Locus 3685

Sequence ID 2R_DroMel_CAF1
Location 12,238,013 – 12,238,177
Length 164
Max. P 0.903932
window5991 window5992 window5993

overview

Window 1

Location 12,238,013 – 12,238,108
Length 95
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 78.97
Mean single sequence MFE -27.97
Consensus MFE -14.78
Energy contribution -15.02
Covariance contribution 0.24
Combinations/Pair 1.18
Mean z-score -1.95
Structure conservation index 0.53
SVM decision value 0.20
SVM RNA-class probability 0.632856
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12238013 95 - 20766785
GCUGAAG-UCACCUCGAGCCAACUGAAGAGUUAGCCAUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUG---CCGGCCAAAUCGAAAACGAAGUCAGU
(((((..-((...(((((((.(((((.............)))))((((((..(((.....)))...))))---)))))....))))....))..))))) ( -28.62)
>DroSec_CAF1 98955 95 - 1
GCUGAAG-UCACCUCGAGACAACUCGAGAGUUGCCCAUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUG---UCGGCCAAUUCGAAAACUAAGUCAGA
.((((..-.....(((((....)))))((((((((.((((...((((((((........)))))))))))---).)).))))))..........)))). ( -27.70)
>DroSim_CAF1 95944 95 - 1
GCUGAAG-UCACCUCGAGCCAACUCGAGAGUUGGCCAUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUG---UCGGCCAAAUCGAAAACGAAGUCAGA
.((((..-((..((((((....))))))..((((((....((.((((((((........)))))))).))---..)))))).........))..)))). ( -35.60)
>DroEre_CAF1 106897 92 - 1
GUUGAAG-UCACCUCGAGCGAA---GAGAGACAGCCAUAUCGGUGGCAUUUAACCAGGAAGGUGCCAGUG---CUGGCCAAAUCGAAAACGAAGUCAGA
.((((..-((..(((.......---))).....((((...((.((((((((........)))))))).))---.))))............))..)))). ( -23.80)
>DroYak_CAF1 102201 92 - 1
GCUGAAG-UCACCUCGAGCGCA---GAGAGAGAGGCAUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUG---CCGGCCAAAUCGAAAACGAAGUCAGA
.((((..-((..(((.......---))).((..(((....((.((((((((........)))))))).))---...)))...))......))..)))). ( -25.80)
>DroAna_CAF1 90866 80 - 1
GCUGUGGCUCAC-------------------GGGCCGUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUGAGGUUGGCAUUUUUAGAUACGAAUUUGGG
.....((((...-------------------.))))(((((..(((.......))).((((((((((((...)))))))))))).)))))......... ( -26.30)
>consensus
GCUGAAG_UCACCUCGAGCCAA___GAGAGUUAGCCAUAUCAGUGGCAUUUAACCAGGAAGGUGCCAAUG___CCGGCCAAAUCGAAAACGAAGUCAGA
.((((...((..(((............)))...(((....((.((((((((........)))))))).)).....)))............))..)))). (-14.78 = -15.02 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,238,074 – 12,238,177
Length 103
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -43.40
Consensus MFE -19.14
Energy contribution -20.83
Covariance contribution 1.70
Combinations/Pair 1.17
Mean z-score -3.75
Structure conservation index 0.44
SVM decision value 1.03
SVM RNA-class probability 0.903932
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12238074 103 + 20766785
GCUAACUCUUCAGUUGGC-----UCGAGGUGACUUCAGCUUCAACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC---AGGUGAGCUAGAGAGCUUGACAA
(((((((....)))))))-----(((((.(..((..(((((..((((((((((..(((....)))..))).((.....))..)))---)))))))))..))).)))))... ( -39.90)
>DroSec_CAF1 99016 101 + 1
GGCAACUCUCGAGUUGUC-----UCGAGGUGACUUCAGCUC--ACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC---AGGUGAGCUCAAGAGCUUGACAA
(((.((.((((((....)-----)))))))..(((.(((((--((((((((((..(((....)))..))).((.....))..)))---))))))))).))).)))...... ( -47.20)
>DroSim_CAF1 96005 101 + 1
GCCAACUCUCGAGUUGGC-----UCGAGGUGACUUCAGCUC--ACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC---AGGUGAGCUCGAGAGCUUGACAA
..((((((((((((((((-----(.(((....))).))))(--((((((((((..(((....)))..))).((.....))..)))---))))))))))))))).))).... ( -50.30)
