Locus 589

Sequence ID	X_DroMel_CAF1
Location	1,656,165 – 1,656,298
Length	133
Max. P	0.822823

overview

Window 8

Location	1,656,165 – 1,656,279
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	66.55
Mean single sequence MFE	-28.48
Consensus MFE	-12.72
Energy contribution	-12.39
Covariance contribution	-0.33
Combinations/Pair	1.26
Mean z-score	-1.51
Structure conservation index	0.45
SVM decision value	0.08
SVM RNA-class probability	0.571336
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1656165 114 - 22224390
AAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCAAACGACACUGGUUGUGGGCCCUU---GCAUUGUAUUGUAGAUGGCAAUCAUAAAAUCAUAAAUGUCGGACAAUCGCU---
.....(((....(((.(((......(((((((.....))..(((((....))))))))))...---))).)))(((((...(((((................))))).))))).)))--- ( -27.19)
>DroPse_CAF1 41237 97 - 1
GCAUAAGCUGUCAGAUUGUUUUAACGAGCAGCG-----------GGGCAGGUUCAAGUUCAAUUCUGGAAU----AGUAGAUUCCAGCUG--------AAAAUAUCGGUCAAUGUACAAA
((((..(((((....((((....))))))))).-----------.(((.(((.....((((...(((((((----.....))))))).))--------))...))).))).))))..... ( -23.00)
>DroSec_CAF1 21023 109 - 1
AAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCUAACGACGCUGGUUGUGGGCCCUU---GCAUU-----GUAGAUGGCAAUCAUAAAAUCAUAAAUGCCGGACAAUCGCU---
((((((((....)).))))))....(((((((((...((.......))...)))))))))...---(((((-----((...(((((................))))).))))).)).--- ( -32.59)
>DroSim_CAF1 10281 109 - 1
AAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCUAACGACGCUGGUUGUGGGCCCUU---GCAUU-----GUAGAUGGCAAUCAUAAAAUCAUAAAUGCCGGACAAUCGCU---
((((((((....)).))))))....(((((((((...((.......))...)))))))))...---(((((-----((...(((((................))))).))))).)).--- ( -32.59)
>DroYak_CAF1 21613 104 - 1
AAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCA-AAUGCUAACGAUAGUGGCUGUGGGCCCUUCCUGCAUU----UGUAGAUGGCAAUCA--------AAAAUGUCGGACAAUCGCU---
............((((((.......((((((((-..(((((....)))))..))))))))..(((.(((((----(...(((....))).--------.)))))).))))))).)).--- ( -32.50)
>DroPer_CAF1 43169 97 - 1
GCAUAAGCUGUCAGAUUGUUUUAACGAGCAGCG-----------GGGCAGGUUCAAGUUCAAUUCUGGAAU----AGUAGAUUCCAGCUG--------AAAAUAUCGGUCAAUGUACAAA
((((..(((((....((((....))))))))).-----------.(((.(((.....((((...(((((((----.....))))))).))--------))...))).))).))))..... ( -23.00)
>consensus
AAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCA_AAUGCUAACGACGCUGGUUGUGGGCCCUU___GCAUU_____GUAGAUGGCAAUCA________AAAAUGUCGGACAAUCGCU___
............(((((((((....((((((((...................))))))))......((...............)).....................))))))).)).... (-12.72 = -12.39 +  -0.33)

alignment

secondary structure

dotplot

Window 9

Location	1,656,202 – 1,656,298
Length	96
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	86.54
Mean single sequence MFE	-27.33
Consensus MFE	-22.79
Energy contribution	-22.60
Covariance contribution	-0.19
Combinations/Pair	1.09
Mean z-score	-1.78
Structure conservation index	0.83
SVM decision value	0.69
SVM RNA-class probability	0.822823
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1656202 96 - 22224390
UCCCAGCUAUCCGCAGAAUAAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCAAACGACACUGGUUGUGGGCCCUU---GCAUUGUAUUGUAG
............((((..(((((((((....)).)))))))...(((((((.....))..(((((....)))))))))).))---))............ ( -24.60)
>DroSec_CAF1 21060 91 - 1
UCCCAGCUAUCCGCAGAAUAAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCUAACGACGCUGGUUGUGGGCCCUU---GCAUU-----GUAG
............((((..(((((((((....)).)))))))...(((((((((...((.......))...))))))))).))---))...-----.... ( -27.40)
>DroSim_CAF1 10318 91 - 1
UCCCAGCUAUCCGCAGAAUAAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCUAACGACGCUGGUUGUGGGCCCUU---GCAUU-----GUAG
............((((..(((((((((....)).)))))))...(((((((((...((.......))...))))))))).))---))...-----.... ( -27.40)
>DroYak_CAF1 21642 83 - 1
-----------CGCAGAAUAAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCA-AAUGCUAACGAUAGUGGCUGUGGGCCCUUCCUGCAUU----UGUAG
-----------.((((..(((((((((....)).)))))))...((((((((-..(((((....)))))..))))))))....))))...----..... ( -29.90)
>consensus
UCCCAGCUAUCCGCAGAAUAAAUAAGCUGUCGCAUUGUUUAAUUGGCCCGCAAAAUGCUAACGACACUGGUUGUGGGCCCUU___GCAUU_____GUAG
............((....(((((((((....)).)))))))...(((((((((..(((....).))....)))))))))......))............ (-22.79 = -22.60 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:39 2006