Locus 4814

Sequence ID 2L_DroMel_CAF1
Location 13,738,059 – 13,738,257
Length 198
Max. P 0.999908
window7612 window7613 window7614 window7615

overview

Window 2

Location 13,738,059 – 13,738,178
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -35.40
Consensus MFE -30.42
Energy contribution -31.29
Covariance contribution 0.86
Combinations/Pair 1.06
Mean z-score -2.32
Structure conservation index 0.86
SVM decision value 1.59
SVM RNA-class probability 0.966313
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13738059 119 - 22407834
UGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACCCAGACAAAGGCCAAACUUUUUGUCUACAUCUCGGUGUCGCUUAGUGAAUGCCA
.(((...(-(((((((((((.........((((((.((((((....))))))))))))...........))))))))))))(((....((..((((....)))).))..)))....))). ( -37.45)
>DroSec_CAF1 1899 119 - 1
UGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCAAACUUUUUGUCUACAUCUCGGUGUCGCUUAGUGAAUGCCA
.(((...(-(((((((((((.........((((((.((((((....))))))))))))...........))))))))))))(((....((..((((....)))).))..)))....))). ( -37.45)
>DroAna_CAF1 13921 119 - 1
UGGCUCUUUUGGCUUUUGUUGCUGCUAAAAGCCAAACAAUAGCCGUCUAUUGUUUGCCGAACAAACUCAGACAAAGGCCAAACUU-UUGUCUCCAUCUCGCAGUCGCUUAGUGAAUUCCA
.(((......(((((((((....)).)))))))(((((((((....))))))))))))(((...(((.(((((((((.....)))-)))))).......((....))..)))...))).. ( -32.20)
>DroSim_CAF1 3548 119 - 1
UGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCAAACUUUUUGUCUACAUCUCGGUGUCGCUUAGUGAAUGCCA
.(((...(-(((((((((((.........((((((.((((((....))))))))))))...........))))))))))))(((....((..((((....)))).))..)))....))). ( -37.45)
>DroEre_CAF1 3426 119 - 1
UGGCUCUU-ACGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAACCAACGCAGACAAAGGCCAAACUUUUUGUCUACAACUCGGUGUCGCCUAGUGAAUUCCA
(((((.((-(.((..........))))).)))))..((..(((((((....(((((.....)))))(.(((((((((......))))))))).).....))))..)))...))....... ( -32.50)
>DroYak_CAF1 3359 119 - 1
UGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCAAACUUUUUGUCUACAUCUCGGUGUCGCUUAGUGAAUUCCA
.(((..((-(((((((((((.........((((((.((((((....))))))))))))...........)))))))))))))......)))........((..((((...))))...)). ( -35.35)
>consensus
UGGCUCUU_UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCAAACUUUUUGUCUACAUCUCGGUGUCGCUUAGUGAAUGCCA
.(((.....(((((((((((.........((((((.((((((....))))))))))))...........)))))))))))........)))........((((((((...))).))))). (-30.42 = -31.29 +   0.86)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,738,099 – 13,738,217
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.96
Mean single sequence MFE -36.28
Consensus MFE -33.10
Energy contribution -33.38
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -3.64
Structure conservation index 0.91
SVM decision value 4.49
SVM RNA-class probability 0.999908
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13738099 118 + 22407834
UGGCCUUUGUCUGGGUUGAUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAU
((((..((((((...((((....(((.......)))....((((((((((((((.((..........))..-))))))))))))))))))...))))))...))))-............. ( -35.30)
>DroSec_CAF1 1939 118 + 1
UGGCCUUUGUCUGAGUUGAUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAU
((((..((((((...((((....(((.......)))....((((((((((((((.((..........))..-))))))))))))))))))...))))))...))))-............. ( -35.30)
>DroAna_CAF1 13960 120 + 1
UGGCCUUUGUCUGAGUUUGUUCGGCAAACAAUAGACGGCUAUUGUUUGGCUUUUAGCAGCAACAAAAGCCAAAAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCAGAAGGAAAUUAAAU
...((((((((((((((.(((.((((((((((((....)))))))))(((((((.(......))))))))......))).)))))))))))).((........)).)))))......... ( -36.40)
>DroSim_CAF1 3588 118 + 1
UGGCCUUUGUCUGAGUUGAUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAU
((((..((((((...((((....(((.......)))....((((((((((((((.((..........))..-))))))))))))))))))...))))))...))))-............. ( -35.30)
>DroEre_CAF1 3466 118 + 1
UGGCCUUUGUCUGCGUUGGUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCGU-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAU
((((..((((((..((((((...(((.......))).)))(((((((((((((((((..........)).)-))))))))))))))...))).))))))...))))-............. ( -40.20)
>DroYak_CAF1 3399 118 + 1
UGGCCUUUGUCUGAGUUGAUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUGGGACAAUAAGCCA-ACGGAAAUUAAAU
((((..((((((.(.((((....(((.......)))....((((((((((((((.((..........))..-)))))))))))))))))).).))))))...))))-............. ( -35.20)
>consensus
UGGCCUUUGUCUGAGUUGAUUCAGCCAACAAUAGGCGGCCAUUGUUUGGCUUUUAGCAGCAACAAAAGCCA_AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA_ACGGAAAUUAAAU
((((..((((((...((((....(((.......)))....((((((((((((((....((.......))...))))))))))))))))))...))))))...)))).............. (-33.10 = -33.38 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,738,099 – 13,738,217
