Locus 6212

Sequence ID	2L_DroMel_CAF1
Location	17,302,798 – 17,302,890
Length	92
Max. P	0.975476

overview

Window 7

Location	17,302,798 – 17,302,890
Length	92
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	67.26
Mean single sequence MFE	-21.65
Consensus MFE	-9.27
Energy contribution	-8.65
Covariance contribution	-0.62
Combinations/Pair	1.21
Mean z-score	-2.15
Structure conservation index	0.43
SVM decision value	0.69
SVM RNA-class probability	0.822727
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17302798 92 + 22407834
GGCAAAUGCAAAUUGCAAUAGCAGCCC---CUACUAAUGCAAUUCCGCG--------------CACUUCGCCCCUCCC-----AGGCAUCCGAAUACCCCUCAACAUAAAGCCG
(((....((.(((((((.(((.((...---)).))).)))))))..)).--------------......(((......-----.))).......................))). ( -19.60)
>DroSec_CAF1 360 97 + 1
GGCAAAUGCAAAUUGCAAUAGCAGCCC---CUACUAAUGCAAUUCCGCG--------------CACUUUCCCCCUUCCCCGUCGGGCAUUCGAAUACCCCUCAACAUAAAGCCG
(((.(((((.(((((((.(((.((...---)).))).)))))))(((((--------------................)).)))))))).((.......))........))). ( -19.39)
>DroEre_CAF1 3203 85 + 1
GGCAAAUGCAAAUUGCAAUAGCAGCCC---CUACUAAUGCAAUUCCGCG--------------CACUCCCCC-----C-----UGCCAUCCGAGUGCCCCU--ACAUAAAGCCG
(((....((.(((((((.(((.((...---)).))).)))))))..))(--------------(((((....-----.-----........))))))....--.......))). ( -23.22)
>DroAna_CAF1 12128 105 + 1
ACCAAAUGGAAAUUGCAACAGAUUUCGCAGAAACUAAUGCAAUACUGCUACGGCGGAGGCUGCCACCCCACC-----C-UAU-UCACACCCCAAUUGCCGG--CCAUAAUGCCG
..(((.(((..((((((..((.((((...))))))..)))))).((((....))))(((.((......)).)-----)-)..-.......))).))).(((--(......)))) ( -24.40)
>consensus
GGCAAAUGCAAAUUGCAAUAGCAGCCC___CUACUAAUGCAAUUCCGCG______________CACUCCCCC_____C_____UGGCAUCCGAAUACCCCU__ACAUAAAGCCG
.((....)).(((((((.(((.((......)).))).)))))))...................................................................... ( -9.27 =  -8.65 +  -0.62)

alignment

secondary structure

dotplot

Window 8

Location	17,302,798 – 17,302,890
Length	92
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	67.26
Mean single sequence MFE	-33.38
Consensus MFE	-18.14
Energy contribution	-18.83
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-1.93
Structure conservation index	0.54
SVM decision value	1.75
SVM RNA-class probability	0.975476
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17302798 92 - 22407834
CGGCUUUAUGUUGAGGGGUAUUCGGAUGCCU-----GGGAGGGGCGAAGUG--------------CGCGGAAUUGCAUUAGUAG---GGGCUGCUAUUGCAAUUUGCAUUUGCC
((((.....))))..((((((....))))))-----......(((.(((((--------------(...((((((((.((((((---...)))))).))))))))))))))))) ( -31.00)
>DroSec_CAF1 360 97 - 1
CGGCUUUAUGUUGAGGGGUAUUCGAAUGCCCGACGGGGAAGGGGGAAAGUG--------------CGCGGAAUUGCAUUAGUAG---GGGCUGCUAUUGCAAUUUGCAUUUGCC
...((((.((((...((((((....))))))))))..))))..((.(((((--------------(...((((((((.((((((---...)))))).)))))))))))))).)) ( -31.80)
>DroEre_CAF1 3203 85 - 1
CGGCUUUAUGU--AGGGGCACUCGGAUGGCA-----G-----GGGGGAGUG--------------CGCGGAAUUGCAUUAGUAG---GGGCUGCUAUUGCAAUUUGCAUUUGCC
.(((...((((--..(.((((((........-----.-----....)))))--------------).).((((((((.((((((---...)))))).))))))))))))..))) ( -31.82)
>DroAna_CAF1 12128 105 - 1
CGGCAUUAUGG--CCGGCAAUUGGGGUGUGA-AUA-G-----GGUGGGGUGGCAGCCUCCGCCGUAGCAGUAUUGCAUUAGUUUCUGCGAAAUCUGUUGCAAUUUCCAUUUGGU
((((......)--))).(((.(((((.....-...-.-----((((((((....))).)))))(((((((..(((((........)))))...)))))))...))))).))).. ( -38.90)
>consensus
CGGCUUUAUGU__AGGGGUAUUCGGAUGCCA_____G_____GGGGAAGUG______________CGCGGAAUUGCAUUAGUAG___GGGCUGCUAUUGCAAUUUGCAUUUGCC
.(((...((((.....................................((((((((....)))))))).((((((((.((((((......)))))).))))))))))))..))) (-18.14 = -18.83 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:22 2006