Locus 1667

Sequence ID	X_DroMel_CAF1
Location	4,686,099 – 4,686,298
Length	199
Max. P	0.856995

overview

Window 2

Location	4,686,099 – 4,686,204
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.43
Mean single sequence MFE	-41.68
Consensus MFE	-35.88
Energy contribution	-35.51
Covariance contribution	-0.37
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.86
SVM decision value	0.81
SVM RNA-class probability	0.856995
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4686099 105 - 22224390
UCGGCUGGCUGAGCG-------------GCUCA--GUUGGCUCAGCCAAAUCGGUUGGCUUCUGUUUGUGUCCUGGGGGUUAAUUCACCAGCCGGCUGACAACAAACAGCAGCAGAGUUC
..(((..((((((..-------------.))))--))..)))(((((.....)))))(((.(((((((((((((((.(((......)))..))))..))).)))))))).)))....... ( -45.10)
>DroSec_CAF1 39710 105 - 1
UCGGCUGGCUGAGUG-------------GCUCAGAGUUGGCUCAGCCAAAUCGGUUGGCUUCUGU--GUGUCCUGGGGGUUAAUUCACCAGCCGGCUGACAACAAACAGCAGCAGAGUUC
(((((((((((.(((-------------((.((((...(((.(((((.....)))))))))))).--))..((....))......))))))))))))))..................... ( -39.70)
>DroEre_CAF1 40098 103 - 1
UCGGCUGGCUGAGUG-------------GCUCA--GUUGGCUCAGCCAAAUCGGAUGGCUUCUGU--GUGUCCUGGGGGUUAAUUCACCAGCCGGCUGACAACAAACAGCAGCAGAGUUC
..(((((((..(.((-------------...))--.)..)).))))).....((((.(((.((((--.((((((((.(((......)))..))))..))))....)))).)))...)))) ( -37.80)
>DroYak_CAF1 36943 116 - 1
UCGGCUGGCUGAGUGGUUGGCUCAGUUGGCUCA--AUUGGCUCAGCCAAAUCGAAUGGCUUCUGU--GUGUCCUGGGGGUUAAUUCACCAGCCGGCUGACAACAAACAGCAGCAGAGUUC
..(((..(((((((.....)))))))..)))..--.(((((...)))))...((((.(((.((((--.((((((((.(((......)))..))))..))))....)))).)))...)))) ( -44.10)
>consensus
UCGGCUGGCUGAGUG_____________GCUCA__GUUGGCUCAGCCAAAUCGGAUGGCUUCUGU__GUGUCCUGGGGGUUAAUUCACCAGCCGGCUGACAACAAACAGCAGCAGAGUUC
((((.(((((((((.........................)))))))))..))))...(((.((((...((((((((.(((......)))..))))..))))....)))).)))....... (-35.88 = -35.51 +  -0.37)

alignment

secondary structure

dotplot

Window 3

Location	4,686,204 – 4,686,298
Length	94
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.75
Mean single sequence MFE	-33.28
Consensus MFE	-22.62
Energy contribution	-22.68
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-1.73
Structure conservation index	0.68
SVM decision value	0.34
SVM RNA-class probability	0.695782
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4686204 94 - 22224390
CACAGGACACCUUAAGGACCUGAGGUCUCUGGUUUCUG--------------------GGUUUCUGGUCUUAAACAACACGUCGCGAAUUGUCGUGG------UCGUGGUCCUUCGUCCU
...(((((......((((((.((((.(((........)--------------------)))))).))))))......((((((((((....))))))------.)))).......))))) ( -32.20)
>DroSec_CAF1 39815 94 - 1
CACAGGACACCAUAAGGACCUGAGGUCUCUGGUUUCUG--------------------GGUUUCUGGUCUCAAACAACACGUCGCGAAUUGUCGUGG------UCGUGGUCCUUCGUCCU
...(((((.....(((((((((((..(...((..(...--------------------.)..)).)..))))......(((((((((....))))))------.)))))))))).))))) ( -31.40)
>DroEre_CAF1 40201 86 - 1
CACAGGACACCUUUAGGACCUGAGGUCUCUGGUUU----------------------------AUGGUCUUAAACAACGCGUCGCGAAUUGUCGUGG------UCGUGGUCCUUCGUCCU
...(((((......((((((((((..(........----------------------------..)..))))......(((((((((....))))))------.)))))))))..))))) ( -28.80)
>DroYak_CAF1 37059 120 - 1
CACAGGACACCAUUAGGACCUGAGGUCUCUGGUUUCUUGCUACUGGUUUCUUGCUACUGGCUUCUGGUCUUUAACAACGCGUCCCGAAUUGUCGUGGUCGUGGUCGUGGUCCUUCGUCCU
...((((((((((.((((((.((((((..((((.....((.....)).....))))..)))))).))))))......((((.(((((....))).)).))))...))))).....))))) ( -40.70)
>consensus
CACAGGACACCAUAAGGACCUGAGGUCUCUGGUUUCUG____________________GGUUUCUGGUCUUAAACAACACGUCGCGAAUUGUCGUGG______UCGUGGUCCUUCGUCCU
...(((((......((((((((((..(......................................)..)))).....((((.((.....)).))))...........))))))..))))) (-22.62 = -22.68 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:14 2006