Locus 5124

Sequence ID 3R_DroMel_CAF1
Location 13,492,211 – 13,492,321
Length 110
Max. P 0.999621
window8360 window8361

overview

Window 0

Location 13,492,211 – 13,492,321
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 92.60
Mean single sequence MFE -31.00
Consensus MFE -28.78
Energy contribution -29.18
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.93
SVM decision value 3.80
SVM RNA-class probability 0.999621
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13492211 110 + 27905053
UCGCUCAAGUUCUCUCUCUCUGUCUGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGUCUUCGUGCCUGUUGCUUGCCUCCUUUCCUUGCUCUCUCU
.((((..(((...(.......)...)))...)))).((((((((.....((((.((.(((((.((...((....))..)).)))))..))..)))).....)))))))). ( -32.30)
>DroSec_CAF1 42137 108 + 1
UCGCUCAAGUUCUCUCUCUC--UCUGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGACUUCGUGCCUGUUGCUUGCCUCCUUUCCUUGCUCUCUCU
.((((..(((..........--...)))...)))).((((((((.....((((.((.(((((.((...((....))..)).)))))..))..)))).....)))))))). ( -32.12)
>DroSim_CAF1 41040 106 + 1
UCGCUCAAGUUCUCU--CUC--UCUGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGUCUUCGUGCCUGUUGCUUGCCUCCUUUCCUUGCUCUCUCU
.((((..(((.....--...--...)))...)))).((((((((.....((((.((.(((((.((...((....))..)).)))))..))..)))).....)))))))). ( -31.70)
>DroEre_CAF1 38988 100 + 1
UCGCUCAAGUUCUC--------UUCGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGUCUUCGUGCCUGUUGCUUGAUUCCUUUCCUUGCUCUCU--
.((((..(((....--------...)))...))))..(((((((.....((((..(.(((((.((...((....))..)).)))))..)...)))).....)))))))-- ( -25.60)
>DroYak_CAF1 48066 104 + 1
UCGCUUAAGUUCUCUC------UCUGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGUCUUCGUGCCUGUUGCUUGCUUCCUUUUCUUGCUCUCUCU
.(((((.(((......------...)))..))))).((((((((.....((((.((.(((((.((...((....))..)).)))))..))..)))).....)))))))). ( -33.30)
>consensus
UCGCUCAAGUUCUCUC_CUC__UCUGCUGCAAGUGUGAGAGAGCCUUCCAAGGCGCUGCAACUGGAAUUGUCUUCGUGCCUGUUGCUUGCCUCCUUUCCUUGCUCUCUCU
.((((..(((...............)))...)))).((((((((.....((((.((.(((((.((...((....))..)).)))))..))..)))).....)))))))). (-28.78 = -29.18 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,492,211 – 13,492,321
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 92.60
Mean single sequence MFE -29.02
Consensus MFE -25.66
Energy contribution -26.06
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.88
SVM decision value 0.74
SVM RNA-class probability 0.839302
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13492211 110 - 27905053
AGAGAGAGCAAGGAAAGGAGGCAAGCAACAGGCACGAAGACAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCAGACAGAGAGAGAGAACUUGAGCGA
.((((((((.....((((..((..(((((.((.............)).))))).)).)))).....)))))))).........((.....(((........)))..)).. ( -29.72)
>DroSec_CAF1 42137 108 - 1
AGAGAGAGCAAGGAAAGGAGGCAAGCAACAGGCACGAAGUCAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCAGA--GAGAGAGAGAACUUGAGCGA
.((((((((.....((((..((..(((((.((...(....)....)).))))).)).)))).....)))))))).........((...--(((........)))..)).. ( -31.20)
>DroSim_CAF1 41040 106 - 1
AGAGAGAGCAAGGAAAGGAGGCAAGCAACAGGCACGAAGACAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCAGA--GAG--AGAGAACUUGAGCGA
.((((((((.....((((..((..(((((.((.............)).))))).)).)))).....)))))))).........((...--(((--......)))..)).. ( -31.32)
>DroEre_CAF1 38988 100 - 1
--AGAGAGCAAGGAAAGGAAUCAAGCAACAGGCACGAAGACAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCGAA--------GAGAACUUGAGCGA
--(((((((.....((((......(((((.((.............)).)))))....)))).....)))))))..........((.((--------(....)))..)).. ( -23.72)
>DroYak_CAF1 48066 104 - 1
AGAGAGAGCAAGAAAAGGAAGCAAGCAACAGGCACGAAGACAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCAGA------GAGAGAACUUAAGCGA
.((((((((.....((((..((..(((((.((.............)).))))).)).)))).....)))))))).........((.((------(......)))..)).. ( -29.12)
>consensus
AGAGAGAGCAAGGAAAGGAGGCAAGCAACAGGCACGAAGACAAUUCCAGUUGCAGCGCCUUGGAAGGCUCUCUCACACUUGCAGCAGA__GAG_GAGAGAACUUGAGCGA
.((((((((.....((((..((..(((((.((.............)).))))).)).)))).....)))))))).................................... (-25.66 = -26.06 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:54 2006