Locus 7560

Sequence ID	3R_DroMel_CAF1
Location	20,259,568 – 20,259,663
Length	95
Max. P	0.999874

overview

Window 2

Location	20,259,568 – 20,259,663
Length	95
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	88.85
Mean single sequence MFE	-19.00
Consensus MFE	-17.12
Energy contribution	-17.12
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.09
Structure conservation index	0.90
SVM decision value	4.33
SVM RNA-class probability	0.999874
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20259568 95 + 27905053
AAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCAUCCAUA----------------UAACCAUACAUCCUCGUGUACACACAC
.....(((((((((((((.((.....)).))))................(((.....)))........----------------....)))))))))..(((....))).. ( -19.80)
>DroSec_CAF1 69264 94 + 1
CAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCACCCAUA----------------UUACCAUACAUCCUCGUGGACACACA-
.....(((((((((((((.((.....)).))))................(((.....)))........----------------....)))))))))..(((....))).- ( -20.30)
>DroSim_CAF1 74531 94 + 1
CAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCACCCAUA----------------UAACCAUACAUCCUCGUGUACACACA-
.....(((((((((((((.((.....)).))))................(((.....)))........----------------....)))))))))..(((....))).- ( -19.80)
>DroEre_CAF1 71024 111 + 1
CAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCACCCAUACAGCCAUACAAGCAUACAACCAUACAUCCCCAAGAAUACACAC
.....((((((((((((((.......(((...((....))...)))...(((.....)))...................)))))))....))))))).............. ( -17.90)
>DroYak_CAF1 72180 95 + 1
CAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCACCCAUA----------------UAACCAUACAUCCUCAUGUAUACACAC
.....(((((((((((((.((.....)).))))................(((.....)))........----------------....))))))))).............. ( -17.20)
>consensus
CAAUCGGGUGUAUGUGUGCCAACUAUUGACACAGAACUCUCACUCACACGCUCAUCCAGCCACCCAUA________________UAACCAUACAUCCUCGUGUACACACAC
.....(((((((((((((.((.....)).))))................(((.....)))............................))))))))).............. (-17.12 = -17.12 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	20,259,568 – 20,259,663
Length	95
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	88.85
Mean single sequence MFE	-28.44
Consensus MFE	-21.14
Energy contribution	-21.30
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.53
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.508905
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20259568 95 - 27905053
GUGUGUGUACACGAGGAUGUAUGGUUA----------------UAUGGAUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUU
((((((((.(((..(.((((.((((((----------------(....))))))).....)))).)..)))........((((((.....))))))))))))))....... ( -25.90)
>DroSec_CAF1 69264 94 - 1
-UGUGUGUCCACGAGGAUGUAUGGUAA----------------UAUGGGUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUG
-.(((..(((....)))..))).....----------------..(((((((((.....)))((((((((....)))).((((((.....)))))))))).)))))).... ( -28.40)
>DroSim_CAF1 74531 94 - 1
-UGUGUGUACACGAGGAUGUAUGGUUA----------------UAUGGGUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUG
-.(((....)))....(((((....))----------------)))((((((((.....)))((((((((....)))).((((((.....)))))))))).)))))..... ( -24.80)
>DroEre_CAF1 71024 111 - 1
GUGUGUAUUCUUGGGGAUGUAUGGUUGUAUGCUUGUAUGGCUGUAUGGGUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUG
.............(((.((((((.(..((((((..(.((((..(....)..)))).)..))))))..)..........(((((((.....))))))))))))))))..... ( -36.40)
>DroYak_CAF1 72180 95 - 1
GUGUGUAUACAUGAGGAUGUAUGGUUA----------------UAUGGGUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUG
((((((((((((....)))))))..))----------------)))((((((((.....)))((((((((....)))).((((((.....)))))))))).)))))..... ( -26.70)
>consensus
GUGUGUGUACACGAGGAUGUAUGGUUA________________UAUGGGUGGCUGGAUGAGCGUGUGAGUGAGAGUUCUGUGUCAAUAGUUGGCACACAUACACCCGAUUG
..(((....))).................................(((((((((.....)))((((((((....)))).((((((.....)))))))))).)))))).... (-21.14 = -21.30 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:54 2006