Locus 3618

Sequence ID	3L_DroMel_CAF1
Location	10,650,638 – 10,650,864
Length	226
Max. P	0.999317

overview

Window 1

Location	10,650,638 – 10,650,748
Length	110
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	92.99
Mean single sequence MFE	-27.08
Consensus MFE	-25.04
Energy contribution	-24.80
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	3.51
SVM RNA-class probability	0.999317
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10650638 110 - 23771897
GACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUAUGCGUGUGCUUAAGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((((((((((.......------..))))))))......((((((((((((((........))))))))..)))))).((((((.....)))))).)))))).. ( -27.10)
>DroSec_CAF1 12964 110 - 1
GACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUGUGCUUAGGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((((((((((.......------..))))))))......((((((.(((((((........)))))))...)))))).((((((.....)))))).)))))).. ( -27.20)
>DroSim_CAF1 12338 110 - 1
GACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUGUGCUUAGGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((((((((((.......------..))))))))......((((((.(((((((........)))))))...)))))).((((((.....)))))).)))))).. ( -27.20)
>DroEre_CAF1 13400 116 - 1
GACACUUACAAAUUUGUAUGUACAACACAUGCAUAUGUACAUGCACACAAACGGACCAAGUACAUAAGUGUGAGUGUGUUUAGGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((((((((((((...........))))))))))......((((((....(((((........)))))....)))))).((((((.....)))))).)))))).. ( -28.00)
>DroYak_CAF1 13294 112 - 1
GACACUUACAAAUUUGUAUGUACAA----UGCAUACAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGAGUGUGUUUAGGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((..(((((((..----(((((......)))))......((((((....(((((........)))))....))))))....)))))))........)))))).. ( -25.90)
>consensus
GACACUUACAAAUUUGUAUGUACAACACA______UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUGUGCUUAGGGUCUGAAGAGUACGUAAUACUUUCAAUUUGAC
........((((((((((((((...............))))))))......((((((((((((((........))))))))..)))))).((((((.....)))))).)))))).. (-25.04 = -24.80 +  -0.24)

alignment

secondary structure

dotplot

Window 2

Location	10,650,678 – 10,650,771
Length	93
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	92.80
Mean single sequence MFE	-24.91
Consensus MFE	-19.38
Energy contribution	-19.58
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.78
SVM decision value	1.36
SVM RNA-class probability	0.945787
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10650678 93 - 23771897
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUAUGCGUG
(((((...(((....))))))))..............(((((((.....)))------))))((((((.((...................)).)))))) ( -18.11)
>DroSec_CAF1 13004 93 - 1
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUG
(((((...(((....))))))))..............(((((((.....)))------))))(((((((((...................))))))))) ( -24.11)
>DroSim_CAF1 12378 93 - 1
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAACACA------UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUG
(((((...(((....))))))))..............(((((((.....)))------))))(((((((((...................))))))))) ( -24.11)
>DroEre_CAF1 13440 99 - 1
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAACACAUGCAUAUGUACAUGCACACAAACGGACCAAGUACAUAAGUGUGAGUG
(((((...(((....))))))))..((((((((....(((((((.....)))))))(((((((.((..(......)...)).)))))))..)))))))) ( -30.50)
>DroYak_CAF1 13334 95 - 1
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAA----UGCAUACAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGAGUG
(((((...(((....))))))))..((((((((......(((((((..----(((((......)))))(......)......)))))))..)))))))) ( -27.70)
>consensus
GCUCUCUAGCUGAUAAGCAGGGCGACACUUACAAAUUUGUAUGUACAACACA______UAUACAUGCACACAAACGGACCAAGUACAUAAGUGUGCGUG
(((((...(((....)))))))).(((((((......((((((((...............)))))))).....((.......))...)))))))..... (-19.38 = -19.58 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	10,650,771 – 10,650,864
Length	93
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	82.34
Mean single sequence MFE	-18.25
Consensus MFE	-11.36
Energy contribution	-11.92
Covariance contribution	0.56
Combinations/Pair	1.19
Mean z-score	-2.25
Structure conservation index	0.62
SVM decision value	0.31
SVM RNA-class probability	0.682472
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10650771 93 - 23771897
CCAAGUACUUGUACAUUUGUCUGUGAAUAUGCA----UGGCGUAUAAAAAUAAAUGUCAGCGAAAA-----AAAAAUGGA--------------AAAAGAGAAAACAUU---UUUUCUA
(((.(((....)))...............(((.----((((((.((....)).)))))))))....-----.....))).--------------...(((((((....)---)))))). ( -14.10)
>DroSec_CAF1 13097 94 - 1
CCAAGUACUUGUACAU-UGUCUGUGCAUAUGCA----UGGCGUAUAAAAAUAAAUGUCAGCGAAAAA---AAAAAAUGGA--------------AAAAGAGAAAACAUU---UUUUCUA
(((.(((..((((((.-....))))))..))).----((((((.((....)).))))))........---......))).--------------...(((((((....)---)))))). ( -18.30)
>DroSim_CAF1 12471 98 - 1
CCAAGUACUUGUACAUUUGUCUGUGCAUAUGCA----UGGCGUAUAAAAAUAAAUGUCAGCGAAAAAAAAAAAAAAUGGA--------------AAAAGAGAAAACAUU---UUUUCUA
(((.(((..((((((......))))))..))).----((((((.((....)).)))))).................))).--------------...(((((((....)---)))))). ( -18.50)
>DroEre_CAF1 13539 94 - 1
CCAAGUACUUGUACAUUUGUCUGUGCAUAUGCA----UGGCGUAUAAAAAUAAAUGCCAGCGAAAAA----AAAAAUGGA--------------AAAAGAGAAAACAUU---UUUUCUA
(((.(((..((((((......))))))..))).----((((((.((....)).))))))........----.....))).--------------...(((((((....)---)))))). ( -21.20)
>DroWil_CAF1 13575 116 - 1
AUACAUAUAUGUAGAUGUCCCGAUGUAUGUGUAAAAAGUACGUAUAAAAAUAAAUGCCAGCAGAAAAA---AAAAGCGGAAAAAUAUAUAAAGUAAAAGAGAAAACAUUCUGUUUUCUA
.(((...((((((....(((...((((((((.......)))))))).............((.......---....)))))....))))))..)))....(((((((.....))))))). ( -19.10)
>DroYak_CAF1 13429 98 - 1
CCAAGUACUUGUGCAUUUGUCUGUGCAUAUGCA---AUGGCGUAUAAAAAUAAAUGUCAGCGAAAAAA-AAAAAAAUGGA--------------AAAAGAGAAAACAUU---UUUUCUA
(((......(((((((......)))))))(((.---.((((((.((....)).)))))))))......-.......))).--------------...(((((((....)---)))))). ( -18.30)
>consensus
CCAAGUACUUGUACAUUUGUCUGUGCAUAUGCA____UGGCGUAUAAAAAUAAAUGUCAGCGAAAAA____AAAAAUGGA______________AAAAGAGAAAACAUU___UUUUCUA
(((.(((..((((((......))))))..))).....((((((.((....)).)))))).................)))....................((((((.......)))))). (-11.36 = -11.92 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:25 2006