Locus 9399

Sequence ID 3R_DroMel_CAF1
Location 24,918,086 – 24,918,246
Length 160
Max. P 0.893504
window15053 window15054 window15055

overview

Window 3

Location 24,918,086 – 24,918,206
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.25
Mean single sequence MFE -26.08
Consensus MFE -20.52
Energy contribution -20.96
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value -0.03
SVM RNA-class probability 0.516401
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24918086 120 + 27905053
GAGAAGUUGUGGCAGCGAAAUCAGCCAUCCGCAAGCUGAAUCAGCAACAACAAUCCGAAAACAAUAGAUUUCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAG
..((((((((((..((.......))...))))..((((...)))).....................)))))).....................((((((((..(....)...)))))))) ( -24.20)
>DroSec_CAF1 31247 120 + 1
GAGAAGUUGUGGCAGCGAAAUCAGCCAUCCACAAGCUGAAUCAGCAACAACACAACGAAAACAAUGGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAG
.....((((((...((....(((((.........)))))....)).....)))))).....((....((((......))))...)).......((((((((..(....)...)))))))) ( -25.90)
>DroSim_CAF1 26992 120 + 1
GAGAAGUUGUGGCAGCGAAAUCAGCCAUCCACAAGCUGAAUCAGCAACAACACAACGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAG
.....((((((...((....(((((.........)))))....)).....)))))).....((....((((......))))...)).......((((((((..(....)...)))))))) ( -25.90)
>DroEre_CAF1 29937 120 + 1
GAGAAGUUGUGGCUGCGAAAUCAGCCAUCCACAAGCUGAAUCAGCAGCAACAAUCCGAAAACAAUUGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGGAAUGAAAAUACAAG
......((((((((((....(((((.........)))))....)))))..((.((((...(((((((.((....)).)))).)))..(((((....)))))..)))).))....))))). ( -27.50)
>DroYak_CAF1 30336 120 + 1
GAGAAGUUGUGGCUGCGAAAUCAGCCAUCCACAAGCUGAAUCAGCAGCAACAAUCCGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGAUGAAAGGAAAAUACAAG
........(((((((......))))))).((((.((((......))))..(((((...........)))))...........)))).......((((((((..(....)...)))))))) ( -26.90)
>consensus
GAGAAGUUGUGGCAGCGAAAUCAGCCAUCCACAAGCUGAAUCAGCAACAACAAUCCGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAG
.....(((((....((....(((((.........)))))....)).)))))..........((....((((......))))...)).......((((((((..(....)...)))))))) (-20.52 = -20.96 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 24,918,086 – 24,918,206
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -29.22
Consensus MFE -22.48
Energy contribution -22.44
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.77
SVM decision value -0.01
SVM RNA-class probability 0.529631
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24918086 120 - 27905053
CUUGUAUUUUCCUUUCGUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGAAAUCUAUUGUUUUCGGAUUGUUGUUGCUGAUUCAGCUUGCGGAUGGCUGAUUUCGCUGCCACAACUUCUC
((((((((..(.....)..))))))))((((....(((...((((((.((((........)))))))))).))).((.((.((((((.......)))))).)).)))))).......... ( -28.10)
>DroSec_CAF1 31247 120 - 1
CUUGUAUUUUCCUUUCGUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGCAAUCCAUUGUUUUCGUUGUGUUGUUGCUGAUUCAGCUUGUGGAUGGCUGAUUUCGCUGCCACAACUUCUC
((((((((..(.....)..))))))))((((....(((((.(((....((((....))))..))).)))))....((.((.((((((.......)))))).)).)))))).......... ( -27.50)
>DroSim_CAF1 26992 120 - 1
CUUGUAUUUUCCUUUCGUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGCAAUCUAUUGUUUUCGUUGUGUUGUUGCUGAUUCAGCUUGUGGAUGGCUGAUUUCGCUGCCACAACUUCUC