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.96
Mean single sequence MFE -38.04
Consensus MFE -33.42
Energy contribution -33.92
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -4.28
Structure conservation index 0.88
SVM decision value 4.07
SVM RNA-class probability 0.999785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13738099 118 - 22407834
AUUUAAUUUCCGU-UGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACCCAGACAAAGGCCA
.............-((((((.(((((........(((((((((((.((-((((..........)))))))))))))))))(((((.(....).)))))...........))))))))))) ( -38.60)
>DroSec_CAF1 1939 118 - 1
AUUUAAUUUCCGU-UGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCA
.............-((((((.(((((........(((((((((((.((-((((..........)))))))))))))))))(((((.(....).)))))...........))))))))))) ( -38.60)
>DroAna_CAF1 13960 120 - 1
AUUUAAUUUCCUUCUGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUUUUGGCUUUUGUUGCUGCUAAAAGCCAAACAAUAGCCGUCUAUUGUUUGCCGAACAAACUCAGACAAAGGCCA
...............(((((.(((((.........(((((((((......(((((((((....)).)))))))(((((((((....)))))))))))))))))).....)))))))))). ( -38.44)
>DroSim_CAF1 3588 118 - 1
AUUUAAUUUCCGU-UGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCA
.............-((((((.(((((........(((((((((((.((-((((..........)))))))))))))))))(((((.(....).)))))...........))))))))))) ( -38.60)
>DroEre_CAF1 3466 118 - 1
AUUUAAUUUCCGU-UGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUU-ACGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAACCAACGCAGACAAAGGCCA
.............-((((((.(((((........(((((((((((.((-(.((..........))))).)))))))))))(((((.(....).)))))...........))))))))))) ( -35.40)
>DroYak_CAF1 3399 118 - 1
AUUUAAUUUCCGU-UGGCUUAUUGUCCCAUCUAAAUUGUUUGGCUCUU-UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCA
.............-((((((.(((((........(((((((((((.((-((((..........)))))))))))))))))(((((.(....).)))))...........))))))))))) ( -38.60)
>consensus
AUUUAAUUUCCGU_UGGCUUAUUGUCCUAUCUAAAUUGUUUGGCUCUU_UGGCUUUUGUUGCUGCUAAAAGCCAAACAAUGGCCGCCUAUUGUUGGCUGAAUCAACUCAGACAAAGGCCA
...............(((((.(((((........(((((((((((.((..(((.......)))...)).)))))))))))(((((.(....).)))))...........)))))))))). (-33.42 = -33.92 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,738,139 – 13,738,257
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.42
Mean single sequence MFE -29.40
Consensus MFE -25.41
Energy contribution -25.44
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -2.84
Structure conservation index 0.86
SVM decision value 2.34
SVM RNA-class probability 0.992602
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13738139 118 + 22407834
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCCAUCAUCU
((((((((((((((.((..........))..-))))))))))))))...(((.((.(....(((((-(...........))))))((((((.......))).)))....))).))).... ( -28.90)
>DroSec_CAF1 1979 118 + 1
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCCAUCAUCA
((((((((((((((.((..........))..-))))))))))))))...(((.((.(....(((((-(...........))))))((((((.......))).)))....))).))).... ( -28.90)
>DroAna_CAF1 14000 108 + 1
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCAAAAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCAGAAGGAAAUUAAAUUGGCUGCUCCACUUUACAAACUACAC-----------UC-
((((((((((((((....((.......))...)))))))))))))).......(((.....((((((............))))))..)))................-----------..- ( -25.20)
>DroSim_CAF1 3628 118 + 1
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCCAUCAUCA
((((((((((((((.((..........))..-))))))))))))))...(((.((.(....(((((-(...........))))))((((((.......))).)))....))).))).... ( -28.90)
>DroEre_CAF1 3506 118 + 1
AUUGUUUGGCUUUUAGCAGCAACAAAAGCGU-AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA-ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCCAUCAUCU
(((((((((((((((((..........)).)-))))))))))))))...(((.((.(....(((((-(...........))))))((((((.......))).)))....))).))).... ( -31.40)
>DroYak_CAF1 3439 118 + 1
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCA-AAGAGCCAAACAAUUUAGAUGGGACAAUAAGCCA-ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCUAUCAUCU
((((((((((((((.((..........))..-))))))))))))))...((((((.(....(((((-(...........))))))((((((.......))).)))....))))))).... ( -33.10)
>consensus
AUUGUUUGGCUUUUAGCAGCAACAAAAGCCA_AAGAGCCAAACAAUUUAGAUAGGACAAUAAGCCA_ACGGAAAUUAAAUUGGCUGCUCUAGUUUACAUAGUAGUUCUCGCCCAUCAUCU
((((((((((((((....((.......))...)))))))))))))).(((((.(((.....(((((..............)))))..))).)))))........................ (-25.41 = -25.44 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:02 2006