Locus 1180

Sequence ID 2L_DroMel_CAF1
Location 3,221,438 – 3,221,538
Length 100
Max. P 0.558798
window1912 window1913

overview

Window 2

Location 3,221,438 – 3,221,538
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.14
Mean single sequence MFE -24.13
Consensus MFE -14.90
Energy contribution -15.65
Covariance contribution 0.75
Combinations/Pair 1.09
Mean z-score -1.49
Structure conservation index 0.62
SVM decision value -0.01
SVM RNA-class probability 0.529634
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3221438 100 + 22407834
UUUGCAAAAGUCGAAAGUU-UCC----------------GCUGCG---AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUUGCGAUGCGGUUUGCAAAAAGUAUGUACAUGGACAAUUUG
..((((.....(....)..-...----------------..))))---(((((((((((((...((((((((((......)))..(((.....))))))))))..)))).))))))))). ( -25.70)
>DroSec_CAF1 55529 100 + 1
UUUGCAAAAGUCGAAAGUU-UCC----------------GCUGCG---AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUUGCGGUGCGGUUUGCAAAAAGUGUGUACAUGGACAAUUUG
..((((.....(....)..-...----------------..))))---(((((((((((((...((((((((((......)))..(((.....))))))))))..)))).))))))))). ( -25.30)
>DroSim_CAF1 54012 100 + 1
UUUGCAAAAGUCGAAAGUU-UCC----------------GCUGCG---AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUUGCUGUGCGGUUUGCAAAAAGUGUGUACAUGGACAAUUUG
..((((.....(....)..-...----------------..))))---(((((((((((((...((((((((((.((....((...)).)).))).)))))))..)))).))))))))). ( -25.00)
>DroEre_CAF1 52054 94 + 1
UUUGCCAAAGUCGAAAGUU-UCC----------------GCAGCG---AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUU--UGUGCGGUUUGCAAAAAC----UACAUGGACAAUUUG
.((((((.(((.....((.-.((----------------(((.((---((((.((..((((((.....)))))).))))))--)))))))...))....))----)...))).))).... ( -21.60)
>DroYak_CAF1 50809 92 + 1
UUUGCAAAAGUCGAAAGUUCUGC----------------GCAGUG---AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUU--UAUGCGGUUUGCAAAAAG----UACAUGGA---AUUG
((((((((((.(....)..)).(----------------(((.((---((((.((..((((((.....)))))).))))))--)))))).))))))))...----........---.... ( -20.90)
>DroPer_CAF1 65961 113 + 1
CUUGGAGAAGUUGAAAGUU-UCUCUGACAGUUUGUGUGCUCCUUGAAAGAAUUGUCUUGCAAAUUACUUUUGCAUACAUUUGC--UGAGGUCGAAAAAAAG----UGCAGGGACAAUUUA
.(..((((((.......))-))))..)..((((.((..(((((((...((((.((..((((((.....)))))).))))))..--))))).........))----..)).))))...... ( -26.30)
>consensus
UUUGCAAAAGUCGAAAGUU_UCC________________GCUGCG___AAAUUGUCUUGUAAAUUACUUUUGCAUACAUUUGCUGUGCGGUUUGCAAAAAG____UACAUGGACAAUUUG
................................................(((((((((((((......(((((((.((............)).)))))))......)))).))))))))). (-14.90 = -15.65 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,221,438 – 3,221,538
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.14
Mean single sequence MFE -17.78
Consensus MFE -11.93
Energy contribution -12.68
Covariance contribution 0.75
Combinations/Pair 1.09
Mean z-score -1.30
Structure conservation index 0.67
SVM decision value 0.05
SVM RNA-class probability 0.558798
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3221438 100 - 22407834
CAAAUUGUCCAUGUACAUACUUUUUGCAAACCGCAUCGCAAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU---CGCAGC----------------GGA-AACUUUCGACUUUUGCAAA
.((((((((..((((..(((((((.(((....((((.....)))).))))))))))...)))).))))))))---.(((((----------------(((-....))))....))))... ( -21.00)
>DroSec_CAF1 55529 100 - 1
CAAAUUGUCCAUGUACACACUUUUUGCAAACCGCACCGCAAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU---CGCAGC----------------GGA-AACUUUCGACUUUUGCAAA
.((((((((..((((...(((((((((.....)))..(((......)))))))))....)))).))))))))---.(((((----------------(((-....))))....))))... ( -19.20)
>DroSim_CAF1 54012 100 - 1
CAAAUUGUCCAUGUACACACUUUUUGCAAACCGCACAGCAAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU---CGCAGC----------------GGA-AACUUUCGACUUUUGCAAA
.((((((((..((((...(((((((((.....)))..(((......)))))))))....)))).))))))))---.(((((----------------(((-....))))....))))... ( -19.10)
>DroEre_CAF1 52054 94 - 1
CAAAUUGUCCAUGUA----GUUUUUGCAAACCGCACA--AAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU---CGCUGC----------------GGA-AACUUUCGACUUUGGCAAA
.((((((((..((((----(((((((((.((......--....)).))))))))....))))).))))))))---.(((.(----------------(((-....)))).....)))... ( -18.60)
>DroYak_CAF1 50809 92 - 1
CAAU---UCCAUGUA----CUUUUUGCAAACCGCAUA--AAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU---CACUGC----------------GCAGAACUUUCGACUUUUGCAAA
....---.....(((----((((((((.....))).)--))).))))((((((((.........((.....)---).((..----------------..))........))))))))... ( -13.20)
>DroPer_CAF1 65961 113 - 1
UAAAUUGUCCCUGCA----CUUUUUUUCGACCUCA--GCAAAUGUAUGCAAAAGUAAUUUGCAAGACAAUUCUUUCAAGGAGCACACAAACUGUCAGAGA-AACUUUCAACUUCUCCAAG
..(((((((..(((.----................--(((......))).(((....)))))).))))))).......((((.(((.....)))..((((-...)))).....))))... ( -15.60)
>consensus
CAAAUUGUCCAUGUA____CUUUUUGCAAACCGCACAGCAAAUGUAUGCAAAAGUAAUUUACAAGACAAUUU___CGCAGC________________GGA_AACUUUCGACUUUUGCAAA
.((((((((..((((.....((((((((.((............)).)))))))).....)))).))))))))................................................ (-11.93 = -12.68 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:37 2006