Locus 3775

Sequence ID	3R_DroMel_CAF1
Location	10,237,914 – 10,238,053
Length	139
Max. P	0.950234

overview

Window 6

Location	10,237,914 – 10,238,015
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	84.27
Mean single sequence MFE	-39.85
Consensus MFE	-33.08
Energy contribution	-33.50
Covariance contribution	0.42
Combinations/Pair	1.11
Mean z-score	-2.68
Structure conservation index	0.83
SVM decision value	1.20
SVM RNA-class probability	0.930099
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10237914 101 - 27905053
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUGAGAUGAU--------CAGAUGCUCAGAUGGCAUCGCCAUCGCCUUUG
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))((((.....)--------))).......((((((...))))))....... ( -40.40)
>DroVir_CAF1 112807 103 - 1
AUGGCCGCCCAAUUAAUGCGUCGCCAGCGAGAGUUGGCGGCUCAUUAACACGCAGUUGGCCCGUACGCC---AUGC-CAUUGG-GUA-UUGGUAUCGGCAUCGACAAUG
..((((((....((((((.(((((((((....))))))))).))))))...))....))))((...(((---((((-((....-...-.)))))).)))..))...... ( -43.10)
>DroSec_CAF1 95801 101 - 1
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUUAU--------CAGAUGCUCAGAUGGCAUCGCCAUCGUCUUUG
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))...((((.((--------..((((((.....))))))...)).))))... ( -37.00)
>DroSim_CAF1 94238 101 - 1
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUGAU--------CAGAUGCUCAGAUGGCAUCGCCAUCGCCUUUG
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))....((((..--------..((((((.....))))))..))))....... ( -39.30)
>DroEre_CAF1 96732 105 - 1
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUGCUCCGAUGCUCAGAUGUUCAGAUGGCAUCGCCAUCGAC----
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))....((((...((((((.((..(....)..)))))))).))))...---- ( -41.30)
>DroYak_CAF1 102134 93 - 1
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUGCU----------------CAGAUGGCAUCGCCAUCGCCUUUG
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))..((((.((.----------------..((((((...)))))))).)))) ( -38.00)
>consensus
CUGGACGCCCAAUUAAUGCGUCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUGAU________CAGAUGCUCAGAUGGCAUCGCCAUCGCCUUUG
.(((((((....((((((.(((((((((....))))))))).))))))...)).)))))............................((((((...))))))....... (-33.08 = -33.50 +   0.42)

alignment

secondary structure

dotplot

Window 7

Location	10,237,946 – 10,238,053
Length	107
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.07
Mean single sequence MFE	-36.03
Consensus MFE	-22.69
Energy contribution	-22.55
Covariance contribution	-0.14
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	0.63
SVM decision value	1.40
SVM RNA-class probability	0.950234
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10237946 107 - 27905053
AUGUUCGGUGCCCGGCCAUGCCCAUAAACGCCA--AUGAUCUGGACGCCCAAUUAAUGCGU-CGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUGAGAUGAU-----
...(((((((..((((...))).......((..--......(((....))).((((((.((-(((((((....))))))))).))))))...)).)..))))))).....----- ( -37.00)
>DroVir_CAF1 112839 103 - 1
-----UCAUGUGUG--GAUGCCCAUAAAAGACGUGGCGG-AUGGCCGCCCAAUUAAUGCGU-CGCCAGCGAGAGUUGGCGGCUCAUUAACACGCAGUUGGCCCGUACGCC---AU
-----...((((((--................(.(((((-....))))))..((((((.((-(((((((....))))))))).))))))))))))..((((......)))---). ( -45.80)
>DroPse_CAF1 103932 92 - 1
-----CGAUGCGUAGCCAUGCCCAUAAACGACA--AUGAUCCGGACGCCCAAUUAAUGCGUCCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUG----------------
-----...(((((.((...))...........(--((((.((((((((.........))))))((((((....)))))))).)))))...)))))....---------------- ( -33.70)
>DroEre_CAF1 96763 112 - 1
AUGCCUGCUUCCCUACCAUGCCCAUAAACGCCA--AUGAUCUGGACGCCCAAUUAAUGCGU-CGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCACUCAGAUGCUCCGAU
.............................((..--.(((..(((((((....((((((.((-(((((((....))))))))).))))))...)).))))).)))...))...... ( -32.50)
>DroAna_CAF1 87118 93 - 1
AUG----AUUCGCGGCCAUGCCCGUAAACGACU--AUGAUCCGGAUGCCCAAUUAAUGCGU-CGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUCG---------------
...----(((((.(..((((..((....))..)--)))..))))))((....((((((.((-(((((((....))))))))).))))))...))......--------------- ( -33.50)
>DroPer_CAF1 106559 92 - 1
-----CGAUGCGUAGCCAUGCCCAUAAACGACA--AUGAUCCGGACGCCCAAUUAAUGCGUCCGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUG----------------
-----...(((((.((...))...........(--((((.((((((((.........))))))((((((....)))))))).)))))...)))))....---------------- ( -33.70)
>consensus
_____CGAUGCGCGGCCAUGCCCAUAAACGACA__AUGAUCCGGACGCCCAAUUAAUGCGU_CGCCGGCGAGAGUUGGCGGCUCAUUAACACGCAGUUC________________
..................(((.....................((....))..((((((.((.(((((((....))))))))).))))))...))).................... (-22.69 = -22.55 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:43 2006