Locus 7166

Sequence ID	X_DroMel_CAF1
Location	17,975,653 – 17,975,883
Length	230
Max. P	0.547795

overview

Window 7

Location	17,975,653 – 17,975,765
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.67
Mean single sequence MFE	-33.56
Consensus MFE	-26.02
Energy contribution	-26.26
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.78
SVM decision value	0.03
SVM RNA-class probability	0.547795
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17975653 112 + 22224390
UGGGGUUCUUCGGCAGUCGUGGAGGCGCCACCAACACGACAAAGUUGUCGCUGGCGAAUCUGGAAUUAUUAUUGAAUGAACUUGCACCAUAUCCGCC--------GUCCAUUUCGCCAUA
((((((.((((.((....)).)))).))).)))...(((((....))))).(((((((..((((.(((((....)))))....((.........)).--------.)))).))))))).. ( -33.50)
>DroSec_CAF1 6593 103 + 1
---------GCGGCAGUCGUGGAGGCGCCACCAACACGACAAAGUUGUCGCUGGCGAAUCUGGAAUUAUUAGUGAAUGAACUUGCGCCAUAUCCGCC--------GUCCAUUUCGCCAUA
---------((((((((((((..((.....))..)))))).....))))))(((((((..((((......(((......))).(((.......))).--------.)))).))))))).. ( -35.70)
>DroSim_CAF1 6284 103 + 1
---------GCGGCAGUCGUGGAGGCGCCACCAACACGACAAAGUUGUCGCUGGCGAAUCUGGAAUUAUUAUUGAAUGAACUUGCGCCAUAUCCGCC--------GUCCAUUUCGCCAUA
---------((((((((((((..((.....))..)))))).....))))))(((((((..((((.(((((....)))))....(((.......))).--------.)))).))))))).. ( -35.50)
>DroEre_CAF1 8214 100 + 1
-----------GGCAGUCGCGAAGGCGCCAGCAACACGACAAAGUUGUCGCAGGCGAAUC-GAAAUUAUUAUUGAAUGAACUAGCGCCAUAUCCGCA--------GUCCAUUUCGCCAUA
-----------.((.(.(((....))).).))....(((((....)))))..((((((((-((........))))(((.(((.(((.......))))--------)).)))))))))... ( -28.20)
>DroYak_CAF1 5610 108 + 1
-----------GGCAGCCGUGGAGGCGCCACCAACACGACAAAGUUGUCGCUGGCGAAUU-GGAAUUAUUAUUGAAUGAACAUGCGCCACAUCCGCAGAUCCACCGUCCACUUCGCCAUA
-----------(((.(((.....)))))).......(((((....))))).(((((((.(-(((.(((((....)))))...((((.......)))).........)))).))))))).. ( -34.90)
>consensus
__________CGGCAGUCGUGGAGGCGCCACCAACACGACAAAGUUGUCGCUGGCGAAUCUGGAAUUAUUAUUGAAUGAACUUGCGCCAUAUCCGCC________GUCCAUUUCGCCAUA
...........(((.(((.....)))))).......(((((....)))))..((((((...(((.(((((....)))))....(((.......)))..........)))..))))))... (-26.02 = -26.26 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	17,975,765 – 17,975,883
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.97
Mean single sequence MFE	-39.10
Consensus MFE	-31.26
Energy contribution	-31.94
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.80
SVM decision value	0.01
SVM RNA-class probability	0.537488
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17975765 118 - 22224390
AUACGCGCCUGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGGCAGCGGCGAGUCCGAAGUUUUUGGAUAUCCCCA--CCUCAUCUUGGCUGCUUUAUUGGCGGCGCUUCAAUAAUUGAU
.........(((((.(((((((((((.........(....)((((((((.((((((((.....)))))).)).)).--.(.......)))))))))))))))))).)))))......... ( -36.20)
>DroSec_CAF1 6696 116 - 1
AUACGCGCCUGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGGCAGCGGCGAGGCCAGGGUUUUUG-GUAUC-CCA--CCUCGUCCUGGCUGCUUUAUUGGCGGCGCUUCAAUAAUUGAU
.........(((((.(((((((((((.........(....)(((((((((((((...(((......-....)-)).--)))))))...))))))))))))))))).)))))......... ( -42.80)
>DroSim_CAF1 6387 117 - 1
AUACGCGCCUGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGGCAGCGGCGAGGCCAGGGUUUUUGGGUAUC-CCA--CCUCGUCCUGGCUGCUUUAUUGGCGGCGCUUCAAUAAUUGAU
.........(((((.(((((((((((......(..(....)..)((((((.(((.(..(((....(((...)-)))--))..).))).))))))))))))))))).)))))......... ( -43.60)
>DroEre_CAF1 8314 116 - 1
AUACGCGCCUGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGGCAGCGGCGAGGCCGUAGUUUUUGGGUAUC-CCA--ACUCAUC-UGGCUGCUUUAUGGGCGGCGCUUCAAUAAUUGAU
....(((((.((....))..............(..((...((((((((((...))).(((...(((((...)-)))--).....)-)))))))))..))..))))))............. ( -34.10)
>DroYak_CAF1 5718 118 - 1
AUACGCGCCAGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGCCAGCGGCGAGGCCGAAGUUUUUGGUUAUA-CCAAAACUCAUC-UGGCUGCUUUAUUGGCGGCGCUUCAAUAAUUGAU
....(((((.((....))((((((((......(..(....)..)((((((.(((..((.(((((.((.....-))))))))).))-).)))))))))))))))))))............. ( -38.80)
>consensus
AUACGCGCCUGGGGAGCCGUCAAUAAUUAAUCGAACAAAUGGGCAGCGGCGAGGCCGAAGUUUUUGGGUAUC_CCA__CCUCAUC_UGGCUGCUUUAUUGGCGGCGCUUCAAUAAUUGAU
....(((((.((....))((((((((......(..(....)..)((((((.(((....((....(((......)))...))...))).)))))))))))))))))))............. (-31.26 = -31.94 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:48 2006