Locus 9740

Sequence ID 3R_DroMel_CAF1
Location 25,776,296 – 25,776,431
Length 135
Max. P 0.970013
window15560 window15561

overview

Window 0

Location 25,776,296 – 25,776,398
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 86.73
Mean single sequence MFE -18.96
Consensus MFE -13.68
Energy contribution -13.92
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.86
Structure conservation index 0.72
SVM decision value 1.51
SVM RNA-class probability 0.960395
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25776296 102 + 27905053
AUUUUCGAGAGUGUUUGCCACUCCUGGCGACUCCCGUUGCCCCGUUGCCCGGUUGCCCCAUUCCCCAACUCCCAUUCCCCCAUUCACACUCCGAAUAUAAUA
...((((.((((((..((.((....((((((....))))))..)).))..(((((..........)))))...............))))))))))....... ( -22.90)
>DroSec_CAF1 19899 94 + 1
AUUUUCGAGAGUGUUUGCCACUCCUGGCGACUCUCUUUGCCCCGUU--------GCCCCAUUCCCGAACUCCCACUCCCCCAUUUACACUCCGAAUAUAAUA
...((((.((((((((((((....))))))........((......--------)).............................))))))))))....... ( -17.60)
>DroSim_CAF1 20064 94 + 1
AUUUUCGAGAGUGUUUGCCACUCCUGGCGACUCUCGUUGCCCCGUU--------GCCCCAUUCCCGAACUCCCACUCCCCCAUUCACACUCCGAAUAUAAUA
...((((.((((((..((.((....((((((....))))))..)).--------)).........(((..............)))))))))))))....... ( -20.04)
>DroYak_CAF1 18755 87 + 1
AUUUUCGAGUGUGUUUGCCACUCCUGGCGACUCCCAUU-CCCCGUU--------CCCCCAUUUCU------CCGUUCCCCCAUUCACACUCCGAAUAUAAUA
...((((((((((.((((((....))))))........-....(..--------....)......------.............)))))).))))....... ( -15.30)
>consensus
AUUUUCGAGAGUGUUUGCCACUCCUGGCGACUCCCGUUGCCCCGUU________GCCCCAUUCCCGAACUCCCACUCCCCCAUUCACACUCCGAAUAUAAUA
...((((.((((((..((((....))))(((............))).......................................))))))))))....... (-13.68 = -13.92 +   0.25)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 25,776,335 – 25,776,431
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 88.59
Mean single sequence MFE -30.75
Consensus MFE -25.84
Energy contribution -25.46
Covariance contribution -0.38
Combinations/Pair 1.10
Mean z-score -2.40
Structure conservation index 0.84
SVM decision value 1.65
SVM RNA-class probability 0.970013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25776335 96 - 27905053
UCCCCGACUUUGUUUAUUCAGCUAUUCCAUCCAUAUUAUAUUCGGAGUGUGAAUGGGGGAAUGGGAGUUGGGGAAUGGGGCAACCGGGCAACGGGG
((((((((((((......)).(((((((.(((((.((((((.....)))))))))))))))))))))))))))).........((.(....).)). ( -37.60)
>DroSec_CAF1 19938 88 - 1
UCCCCGACUUUGUUUAUUCAGCUAUUCCAUCCAUAUUAUAUUCGGAGUGUAAAUGGGGGAGUGGGAGUUCGGGAAUGGGGC--------AACGGGG
.(((((.(((..(((((((..(((((((.(((((.((((((.....))))))))))))))))))))))....)))..))).--------..))))) ( -29.20)
>DroSim_CAF1 20103 88 - 1
UCCCCGACUUUGUUUAUUCAGCUAUUCCAUCCAUAUUAUAUUCGGAGUGUGAAUGGGGGAGUGGGAGUUCGGGAAUGGGGC--------AACGGGG
.(((((.(((..(((((((..(((((((.(((((.((((((.....))))))))))))))))))))))....)))..))).--------..))))) ( -29.30)
>DroYak_CAF1 18793 82 - 1
UCCCCGACUUUGUUUAUUCAGCUAUUCCAUCCAUAUUAUAUUCGGAGUGUGAAUGGGGGAACGG------AGAAAUGGGGG--------AACGGGG
.(((((.(((..(((......(..((((.(((((.((((((.....)))))))))))))))..)------..)))..))).--------..))))) ( -26.90)
>consensus
UCCCCGACUUUGUUUAUUCAGCUAUUCCAUCCAUAUUAUAUUCGGAGUGUGAAUGGGGGAAUGGGAGUUCGGGAAUGGGGC________AACGGGG
.(((((.(((..(((......(((((((.(((((.((((((.....))))))))))))))))))........)))..)))...........))))) (-25.84 = -25.46 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:41:07 2006