Locus 3265

Sequence ID 2R_DroMel_CAF1
Location 11,158,169 – 11,158,290
Length 121
Max. P 0.999638
window5353 window5354 window5355 window5356

overview

Window 3

Location 11,158,169 – 11,158,259
Length 90
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 82.47
Mean single sequence MFE -31.76
Consensus MFE -21.26
Energy contribution -22.34
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -2.01
Structure conservation index 0.67
SVM decision value 0.61
SVM RNA-class probability 0.799389
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11158169 90 + 20766785
UGCCCAUACAACUGGCGGUGGUGAUG---------GUGCUGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
.(((.........))).((.(..(((---------.(((((((((..((((....((---(((....))))).))))..).))))))))...)))..).)). ( -33.80)
>DroSec_CAF1 72940 84 + 1
UGCCCAUACAACUGGCGGUG---------------GUGCAGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
.(((.........)))..((---------------.((((((((((..(((......---.)))..)))))))))).))(((.(((((.....)))))))). ( -33.20)
>DroSim_CAF1 72536 84 + 1
UGCCCAUACAACUGGCGGUG---------------GUGCAGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
.(((.........)))..((---------------.((((((((((..(((......---.)))..)))))))))).))(((.(((((.....)))))))). ( -33.20)
>DroEre_CAF1 75584 69 + 1
UGCCCAUACAAC------------------------------UGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
...........(------------------------------((((..(((......---.)))..))))).((((((((((......))).)))))))... ( -22.20)
>DroYak_CAF1 72612 102 + 1
UGCCCAUACAACUGGCGGCGAUGGUGGCAACGCUGGUGGCACUGCAAUUGCUACUGCUACUGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
.............(((.(((((((((....))).(((((((..((....))...))))))).)))).)).)))(((((((((......))).)))))).... ( -36.40)
>consensus
UGCCCAUACAACUGGCGGUG_______________GUGCAGUUGCAAUUGCUACUGC___UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACA
.(((.........)))........................((((((..(((..........)))..))))))((((((((((......))).)))))))... (-21.26 = -22.34 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,158,169 – 11,158,259
Length 90
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 82.47
Mean single sequence MFE -31.72
Consensus MFE -23.11
Energy contribution -23.27
Covariance contribution 0.16
Combinations/Pair 1.07
Mean z-score -2.13
Structure conservation index 0.73
SVM decision value 1.06
SVM RNA-class probability 0.908395
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11158169 90 - 20766785
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACAGCAC---------CAUCACCACCGCCAGUUGUAUGGGCA
....((((((.((((....)))))))))).(((((....)))---)).((.((....)).)).((.(---------(((.((.((.....)).)))))))). ( -30.80)
>DroSec_CAF1 72940 84 - 1
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACUGCAC---------------CACCGCCAGUUGUAUGGGCA
....((((((.((((....)))))))))).(((((....)))---))....((...(((((((((..---------------....).))))))))...)). ( -33.70)
>DroSim_CAF1 72536 84 - 1
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACUGCAC---------------CACCGCCAGUUGUAUGGGCA
....((((((.((((....)))))))))).(((((....)))---))....((...(((((((((..---------------....).))))))))...)). ( -33.70)
>DroEre_CAF1 75584 69 - 1
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCA------------------------------GUUGUAUGGGCA
.(((((((((.((((....))))))))))((((((((.(((.---......))).)))))------------------------------))).....))). ( -27.70)
>DroYak_CAF1 72612 102 - 1
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCAGUAGCAGUAGCAAUUGCAGUGCCACCAGCGUUGCCACCAUCGCCGCCAGUUGUAUGGGCA
.((.(((((.((..(.(((((...(((((.(((((..........))))).)))))..))))).)..))..))))).)).......(((.........))). ( -32.70)
>consensus
UGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA___GCAGUAGCAAUUGCAACUGCAC_______________CACCGCCAGUUGUAUGGGCA
