Locus 2930

Sequence ID	3R_DroMel_CAF1
Location	7,858,019 – 7,858,126
Length	107
Max. P	0.762809

overview

Window 4

Location	7,858,019 – 7,858,126
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.38
Mean single sequence MFE	-30.48
Consensus MFE	-15.80
Energy contribution	-17.72
Covariance contribution	1.92
Combinations/Pair	1.20
Mean z-score	-1.98
Structure conservation index	0.52
SVM decision value	0.51
SVM RNA-class probability	0.762809
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7858019 107 + 27905053
AGG-CUG-AAAGAAAGUUUUCCUUCUCUCACCAGAUUCAUGGCCCAAACGCCAUCAUAAAGUAAUUUAUGUGAUUUG-ACCAUUCUUCUGGUGACCAC-CCCAGUCCGGCC---------
.((-(((-..((((........)))).((((((((...((((..((((...((.((((((....)))))))).))))-.))))...))))))))....-.......)))))--------- ( -30.50)
>DroPse_CAF1 20907 112 + 1
AGG-CCGGACCGAAAGUUUUCCU------ACCAGAUUCCUGGCUGGGAUGCCAUCAUAAAGUAAUUUAUGUGAUUUGUCCCAUUCUUCUGCGGAGAGGCCCCG-CCUCGUUUUUCUCCGC
...-..((((.((..((..((((------(((((....)))).))))).))((.((((((....)))))))).)).)))).........((((((((((...)-))))(.....)))))) ( -33.90)
>DroEre_CAF1 19106 106 + 1
AGG-CUG-AAAGAAAGUUUUCCCUCUCUCACCAGAUUCAUGGCCCAAGCGCCAUCAUAAAGUAAUUUAUGUGAUUUG-CCCAUUCUUCUGGUGAC----CCCGGUCCCGCCAU-------
.((-(.(-((((....)))))((....((((((((...((((..((((...((.((((((....)))))))).))))-.))))...)))))))).----...))....)))..------- ( -28.90)
>DroYak_CAF1 19363 106 + 1
AGG-CUG-AAAGAAAGUUUUCCUUCUCUCACCAGAUUCAUGGCCCAAACGCCAUCAUAAAGUAAUUUAUGUGAUUUG-CCCAUUCUUCUGGUGAC----CCUGGUCCGGCGGC-------
..(-(((-..((((........)))).((((((((...((((..((((...((.((((((....)))))))).))))-.))))...)))))))).----.......))))...------- ( -27.90)
>DroAna_CAF1 21183 106 + 1
GGGCCUG-AAAGAAACUUUUCCUU-ACACGCCAGAUUCAUGGCCCGGUCGCCAUCAUAAAGUAAUUUAUGUGAUUUG-CCCAUUCUUCUGGUGAC----CCCAGCCUGCCUCC-------
((((..(-((((....)))))...-...(((((((...((((.(..(((((....(((((....))))))))))..)-.))))...)))))))..----....))))......------- ( -29.20)
>DroPer_CAF1 20923 105 + 1
AGG-CCGGACCGAAAGUUUUCCU------ACCAGAUUCCUGGCUGGGAUGCCAUCAUAAAGUAAUUUAUGUGAUUUGUCCCAUUCUUCUGCGGAGAGGCCCCG-CCUCGUUUU-------
.((-((((((.((..((..((((------(((((....)))).))))).))((.((((((....)))))))).)).))))...((((.....))))))))...-.........------- ( -32.50)
>consensus
AGG_CUG_AAAGAAAGUUUUCCUU_UCUCACCAGAUUCAUGGCCCAAACGCCAUCAUAAAGUAAUUUAUGUGAUUUG_CCCAUUCUUCUGGUGAC____CCCGGCCCCGCUUU_______
.((.(((....(((....))).......(((((((....((((......)))).((((((....))))))................)))))))........))).))............. (-15.80 = -17.72 +   1.92)

alignment

secondary structure

dotplot

Window 5

Location	7,858,019 – 7,858,126
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.38
Mean single sequence MFE	-34.90
Consensus MFE	-14.94
Energy contribution	-14.42
Covariance contribution	-0.52
Combinations/Pair	1.23
Mean z-score	-2.19
Structure conservation index	0.43
SVM decision value	0.22
SVM RNA-class probability	0.641006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7858019 107 - 27905053
---------GGCCGGACUGGG-GUGGUCACCAGAAGAAUGGU-CAAAUCACAUAAAUUACUUUAUGAUGGCGUUUGGGCCAUGAAUCUGGUGAGAGAAGGAAAACUUUCUUU-CAG-CCU
---------(((..((((...-..))))((((((...(((((-(((((((((((((....)))))).))..)))).))))))...))))))(((((((((....))))))))-).)-)). ( -37.50)
>DroPse_CAF1 20907 112 - 1
GCGGAGAAAAACGAGG-CGGGGCCUCUCCGCAGAAGAAUGGGACAAAUCACAUAAAUUACUUUAUGAUGGCAUCCCAGCCAGGAAUCUGGU------AGGAAAACUUUCGGUCCGG-CCU
(((((((.......((-(...)))))))))).......(((((....(((((((((....)))))).)))..)))))(((.(((..((((.------((.....)).)))))))))-).. ( -34.81)
>DroEre_CAF1 19106 106 - 1
-------AUGGCGGGACCGGG----GUCACCAGAAGAAUGGG-CAAAUCACAUAAAUUACUUUAUGAUGGCGCUUGGGCCAUGAAUCUGGUGAGAGAGGGAAAACUUUCUUU-CAG-CCU
-------..(((..(((....----)))((((((...((((.-(...(((((((((....)))))).)))......).))))...))))))(((((((((....))))))))-).)-)). ( -36.00)
>DroYak_CAF1 19363 106 - 1
-------GCCGCCGGACCAGG----GUCACCAGAAGAAUGGG-CAAAUCACAUAAAUUACUUUAUGAUGGCGUUUGGGCCAUGAAUCUGGUGAGAGAAGGAAAACUUUCUUU-CAG-CCU
-------......(((((((.----.((.(((......))).-.......((((((....))))))(((((......)))))))..)))))(((((((((....))))))))-)..-)). ( -32.80)
>DroAna_CAF1 21183 106 - 1
-------GGAGGCAGGCUGGG----GUCACCAGAAGAAUGGG-CAAAUCACAUAAAUUACUUUAUGAUGGCGACCGGGCCAUGAAUCUGGCGUGU-AAGGAAAAGUUUCUUU-CAGGCCC
-------(((..((((((.((----(((((((......))).-.......((((((....)))))).))))..)).)))).))..)))(((.((.-((((((....))))))-)).))). ( -34.00)
>DroPer_CAF1 20923 105 - 1
-------AAAACGAGG-CGGGGCCUCUCCGCAGAAGAAUGGGACAAAUCACAUAAAUUACUUUAUGAUGGCAUCCCAGCCAGGAAUCUGGU------AGGAAAACUUUCGGUCCGG-CCU
-------......(((-(.((((((((....))).((((((((....(((((((((....)))))).)))..)))))(((((....)))))------.........)))))))).)-))) ( -34.30)
>consensus
_______AAAGCCAGACCGGG____GUCACCAGAAGAAUGGG_CAAAUCACAUAAAUUACUUUAUGAUGGCGUCCGGGCCAUGAAUCUGGUGAGA_AAGGAAAACUUUCUUU_CAG_CCU
...............((((((.....((((((......))).........((((((....)))))).((((......))))))).))))))............................. (-14.94 = -14.42 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:01 2006