Locus 9697

Sequence ID	3R_DroMel_CAF1
Location	25,652,176 – 25,652,284
Length	108
Max. P	0.837175

overview

Window 2

Location	25,652,176 – 25,652,284
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.12
Mean single sequence MFE	-32.78
Consensus MFE	-28.75
Energy contribution	-28.78
Covariance contribution	0.03
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.88
SVM decision value	0.74
SVM RNA-class probability	0.837175
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25652176 108 + 27905053
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCU------------GCUGGAGGAGCGCUCUCGCAUACGGGAAAGUGACUCCU
.......((((......))))...((((((((..((((.(((((((......)).))))).))))..)))------------)))))(((((((((((((....)))))..))).))))) ( -33.70)
>DroSec_CAF1 8719 108 + 1
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCU------------GCUGGAGGAGCGCUCUCGCAUACGGGAAAGUGACUCCU
.......((((......))))...((((((((..((((.(((((((......)).))))).))))..)))------------)))))(((((((((((((....)))))..))).))))) ( -33.70)
>DroSim_CAF1 7674 108 + 1
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCU------------GCUGGAGGAGCGCUCUCGCAUACGGGAAAGUGACUCCU
.......((((......))))...((((((((..((((.(((((((......)).))))).))))..)))------------)))))(((((((((((((....)))))..))).))))) ( -33.70)
>DroEre_CAF1 7646 108 + 1
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCU------------GCUGGAGGAGCGCUCUCGCAUACGGGAAAGUGACUCCU
.......((((......))))...((((((((..((((.(((((((......)).))))).))))..)))------------)))))(((((((((((((....)))))..))).))))) ( -33.70)
>DroYak_CAF1 8170 120 + 1
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCUUUAGCUGGUGGAGCUGGAGGAGCGCUCUUGCAUACGGGAAAGUGACUCCU
......((((((((...(((((....(((......(....)..)))..))))).))))))))(((((((.......)))))))..((((..((..(((((....)))))..))..)))). ( -33.60)
>DroAna_CAF1 4001 111 + 1
UGAAUCAUGCAAAUAAAUGCACCCUCAGCACAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCUUUAGC-------GCUGAAGGAGCGCU--CGCAUACGGGAAAGUGACUCCU
.......((((......))))...(((((......(....)..(((..(((.((((....)))).)))....)))-------)))))(((((((((--..(......)..)))).))))) ( -28.30)
>consensus
UGAAUCAUGCAAAUAAAUGCACCCUCAGCAGAACAGGAAACAGGCUUCGUGCAGAUUUGUAUCUUUAUCU____________GCUGGAGGAGCGCUCUCGCAUACGGGAAAGUGACUCCU
......((((((((...(((((....(((......(....)..)))..))))).)))))))).........................(((((((((.((.(....).)).)))).))))) (-28.75 = -28.78 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	25,652,176 – 25,652,284
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.12
Mean single sequence MFE	-33.82
Consensus MFE	-27.50
Energy contribution	-27.70
Covariance contribution	0.20
Combinations/Pair	1.03
Mean z-score	-1.98
Structure conservation index	0.81
SVM decision value	-0.04
SVM RNA-class probability	0.510838
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25652176 108 - 27905053
AGGAGUCACUUUCCCGUAUGCGAGAGCGCUCCUCCAGC------------AGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((((.((((.((((.(((------------(((...((((....))))(((.((((....)))).))))))))))))))))).....)))))))))))). ( -34.70)
>DroSec_CAF1 8719 108 - 1
AGGAGUCACUUUCCCGUAUGCGAGAGCGCUCCUCCAGC------------AGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((((.((((.((((.(((------------(((...((((....))))(((.((((....)))).))))))))))))))))).....)))))))))))). ( -34.70)
>DroSim_CAF1 7674 108 - 1
AGGAGUCACUUUCCCGUAUGCGAGAGCGCUCCUCCAGC------------AGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((((.((((.((((.(((------------(((...((((....))))(((.((((....)))).))))))))))))))))).....)))))))))))). ( -34.70)
>DroEre_CAF1 7646 108 - 1
AGGAGUCACUUUCCCGUAUGCGAGAGCGCUCCUCCAGC------------AGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((((.((((.((((.(((------------(((...((((....))))(((.((((....)))).))))))))))))))))).....)))))))))))). ( -34.70)
>DroYak_CAF1 8170 120 - 1
AGGAGUCACUUUCCCGUAUGCAAGAGCGCUCCUCCAGCUCCACCAGCUAAAGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..((((((....(((....(((.((((((..((..((((.....))))..))....((((....))))))..((((....))))..)))))))...)))((((......)))))))))). ( -29.90)
>DroAna_CAF1 4001 111 - 1
AGGAGUCACUUUCCCGUAUGCG--AGCGCUCCUUCAGC-------GCUAAAGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUGUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((--((.((.((((((((-------((.........((((....))))(((.((((....)))).))).)))))))))).)).....)))))))))))). ( -34.20)
>consensus
AGGAGUCACUUUCCCGUAUGCGAGAGCGCUCCUCCAGC____________AGAUAAAGAUACAAAUCUGCACGAAGCCUGUUUCCUGUUCUGCUGAGGGUGCAUUUAUUUGCAUGAUUCA
..(((((((......))(((((((.((((.(((.((((..................((((....))))(((.((((....)))).)))...))))))))))).....)))))))))))). (-27.50 = -27.70 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:07 2006