Locus 2348

Sequence ID	X_DroMel_CAF1
Location	6,272,744 – 6,272,889
Length	145
Max. P	0.999537

overview

Window 2

Location	6,272,744 – 6,272,856
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.70
Mean single sequence MFE	-33.26
Consensus MFE	-26.97
Energy contribution	-27.05
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.52
Structure conservation index	0.81
SVM decision value	0.40
SVM RNA-class probability	0.722947
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6272744 112 - 22224390
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU-------UCUCAGGAUUUUUCCG-GCUCUUCCGGCUUUUU
.......(((((((((.(((((.....)))))))..((((.((......)))))).)))))))((((((((.((((((..-------((....))...)))))-)...)))))))).... ( -34.90)
>DroSec_CAF1 15029 110 - 1
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU-------UUUCAGGGUU-UUCCG-GCUCUUCCGGCUU-CU
.......(((((((((.(((((.....)))))))..((((.((......)))))).)))))))((((((((.((((((..-------((....))..-)))))-)...)))))))).-.. ( -33.50)
>DroSim_CAF1 16587 110 - 1
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU-------UUUCAGGGUU-UUCCG-GCUCUUCCGGCUU-CU
.......(((((((((.(((((.....)))))))..((((.((......)))))).)))))))((((((((.((((((..-------((....))..-)))))-)...)))))))).-.. ( -33.50)
>DroEre_CAF1 4042 112 - 1
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAACCGGGGUCCGGGGUU-------UUUCAGGGGUUUUCAGGGUUUUUCCGGCUU-CU
......(((((..(((.(((((.....))))))))............(((((...)))))..)))))((((.((((((..-------..((..((....))..))...)))))))))-). ( -27.70)
>DroYak_CAF1 12228 118 - 1
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGAGUUCUUUUUUUUUCCAGGCUUUUCCG-GCUUCUCCGGCUU-CU
.......(((((((((.(((((.....)))))))..((((.((......)))))).)))))))((((((((.((((((..(((.........)))...)))))-)...)))))))).-.. ( -36.70)
>consensus
UCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU_______UUUCAGGGUUUUUCCG_GCUCUUCCGGCUU_CU
.......(((((((((.(((((.....)))))))..((((.((......)))))).)))))))((((((((.((((((....................))))).)...)))))))).... (-26.97 = -27.05 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	6,272,776 – 6,272,889
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.34
Mean single sequence MFE	-36.84
Consensus MFE	-35.06
Energy contribution	-35.18
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-2.14
Structure conservation index	0.95
SVM decision value	3.70
SVM RNA-class probability	0.999537
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6272776 113 - 22224390
GCG-------GCACUUGCGGUCGAAAGGCAAACUCUGAGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU
...-------((....)).(((....))).(((((((..(((.((((.((((((((.(((((.....)))))))..((((.((......)))))).))))))))))..)))..))))))) ( -31.90)
>DroSec_CAF1 15059 113 - 1
GCG-------GCACUUGCGGUCGAAAGACAAACUCUGGGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU
...-------((....)).(((....))).(((((((((..(.((((.((((((((.(((((.....)))))))..((((.((......)))))).))))))))))..)..))))))))) ( -37.80)
>DroSim_CAF1 16617 113 - 1
GCG-------GCACUUGCGGUCGAAAGGCAAACUCUGGGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU
...-------((....)).(((....))).(((((((((..(.((((.((((((((.(((((.....)))))))..((((.((......)))))).))))))))))..)..))))))))) ( -37.20)
>DroEre_CAF1 4074 113 - 1
GCG-------GCACUUGCGGUCGAAAGGCAAACUCGGGGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAACCGGGGUCCGGGGUU
...-------((....)).(((....)))...((((((.(((.((((.((((((((.(((((.....)))))))..((((.((......)))))).)))))))))).))).))))))... ( -35.50)
>DroYak_CAF1 12266 120 - 1
GCUGCAAGGAGCACUUGCGGUCGAAAGGCAAACUCGGGGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGAGUU
..((((((.....))))))(((....))).(((((.(((..(.((((.((((((((.(((((.....)))))))..((((.((......)))))).))))))))))..)..))).))))) ( -41.80)
>consensus
GCG_______GCACUUGCGGUCGAAAGGCAAACUCUGGGUUCAGUUGGUUGAGUGAAUGGAUUAAAAGUCCAUCAGAAUGUACAUAAAAGUCAUUGACUUAACAGCCGGGGUCCGGGGUU
..........((....)).(((....))).(((((((((..(.((((.((((((((.(((((.....)))))))..((((.((......)))))).))))))))))..)..))))))))) (-35.06 = -35.18 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:24 2006