Locus 6092

Sequence ID	3R_DroMel_CAF1
Location	15,974,413 – 15,974,533
Length	120
Max. P	0.592390

overview

Window 6

Location	15,974,413 – 15,974,533
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.78
Mean single sequence MFE	-29.62
Consensus MFE	-25.61
Energy contribution	-26.33
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-1.42
Structure conservation index	0.86
SVM decision value	0.08
SVM RNA-class probability	0.571637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15974413 120 + 27905053
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUUGUGUUUUUGCUGGUCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
.(((((((..................(((((((((((....(((((((.((....))....)))))))..))))....)))))))(((....))))))))))...((.....))...... ( -30.30)
>DroSec_CAF1 100362 120 + 1
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUGGUUUUUUUGCUGGCCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
.(((((((..................(((((((((((....(((((((((........)))).)))))..))))....)))))))(((....))))))))))...((.....))...... ( -31.30)
>DroSim_CAF1 77159 120 + 1
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUUGUGUUUUUGCUGGCCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
.(((((((..................(((((((((((....(((((((.(((......))))))))))..))))....)))))))(((....))))))))))...((.....))...... ( -32.40)
>DroEre_CAF1 75640 120 + 1
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUUGUGUUUUUGCUGGCCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
.(((((((..................(((((((((((....(((((((.(((......))))))))))..))))....)))))))(((....))))))))))...((.....))...... ( -32.40)
>DroYak_CAF1 106046 118 + 1
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGG--UACCUUUAACUUUGUGUUUUUGCUGGUCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
.(((((((..................((((((--(((....(((((((.((....))....)))))))..))))......)))))(((....))))))))))...((.....))...... ( -25.20)
>DroAna_CAF1 69374 120 + 1
CUCUCAUUGGCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUUGUGUUUUUGCUGGCCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAAAAUGAACGAAGCAAGAAGCAAACAA
.((((((.((..((.......))..))))))))((((....(((((((.(((......))))))))))..))))...((((..(((((((((.....)))))..)))).))))....... ( -26.10)
>consensus
UGCUCAUUGCCCUGAUUUAUCCAAUCCAUGGGAGCACCUUUAACUUUGUGUUUUUGCUGGCCAAAGUUUUGUGCAAUUUUCCAUGCUGUUUACAGAAUGAGCGAAGCAAGAAGCAAACAA
((((((((..................(((((((((((....(((((((.(((......))))))))))..))))....)))))))(((....)))))))))))..((.....))...... (-25.61 = -26.33 +   0.72)

alignment

secondary structure

dotplot

Window 7

Location	15,974,413 – 15,974,533
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.78
Mean single sequence MFE	-27.62
Consensus MFE	-25.42
Energy contribution	-26.12
Covariance contribution	0.70
Combinations/Pair	1.03
Mean z-score	-0.99
Structure conservation index	0.92
SVM decision value	0.12
SVM RNA-class probability	0.592390
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15974413 120 - 27905053
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGACCAGCAAAAACACAAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((......((((..(((((((.............)))))))....))))..)))))((((.....))))).)).))))))). ( -28.92)
>DroSec_CAF1 100362 120 - 1
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGGCCAGCAAAAAAACCAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((......((((..(((((.((............)))))))....))))..)))))((((.....))))).)).))))))). ( -27.60)
>DroSim_CAF1 77159 120 - 1
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGGCCAGCAAAAACACAAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((......((((..(((((((.............)))))))....))))..)))))((((.....))))).)).))))))). ( -30.22)
>DroEre_CAF1 75640 120 - 1
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGGCCAGCAAAAACACAAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((......((((..(((((((.............)))))))....))))..)))))((((.....))))).)).))))))). ( -30.22)
>DroYak_CAF1 106046 118 - 1
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGACCAGCAAAAACACAAAGUUAAAGGUA--CCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((.....(((....(((((((.............)))))))....)))--.)))))((((.....))))).)).))))))). ( -24.32)
>DroAna_CAF1 69374 120 - 1
UUGUUUGCUUCUUGCUUCGUUCAUUUUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGGCCAGCAAAAACACAAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGCCAAUGAGAG
((((((((....((.......))....))))))))(((((......((((..(((((((.............)))))))....))))..))))).(((((..........)))))..... ( -24.42)
>consensus
UUGUUUGCUUCUUGCUUCGCUCAUUCUGUAAACAGCAUGGAAAAUUGCACAAAACUUUGGCCAGCAAAAACACAAAGUUAAAGGUGCUCCCAUGGAUUGGAUAAAUCAGGGCAAUGAGCA
......((.....))...(((((((((.(......(((((......((((..(((((((.............)))))))....))))..)))))((((.....))))).)).))))))). (-25.42 = -26.12 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:30 2006