Locus 1004

Sequence ID 3R_DroMel_CAF1
Location 3,193,321 – 3,193,481
Length 160
Max. P 0.951943
window1624 window1625

overview

Window 4

Location 3,193,321 – 3,193,441
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -27.17
Consensus MFE -27.20
Energy contribution -26.43
Covariance contribution -0.77
Combinations/Pair 1.18
Mean z-score -1.98
Structure conservation index 1.00
SVM decision value 1.42
SVM RNA-class probability 0.951943
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3193321 120 - 27905053
UCACCGAAAACUAAUAUUCGUCAAUCGGGAGUAUGAUCUAUUUUAUAUUCGUCAAAUGGCAGCCCCCUGUCCUCAUAAGUGCGAGUGUUGUUAUAGCCGCGAUUCACUUAUUUUAAAAAU
...((((..((........))...))))((((((((......)))))))).......(((((....)))))...(((((((....(((.((....)).)))...)))))))......... ( -22.40)
>DroSec_CAF1 12830 120 - 1
ACAUCAAAAACUAAUACUCGUCAAUCAGGAGUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAUGCGAGUGUUGUUACAGCCGCGAUUCACUUAUUUUUAAAAU
........(((.(((((((((...(((.((((((((......)))))))).)))...(((((....))))).........))))))))))))............................ ( -29.70)
>DroSim_CAF1 19557 120 - 1
UCACCAAAAACUGAUACUCGUCAAUCAGGAAUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAUGCGAGUGUUGUUACAGCCGCGAUUCACUUAUUUUAAAAAU
........(((.(((((((((...(((.((((((((......)))))))).)))...(((((....))))).........))))))))))))............................ ( -29.40)
>consensus
UCACCAAAAACUAAUACUCGUCAAUCAGGAGUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAUGCGAGUGUUGUUACAGCCGCGAUUCACUUAUUUUAAAAAU
........(((.(((((((((...(((.((((((((......)))))))).)))...(((((....))))).........))))))))))))............................ (-27.20 = -26.43 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,193,361 – 3,193,481
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -29.70
Consensus MFE -24.80
Energy contribution -24.25
Covariance contribution -0.55
Combinations/Pair 1.12
Mean z-score -3.18
Structure conservation index 0.83
SVM decision value 1.22
SVM RNA-class probability 0.932350
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3193361 120 - 27905053
UUAAUACAAUUAUGAGCAUCUAUAAGUAUAUGGAAUGGCUUCACCGAAAACUAAUAUUCGUCAAUCGGGAGUAUGAUCUAUUUUAUAUUCGUCAAAUGGCAGCCCCCUGUCCUCAUAAGU
.........(((((((..((((((....)))))).((((....((((..((........))...))))((((((((......))))))))))))...(((((....)))))))))))).. ( -27.80)
>DroSec_CAF1 12870 120 - 1
UUACUACGAUUAUGAGCAUCUAUAAGAAUAUGGAAUGGCUACAUCAAAAACUAAUACUCGUCAAUCAGGAGUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAU
.........(((((((.........(((((((((((((....((((........(((((.(.....).)))))))))))))))))))))).......(((((....)))))))))))).. ( -29.30)
>DroSim_CAF1 19597 120 - 1
UAACUACAAUUAUGAGCAUUUAUAAGAAUAUGGAAUGGCUUCACCAAAAACUGAUACUCGUCAAUCAGGAAUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAU
.........(((((((.((((....(((((((((((((..(((.......(((((........))))).....))).)))))))))))))...))))(((((....)))))))))))).. ( -32.00)
>consensus
UUACUACAAUUAUGAGCAUCUAUAAGAAUAUGGAAUGGCUUCACCAAAAACUAAUACUCGUCAAUCAGGAGUAUGAUCUAUUUUAUAUUCGUGAAAUGGCAGCCCCCUGCCCUCAUAAAU
.........(((((((..((((((....)))))).((((....................)))).(((.((((((((......)))))))).)))...(((((....)))))))))))).. (-24.80 = -24.25 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:07 2006