36
Combinations/Pair 1.04
Mean z-score -1.33
Structure conservation index 0.90
SVM decision value 0.61
SVM RNA-class probability 0.799469
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25220200 105 + 27905053
GCAGGAAA-UGGGGAAACCUCACAGACAGGCCGACCAAGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
...((((.-.(((....)))........(((((.....(((........)))....)))))..(((....)))...))))...(((((....)))))......... ( -30.50)
>DroSec_CAF1 78437 105 + 1
GCGGAAAA-UGGGGAAACCUCACAGACAGGCCGACCAAGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
..((((..-.(((....)))........(((((.....(((........)))....)))))..(((....)))...))))...(((((....)))))......... ( -30.60)
>DroSim_CAF1 78785 105 + 1
GCUGAAAA-UGGGGAAACCUCACAGACAGGCCGACCAAGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
((..(...-.(((....)))........((((..(((.(((........)))....)))...))))..)..)).....((((.(((((....))))).....)))) ( -30.60)
>DroEre_CAF1 81605 105 + 1
GCGGAAAA-UGGGGAAACCUCACAGACAGGCCGACCAAGACCGAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
(((.....-.(((....)))........((((..(((....((((.......)))))))...))))......)))...((((.(((((....))))).....)))) ( -31.60)
>DroYak_CAF1 81536 106 + 1
GCGGAAAACUGGGGAAACCUCACAGACAGGCCGACCAAGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
..((((..(((((....))...)))...(((((.....(((........)))....)))))..(((....)))...))))...(((((....)))))......... ( -31.30)
>DroAna_CAF1 76612 99 + 1
GUGGAAA---GGGGAAACCUCACAGACAGGCCG----AGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCUUUCCAGACAAGUGAAAACUUGAUAAACUGG
.((((((---(((....))..........((((----((..((.....))..)))(((((...)))))..))).)))))))..(((((....)))))......... ( -35.20)
>consensus
GCGGAAAA_UGGGGAAACCUCACAGACAGGCCGACCAAGACCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGG
((........(((....)))........(((((.....(((........)))....)))))..(((....)))))...((((.(((((....))))).....)))) (-28.47 = -29.83 +   1.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,220,239 – 25,220,332
Length 93
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.25
Mean single sequence MFE -35.83
Consensus MFE -25.27
Energy contribution -27.38
Covariance contribution 2.11
Combinations/Pair 1.14
Mean z-score -2.23
Structure conservation index 0.71
SVM decision value 0.87
SVM RNA-class probability 0.871783
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25220239 93 + 27905053
-----------CCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCAGCCCAAAAAGGGGCGGAUUGGGG-------------
-----------((((...(((((((.(((((...)))))((((.((..(((((.(((((....))))).....)))))...))))))...))))))).))))..------------- ( -34.90)
>DroPse_CAF1 83936 93 + 1
GAGAGGAGCAGCCAAGUAUUGU---UGUGGCCGGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCACC--------GGGCGGUCUGCGG-------------
.......((((((..((.(((.---.(((((((((...)))))).)))..))).(((((....)))))))...((((....))--------))..)).))))..------------- ( -32.80)
>DroSec_CAF1 78476 92 + 1
-----------CCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCAGCCCAAAA-CGGGCGGAUUGGGG-------------
-----------((((...((((((..(((((...)))))((((.((..(((((.(((((....))))).....)))))...))))))..-.)))))).))))..------------- ( -34.40)
>DroEre_CAF1 81644 92 + 1
-----------CCGAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCAGCCCAAAAGGGGGCGGAUUGG-G-------------
-----------((((...(((((((((((((...)))))((((.((..(((((.(((((....))))).....)))))...))))))..)))))))).))))-.------------- ( -38.10)
>DroYak_CAF1 81576 92 + 1
-----------CCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCAGCCCAAAAGGGGGCAGAUUGG-G-------------
-----------((((...(((((((((((((...)))))((((.((..(((((.(((((....))))).....)))))...))))))..)))))))).))))-.------------- ( -39.20)
>DroAna_CAF1 76645 103 + 1
-----------CCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCUUUCCAGACAAGUGAAAACUUGAUAAACUGGGUCAGCCAGC---UCGAUGGCUUGGGGAGGUGACACAGGC
-----------((((((((((..(..(((((...))))).((((....(((((.(((((....))))).....)))))...))))).---.)))).))))))...(....)...... ( -35.60)
>consensus
___________CCAAGUAUUGUCCUCGUGGCCAGGCCACUUGGCGCAUUCCAGACAAGUGAAAACUUGACAAACUGGGUCAGCCCAAAA_GGGGCGGAUUGGGG_____________
...........((((...((((((..(((((...)))))..(((....(((((.(((((....))))).....)))))...))).......)))))).))))............... (-25.27 = -27.38 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:50 2006