>DroEre_CAF1 106958 98 + 1
GCUGUCUCUC---UUCGC-----UCGAGGUGACUUCAACUC--ACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC---AGGUGAGCUCGAUAGCUUGACAA
((((((((.(---(((..-----..)))).))......(((--((((((((((..(((....)))..))).((.....))..)))---)))))))...))))))....... ( -40.50)
>DroYak_CAF1 102262 98 + 1
CCUCUCUCUC---UGCGC-----UCGAGGUGACUUCAGCUC--ACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC---AGGUGAGCUCGAGAGCUUGACAA
......((..---.((.(-----(((((....)....((((--((((((((((..(((....)))..))).((.....))..)))---))))))))))))).))..))... ( -43.10)
>DroPer_CAF1 103082 100 + 1
GG-GGCUCUCUAUGAAGCUCUCCUAAAGG------CAGC----CCCUGAGGCAUUUGCAUUGGCAUUUGCCGCAAUGUUUAGCUUCAGAGGCGACACCGAGAGCUUGACAA
.(-(((((((..((..(((........))------).((----(.(((((((....((((((((....)))..)))))...))))))).)))..))..))))))))..... ( -39.40)
>consensus
GCUAACUCUC_AGUUGGC_____UCGAGGUGACUUCAGCUC__ACCUGAGGCAUUUGCAUUGGCAUUUGCGGCAAUGUGCGGCUC___AGGUGAGCUCGAGAGCUUGACAA
.......................(((((.(..(((.(((((..((((((((((..(((....)))..))).((.....))..)))...))))))))).)))).)))))... (-19.14 = -20.83 +   1.70)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,238,074 – 12,238,177
Length 103
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -37.25
Consensus MFE -15.18
Energy contribution -16.93
Covariance contribution 1.75
Combinations/Pair 1.17
Mean z-score -3.01
Structure conservation index 0.41
SVM decision value 0.02
SVM RNA-class probability 0.542082
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12238074 103 - 20766785
UUGUCAAGCUCUCUAGCUCACCU---GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGUUGAAGCUGAAGUCACCUCGA-----GCCAACUGAAGAGUUAGC
......((((((.(((.((((((---(((..(((..((((.((....))....)))).))))))))).))).(((..((....))..)-----))...))).))))))... ( -27.30)
>DroSec_CAF1 99016 101 - 1
UUGUCAAGCUCUUGAGCUCACCU---GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGU--GAGCUGAAGUCACCUCGA-----GACAACUCGAGAGUUGCC
.......((.(((.(((((((((---(((..(((..((((.((....))....)))).))))))))))--))))).)))..(((((((-----(....)))))).)).)). ( -41.70)
>DroSim_CAF1 96005 101 - 1
UUGUCAAGCUCUCGAGCUCACCU---GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGU--GAGCUGAAGUCACCUCGA-----GCCAACUCGAGAGUUGGC
..(((((.(((((.(((((((((---(((..(((..((((.((....))....)))).))))))))))--)))))...........((-----(....))))))))))))) ( -42.50)
>DroEre_CAF1 106958 98 - 1
UUGUCAAGCUAUCGAGCUCACCU---GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGU--GAGUUGAAGUCACCUCGA-----GCGAA---GAGAGACAGC
(((((..(((.((.(((((((((---(((..(((..((((.((....))....)))).))))))))))--))))))))))...(((..-----.....---))).))))). ( -34.80)
>DroYak_CAF1 102262 98 - 1
UUGUCAAGCUCUCGAGCUCACCU---GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGU--GAGCUGAAGUCACCUCGA-----GCGCA---GAGAGAGAGG
........(((((.(((((((((---(((..(((..((((.((....))....)))).))))))))))--)))))........(((..-----.....---))).))))). ( -38.70)
>DroPer_CAF1 103082 100 - 1
UUGUCAAGCUCUCGGUGUCGCCUCUGAAGCUAAACAUUGCGGCAAAUGCCAAUGCAAAUGCCUCAGGG----GCUG------CCUUUAGGAGAGCUUCAUAGAGAGCC-CC
((((.((((((((((.((.((((((((.((........))((((..(((....)))..))))))))))----)).)------)))....)))))))).))))......-.. ( -38.50)
>consensus
UUGUCAAGCUCUCGAGCUCACCU___GAGCCGCACAUUGCCGCAAAUGCCAAUGCAAAUGCCUCAGGU__GAGCUGAAGUCACCUCGA_____GCCAACU_GAGAGUUAGC
.......((((((.(((((((((...(((..(((..((((.((....))....)))).))))))))))..)))))((.......))...............)))))).... (-15.18 = -16.93 +   1.75)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:53 2006