Locus 1441

Sequence ID	3R_DroMel_CAF1
Location	4,156,840 – 4,156,933
Length	93
Max. P	0.864036

overview

Window 1

Location	4,156,840 – 4,156,933
Length	93
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	95.74
Mean single sequence MFE	-29.25
Consensus MFE	-27.00
Energy contribution	-27.12
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-1.76
Structure conservation index	0.92
SVM decision value	0.62
SVM RNA-class probability	0.802089
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4156840 93 + 27905053
UGAGUUUGCUUCCAAGAACAUGAACUACACUUGUCAGAUGUCAGAGGUUGUGGAUCCAUGGGGAGAUGUCCACG-CCC-AAAGGGAGCAAAUGUC
...((((((((((..((...(((.(.......))))....))...((.(((((((((....)))....))))))-.))-...))))))))))... ( -28.50)
>DroSec_CAF1 827 93 + 1
UGAGUUUGCUCCCAAGAACAUGAAGUACACUUGUCAGAUGUCAGAGGUUGUGGAUCCAUGGGGAGAUGUCCACG-CCC-AAAGGGAGCAAAUGUC
...((((((((((..((...(((((....))..)))....))...((.(((((((((....)))....))))))-.))-...))))))))))... ( -31.50)
>DroSim_CAF1 5507 93 + 1
UGAGUUCGCUCCCAAGAACAUGAAGUACACUUGUCAGAUGUCAGAGGUUGUGGAUCCAUGGGGAGAUGUCCACG-CCC-AAAGGGAGCAAAUGUC
.......((((((..((...(((((....))..)))....))...((.(((((((((....)))....))))))-.))-...))))))....... ( -27.70)
>DroYak_CAF1 5724 95 + 1
UGAGUUUACUCCCAAGAACAUGAAGUACACUUGUCAGAUGUCAGAGGUUGUGGAUCCAUGGGGAGAUGUCCACAGCCCAAAAGGGAGGAAAUGUC
...((((.(((((..((...(((((....))..)))....)).(.((((((((((((....)))....))))))))))....))))).))))... ( -29.30)
>consensus
UGAGUUUGCUCCCAAGAACAUGAAGUACACUUGUCAGAUGUCAGAGGUUGUGGAUCCAUGGGGAGAUGUCCACG_CCC_AAAGGGAGCAAAUGUC
...((((((((((..((...(((..........)))....))...((.(((((((((....)))....)))))).)).....))))))))))... (-27.00 = -27.12 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	4,156,840 – 4,156,933
Length	93
Sequences	4
Columns	95
Reading direction	reverse
Mean pairwise identity	95.74
Mean single sequence MFE	-26.35
Consensus MFE	-23.11
Energy contribution	-23.43
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.12
Structure conservation index	0.88
SVM decision value	0.84
SVM RNA-class probability	0.864036
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4156840 93 - 27905053
GACAUUUGCUCCCUUU-GGG-CGUGGACAUCUCCCCAUGGAUCCACAACCUCUGACAUCUGACAAGUGUAGUUCAUGUUCUUGGAAGCAAACUCA
((..((((((.((...-(((-(((((((...(((....))).............(((.((....))))).))))))))))..)).)))))).)). ( -25.10)
>DroSec_CAF1 827 93 - 1
GACAUUUGCUCCCUUU-GGG-CGUGGACAUCUCCCCAUGGAUCCACAACCUCUGACAUCUGACAAGUGUACUUCAUGUUCUUGGGAGCAAACUCA
((..(((((((((...-(((-((((((....(((....))))))))........(((.((....))))).......))))..))))))))).)). ( -29.00)
>DroSim_CAF1 5507 93 - 1
GACAUUUGCUCCCUUU-GGG-CGUGGACAUCUCCCCAUGGAUCCACAACCUCUGACAUCUGACAAGUGUACUUCAUGUUCUUGGGAGCGAACUCA
((..(((((((((...-(((-((((((....(((....))))))))........(((.((....))))).......))))..))))))))).)). ( -28.70)
>DroYak_CAF1 5724 95 - 1
GACAUUUCCUCCCUUUUGGGCUGUGGACAUCUCCCCAUGGAUCCACAACCUCUGACAUCUGACAAGUGUACUUCAUGUUCUUGGGAGUAAACUCA
((..(((.(((((....(((.((((((....(((....))))))))).)))..(((((...((....)).....)))))...))))).))).)). ( -22.60)
>consensus
GACAUUUGCUCCCUUU_GGG_CGUGGACAUCUCCCCAUGGAUCCACAACCUCUGACAUCUGACAAGUGUACUUCAUGUUCUUGGGAGCAAACUCA
((..(((((((((....((...(((((....(((....))))))))..))...(((((...((....)).....)))))...))))))))).)). (-23.11 = -23.43 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:41 2006