Locus 1573

Sequence ID	X_DroMel_CAF1
Location	4,482,992 – 4,483,087
Length	95
Max. P	0.997041

overview

Window 2

Location	4,482,992 – 4,483,087
Length	95
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	83.13
Mean single sequence MFE	-30.48
Consensus MFE	-20.22
Energy contribution	-20.22
Covariance contribution	0.00
Combinations/Pair	1.20
Mean z-score	-1.97
Structure conservation index	0.66
SVM decision value	0.46
SVM RNA-class probability	0.743649
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4482992 95 + 22224390
-------AGAGGACACGGAGAAGCUGCUCGAGC------AGGACCGCGAAGCAGAGGUGAUUCUCGAGCAGGAGAAGAUUCUAGAGCAGGAGAUGGUCUCAGAGCGGG
-------........((......(((((((((.------(..(((.(......).)))..).))))))))).......(((((((.((.....)).))).)))))).. ( -28.00)
>DroSec_CAF1 1283 101 + 1
-------GGAGGACAAGGAGAAGCUGCUCGAGCUGCUCGAGGACCCCGAAACAGAGGUGAUUCUCGAGCAGGAGAAGAUUCUAGAGCAGGAGAUGCUCUUGGAGCGGG
-------................((((((...(((((((((((.(((........)).).))))))))))).........(.((((((.....)))))).))))))). ( -39.50)
>DroSim_CAF1 315 95 + 1
-------GGAGGACAAGGAGAAGCUGCUCGAGC------AGGACCCCGAAACAGAGGUGAUUCUCGAGCAGGAGAAGAUUCUAGAGCAGGAGAUGCUCUUGGAGCGGG
-------................(((((((((.------(..(((.(......).)))..).))))))))).....(.((((((((((.....))))).))))))... ( -31.00)
>DroEre_CAF1 7581 95 + 1
-------GGAGGAGAAGGAGAAGCCUCUUGAGA------AGGACCCCGAGGCAGAGGCGAUUCUCGAGCAGGAGAGGAUUCUAGAGCAGGAGAUGCUCUUAGAGAGGG
-------................((((((((((------(...((.(......).))...)))))))).)))......((((((((((.....))))).))))).... ( -26.90)
>DroYak_CAF1 5903 102 + 1
AGGUGGAGGAGGACAAGGAGGAACUGCUCGAAA------AAGAUCCCGAGGCCGAGGAGAUUCGCGAGCAGGAGAGGAUGCUAGAGCAAGAGAUGCUCUCAGAGAGGG
.......................(((((((...------((..(((((....)).)))..))..)))))))(((((.((.((........)))).)))))........ ( -27.00)
>consensus
_______GGAGGACAAGGAGAAGCUGCUCGAGC______AGGACCCCGAAGCAGAGGUGAUUCUCGAGCAGGAGAAGAUUCUAGAGCAGGAGAUGCUCUUAGAGCGGG
.......................((((((.........................(((...(((((......)))))...)))((((((.....))))))..)))))). (-20.22 = -20.22 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	4,482,992 – 4,483,087
Length	95
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	83.13
Mean single sequence MFE	-28.11
Consensus MFE	-19.60
Energy contribution	-20.56
Covariance contribution	0.96
Combinations/Pair	1.15
Mean z-score	-3.58
Structure conservation index	0.70
SVM decision value	2.79
SVM RNA-class probability	0.997041
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4482992 95 - 22224390
CCCGCUCUGAGACCAUCUCCUGCUCUAGAAUCUUCUCCUGCUCGAGAAUCACCUCUGCUUCGCGGUCCU------GCUCGAGCAGCUUCUCCGUGUCCUCU-------
...((...(((.....)))..))..............(((((((((....(((.(......).)))...------.)))))))))................------- ( -23.60)
>DroSec_CAF1 1283 101 - 1
CCCGCUCCAAGAGCAUCUCCUGCUCUAGAAUCUUCUCCUGCUCGAGAAUCACCUCUGUUUCGGGGUCCUCGAGCAGCUCGAGCAGCUUCUCCUUGUCCUCC-------
...((((..((((((.....))))))...........(((((((((....(((((......))))).)))))))))...))))..................------- ( -34.50)
>DroSim_CAF1 315 95 - 1
CCCGCUCCAAGAGCAUCUCCUGCUCUAGAAUCUUCUCCUGCUCGAGAAUCACCUCUGUUUCGGGGUCCU------GCUCGAGCAGCUUCUCCUUGUCCUCC-------
.........((((((.....))))))...........(((((((((....(((((......)))))...------.)))))))))................------- ( -30.20)
>DroEre_CAF1 7581 95 - 1
CCCUCUCUAAGAGCAUCUCCUGCUCUAGAAUCCUCUCCUGCUCGAGAAUCGCCUCUGCCUCGGGGUCCU------UCUCAAGAGGCUUCUCCUUCUCCUCC-------
.((((((((.(((((.....)))))))))..............(((((..(((((......)))))..)------))))..))))................------- ( -27.20)
>DroYak_CAF1 5903 102 - 1
CCCUCUCUGAGAGCAUCUCUUGCUCUAGCAUCCUCUCCUGCUCGCGAAUCUCCUCGGCCUCGGGAUCUU------UUUCGAGCAGUUCCUCCUUGUCCUCCUCCACCU
.........((((((.....)))))).(((.......(((((((.(((..(((.((....)))))...)------)).)))))))........)))............ ( -25.06)
>consensus
CCCGCUCUAAGAGCAUCUCCUGCUCUAGAAUCUUCUCCUGCUCGAGAAUCACCUCUGCUUCGGGGUCCU______GCUCGAGCAGCUUCUCCUUGUCCUCC_______
.........((((((.....))))))...........(((((((((....(((((......)))))..........)))))))))....................... (-19.60 = -20.56 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:48 2006