Locus 6652

Sequence ID	3L_DroMel_CAF1
Location	17,715,875 – 17,716,003
Length	128
Max. P	0.847545

overview

Window 6

Location	17,715,875 – 17,715,981
Length	106
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.25
Mean single sequence MFE	-26.21
Consensus MFE	-15.49
Energy contribution	-15.99
Covariance contribution	0.50
Combinations/Pair	1.18
Mean z-score	-1.69
Structure conservation index	0.59
SVM decision value	0.78
SVM RNA-class probability	0.847545
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17715875 106 + 23771897
GCCGAAUGUGUCAAUAGGCCGCACAUUUGUUUGCGCCC------UGCCAUUGCCGUUAU-AUACACACCCCGUGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACU
((.((((((((...((((.((((........)))).))------)).....((((((..-...(((.....))).....)))))).....))))).))).))........... ( -26.20)
>DroPse_CAF1 77441 91 + 1
CCCGAAUGUGUCAAUAGGCCGCACAUUUGUUAGCGCCUCAAAUCCGCUUCCACCGUUA-----------CGCCGCACAAAAUGGCGGCCAACGCAUUUCCGC-----------
...((((((((.....((((((.((((((..((((.........))))..)...((..-----------....))...))))))))))).))))))))....----------- ( -26.00)
>DroSec_CAF1 93628 106 + 1
GCCGAAUGUGUCAAUAGGCCGCACAUUUGUUUGCGCCG------UGCCAUUGCCGUUAU-AGACACAACCUGCGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACU
((.((((((((.....(((.(((........))))))(------(((((((..(((...-...........))).....))))))))...))))).))).))........... ( -26.94)
>DroSim_CAF1 87724 106 + 1
GCCGAAUGUGUCAAUAGGCCGCACAUUUGUUUGCGCCC------UGCCAUUGCCGUUAU-ACACACACCCUGCUCACAAAAUGGCUCCCAACGCAUUUCCGCUUUAACACACU
((.((((((((....(((.((((........)))).))------)((((((........-...................)))))).....))))).))).))........... ( -22.03)
>DroAna_CAF1 82805 103 + 1
CCGGAAUGUGUCAAUAGGCCGCGCAUUUGUUAGCGCCC------CGCCAUU----UUAUUCCGCACAAAAAACGCACAAAAUGGUGGCCAACGCAUUUCCGCUUUAACACACU
.((((((((((.....((((((((........))))..------.((((((----((.....((.........))..)))))))))))).))))).)))))............ ( -30.10)
>DroPer_CAF1 75724 91 + 1
CCCGAAUGUGUCAAUAGGCCGCACAUUUGUUAGCGCCUCAAAUCCGCUUCCACCGUUA-----------CGCCGCACAAAAUGGCGGCCAACGCAUUUCCGC-----------
...((((((((.....((((((.((((((..((((.........))))..)...((..-----------....))...))))))))))).))))))))....----------- ( -26.00)
>consensus
CCCGAAUGUGUCAAUAGGCCGCACAUUUGUUAGCGCCC______CGCCAUUGCCGUUAU_A_ACACA_CCGGCGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACU
...((((((((.....(((.((((....))..))))).......(((((((............................)))))))....))))))))............... (-15.49 = -15.99 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	17,715,909 – 17,716,003
Length	94
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	85.36
Mean single sequence MFE	-16.44
Consensus MFE	-12.38
Energy contribution	-12.69
Covariance contribution	0.31
Combinations/Pair	1.19
Mean z-score	-1.54
Structure conservation index	0.75
SVM decision value	0.15
SVM RNA-class probability	0.606018
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17715909 94 + 23771897
GCCCUGCCAUUGCCGUUAU-AUACACACCCCGUGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACUAAAGCCGCGACCCCGUCAACUA
((..(((...(((((((..-...(((.....))).....)))))))......))).....((((((......)))))).))(((...)))..... ( -17.20)
>DroSec_CAF1 93662 94 + 1
GCCGUGCCAUUGCCGUUAU-AGACACAACCUGCGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACUAAAGCCGCGACCCCGUCAACUA
((.((((((((..(((...-...........))).....)))))))).............((((((......)))))).))(((...)))..... ( -18.64)
>DroSim_CAF1 87758 94 + 1
GCCCUGCCAUUGCCGUUAU-ACACACACCCUGCUCACAAAAUGGCUCCCAACGCAUUUCCGCUUUAACACACUAAAGCCGCGACCCCGUCAACUA
((..(((....((((((..-...................)))))).......))).....((((((......)))))).))(((...)))..... ( -13.20)
>DroAna_CAF1 82839 86 + 1
GCCCCGCCAUU----UUAUUCCGCACAAAAAACGCACAAAAUGGUGGCCAACGCAUUUCCGCUUUAACACACUAAAGCCGC-----CAUCAACUA
((.((((((((----((.....((.........))..)))))))))).............((((((......)))))).))-----......... ( -16.70)
>consensus
GCCCUGCCAUUGCCGUUAU_ACACACAACCUGCGCACAAAAUGGCGCCCAACGCAUUUCCGCUUUAACACACUAAAGCCGCGACCCCGUCAACUA
((.((((((((............................)))))))).............((((((......)))))).)).............. (-12.38 = -12.69 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:33 2006