Locus 190

Sequence ID	3L_DroMel_CAF1
Location	542,871 – 543,010
Length	139
Max. P	0.831022

overview

Window 3

Location	542,871 – 542,984
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	97.55
Mean single sequence MFE	-28.60
Consensus MFE	-27.56
Energy contribution	-27.80
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.96
SVM decision value	0.71
SVM RNA-class probability	0.831022
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 542871 113 - 23771897
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACAA---
....((((.....)))).....(((((((((..((((.(((((((((..(((.....)))..))))).(((((...)))))......)))).))))..))))..)))))....--- ( -28.20)
>DroSec_CAF1 16886 113 - 1
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAAUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACAA---
....((((.....)))).....(((((((((...((.((((((((((((((...........)))))(((....)))..))))))))).)).......))))..)))))....--- ( -27.50)
>DroSim_CAF1 17795 113 - 1
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGCCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACAA---
....((((.....)))).....(((((((((..((((.(((((((((..(((.....)))..))))).(((((...)))))......)))).))))..))))..)))))....--- ( -30.90)
>DroEre_CAF1 17266 113 - 1
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGCUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACAA---
....((((.....)))).....(((((((((...........(((((..(((.....)))..)))))...........((.(((....))).))....))))..)))))....--- ( -25.90)
>DroYak_CAF1 17497 116 - 1
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACGAGCA
...(((((((..........(((.(((((....))))).)))(((((..(((.....)))..))))).((((((.(((((.(((....))).).))))...))))))))))))).. ( -30.50)
>consensus
AACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAUGGAUCAAUCGAUGCAAUAUGAAUUAUGGCUACAA___
....((((.....)))).....(((((((((..((((.(((((((((..(((.....)))..))))).(((((...)))))......)))).))))..))))..)))))....... (-27.56 = -27.80 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	542,905 – 543,010
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	98.48
Mean single sequence MFE	-27.54
Consensus MFE	-26.20
Energy contribution	-26.44
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.20
Structure conservation index	0.95
SVM decision value	0.04
SVM RNA-class probability	0.553682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 542905 105 - 23771897
UAGUUUAGCCUCGUUUUUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
..(((((...((((((((..(((........))).))))))))...)))))((((((.....))))))(((((..(((.....)))..)))))............ ( -26.80)
>DroSec_CAF1 16920 105 - 1
UAGUUUAGCCUCGUUUUUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAAUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
..(((((...((((((((..(((........))).))))))))...)))))((((((.....))))))(((((..(((.....)))..)))))............ ( -26.80)
>DroSim_CAF1 17829 105 - 1
UAGUUUAGCCUCGUUUUUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGCCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
..(((((...((((((((..(((........))).))))))))...)))))((((((.....))))))(((((..(((.....)))..)))))............ ( -29.50)
>DroEre_CAF1 17300 105 - 1
UAGUUUAGCCUCGUUUUUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGCUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
.....(((((((((((((..(((........))).))))))))........((((....)))))))))(((((..(((.....)))..)))))............ ( -27.30)
>DroYak_CAF1 17534 105 - 1
UAGUUUAGCCUCGUUUCUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
..((((((........))))))...((((((..(((((................)))))...))))))(((((..(((.....)))..)))))............ ( -27.29)
>consensus
UAGUUUAGCCUCGUUUUUAGACGCCCAACCUCGUGGAAAACGAAAAUAAGCCAAUUCCAAUUGGGUUGGUCCGCUCGCUGUUUGUGUUCGGGCAUUAUAAAAUAU
..(((((...((((((((..(((........))).))))))))...)))))((((((.....))))))(((((..(((.....)))..)))))............ (-26.20 = -26.44 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:22 2006