Locus 7209

Sequence ID	3L_DroMel_CAF1
Location	19,351,407 – 19,351,607
Length	200
Max. P	0.945931

overview

Window 5

Location	19,351,407 – 19,351,527
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-32.45
Consensus MFE	-31.20
Energy contribution	-31.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.96
SVM decision value	0.75
SVM RNA-class probability	0.842027
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351407 120 - 23771897
GUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCACCUGACAAUUUGUUGACUCAACUAAUCUCCUUCUCCGCCGC
...((.(((((((((((......)))).))))))).)).......((((.((.(((((....((((...(((((..((....)).....)))))..)))).....)))))..)).)))). ( -33.10)
>DroSec_CAF1 1573 120 - 1
GUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCACCUGACAAUUUGUUGACUCAACUAAUCUCCUUCUCCGUUGC
..(((((((((((((((......)))).)))))))...........((..((.(((((....((((...(((((..((....)).....)))))..)))).....))))))).)))))). ( -31.80)
>DroSim_CAF1 1599 120 - 1
GUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCACCUGACAAUUUGUUGACUCAACUAAUCUCCUUCUCCGUUGC
..(((((((((((((((......)))).)))))))...........((..((.(((((....((((...(((((..((....)).....)))))..)))).....))))))).)))))). ( -31.80)
>DroYak_CAF1 4814 120 - 1
GUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCACCUGACAAUUUGUUGACUCAACUAAUCUCCUUCUCCGCCGC
...((.(((((((((((......)))).))))))).)).......((((.((.(((((....((((...(((((..((....)).....)))))..)))).....)))))..)).)))). ( -33.10)
>consensus
GUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCACCUGACAAUUUGUUGACUCAACUAAUCUCCUUCUCCGCCGC
(((((((((((((((((......)))).))))))............)))))))(((((....((((...(((((..((....)).....)))))..)))).....))))).......... (-31.20 = -31.20 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	19,351,447 – 19,351,567
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-35.05
Consensus MFE	-34.78
Energy contribution	-35.03
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.99
SVM decision value	1.36
SVM RNA-class probability	0.945931
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351447 120 - 23771897
AACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCAC
..........((((((.(((((...((.((..(((.(((((..((.(((((((((((......)))).))))))).)).....))))).)))..)).))..)))))...))).))).... ( -36.20)
>DroSec_CAF1 1613 120 - 1
AACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCAC
..........((((((.(((((...((.((..(((.(((((..((.(((((((((((......)))).))))))).)).....))))).)))..)).))..)))))...))).))).... ( -36.20)
>DroSim_CAF1 1639 120 - 1
AACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCAC
..........((((((.(((((...((.((..(((.(((((..((.(((((((((((......)))).))))))).)).....))))).)))..)).))..)))))...))).))).... ( -36.20)
>DroYak_CAF1 4854 120 - 1
AACAACCCCCUGUCUGUUCAAAUUCGCACCACUCAUCUAGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCAC
..........((((((.(((((...((.((.((.....))(((((((((((((((((......)))).))))))............))))))).)).))..)))))...))).))).... ( -31.60)
>consensus
AACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCAUUUUCCGGUUGACAGGAGCCCUUUGAUUCCAGCACAUCAC
..........((((((.(((((...((.((..(((.(((((..((.(((((((((((......)))).))))))).)).....))))).)))..)).))..)))))...))).))).... (-34.78 = -35.03 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	19,351,487 – 19,351,607
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-43.65
Consensus MFE	-41.35
Energy contribution	-42.10
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.95
SVM decision value	1.00
SVM RNA-class probability	0.898642
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351487 120 - 23771897
UUUGUUUGCUUCCUGAUCCGCGUGGCCAGGUGACGGGGUGAACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCA
............((((((((.((((...((((.(((..((((((.((....)).))))))...)))))))..)))).)))))))).(((((((((((......)))).)))))))..... ( -45.20)
>DroSec_CAF1 1653 120 - 1
UUUGUUUGCUUCCUGAUCCGCGUGGCAAGGUGACGGGGUGAACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCA
............((((((((.((((...((((.(((..((((((.((....)).))))))...)))))))..)))).)))))))).(((((((((((......)))).)))))))..... ( -45.20)
>DroSim_CAF1 1679 120 - 1
UUUGUUUGCUUCCUGAUCCGCGUGGCCAGGUGACGGGGUGAACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCA
............((((((((.((((...((((.(((..((((((.((....)).))))))...)))))))..)))).)))))))).(((((((((((......)))).)))))))..... ( -45.20)
>DroYak_CAF1 4894 120 - 1
UUUGUUUGCUUCCUGAUCCGCGUGGCCAGCUGACGGGGUGAACAACCCCCUGUCUGUUCAAAUUCGCACCACUCAUCUAGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCA
..............(((..((...(((((((((((((((.....))))).....(((........)))............))))))))))(((((((......)))).))))).)))... ( -39.00)
>consensus
UUUGUUUGCUUCCUGAUCCGCGUGGCCAGGUGACGGGGUGAACAAACCCCUGUCUGUUCAAAUUCGCACCACUCAUCUGGGUCAGCUGGCGGUCGUUUCCUCCGACGCACCGCCAUCUCA
............((((((((.((((...((((.(((..((((((.((....)).))))))...)))))))..)))).)))))))).(((((((((((......)))).)))))))..... (-41.35 = -42.10 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:53 2006