.(((((((((.((((....)))))))))).(((((...(((....))))))))...((((((............................))))))..))). (-23.11 = -23.27 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,158,196 – 11,158,290
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 86.80
Mean single sequence MFE -37.18
Consensus MFE -30.84
Energy contribution -31.84
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -4.11
Structure conservation index 0.83
SVM decision value 3.82
SVM RNA-class probability 0.999638
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11158196 94 + 20766785
UGCUGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUCUGCAUCCGCAGCCCCGC
.((((((((((((((....((---(((....))))).(((((((((......))).))))))).))))))))..(((....)))...)))))..... ( -37.30)
>DroSec_CAF1 72961 94 + 1
UGCAGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUUUGCAUCCGCAGCCCCGC
(((((.(((((((((....((---(((....))))).(((((((((......))).))))))).)))))))).))))).((((....))))...... ( -39.90)
>DroSim_CAF1 72557 94 + 1
UGCAGUUGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUCUGCAUCCGCAGCCCCGC
(((((.(((((((((....((---(((....))))).(((((((((......))).))))))).)))))))).))))).((((....))))...... ( -41.70)
>DroEre_CAF1 75596 75 + 1
------UGCAAUUGCUACUGC---UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUCUGCA-------------
------(((((((((....((---(((....))))).(((((((((......))).))))))).))))))))...((....)).------------- ( -30.30)
>DroYak_CAF1 72648 92 + 1
UGGCACUGCAAUUGCUACUGCUACUGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUCUGCAGCCGCAUU-----
(((((.......))))).(((..(((((..(((((.(((((..(((.(((((.....))))))))..))))).)))))..)))))..)))..----- ( -36.70)
>consensus
UGCAGUUGCAAUUGCUACUGC___UGCAUCUGCAGCUGCAACAGUCAGCGGCGACAUGUUGCGACAAUUGCAUCUGCAUCUGCAUCCGCAGCCCCGC
.......((....))..((((...((((..(((((.(((((..(((.(((((.....))))))))..))))).)))))..))))...))))...... (-30.84 = -31.84 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 11,158,196 – 11,158,290
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 86.80
Mean single sequence MFE -39.64
Consensus MFE -31.74
Energy contribution -32.82
Covariance contribution 1.08
Combinations/Pair 1.04
Mean z-score -3.93
Structure conservation index 0.80
SVM decision value 3.46
SVM RNA-class probability 0.999252
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11158196 94 - 20766785
GCGGGGCUGCGGAUGCAGAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACAGCA
(((...((((....)))).))).(.(((((((((.((((((.((((....)))))))))).(((((....)))---))....))))))))).).... ( -40.30)
>DroSec_CAF1 72961 94 - 1
GCGGGGCUGCGGAUGCAAAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACUGCA
((((..(((((........))))).(((((((((.((((((.((((....)))))))))).(((((....)))---))....))))))))).)))). ( -43.10)
>DroSim_CAF1 72557 94 - 1
GCGGGGCUGCGGAUGCAGAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCAACUGCA
......((((....)))).(((((.(((((((((.((((((.((((....)))))))))).(((((....)))---))....))))))))).))))) ( -43.90)
>DroEre_CAF1 75596 75 - 1
-------------UGCAGAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA---GCAGUAGCAAUUGCA------
-------------(((....)))..(((((((((.((((((.((((....)))))))))).(((((....)))---))....)))))))))------ ( -32.90)
>DroYak_CAF1 72648 92 - 1
-----AAUGCGGCUGCAGAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCAGUAGCAGUAGCAAUUGCAGUGCCA
-----...(((.((((((.(((...(((.......((((((.((((....)))))))))).(((((....))))).)))...))).))))))))).. ( -38.00)
>consensus
GCGGGGCUGCGGAUGCAGAUGCAGAUGCAAUUGUCGCAACAUGUCGCCGCUGACUGUUGCAGCUGCAGAUGCA___GCAGUAGCAAUUGCAACUGCA
.....(((((...((((..(((((.((((((.(((((...........)).))).)))))).)))))..))))...))))).((....))....... (-31.74 = -32.82 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:24 2006