Locus 3251

Sequence ID	3L_DroMel_CAF1
Location	9,507,554 – 9,507,685
Length	131
Max. P	0.886919

overview

Window 6

Location	9,507,554 – 9,507,653
Length	99
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	87.04
Mean single sequence MFE	-26.74
Consensus MFE	-19.30
Energy contribution	-20.30
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.72
SVM decision value	0.94
SVM RNA-class probability	0.886919
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9507554 99 - 23771897
AAU--ACGCACAUUUUGUUGCCGCUCGCAACGCAGCGCGAG-CUUCCUUUGAUUUUCGGUGAAAAUCGAGGGACACCAGCAUUUUGAACAUUUCAUUUCAAA
...--..........(((((..((((((........)))))-).(((((((((((((...)))))))))))))...))))).((((((........)))))) ( -30.50)
>DroSec_CAF1 24043 102 - 1
AACACACGCACAUUUUGUUGCCACUCGCAACGCGCUGCGUUCCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGACACCAGCAUUUUGAACAUUGCAUUUCAAA
.......(((......(((((.....)))))..((((.((....(((((((((((((...))))))))))))).))))))...........)))........ ( -29.30)
>DroSim_CAF1 26234 102 - 1
AACACACGCACAUUUUGUUGCCACUCGCAACGCGCUGCGUUCCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGACACCAGCAUUUUGAACAUUGCAUUUCAAA
.......(((......(((((.....)))))..((((.((....(((((((((((((...))))))))))))).))))))...........)))........ ( -29.30)
>DroEre_CAF1 24151 97 - 1
AAC--ACACGGAUUUUGUUGCCCCUCACAACGCAACUC---GCUUCCUUUGAUUUUCGGUGAAAAUCGCGGGACACCAGCAUUUUGAACAUUGCAUUUCAAA
...--....((.....(((((..........)))))..---...((((.((((((((...)))))))).))))..)).(((..........)))........ ( -19.10)
>DroYak_CAF1 26765 96 - 1
AAC--ACGCAGAUUUUGUUGCCGCUCGCAACGCAACUG---ACUUCCUUUGAUUUUCGG-GUAAAUCGAGGGAUACCCGCAUUUUGCACAUUGCAUUUCAAA
...--..((((.....(((((.....)))))((((.((---...(((((((((((....-..)))))))))))......))..))))...))))........ ( -25.50)
>consensus
AAC__ACGCACAUUUUGUUGCCACUCGCAACGCAACGCG__CCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGACACCAGCAUUUUGAACAUUGCAUUUCAAA
.......((.......(((((.....))))).............(((((((((((((...))))))))))))).....))..((((((........)))))) (-19.30 = -20.30 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	9,507,583 – 9,507,685
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	86.65
Mean single sequence MFE	-29.74
Consensus MFE	-23.28
Energy contribution	-24.04
Covariance contribution	0.76
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.78
SVM decision value	0.05
SVM RNA-class probability	0.558544
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9507583 102 - 23771897
UUGCAACCACGUCAACAGCGACAACAGU------UCGAAAU--ACGCACAUUUUGUUGCCGCUCGCAACGCAGCGCGAG-CUUCCUUUGAUUUUCGGUGAAAAUCGAGGGA
..(((((...(((......)))....((------.((....--.)).)).....))))).((((((........)))))-).(((((((((((((...))))))))))))) ( -34.00)
>DroSec_CAF1 24072 111 - 1
UUGCAACAACGUCAACAGCGACAACAGUCGAAUUUCGAAACACACGCACAUUUUGUUGCCACUCGCAACGCGCUGCGUUCCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGA
..(((((((.(((......))).....(((.....)))..............)))))))....((((......)))).....(((((((((((((...))))))))))))) ( -29.90)
>DroSim_CAF1 26263 111 - 1
UUGCAACAACGUCAACAGCGACAACAGUCGAAUUUCGAAACACACGCACAUUUUGUUGCCACUCGCAACGCGCUGCGUUCCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGA
..(((((((.(((......))).....(((.....)))..............)))))))....((((......)))).....(((((((((((((...))))))))))))) ( -29.90)
>DroEre_CAF1 24180 106 - 1
UUGCAACAACGUCAACAGCGACAACAGUCGAAUUUCGAAAC--ACACGGAUUUUGUUGCCCCUCACAACGCAACUC---GCUUCCUUUGAUUUUCGGUGAAAAUCGCGGGA
..(((((((.(((.....((((....)))).....((....--...))))).)))))))..........((.....---)).((((.((((((((...)))))))).)))) ( -25.70)
>DroYak_CAF1 26794 105 - 1
UUGCAACAACGUCGACAGCGACAACAGUCGAAUUUCGAAAC--ACGCAGAUUUUGUUGCCGCUCGCAACGCAACUG---ACUUCCUUUGAUUUUCGG-GUAAAUCGAGGGA
((((.......((((...((((....))))....))))...--...........(((((.....)))))))))...---...(((((((((((....-..))))))))))) ( -29.20)
>consensus
UUGCAACAACGUCAACAGCGACAACAGUCGAAUUUCGAAAC__ACGCACAUUUUGUUGCCACUCGCAACGCAACGCG__CCUUCCUUUGAUUUUCGGUGAAAAUCGAGGGA
.(((.....((.......((((....)))).....)).................(((((.....))))))))..........(((((((((((((...))))))))))))) (-23.28 = -24.04 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:03 2006