((((((((..(.....)..))))))))((((....(((((.(((....((((....))))..))).)))))....((.((.((((((.......)))))).)).)))))).......... ( -27.50)
>DroEre_CAF1 29937 120 - 1
CUUGUAUUUUCAUUCCGUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGCAAUCAAUUGUUUUCGGAUUGUUGCUGCUGAUUCAGCUUGUGGAUGGCUGAUUUCGCAGCCACAACUUCUC
((((((((..(.....)..))))))))(((..((((((.((((((...((((.(((((.......))))))))).))))))......))))))((((((......))))))..))).... ( -32.30)
>DroYak_CAF1 30336 120 - 1
CUUGUAUUUUCCUUUCAUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGCAAUCUAUUGUUUUCGGAUUGUUGCUGCUGAUUCAGCUUGUGGAUGGCUGAUUUCGCAGCCACAACUUCUC
((((((((...........))))))))(((..((((((.((((((...(((((((.........)))))))....))))))......))))))((((((......))))))..))).... ( -30.70)
>consensus
CUUGUAUUUUCCUUUCGUCAAUACAAGGGUAUUUCACAUAUCGGUCUUGCAAUCUAUUGUUUUCGGAUUGUUGUUGCUGAUUCAGCUUGUGGAUGGCUGAUUUCGCUGCCACAACUUCUC
((((((((...........))))))))(((.........((((((...(((((....((....))....))))).))))))((((((.......)))))).......))).......... (-22.48 = -22.44 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 24,918,126 – 24,918,246
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -28.72
Consensus MFE -22.48
Energy contribution -24.76
Covariance contribution 2.28
Combinations/Pair 1.03
Mean z-score -2.15
Structure conservation index 0.78
SVM decision value 0.98
SVM RNA-class probability 0.893504
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24918126 120 + 27905053
UCAGCAACAACAAUCCGAAAACAAUAGAUUUCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAGGUCAUUAUCGUCUAGAAAUAAUUGCGUGUGAUUUUGGGUA
............(((((((((((....(((((.((((.((((.((((.....(((((((((..(....)...))))))))))))))))))))).))))).......)))..)))))))). ( -33.60)
>DroSec_CAF1 31287 120 + 1
UCAGCAACAACACAACGAAAACAAUGGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAGGUCAUUAUCGUCUGAAAAUAAUUGCGUGUGAUUUUGGGUA
....(((...((((.((....((((..(((...((((.((((.((((.....(((((((((..(....)...)))))))))))))))))))))...))).))))))))))...))).... ( -29.40)
>DroSim_CAF1 27032 120 + 1
UCAGCAACAACACAACGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAGGUCAUUAUCGUCUGGAAAUAAUUGCGUGUGAUUUUGGGUA
....(((...((((.((....((((..(((...((((.((((.((((.....(((((((((..(....)...)))))))))))))))))))))...))).))))))))))...))).... ( -28.20)
>DroEre_CAF1 29977 120 + 1
UCAGCAGCAACAAUCCGAAAACAAUUGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGGAAUGAAAAUACAAGGCCAUUAUCGUCUGGAAAUAAUUGCGUGUGAUUUUGGGUA
............(((((((((((...(((((..((((.((((.(((......(((((((((...........))))))))).))))))))))).....)))))...)))..)))))))). ( -24.10)
>DroYak_CAF1 30376 120 + 1
UCAGCAGCAACAAUCCGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGAUGAAAGGAAAAUACAAGGUCAUUAUCGUCUGCAUAUAAUUGCGUGUGAUUUUUGGUA
.......(((.((((((....((((....((((.(((.((((.((((.....(((((((((..(....)...))))))))))))))))))))))))....))))..)).)))).)))... ( -28.30)
>consensus
UCAGCAACAACAAUCCGAAAACAAUAGAUUGCAAGACCGAUAUGUGAAAUACCCUUGUAUUGACGAAAGGAAAAUACAAGGUCAUUAUCGUCUGGAAAUAAUUGCGUGUGAUUUUGGGUA
............(((((((((((...(((((..((((.((((.((((.....(((((((((..(....)...))))))))))))))))))))).....)))))...)))..)))))))). (-22.48 = -24.76 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:46 2006