Locus 1632

Sequence ID	2R_DroMel_CAF1
Location	6,132,517 – 6,132,613
Length	96
Max. P	0.901599

overview

Window 2

Location	6,132,517 – 6,132,613
Length	96
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.81
Mean single sequence MFE	-17.18
Consensus MFE	-13.53
Energy contribution	-14.08
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-1.84
Structure conservation index	0.79
SVM decision value	1.02
SVM RNA-class probability	0.901599
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6132517 96 + 20766785
-------CACACUCAUGCAAAUUGCAUGCCUGA-UUUCACCAAUUGAUUGCAUGCAAUUGUUU---------UUUCCUUCGACUUCCACUUGUUUGCUCAUCCCGAGCCAAAU
-------.........((((.((((((((..((-((.........))))))))))))))))..---------...................((((((((.....))).))))) ( -17.50)
>DroSec_CAF1 141595 96 + 1
-------CACACUCAUGCAAAUUGCAUGCCUGA-UUUCACCAAUUGAUUGCAUGCAAUUGUUU---------UUUCCUUCGACUUCCACUUGUUUGCUCAUCCCGAGCCAAAU
-------.........((((.((((((((..((-((.........))))))))))))))))..---------...................((((((((.....))).))))) ( -17.50)
>DroSim_CAF1 149568 103 + 1
UCAGACACACACUCAUGCAAAUUGCAUGCCUGA-UUUCACCAAUUGAUUGCAUGCAAUUGUUU---------UUUCCUUCGACUUCCACUUGUUUGCUCAUCCCGAGCCAAAU
..(((((............((((((((((..((-((.........))))))))))))))(((.---------........))).......)))))((((.....))))..... ( -17.70)
>DroEre_CAF1 145808 108 + 1
----ACACACACUCAUGCAAAUUGCAUGCCUGA-UUUCCCCAAUUGAUUGCAUGCAAUUGUGUUUUUUUCUGUUUCCUUCGACUUCCACUUGUUUGCUCAUCCAGAGCCAAAU
----..(((.......(((((((((((((..((-((.........)))))))))))))).))).......)))..................((((((((.....))).))))) ( -19.24)
>DroYak_CAF1 144934 97 + 1
------ACACACUCAUGCAAAUUGCAUGCCUGA-UUUCCCCAAUUGAUUGCAUGCAAUUGUUU---------UUUCCUUCGACUUCCACUUGUUUGCUCAUCCCGAGCCAAAU
------..........((((.((((((((..((-((.........))))))))))))))))..---------...................((((((((.....))).))))) ( -17.50)
>DroPer_CAF1 134884 78 + 1
-------C----------ACAUCGCAUGCUCGACUUUCUCCAAUGCAUUGCAUGCAAUGGUUU---------C-UCCCAGAACUUUCACAUCU--------CCCUGGCCAGCC
-------.----------.....((((((....................))))))...((((.---------.-..((((.............--------..))))..)))) ( -13.61)
>consensus
_______CACACUCAUGCAAAUUGCAUGCCUGA_UUUCACCAAUUGAUUGCAUGCAAUUGUUU_________UUUCCUUCGACUUCCACUUGUUUGCUCAUCCCGAGCCAAAU
...................((((((((((....................))))))))))....................................((((.....))))..... (-13.53 = -14.08 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	6,132,517 – 6,132,613
Length	96
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	79.81
Mean single sequence MFE	-22.52
Consensus MFE	-15.92
Energy contribution	-17.03
Covariance contribution	1.11
Combinations/Pair	1.12
Mean z-score	-1.40
Structure conservation index	0.71
SVM decision value	0.37
SVM RNA-class probability	0.710588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6132517 96 - 20766785
AUUUGGCUCGGGAUGAGCAAACAAGUGGAAGUCGAAGGAAA---------AAACAAUUGCAUGCAAUCAAUUGGUGAAA-UCAGGCAUGCAAUUUGCAUGAGUGUG-------
.....((((.....))))..(((.(((.((.((....))..---------.....(((((((((..(((.....)))..-....))))))))))).)))...))).------- ( -22.10)
>DroSec_CAF1 141595 96 - 1
AUUUGGCUCGGGAUGAGCAAACAAGUGGAAGUCGAAGGAAA---------AAACAAUUGCAUGCAAUCAAUUGGUGAAA-UCAGGCAUGCAAUUUGCAUGAGUGUG-------
.....((((.....))))..(((.(((.((.((....))..---------.....(((((((((..(((.....)))..-....))))))))))).)))...))).------- ( -22.10)
>DroSim_CAF1 149568 103 - 1
AUUUGGCUCGGGAUGAGCAAACAAGUGGAAGUCGAAGGAAA---------AAACAAUUGCAUGCAAUCAAUUGGUGAAA-UCAGGCAUGCAAUUUGCAUGAGUGUGUGUCUGA
.(((.(((...(((..(((..(((.((....((....))..---------...)).)))..))).)))....))).)))-(((((((((((.((.....)).))))))))))) ( -26.10)
>DroEre_CAF1 145808 108 - 1
AUUUGGCUCUGGAUGAGCAAACAAGUGGAAGUCGAAGGAAACAGAAAAAAACACAAUUGCAUGCAAUCAAUUGGGGAAA-UCAGGCAUGCAAUUUGCAUGAGUGUGUGU----
.((((((((.....)))).............((....))..)))).....((((((((((((((.....(((.....))-)...)))))))))).(((....)))))))---- ( -24.50)
>DroYak_CAF1 144934 97 - 1
AUUUGGCUCGGGAUGAGCAAACAAGUGGAAGUCGAAGGAAA---------AAACAAUUGCAUGCAAUCAAUUGGGGAAA-UCAGGCAUGCAAUUUGCAUGAGUGUGU------
.....((((.....))))..(((.(((.((.((....))..---------.....(((((((((.....(((.....))-)...))))))))))).)))...)))..------ ( -21.70)
>DroPer_CAF1 134884 78 - 1
GGCUGGCCAGGG--------AGAUGUGAAAGUUCUGGGA-G---------AAACCAUUGCAUGCAAUGCAUUGGAGAAAGUCGAGCAUGCGAUGU----------G-------
......((((((--------...(.....).))))))..-.---------....((((((((((..((.(((......))))).)))))))))).----------.------- ( -18.60)
>consensus
AUUUGGCUCGGGAUGAGCAAACAAGUGGAAGUCGAAGGAAA_________AAACAAUUGCAUGCAAUCAAUUGGUGAAA_UCAGGCAUGCAAUUUGCAUGAGUGUG_______
.....((((.....))))..(((.(((....((....))...............((((((((((......((.....)).....))))))))))..)))...)))........ (-15.92 = -17.03 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:21 2006