Locus 592

Sequence ID	X_DroMel_CAF1
Location	1,662,394 – 1,662,507
Length	113
Max. P	0.895693

overview

Window 3

Location	1,662,394 – 1,662,507
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.83
Mean single sequence MFE	-40.02
Consensus MFE	-24.98
Energy contribution	-26.60
Covariance contribution	1.62
Combinations/Pair	1.11
Mean z-score	-2.40
Structure conservation index	0.62
SVM decision value	0.99
SVM RNA-class probability	0.895693
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1662394 113 + 22224390
UUCGAGUGGAUGUGUCGCGGCAACUUAAGUGUAUCAUU------UGCUUGGCCAGAAUCA-GGCGGCAAUUGAUGGGGCUUCAUUGAAGCCGCGAAAGUGUUGCGGAAUUAAGUUACUCG
..(((((((..((..(((((((.(((..((.(((((.(------((((..(((.......-)))))))).))))).((((((...))))))))..))))))))))..))....))))))) ( -42.00)
>DroSim_CAF1 405 117 + 1
UUGGAGUGGAUGUGUCGCGGCAACUUAAGUGUAUCAUUGCUUGGUGCUUGGCCAGCACCA-GGCGGCAAUUGAUGGGGCUUCAUUGAAGCCGCGAAAGUGUUGCGAAAUUAAGUUACU--
....(((((..((.((((((((.(((..((.(((((((((((((((((.....)))))))-)))))....))))).((((((...))))))))..))))))))))).))....)))))-- ( -44.60)
>DroEre_CAF1 8120 101 + 1
UUCGAGUGGCUGUGUCG------------UGUAUCUUU------UGCUCGGCCAGCAGCAAAGCGGCCAUUGAUGGGGUUUCACUGAAGCCGCGAAAGUGUUGCGAA-CCAACUUACUCG
..(((((((.((..(((------------((...((((------(((..((((.((......))))))........((((((...)))))))))))))...))))).-.)).).)))))) ( -37.20)
>DroYak_CAF1 567 113 + 1
UUCGAGUGGAUGUGUCGCGGCAACUUAAGUGUAUCAUU------UGCUUGGCCAGCAGCA-AGCGGCAAUUGAUGGGGUUUUAUUGAAGCCGCGAAAGUGGUGCGAAAUGAAGUUACUCG
..(((((((.....((((..(((...((.(.(((((.(------((((..((.....)).-...))))).))))).).))...)))..(((((....))))))))).......))))))) ( -36.30)
>consensus
UUCGAGUGGAUGUGUCGCGGCAACUUAAGUGUAUCAUU______UGCUUGGCCAGCAGCA_AGCGGCAAUUGAUGGGGCUUCAUUGAAGCCGCGAAAGUGUUGCGAAAUUAAGUUACUCG
..(((((((.....((((((((............................(((.((......)))))......((.((((((...)))))).))....)))))))).......))))))) (-24.98 = -26.60 +   1.62)

alignment

secondary structure

dotplot

Window 4

Location	1,662,394 – 1,662,507
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.83
Mean single sequence MFE	-29.39
Consensus MFE	-16.20
Energy contribution	-17.52
Covariance contribution	1.31
Combinations/Pair	1.05
Mean z-score	-2.22
Structure conservation index	0.55
SVM decision value	0.02
SVM RNA-class probability	0.543151
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1662394 113 - 22224390
CGAGUAACUUAAUUCCGCAACACUUUCGCGGCUUCAAUGAAGCCCCAUCAAUUGCCGCC-UGAUUCUGGCCAAGCA------AAUGAUACACUUAAGUUGCCGCGACACAUCCACUCGAA
(((((........((((((((......(.((((((...)))))).)((((.((((.(((-.......)))...)))------).))))........)))).)).)).......))))).. ( -30.56)
>DroSim_CAF1 405 117 - 1
--AGUAACUUAAUUUCGCAACACUUUCGCGGCUUCAAUGAAGCCCCAUCAAUUGCCGCC-UGGUGCUGGCCAAGCACCAAGCAAUGAUACACUUAAGUUGCCGCGACACAUCCACUCCAA
--.(((((((((....((((.......(.((((((...)))))))......)))).((.-(((((((.....))))))).))..........)))))))))................... ( -33.12)
>DroEre_CAF1 8120 101 - 1
CGAGUAAGUUGG-UUCGCAACACUUUCGCGGCUUCAGUGAAACCCCAUCAAUGGCCGCUUUGCUGCUGGCCGAGCA------AAAGAUACA------------CGACACAGCCACUCGAA
(((((..((((.-.(((.....((((..(((((.(((..((...(((....)))....))..)))..)))))....------)))).....------------)))..)))).))))).. ( -29.90)
>DroYak_CAF1 567 113 - 1
CGAGUAACUUCAUUUCGCACCACUUUCGCGGCUUCAAUAAAACCCCAUCAAUUGCCGCU-UGCUGCUGGCCAAGCA------AAUGAUACACUUAAGUUGCCGCGACACAUCCACUCGAA
(((((.........((((.(.((((..(((((.....................)))))(-((((........))))------)...........)))).)..)))).......))))).. ( -23.99)
>consensus
CGAGUAACUUAAUUUCGCAACACUUUCGCGGCUUCAAUGAAACCCCAUCAAUUGCCGCC_UGCUGCUGGCCAAGCA______AAUGAUACACUUAAGUUGCCGCGACACAUCCACUCGAA
(((((.........((((.........(((((....(((......))).....))))).....((((.....))))..........................)))).......))))).. (-16.20 = -17.52 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:44 2006