Locus 4267

Sequence ID	2R_DroMel_CAF1
Location	14,078,250 – 14,078,356
Length	106
Max. P	0.880454

overview

Window 7

Location	14,078,250 – 14,078,356
Length	106
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.60
Mean single sequence MFE	-31.13
Consensus MFE	-23.34
Energy contribution	-23.12
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-3.32
Structure conservation index	0.75
SVM decision value	0.91
SVM RNA-class probability	0.880454
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14078250 106 + 20766785
CAACAAAUUCAGCCUGUCAACCGGGC----GAAACAAUGCAAAGUAAGCUCUCUGUCAUUU-------UGCAAUUUGCAAUUGGAGUAGCCCACCUCAUGGCUGCACAAAAAGC---AAA
.......(((.(((((.....)))))----)))....((((((((..((.....)).))))-------)))).(((((..(((..((((((........)))))).)))...))---))) ( -29.00)
>DroSim_CAF1 2802 106 + 1
CAACAAAUUCAGCCUGUCAACCAGGC----GAAACAAUGCAAAGUAAGCUCUCUGUCAUUU-------UGCAAUUUGCAAUUGGAGUAGCCCACCUCACGGCUGCACAAAAAGC---AAA
.......(((.(((((.....)))))----)))....((((((((..((.....)).))))-------)))).(((((..(((..((((((........)))))).)))...))---))) ( -29.80)
>DroYak_CAF1 3465 120 + 1
CAACAAAUGCAGCCUGUCAACCGGGCAACCGAAACAAUGCAAAGUAAGCUCUCUGUCAUUUUGCAUUUUGCAAUUUGCAAUUGGAGUAGCCCACCUCACGGCUGCACAAAAAGUGAAAAA
.......(((((((((......((((..((((...((((((((((..((.....)).))))))))))((((.....))))))))....))))....)).))))))).............. ( -34.60)
>consensus
CAACAAAUUCAGCCUGUCAACCGGGC____GAAACAAUGCAAAGUAAGCUCUCUGUCAUUU_______UGCAAUUUGCAAUUGGAGUAGCCCACCUCACGGCUGCACAAAAAGC___AAA
...........(((((.....)))))........(((((((((....((....................))..))))).))))..((((((........))))))............... (-23.34 = -23.12 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	14,078,250 – 14,078,356
Length	106
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.60
Mean single sequence MFE	-35.07
Consensus MFE	-27.22
Energy contribution	-27.33
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.78
SVM decision value	0.11
SVM RNA-class probability	0.586577
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14078250 106 - 20766785
UUU---GCUUUUUGUGCAGCCAUGAGGUGGGCUACUCCAAUUGCAAAUUGCA-------AAAUGACAGAGAGCUUACUUUGCAUUGUUUC----GCCCGGUUGACAGGCUGAAUUUGUUG
...---..........(((((.(.((.(((((........((((.....)))-------)((((.(((((......))))))))).....----))))).)).)..)))))......... ( -28.20)
>DroSim_CAF1 2802 106 - 1
UUU---GCUUUUUGUGCAGCCGUGAGGUGGGCUACUCCAAUUGCAAAUUGCA-------AAAUGACAGAGAGCUUACUUUGCAUUGUUUC----GCCUGGUUGACAGGCUGAAUUUGUUG
...---(((((((((((.(((....)))..))........((((.....)))-------)....))))))))).......(((..((((.----(((((.....))))).)))).))).. ( -34.70)
>DroYak_CAF1 3465 120 - 1
UUUUUCACUUUUUGUGCAGCCGUGAGGUGGGCUACUCCAAUUGCAAAUUGCAAAAUGCAAAAUGACAGAGAGCUUACUUUGCAUUGUUUCGGUUGCCCGGUUGACAGGCUGCAUUUGUUG
.............(((((((((..(((((((((.(((....((((..((((.....))))..)).))))))))))))))..)..((((((((....))))..))))))))))))...... ( -42.30)
>consensus
UUU___GCUUUUUGUGCAGCCGUGAGGUGGGCUACUCCAAUUGCAAAUUGCA_______AAAUGACAGAGAGCUUACUUUGCAUUGUUUC____GCCCGGUUGACAGGCUGAAUUUGUUG
................(((((((.((.(((((.........(((.....)))........((((.(((((......))))))))).........))))).)).)).)))))......... (-27.22 = -27.33 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:42 2006