Locus 4539

Sequence ID 2L_DroMel_CAF1
Location 12,995,978 – 12,996,100
Length 122
Max. P 0.960056
window7153 window7154

overview

Window 3

Location 12,995,978 – 12,996,072
Length 94
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 77.86
Mean single sequence MFE -30.23
Consensus MFE -19.53
Energy contribution -19.48
Covariance contribution -0.05
Combinations/Pair 1.29
Mean z-score -1.51
Structure conservation index 0.65
SVM decision value 0.50
SVM RNA-class probability 0.758503
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12995978 94 - 22407834
UUCAGAGCAGCGCGGGGA-AACUAAGUGCUGUGCUGGGU-GGGCGUG----------GGUGGAAAUGAACGUGUGUGUGUGUGUGGA-AAACAACUAUUGCUCGAGC
(((((.(((((((.((..-..))..))))))).)))))(-(((((((----------(.((.......(((..(....)..)))...-...)).))).))))))... ( -29.62)
>DroSec_CAF1 21215 92 - 1
UUCAGAGCAGCGCGGGGA-AACUAAGUGCUGCGCUGGGU-GGCCGUG----------GGUGGAAAUGAGCG--UGUGUGUGUGUGGA-AAACAACUAUUGCUCCAGC
......(((((((.((..-..))..)))))))(((((..-(((.(((----------(.((.......(((--......))).....-...)).)))).)))))))) ( -30.96)
>DroSim_CAF1 19968 92 - 1
UUCAGAGCAGCGCGGGGA-AACUAAGUGCUGCGCUGGGU-GGGCGUG----------GGUGGAUAUGAGUG--UGUGUGUGUGUGGA-AAACAACUAUUGCUCGAGC
(((((.(((((((.((..-..))..))))))).)))))(-(((((((----------(..(.((((.....--.)))).).(((...-..))).))).))))))... ( -29.40)
>DroEre_CAF1 22828 89 - 1
UUCAGAGCAGCGCGGGGAAAACUAAGUGCUGCGCUGGGU-GGGCACG----------GGUGGAAAUGAGU------GUGUGUGUGGA-GAACAACUAUUGCUCGAGC
......(((((((..((....))..)))))))((((((.-.(((((.----------.((....))..))------))...(((...-..)))....)..))).))) ( -28.30)
>DroYak_CAF1 20253 98 - 1
UUCAGAGCAGCGCGGGGA-AACUAAGUGCUGUGCUGGGU-GGGCAUGGGUGGUCAUGGGUGGAAAUGAGC------GUGUGUGUGGA-AAACAACUAUUGCCCGAGC
(((((.(((((((.((..-..))..))))))).)))))(-(((((..((((.((((........)))).)------.....(((...-..))))))..))))))... ( -35.10)
>DroPer_CAF1 41127 95 - 1
UUCAGUCCUCCAAAGGGAGAACCGAGUGGUGUGGGGGGGGGGGCGCA-----------GUGGUACUGGUGCU-GGGAAGCGUGUAAAAAAGCAACUAUUGCUCGGGU
....(((((((.........(((....))).......)))))))(((-----------(((((......(((-....))).(((......)))))))))))...... ( -27.99)
>consensus
UUCAGAGCAGCGCGGGGA_AACUAAGUGCUGCGCUGGGU_GGGCGUG__________GGUGGAAAUGAGCG__UGUGUGUGUGUGGA_AAACAACUAUUGCUCGAGC
(((((.(((((((..((....))..))))))).)))))..(((((.............((....))...............(((......))).....))))).... (-19.53 = -19.48 +  -0.05)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 12,996,009 – 12,996,100
Length 91
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.61
Mean single sequence MFE -40.48
Consensus MFE -26.27
Energy contribution -27.58
Covariance contribution 1.31
Combinations/Pair 1.20
Mean z-score -2.03
Structure conservation index 0.65
SVM decision value 1.51
SVM RNA-class probability 0.960056
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12996009 91 - 22407834
--------ACCCACCACCCCGUUGGCACGUCAUAAUUUCAGAGCAGCGCGGGGA-AACUAAGUGCUGUGCUGGGU-GGGCGUG----------GGUGGAAAUGAACGUGUG
--------..(((((.((.....))((((((.....(((((.(((((((.((..-..))..))))))).))))).-.))))))----------)))))............. ( -36.90)
>DroSec_CAF1 21246 95 - 1
--GCCACCACCCACCAUCCCGUUGGCACGUCAUAAUUUCAGAGCAGCGCGGGGA-AACUAAGUGCUGCGCUGGGU-GGCCGUG----------GGUGGAAAUGAGCG--UG
--((((((((((((((......))....(((((....((((.(((((((.((..-..))..))))))).))))))-))).)))----------)))))...)).)).--.. ( -41.50)
>DroSim_CAF1 19999 95 - 1
--CCCACCACCCACCACCCCGUUGGCACGUCAUAAUUUCAGAGCAGCGCGGGGA-AACUAAGUGCUGCGCUGGGU-GGGCGUG----------GGUGGAUAUGAGUG--UG
--....((((((((..((((..(((....)))......(((.(((((((.((..-..))..))))))).))))).-))..)))----------))))).........--.. ( -42.40)
>DroEre_CAF1 22858 95 - 1
CACCCAGCACCCACCACCCCGUUGGCACGUCAUAAUUUCAGAGCAGCGCGGGGAAAACUAAGUGCUGCGCUGGGU-GGGCACG----------GGUGGAAAUGAGU-----
(((((.(..((((((....(((....))).........(((.(((((((..((....))..))))))).))))))-)))..))----------)))).........----- ( -39.30)
>DroYak_CAF1 20283 102 - 1
--CCCAGCAGCCACCACCCCGUCGGCACGUCAUAAUUUCAGAGCAGCGCGGGGA-AACUAAGUGCUGUGCUGGGU-GGGCAUGGGUGGUCAUGGGUGGAAAUGAGC-----
--((((...((((((..(((..(((....)).......(((.(((((((.((..-..))..))))))).))))..-)))....))))))..))))...........----- ( -41.60)
>DroPer_CAF1 41159 98 - 1
UAUCCUGCU-CUCCCACCCCUUUGGCACGUCAUAAUUUCAGUCCUCCAAAGGGAGAACCGAGUGGUGUGGGGGGGGGGGCGCA-----------GUGGUACUGGUGCU-GG
((((((((.-(((((.(((((....(((..(((....((.((.((((....)))).)).)))))..))))))))))))).)))-----------).))))........-.. ( -41.20)
>consensus
__CCCAGCACCCACCACCCCGUUGGCACGUCAUAAUUUCAGAGCAGCGCGGGGA_AACUAAGUGCUGCGCUGGGU_GGGCGUG__________GGUGGAAAUGAGCG__UG
..........(((((..........((((((.....(((((.(((((((..((....))..))))))).)))))...))))))..........)))))............. (-26.27 = -27.58 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:32 2006