Locus 1944

Sequence ID	3R_DroMel_CAF1
Location	5,490,983 – 5,491,088
Length	105
Max. P	0.987250

overview

Window 6

Location	5,490,983 – 5,491,088
Length	105
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	86.81
Mean single sequence MFE	-35.10
Consensus MFE	-30.00
Energy contribution	-29.84
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.28
Structure conservation index	0.85
SVM decision value	2.07
SVM RNA-class probability	0.987250
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5490983 105 + 27905053
CGGCAUUCCAAGGUGGUAUC-CACCACCUCUGCAUCCUC---CACUUAGUCCACCCACUCCACCUUCUUGGCCACUGAAACGGCCACGAGGAAUGUGCGGAGCACGUGC
((((.......((((((...-.))))))(((((((..((---(....(((......)))......((.(((((........))))).)))))..))))))))).))... ( -34.90)
>DroSec_CAF1 21715 106 + 1
CGGCAUUCCAAGGUGGUAUCCCACCACCUCUGCAUCCUC---CACUUAGACCACCCCCUCCACUUCCUUGGCCACUGAAACGGCCACGCGGAAUGUGCGGAGCACGUGC
..((((.....(((((....)))))..((((((((..((---(.....((........))........(((((........)))))...)))..))))))))...)))) ( -33.00)
>DroSim_CAF1 23950 106 + 1
CGGCAUUCCAAGGUGGUAUCCCACCACCUCUGCAUCCUC---CACUUAGGCCACCCCCUCCACUUGCUUGGCCACUGAAACGGCUACGAGGAAUGUGCGGAGCACGUGC
..((((.....(((((....)))))..((((((((..((---(.....(((((...............))))).......((....)).)))..))))))))...)))) ( -34.76)
>DroEre_CAF1 22143 96 + 1
CGGCAUUCCAAGGUGGUAUA-CACCACCUCCGCAUCCUG---CUCCUCGACCU---------CCUCCUUGGCCACUGAAACGGCCACGAGGAAUGUGCGGAGCACGUGC
.((.......(((((((...-.)))))))))((((..((---((((.((...(---------((((..(((((........))))).)))))...)).)))))).)))) ( -40.91)
>DroYak_CAF1 20295 108 + 1
CGGCAUUCCAAGGUGGUAUC-CACCACCUCUGCAUCCUCCAACUCCUCAACAUCCACCUCCACCUUCUUGGCCACUGAAUGGGCCACGAGGAAUGUGCGGAGCACGUGC
((((.......((((((...-.))))))(((((((..(((.........................((.(((((.(.....)))))).)))))..))))))))).))... ( -31.91)
>consensus
CGGCAUUCCAAGGUGGUAUC_CACCACCUCUGCAUCCUC___CACUUAGACCACCCCCUCCACCUCCUUGGCCACUGAAACGGCCACGAGGAAUGUGCGGAGCACGUGC
..(((((((.(((((((.....))))))).......................................(((((........)))))...)))))))(((.....))).. (-30.00 = -29.84 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	5,490,983 – 5,491,088
Length	105
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	86.81
Mean single sequence MFE	-43.40
Consensus MFE	-30.38
Energy contribution	-31.54
Covariance contribution	1.16
Combinations/Pair	1.10
Mean z-score	-1.88
Structure conservation index	0.70
SVM decision value	0.22
SVM RNA-class probability	0.638655
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5490983 105 - 27905053
GCACGUGCUCCGCACAUUCCUCGUGGCCGUUUCAGUGGCCAAGAAGGUGGAGUGGGUGGACUAAGUG---GAGGAUGCAGAGGUGGUG-GAUACCACCUUGGAAUGCCG
((((((.((((((.((((((((.((((((......))))))....)).))))))((....))..)))---))).)))..((((((((.-...))))))))....))).. ( -44.40)
>DroSec_CAF1 21715 106 - 1
GCACGUGCUCCGCACAUUCCGCGUGGCCGUUUCAGUGGCCAAGGAAGUGGAGGGGGUGGUCUAAGUG---GAGGAUGCAGAGGUGGUGGGAUACCACCUUGGAAUGCCG
.(((.(.((((((...((((...((((((......)))))).)))))))))).).))).........---..((((...(((((((((...)))))))))...)).)). ( -44.70)
>DroSim_CAF1 23950 106 - 1
GCACGUGCUCCGCACAUUCCUCGUAGCCGUUUCAGUGGCCAAGCAAGUGGAGGGGGUGGCCUAAGUG---GAGGAUGCAGAGGUGGUGGGAUACCACCUUGGAAUGCCG
....((..((((((..((((.(.((((((..((.....(((......)))..))..))).))).).)---)))..))).(((((((((...))))))))))))..)).. ( -37.90)
>DroEre_CAF1 22143 96 - 1
GCACGUGCUCCGCACAUUCCUCGUGGCCGUUUCAGUGGCCAAGGAGG---------AGGUCGAGGAG---CAGGAUGCGGAGGUGGUG-UAUACCACCUUGGAAUGCCG
((((.((((((.....((((((.((((((......))))))..))))---------)).....))))---)).).))).((((((((.-...))))))))((....)). ( -49.00)
>DroYak_CAF1 20295 108 - 1
GCACGUGCUCCGCACAUUCCUCGUGGCCCAUUCAGUGGCCAAGAAGGUGGAGGUGGAUGUUGAGGAGUUGGAGGAUGCAGAGGUGGUG-GAUACCACCUUGGAAUGCCG
((((((.(((((...((((((((....(((((...(.(((.....))).).)))))....))))))))))))).)))..((((((((.-...))))))))....))).. ( -41.00)
>consensus
GCACGUGCUCCGCACAUUCCUCGUGGCCGUUUCAGUGGCCAAGAAGGUGGAGGGGGUGGUCUAAGUG___GAGGAUGCAGAGGUGGUG_GAUACCACCUUGGAAUGCCG
....((..((((((...(((((.((((((......)))))).........(((......)))........)))))))).(((((((((...))))))))))))..)).. (-30.38 = -31.54 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:31 2006