Locus 4069

Sequence ID	X_DroMel_CAF1
Location	10,768,741 – 10,768,883
Length	142
Max. P	0.994308

overview

Window 1

Location	10,768,741 – 10,768,845
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	91.03
Mean single sequence MFE	-21.77
Consensus MFE	-19.31
Energy contribution	-21.00
Covariance contribution	1.69
Combinations/Pair	1.06
Mean z-score	-3.08
Structure conservation index	0.89
SVM decision value	2.47
SVM RNA-class probability	0.994308
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10768741 104 + 22224390
UGCGAUUGUAUCAAAACAAGUUUUGAAUUAUCAAAAUUGGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUUA
...(((.((.((((((....)))))))).)))......((.((((.....((((((....((((((.......))))))....)))))).)))).))....... ( -19.50)
>DroSec_CAF1 18204 104 + 1
UGCGAUUGUAUAAAAACAUGUUUUGAAUUAUCAAAAUAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAA
.....(((((((((((((((((((((....))))))))))).........))))))))))((((((.......)))))).(((((...)))))........... ( -25.30)
>DroSim_CAF1 16386 103 + 1
UGCGAUUGUA-AAAAACAAGUUUUGAAUUAUCAAAAUAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAA
...((..(((-((.((((.(((((((....))))))).))))...)))))..))......((((((.......)))))).(((((...)))))........... ( -17.70)
>DroYak_CAF1 17870 100 + 1
UGCGAUUGUAUAAAAACAAGUC-CGAAAUUUCAAAAUAUGUUUGAUUUAUUUUUAUGCAACCUUGACCUAUUUUCAAGGACCAAUAAUAUUGGACCCCGCA---
.(((.(((((((((((.(((((-.((.((........)).)).))))).)))))))))))((((((.......)))))).(((((...)))))....))).--- ( -24.60)
>consensus
UGCGAUUGUAUAAAAACAAGUUUUGAAUUAUCAAAAUAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAA
.....(((((((((((((((((((((....))))))))))).........))))))))))((((((.......)))))).(((((...)))))........... (-19.31 = -21.00 +   1.69)

alignment

secondary structure

dotplot

Window 2

Location	10,768,741 – 10,768,845
Length	104
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	91.03
Mean single sequence MFE	-24.20
Consensus MFE	-21.64
Energy contribution	-22.32
Covariance contribution	0.69
Combinations/Pair	1.09
Mean z-score	-2.45
Structure conservation index	0.89
SVM decision value	2.00
SVM RNA-class probability	0.985240
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10768741 104 - 22224390
UAAUGUGGGGUCCAAUCUUAUUGGUCCUUGAAAAUAGGUCAAGGUUGUAUAAAAAUAAAUGGAACCAAUUUUGAUAAUUCAAAACUUGUUUUGAUACAAUCGCA
...(((((((.(((((...))))).)))).............((((((((.(((((((.((....)).((((((....)))))).))))))).))))))))))) ( -24.00)
>DroSec_CAF1 18204 104 - 1
UUAUGUGGGGUCCAAUCUUAUUGGUCCUUGAAAAUAGGUCAAGGUUGUAUAAAAAUAAAUGGAACAUAUUUUGAUAAUUCAAAACAUGUUUUUAUACAAUCGCA
((((.(((((.(((((...))))).)))))...)))).....((((((((((.........((((((.((((((....)))))).))))))))))))))))... ( -26.30)
>DroSim_CAF1 16386 103 - 1
UUAUGUGGGGUCCAAUCUUAUUGGUCCUUGAAAAUAGGUCAAGGUUGUAUAAAAAUAAAUGGAACAUAUUUUGAUAAUUCAAAACUUGUUUUU-UACAAUCGCA
((((.(((((.(((((...))))).)))))...)))).....(((((((...........((((((..((((((....))))))..)))))).-)))))))... ( -22.80)
>DroYak_CAF1 17870 100 - 1
---UGCGGGGUCCAAUAUUAUUGGUCCUUGAAAAUAGGUCAAGGUUGCAUAAAAAUAAAUCAAACAUAUUUUGAAAUUUCG-GACUUGUUUUUAUACAAUCGCA
---.((((((.(((((...))))).)))((((((((((((.(((((.....((((((.........))))))..)))))..-))))))))))))......))). ( -23.70)
>consensus
UUAUGUGGGGUCCAAUCUUAUUGGUCCUUGAAAAUAGGUCAAGGUUGUAUAAAAAUAAAUGGAACAUAUUUUGAUAAUUCAAAACUUGUUUUUAUACAAUCGCA
...(((((((.(((((...))))).)))).............((((((((((((((((..........((((((....)))))).))))))))))))))))))) (-21.64 = -22.32 +   0.69)

alignment

secondary structure

dotplot

Window 3

Location	10,768,777 – 10,768,883
Length	106
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	81.35
Mean single sequence MFE	-15.01
Consensus MFE	-9.90
Energy contribution	-9.52
Covariance contribution	-0.37
Combinations/Pair	1.12
Mean z-score	-2.34
Structure conservation index	0.66
SVM decision value	1.36
SVM RNA-class probability	0.946591
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10768777 106 + 22224390
UUGGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUUAACUUAGAAAACAAUACUUGCCAUGUUCAAUUUUAUUCC-
.((((......(((....)))...((((((.......))))))))))((((((((((((....((....................))....))))))))))))...- ( -15.85)
>DroSec_CAF1 18240 95 + 1
UAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAAACACAGAAAACAACAAUU------------CGUAUUCCA
(((((((((.....((((((....((((((.......))))))....)))))).))))....)))))......(((.((.......------------.)).))).. ( -14.20)
>DroSim_CAF1 16421 95 + 1
UAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAAACACAGAAAGCAACAAUU------------CGUAUUCCA
(((((((((.....((((((....((((((.......))))))....)))))).))))....)))))......(((.((.......------------.)).))).. ( -14.50)
>DroYak_CAF1 17905 89 + 1
UAUGUUUGAUUUAUUUUUAUGCAACCUUGACCUAUUUUCAAGGACCAAUAAUAUUGGACCCCGCA------CAGGAAACAACAAUU------------CUCAUUUUA
..((((.............(((..((((((.......)))))).(((((...))))).....)))------..(....)))))...------------......... ( -15.50)
>consensus
UAUGUUCCAUUUAUUUUUAUACAACCUUGACCUAUUUUCAAGGACCAAUAAGAUUGGACCCCACAUAAACACAGAAAACAACAAUU____________CGUAUUCCA
.............(((((......((((((.......)))))).(((((...)))))................)))))............................. ( -9.90 =  -9.52 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:40 2006