Locus 1330

Sequence ID X_DroMel_CAF1
Location 3,980,580 – 3,980,788
Length 208
Max. P 0.812623
window2120 window2121

overview

Window 0

Location 3,980,580 – 3,980,680
Length 100
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 82.44
Mean single sequence MFE -26.60
Consensus MFE -18.09
Energy contribution -18.82
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.68
SVM decision value -0.05
SVM RNA-class probability 0.509709
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3980580 100 + 22224390
AUGAAAAUAGAAACAGAAGC-GAAUCGA-----AAACGGAUACGGAUACGGUAGCGGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACCGCCCAGUUUG
..........((((....((-..((((.-----(..((....))..).)))).))........((((((((......)))))))).((((((...)))))))))). ( -28.80)
>DroSec_CAF1 2617 100 + 1
AUGAAAAUAGAAACAGAAGC-GAAUCGA-----AAACGGAUACGGAUACGGUAGCGGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACCGCCCAGUUUG
..........((((....((-..((((.-----(..((....))..).)))).))........((((((((......)))))))).((((((...)))))))))). ( -28.80)
>DroSim_CAF1 553 100 + 1
AUGAAAAUAGAAACAGAAGC-GAAUCGA-----AAACGGAUACGGAUACGGUAGCGGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACCGCCCAGUUUG
..........((((....((-..((((.-----(..((....))..).)))).))........((((((((......)))))))).((((((...)))))))))). ( -28.80)
>DroEre_CAF1 473 105 + 1
AUGAAAAUAGCAACGGAAAC-GAAUCGAAUCAAAAACGGAUACGGAUACGGAUACAGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACCGCCCAGUUUG
.............((....)-)..(((.(((.......))).)))...(((((..........((((((((......)))))))).((((((...))))))))))) ( -27.70)
>DroYak_CAF1 564 103 + 1
AUGAAAAUAGAAUAAGAAACAGAAACGAAC---GAACGGAUACGGAUACGGAUAGAGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACAGCCCAAUUUG
...................((((..(((..---.........((....))..........)))((((((((......)))))))).(((((.....))))).)))) ( -24.00)
>DroAna_CAF1 787 89 + 1
ACGGAAACUGAAGCAG----------GA-----UAACUGAAGCGGAGAGAGUGGUAGAG--AGAGGUACGUACAAUGGCGAUGUCAUGGGCGAACCGCCCAGUUUG
....((((((..((..----------..-----...(((..((.......))..)))..--...(((.(((...(((((...)))))..))).))))).)))))). ( -21.50)
>consensus
AUGAAAAUAGAAACAGAAGC_GAAUCGA_____AAACGGAUACGGAUACGGUAGCAGAAGUCGGGGUACGUACAAUGGCGUGCUCAUGGGCGAACCGCCCAGUUUG
..........................................(((((................((((((((......)))))))).(((((.....)))))))))) (-18.09 = -18.82 +   0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,980,680 – 3,980,788
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 91.02
Mean single sequence MFE -38.70
Consensus MFE -32.92
Energy contribution -33.40
Covariance contribution 0.48
Combinations/Pair 1.03
Mean z-score -1.49
Structure conservation index 0.85
SVM decision value 0.65
SVM RNA-class probability 0.812623
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3980680 108 + 22224390
ACGGGCGGCGGCAGUGGCAACGGUGACGGCGGUGGCUCCUUUACCAGCUGGCCACUGCAAUAAGGUAGCGGAAAACGCCAACCGUAAAGACUGCUUGGUUAGAUGGU-----U
.((((((((.((((((((..((....))(((((((.....))))).))..)))))))).....(((.(((.....)))..))).....).)))))))..........-----. ( -42.90)
>DroVir_CAF1 619 113 + 1
ACUGGCGGCGGCAGUGGUAACGGUGAUGGUGGUGGCUCCUUAACCAGCUGUCCACUGCAAUAAGGUAGCGGGAAACGCCAACCAUAAAGACUGCUUGGUUAGAUGAUGGUAAU
..((((.((.(((((((..(((((..((((...(....)...)))))))))))))))).........)).(....)))))(((((...((((....)))).....)))))... ( -36.50)
>DroGri_CAF1 639 113 + 1
ACUGGCGGCGGCAGUGGUAACGGUGAUGGUGGUGGCUCCUUAACCAGCUGUCCACUGCAAUAAGGUAGCGGGAAACGCCAACCAUAAAGACUGCUUGGUUAGAUGAUGAUAAU
.((((((((((((((((..(((((..((((...(....)...)))))))))))))))).....(((.(((.....)))..)))........))))..)))))........... ( -36.20)
>DroWil_CAF1 8787 105 + 1
ACUGGCGGCGGCAGUGGUAGCGGUGACGGUGGUGGCUCCUUAACCAGCUGUCCACUGCAAUAAGGUAGCGGAAAACGCCAACCAUAAAGACUGCUUGGUUAAAU--------U
.(.((((((.((((((((((((....)(((...(....)...))).)))).))))))).....(((.(((.....)))..))).....).))))).).......--------. ( -38.80)
>DroMoj_CAF1 625 113 + 1
ACUGGCGGCGGCAGUGGCAACGGUGAUGGCGGCGGCUCCUUAACCAGCUGUCCACUGCAAUAAGGUAGCGGGAAACGCCAACCAUAAAGACUGCUUGGUUAGAUGUUGAUAAU
.(((((.(.(((((((....)(((..(((((((((((........))))))((.((((......)))).))....))))))))......))))))).)))))........... ( -39.10)
>consensus
ACUGGCGGCGGCAGUGGUAACGGUGAUGGUGGUGGCUCCUUAACCAGCUGUCCACUGCAAUAAGGUAGCGGGAAACGCCAACCAUAAAGACUGCUUGGUUAGAUGAUG_UAAU
.(.((((((.(((((((..(((((...(((...(....)...))).)))))))))))).....(((.(((.....)))..))).....).))))).)................ (-32.92 = -33.40 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:41 2006