Locus 2821

Sequence ID	2R_DroMel_CAF1
Location	9,819,495 – 9,819,590
Length	95
Max. P	0.883966

overview

Window 2

Location	9,819,495 – 9,819,590
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.06
Mean single sequence MFE	-28.12
Consensus MFE	-24.44
Energy contribution	-24.38
Covariance contribution	-0.06
Combinations/Pair	1.09
Mean z-score	-2.00
Structure conservation index	0.87
SVM decision value	0.93
SVM RNA-class probability	0.883966
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9819495 95 + 20766785
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGCCGAUGACGUCGUCAUCGUC---UCAC----------------------CGAAAUUGAAAUGCAACUCACAUUUGGAGCCCGCUCCU
..((((..((((((.((....))))))))..((.(((((((...))))))).)---)...----------------------...........))))..........((((....)))). ( -26.70)
>DroSec_CAF1 57340 95 + 1
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGCCGAUGACGUCGUCAUCGUC---UCAC----------------------UGAAAUUGAAAUGCAACUCACAUUUGGAGCCCGCUCCU
..((((..((((((.((....))))))))..((.(((((((...))))))).)---)...----------------------...........))))..........((((....)))). ( -26.70)
>DroSim_CAF1 58793 95 + 1
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGCCGAUGACGUCGUCAUCGUC---UCAC----------------------UGAAAUUGAAAUGCAACUCACAUUUGGAGCCCGCUCCU
..((((..((((((.((....))))))))..((.(((((((...))))))).)---)...----------------------...........))))..........((((....)))). ( -26.70)
>DroEre_CAF1 62090 95 + 1
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGUCGAUGACGUCGUCAUCGUC---UCAC----------------------UGAAAUUGAAAUGCAACUCACAUUUGGGGCCCGCUCCU
..((((..((((((.((....))))))))..((.(((((((...))))))).)---)...----------------------...........))))..........((((....)))). ( -26.90)
>DroYak_CAF1 59117 95 + 1
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGUCGAUGACGUCGUCAUCGGC---UCAC----------------------UGAAAUUGAAAUGCAACUCACAUUUGGGGCCCGCUCCU
..((((..((((((.((....))))))))..((((((((((...)))))))))---)...----------------------...........))))..........((((....)))). ( -30.20)
>DroAna_CAF1 57709 120 + 1
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGCUGAUGACGUAGUCCCCGUCAAUUCGCUUUUUUUUUUCUCUCUCGGUUGCAAAAUUGAAAUGCAACUCACAUUUGGGGCCCGCUCCU
...(((....)))........(((((((((((((.(((((((.......)))).))).))))))))...........((((.((((..(((........)))..)))).)))).))))). ( -31.50)
>consensus
AAUGCAAAUUUGCUGCCAUAUGGAGCAGAAAAGCCGAUGACGUCGUCAUCGUC___UCAC______________________UGAAAUUGAAAUGCAACUCACAUUUGGAGCCCGCUCCU
..((((..((((((.((....)))))))).....(((((((...)))))))..........................................))))..........((((....)))). (-24.44 = -24.38 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	9,819,495 – 9,819,590
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	88.06
Mean single sequence MFE	-30.50
Consensus MFE	-25.54
Energy contribution	-25.73
Covariance contribution	0.19
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.84
SVM decision value	0.34
SVM RNA-class probability	0.697600
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9819495 95 - 20766785
AGGAGCGGGCUCCAAAUGUGAGUUGCAUUUCAAUUUCG----------------------GUGA---GACGAUGACGACGUCAUCGGCUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((....)))).((((..((((((.(((((......----------------------.)))---))(((((((...))))))))).....((((((....)).))))))))..)))) ( -30.70)
>DroSec_CAF1 57340 95 - 1
AGGAGCGGGCUCCAAAUGUGAGUUGCAUUUCAAUUUCA----------------------GUGA---GACGAUGACGACGUCAUCGGCUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((....)))).((((..((((((.(((((......----------------------.)))---))(((((((...))))))))).....((((((....)).))))))))..)))) ( -30.70)
>DroSim_CAF1 58793 95 - 1
AGGAGCGGGCUCCAAAUGUGAGUUGCAUUUCAAUUUCA----------------------GUGA---GACGAUGACGACGUCAUCGGCUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((....)))).((((..((((((.(((((......----------------------.)))---))(((((((...))))))))).....((((((....)).))))))))..)))) ( -30.70)
>DroEre_CAF1 62090 95 - 1
AGGAGCGGGCCCCAAAUGUGAGUUGCAUUUCAAUUUCA----------------------GUGA---GACGAUGACGACGUCAUCGACUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((((((....((((((.....))))))........----------------------..((---(.(((((((...))))))).))).)))))))).....((((.....))))... ( -27.90)
>DroYak_CAF1 59117 95 - 1
AGGAGCGGGCCCCAAAUGUGAGUUGCAUUUCAAUUUCA----------------------GUGA---GCCGAUGACGACGUCAUCGACUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((((((....((((((.....))))))........----------------------..((---(.(((((((...))))))).))).)))))))).....((((.....))))... ( -28.30)
>DroAna_CAF1 57709 120 - 1
AGGAGCGGGCCCCAAAUGUGAGUUGCAUUUCAAUUUUGCAACCGAGAGAGAAAAAAAAAAGCGAAUUGACGGGGACUACGUCAUCAGCUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.(((((((..........((.((((((.........))))))))............((((((....(((((.......)))))...))))))))))))).....((((.....))))... ( -34.70)
>consensus
AGGAGCGGGCCCCAAAUGUGAGUUGCAUUUCAAUUUCA______________________GUGA___GACGAUGACGACGUCAUCGGCUUUUCUGCUCCAUAUGGCAGCAAAUUUGCAUU
.((((((((....((((((.....)))))).......................................(((((((...))))))).....)))))))).....((((.....))))... (-25.54 = -25.73 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:16 2006