Locus 8229

Sequence ID	X_DroMel_CAF1
Location	20,433,938 – 20,434,071
Length	133
Max. P	0.841364

overview

Window 8

Location	20,433,938 – 20,434,036
Length	98
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	86.34
Mean single sequence MFE	-31.20
Consensus MFE	-24.25
Energy contribution	-25.62
Covariance contribution	1.38
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.78
SVM decision value	0.75
SVM RNA-class probability	0.841364
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20433938 98 - 22224390
-------AAGUCAGCAGACCCAGAUCGUGUGGCAAAGAUCUCGC------------CAGGUCGAGAUCUCAAAACCCAGUUUCUCAAACACAAAGAUCGUUGGUACAAUGUUGGCGC
-------..(((((((.(((..((((.((((....((((((((.------------.....))))))))..((((...))))......))))..))))...)))....))))))).. ( -30.10)
>DroSec_CAF1 7588 110 - 1
-------AAGUCAGCAGACCCAGAUCGUGUGGCAAAGAUCUCGCCCAAGAGAGCUCCAGCUCGAGAUCUCAAAACCCAGUUUCUCAAACACAAAGAUCGUUGGUACAAUGUUGGCGC
-------..(((((((.(((..((((.((((....(((((((.(....).((((....)))))))))))..((((...))))......))))..))))...)))....))))))).. ( -32.60)
>DroSim_CAF1 9668 110 - 1
-------AAGUCAGCAGACCCAGAUCGUGUGGCAAAGAUCUCGCCUAAGAGAGCUCCAGGUCGAGAUCUCAAAACCCAGUUUCUCAAACACAAAGAUCGUUGGUACAAUGUUGGCGC
-------..(((((((.(((..((((.((((....(((((((((((..((....)).))).))))))))..((((...))))......))))..))))...)))....))))))).. ( -34.90)
>DroEre_CAF1 6138 114 - 1
CAACACCAAAUC---AGACCCAGAUCGUGUGGCGAAGAUCUCGCCAAAGAGGGAUCCAGAUCGAGAUCUCAAAACCCAGUUUAUCAAACACAAAGAUAGUUGGUACAAUGUUGGCGU
..((.((((...---..(((...((((((((((((.....))))).....((((((........)))))).................))))...)))....)))......)))).)) ( -27.20)
>consensus
_______AAGUCAGCAGACCCAGAUCGUGUGGCAAAGAUCUCGCC_AAGAGAGCUCCAGGUCGAGAUCUCAAAACCCAGUUUCUCAAACACAAAGAUCGUUGGUACAAUGUUGGCGC
.........(((((((.(((..((((.((((....((((((((.....((....)).....))))))))..((((...))))......))))..))))...)))....))))))).. (-24.25 = -25.62 +   1.38)

alignment

secondary structure

dotplot

Window 9

Location	20,433,978 – 20,434,071
Length	93
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	83.49
Mean single sequence MFE	-32.45
Consensus MFE	-24.14
Energy contribution	-25.32
Covariance contribution	1.19
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.74
SVM decision value	0.49
SVM RNA-class probability	0.757789
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20433978 93 + 22224390
GGGUUUUGAGAUCUCGACCUG------------GCGAGAUCUUUGCCACACGAUCUGGGUCUGCUGACUU--------GUUGUAGUAGACAGUUAAUCUCAACUUUGUUUGCA
.(((...(((((((((.....------------.))))))))).)))..(((((..(((((....)))))--------))))).((((((((............)))))))). ( -30.10)
>DroSec_CAF1 7628 105 + 1
GGGUUUUGAGAUCUCGAGCUGGAGCUCUCUUGGGCGAGAUCUUUGCCACACGAUCUGGGUCUGCUGACUU--------GUUGUAGUAGACAGUUAAUCUCAACUUUGUUUGCC
.(((...(((((((((..(.(((....))).)..))))))))).)))..(((((..(((((....)))))--------))))).((((((((............)))))))). ( -32.50)
>DroSim_CAF1 9708 105 + 1
GGGUUUUGAGAUCUCGACCUGGAGCUCUCUUAGGCGAGAUCUUUGCCACACGAUCUGGGUCUGCUGACUU--------GUUGUAGUAGACAGUUAAUCUCAACUUUGUUUGCC
.(((...(((((((((.((((((....)).))))))))))))).)))..(((((..(((((....)))))--------))))).((((((((............)))))))). ( -35.60)
>DroEre_CAF1 6178 110 + 1
GGGUUUUGAGAUCUCGAUCUGGAUCCCUCUUUGGCGAGAUCUUCGCCACACGAUCUGGGUCU---GAUUUGGUGUUGAUUUGUAGUAGACAGUUAAUUUCAAAUUGCCUUGCC
((((...........((((..((((......(((((((...)))))))...))))..)))).---(((((((.(((((((.((.....))))))))).))))))))))).... ( -31.60)
>consensus
GGGUUUUGAGAUCUCGACCUGGAGCUCUCUU_GGCGAGAUCUUUGCCACACGAUCUGGGUCUGCUGACUU________GUUGUAGUAGACAGUUAAUCUCAACUUUGUUUGCC
.(((...(((((((((....(((....)))....))))))))).)))..(((((..(((((....)))))........))))).((((((((............)))))))). (-24.14 = -25.32 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:54 2006