Locus 9283

Sequence ID	3R_DroMel_CAF1
Location	24,747,621 – 24,747,769
Length	148
Max. P	0.874223

overview

Window 2

Location	24,747,621 – 24,747,730
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.69
Mean single sequence MFE	-23.12
Consensus MFE	-12.73
Energy contribution	-12.45
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-2.68
Structure conservation index	0.55
SVM decision value	0.88
SVM RNA-class probability	0.874223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24747621 109 - 27905053
AAUGCACAGCAACAUGUGCUCGAAGUAUU-UGGAAACAAAGGAUCAAAA---GGGAUCAAU---GGAUUUUUGUAUAAUAAACAU--CUAUACAAGUCAAGUUCAAA-AAUUUA-AAAUA
...(((((......)))))........((-((....)))).((((....---..))))..(---(((((((((((((........--.)))))))...)))))))..-......-..... ( -21.80)
>DroPse_CAF1 1723 119 - 1
GAUGCGCAGCAACAUGCGCAUGGUAAAAU-GGUAUAGUAUGUAUGUAUAUGAGAAAACAAUGUAGGAUUUUUGUAUAAGAAACCUCUCUAUACAAGUCAAGUUAACAAAACUAAAAAGUA
.(((((((......)))))))........-.((((((...((...((((..((((..(......)..))))..))))....))....))))))......((((.....))))........ ( -23.30)
>DroSim_CAF1 1668 110 - 1
AAUGCACAGCAACAUGUGCACGAAGUAUUUUGGAAACAAAGGAUCAAAA---GGGAUCAAU---GGAUUUUUGUAUAAUAAACAU--CUAUACAAGUCAAGUUCAAA-AAUUUA-AAAUA
..((((((......)))))).......(((((....)))))((((....---..))))..(---(((((((((((((........--.)))))))...)))))))..-......-..... ( -23.60)
>DroEre_CAF1 1674 110 - 1
AAUGCACAGCAACAUGUGCACGAAAUAUU-UGGAAACAAUGGAUCAAUA---AGGAUCAAU---GGAUUUUUGUAUAAUAAACAU--CUAUACAAGUCAAGUUCAAAAAAUUUA-GAAUA
..((((((......))))))........(-((....)))..((((....---..))))..(---(((((((((((((........--.)))))))...))))))).........-..... ( -21.80)
>DroYak_CAF1 1668 110 - 1
AAUGCACAGCAACAUGUGCACGAAAUAUU-UGGAAACAAUGGAUCAAUA---AGGAUCAAU---GGAUUUUUGUAUAAUAAACAU--CUAUACAAGUCAAGUUCAAAAAAUUUA-GAAUA
..((((((......))))))........(-((....)))..((((....---..))))..(---(((((((((((((........--.)))))))...))))))).........-..... ( -21.80)
>DroPer_CAF1 1723 119 - 1
GAUGCGCAGCAACAUGCGCAUGGUAAAAU-GGUAUAGUAUGUAUGUAUAUGAGAAAACAAUGUAGGAUUUUUGUAUAAGAAACAUCUCUAUACAAGUCAAGUUAACAAAACUAAAAAGUA
.(((((((......)))))))........-.((((((.((((...((((..((((..(......)..))))..))))....))))..))))))......((((.....))))........ ( -26.40)
>consensus
AAUGCACAGCAACAUGUGCACGAAAUAUU_UGGAAACAAUGGAUCAAUA___GGGAUCAAU___GGAUUUUUGUAUAAUAAACAU__CUAUACAAGUCAAGUUCAAAAAAUUUA_AAAUA
..((((((......)))))).............................................(((..(((((((...........))))))))))...................... (-12.73 = -12.45 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	24,747,657 – 24,747,769
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.36
Mean single sequence MFE	-28.05
Consensus MFE	-18.46
Energy contribution	-17.85
Covariance contribution	-0.61
Combinations/Pair	1.14
Mean z-score	-2.20
Structure conservation index	0.66
SVM decision value	0.42
SVM RNA-class probability	0.728063
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24747657 112 - 27905053
AUGCACAAGCGCAG-CAUGGCGCUACACAGCUCUAAAUAUAAUGCACAGCAACAUGUGCUCGAAGUAUU-UGGAAACAAAGGAUCAAAA---GGGAUCAAU---GGAUUUUUGUAUAAUA
(((((..(((((..-....))))).......(((((((((...(((((......))))).....)))))-))))..((...((((....---..))))..)---)......))))).... ( -27.50)
>DroPse_CAF1 1763 117 - 1
AUGCACAGGCGCAAUCGUGGCGCUACACAGCUCUGAA--UGAUGCGCAGCAACAUGCGCAUGGUAAAAU-GGUAUAGUAUGUAUGUAUAUGAGAAAACAAUGUAGGAUUUUUGUAUAAGA
(((((..(((((.......))))).....(((.(..(--(.(((((((......))))))).))...).-)))......))))).((((..((((..(......)..))))..))))... ( -28.20)
>DroSim_CAF1 1704 113 - 1
AUGCACAAGCGCAA-CAAGGCGCUACACAGCUCUAAAUAUAAUGCACAGCAACAUGUGCACGAAGUAUUUUGGAAACAAAGGAUCAAAA---GGGAUCAAU---GGAUUUUUGUAUAAUA
(((((..(((((..-....))))).......((((.......((((((......)))))).......(((((....)))))((((....---..))))..)---)))....))))).... ( -28.00)
>DroEre_CAF1 1711 112 - 1
AUGCACAAGCGCAA-CAUGGCGCUACACAGCUCUAAAUAUAAUGCACAGCAACAUGUGCACGAAAUAUU-UGGAAACAAUGGAUCAAUA---AGGAUCAAU---GGAUUUUUGUAUAAUA
(((((..(((((..-....))))).......(((((((((..((((((......))))))....)))))-))))..((...((((....---..))))..)---)......))))).... ( -28.20)
>DroYak_CAF1 1705 112 - 1
AUGCACAAGCGCAA-CAUGGCGCUACACAGCUCUAAAUAUAAUGCACAGCAACAUGUGCACGAAAUAUU-UGGAAACAAUGGAUCAAUA---AGGAUCAAU---GGAUUUUUGUAUAAUA
(((((..(((((..-....))))).......(((((((((..((((((......))))))....)))))-))))..((...((((....---..))))..)---)......))))).... ( -28.20)
>DroPer_CAF1 1763 117 - 1
AUGCACAGGCGCAAUCGUGGCGCUACACAGCUCUGAA--UGAUGCGCAGCAACAUGCGCAUGGUAAAAU-GGUAUAGUAUGUAUGUAUAUGAGAAAACAAUGUAGGAUUUUUGUAUAAGA
(((((..(((((.......))))).....(((.(..(--(.(((((((......))))))).))...).-)))......))))).((((..((((..(......)..))))..))))... ( -28.20)
>consensus
AUGCACAAGCGCAA_CAUGGCGCUACACAGCUCUAAAUAUAAUGCACAGCAACAUGUGCACGAAAUAUU_UGGAAACAAUGGAUCAAUA___GGGAUCAAU___GGAUUUUUGUAUAAUA
(((((..(((((.......))))).......(((........((((((......))))))..........((....))..........................)))....))))).... (-18.46 = -17.85 +  -0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:40 2006