Locus 3580

Sequence ID 3R_DroMel_CAF1
Location 9,675,418 – 9,675,634
Length 216
Max. P 0.999865
window5772 window5773 window5774 window5775

overview

Window 2

Location 9,675,418 – 9,675,538
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -27.64
Consensus MFE -25.94
Energy contribution -26.22
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -1.31
Structure conservation index 0.94
SVM decision value 0.77
SVM RNA-class probability 0.845044
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9675418 120 - 27905053
CCACAUUCACGUCCACAUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
......(((((((((......)))))).)))(((((...(((((((.(..........).)))))))......((......((((((.........)))))).))......))))).... ( -26.60)
>DroSec_CAF1 67151 120 - 1
CCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
((...((((.(((((((((....)))).))))).)))).(((((((.(..........).)))))))......))......((((((.........)))))).................. ( -27.90)
>DroSim_CAF1 70078 120 - 1
CCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
((...((((.(((((((((....)))).))))).)))).(((((((.(..........).)))))))......))......((((((.........)))))).................. ( -27.90)
>DroEre_CAF1 68374 112 - 1
--------ACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
--------....(((((((....)))).)))(((((...(((((((.(..........).)))))))......((......((((((.........)))))).))......))))).... ( -26.50)
>DroYak_CAF1 72209 120 - 1
UCACAUCCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
......(((((((((......)))))).)))(((((...(((((((.(..........).)))))))......((......((((((.........)))))).))......))))).... ( -29.30)
>consensus
CCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUUGUCUCGUAAUAACUCAGCGGGAGCCAUUUAACAUGCAAUC
......(((((((((......)))))).)))(((((...(((((((.(..........).)))))))......((......((((((.........)))))).))......))))).... (-25.94 = -26.22 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,675,458 – 9,675,554
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -23.43
Consensus MFE -21.54
Energy contribution -21.85
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -3.27
Structure conservation index 0.92
SVM decision value 3.46
SVM RNA-class probability 0.999252
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9675458 96 - 27905053
ACAUC------------CACAUC------------CACAUCCACAUUCACGUCCACAUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUU
.....------------...(((------------(.(((((.(((...((((((......))))))))))).)))...(((((((.(..........).)))))))......))))... ( -20.50)
>DroSec_CAF1 67191 84 - 1
AC------------------------------------AUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUU
..------------------------------------((((...((((.(((((((((....)))).))))).)))).(((((((.(..........).)))))))......))))... ( -24.70)
>DroSim_CAF1 70118 96 - 1
ACAUC------------CACAUC------------CACAUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUU
.....------------......------------...((((...((((.(((((((((....)))).))))).)))).(((((((.(..........).)))))))......))))... ( -24.70)
>DroYak_CAF1 72249 120 - 1
ACAUCCCCAUCCCCAUCUCCAUCCACAACUACAUCCACAUUCACAUCCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUU
................................((((...((((..((((((((((......)))))).))))..)))).(((((((.(..........).)))))))......))))... ( -23.80)
>consensus
ACAUC____________CACAUC____________CACAUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAAUCGUUUACAAAUAAAUCAGAAAGCGAUAAAUAAGGAUUUU
......................................((((...((((.(((((((((....)))).))))).)))).(((((((.(..........).)))))))......))))... (-21.54 = -21.85 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,675,498 – 9,675,594
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.62
Mean single sequence MFE -27.52
Consensus MFE -23.41
Energy contribution -24.66
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -3.43
Structure conservation index 0.85
SVM decision value 4.30
SVM RNA-class probability 0.999865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9675498 96 - 27905053
GUCCUGUUGGCCAUACUCAGCCACAUCUUGGCCAAGAACCACAUC------------CACAUC------------CACAUCCACAUUCACGUCCACAUCCAUGGGCGAUGGGCAUGAAAA
(((((.(((((((...............))))))).)........------------......------------..............((((((......))))))..))))....... ( -23.76)
>DroSec_CAF1 67231 84 - 1
GUCCUGUUGGCCAUCCUCAGCCACAGCUUGGCCAACAUCCAC------------------------------------AUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAA
....(((((((((.....(((....)))))))))))).....------------------------------------.......((((.(((((((((....)))).))))).)))).. ( -31.90)
>DroSim_CAF1 70158 96 - 1
GUCCUGUUGGCCAUCCUCAGCCACAUCUUGGCCAACAUCCACAUC------------CACAUC------------CACAUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAA
....(((((((((...............)))))))))........------------......------------..........((((.(((((((((....)))).))))).)))).. ( -30.16)
>DroYak_CAF1 72289 120 - 1
GUCCUGUUGGCCAUCCUCAUCCUCAUCUUGGGCCACAUCCACAUCCCCAUCCCCAUCUCCAUCCACAACUACAUCCACAUUCACAUCCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAA
....(((.((((..................)))))))....(((.(((((((((((............................................))))).)))))).))).... ( -24.27)
>consensus
GUCCUGUUGGCCAUCCUCAGCCACAUCUUGGCCAACAUCCACAUC____________CACAUC____________CACAUCCACAUUCACGUCCACGUCCAUGGGCGAUGGGCAUGAAAA
....(((((((((...............)))))))))................................................((((.(((((((((....)))).))))).)))).. (-23.41 = -24.66 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,675,538 – 9,675,634
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.09
Mean single sequence MFE -22.03
Consensus MFE -19.75
Energy contribution -19.50
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.08
Structure conservation index 0.90
SVM decision value 0.32
SVM RNA-class probability 0.687996
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9675538 96 - 27905053
UGGCCAGCCCAUCAAGAUGCCAGUCGAAGUCCAGCUGCAGGUCCUGUUGGCCAUACUCAGCCACAUCUUGGCCAAGAACCACAUC------------CACAUC------------CACAU
((((((((....(....(((.(((.(.....).)))))).)....))))))))..((..((((.....))))..)).........------------......------------..... ( -22.80)
>DroSec_CAF1 67271 84 - 1
UGGCCAGCCCAUCAAGAUGCCAGACGAAGUCCAGCUGCAGGUCCUGUUGGCCAUCCUCAGCCACAGCUUGGCCAACAUCCAC------------------------------------AU
..((.(((.(((....)))...(((...)))..))))).((...(((((((((.....(((....)))))))))))).))..------------------------------------.. ( -22.50)
>DroSim_CAF1 70198 96 - 1
UGGCCAGCCCAUCAAGAUGCCAGUCGAAGUCCAGCUGCAGGUCCUGUUGGCCAUCCUCAGCCACAUCUUGGCCAACAUCCACAUC------------CACAUC------------CACAU
(((.((((.......(((....)))........))))..((...(((((((((...............))))))))).))....)------------))....------------..... ( -22.32)
>DroYak_CAF1 72329 120 - 1
UGGCCAGCCCAUCAAGAUGCCAGUCGAAGUCCAACUGCAGGUCCUGUUGGCCAUCCUCAUCCUCAUCUUGGGCCACAUCCACAUCCCCAUCCCCAUCUCCAUCCACAACUACAUCCACAU
(((((.......(((((((.((((.(.....).))))..((.((....))))...........))))))))))))............................................. ( -20.51)
>consensus
UGGCCAGCCCAUCAAGAUGCCAGUCGAAGUCCAGCUGCAGGUCCUGUUGGCCAUCCUCAGCCACAUCUUGGCCAACAUCCACAUC____________CACAUC____________CACAU
((((((((....(....(((.(((.(.....).)))))).)....))))))))......(((.......)))................................................ (-19.75 = -19.50 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:04 2006