Locus 7459

Sequence ID 2L_DroMel_CAF1
Location 20,699,358 – 20,699,523
Length 165
Max. P 0.973998
window11991 window11992 window11993

overview

Window 1

Location 20,699,358 – 20,699,469
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.01
Mean single sequence MFE -35.04
Consensus MFE -20.32
Energy contribution -21.27
Covariance contribution 0.95
Combinations/Pair 1.25
Mean z-score -2.88
Structure conservation index 0.58
SVM decision value 1.72
SVM RNA-class probability 0.973998
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20699358 111 + 22407834
CGCUAACCGCAGAGUGCUUAAAAGCUGAUUGCUG--GGAAACACUUAAUGGGCGCUAA---GUUAGCCGCAAAAUACAGUCGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUU
.((.....))..((((((((..(((.....))).--(....)......))))))))..---(((((((((.......(((((((.....))))))).....))))----)))))...... ( -37.10)
>DroSec_CAF1 22311 111 + 1
CACUAACCGCAGAGUGCUUAAAAGCUGAUUGCUG--CGAAACACUUAAUGGGCGCUAA---GUUAGCCGCAAAAUACAGUCGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUU
......(((..(((((.((...(((.....))).--..)).)))))..))).......---(((((((((.......(((((((.....))))))).....))))----)))))...... ( -34.60)
>DroSim_CAF1 13294 111 + 1
CGCUAACCGCAGAGUGCUUAAAAGCUGAUUGCUG--CGAAACACUUAAUGGGCGCUAA---GUUAGCCGCAAAAUACAGUCGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUU
.((...(((..(((((.((...(((.....))).--..)).)))))..)))..))...---(((((((((.......(((((((.....))))))).....))))----)))))...... ( -36.50)
>DroEre_CAF1 19403 113 + 1
UGCUAGCCACAGAGUGUUUA--AGCCAAGUGCUG--GGCAACACUUAAUGGCCGCCAA---GUUAGCCGCAAAGUACGAACGCUUGGGAAGCGGCUAACAAGUGGCUGGCUAACCGACUU
.(((((((((.(((((((..--.(((........--))))))))))............---(((((((((.((((......)))).....)))))))))..))))))))).......... ( -45.90)
>DroYak_CAF1 22611 111 + 1
UGCUAGCCACAGAGUGUUUAAAAGCCGAGUGCUU--GGAAACAAUUAAUGGGCGCUAA---GUUAGCUGCAAAACACAGACUCUUAAGAAGCGGCUAACAAGUGG----CUAACCAACUU
...(((((((..((((((((.((((.....))))--(....)......))))))))..---(((((((((....................)))))))))..))))----)))........ ( -35.75)
>DroAna_CAF1 24513 104 + 1
AACUAACCACACCGUAUUAAAUGGCCAACUACUAACGAAAACACUCAAUAACCGCUAACUAGCUGGCCG------------GCUUAAGAAGCGGCUAACAACUCG----GUAACCGAUUU
...........((((.((((.((((((.........((......)).......(((....)))))))))------------..))))...))))........(((----(...))))... ( -20.40)
>consensus
CGCUAACCACAGAGUGCUUAAAAGCCGAUUGCUG__GGAAACACUUAAUGGGCGCUAA___GUUAGCCGCAAAAUACAGUCGCUUAAGAAGCGGCUAACAAGUGG____CUAACCGACUU
......((((...(((((((..(((.....)))...(....)......)))))))......(((((((((....................)))))))))..))))............... (-20.32 = -21.27 +   0.95)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,699,358 – 20,699,469
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.01
Mean single sequence MFE -35.43
Consensus MFE -22.22
Energy contribution -21.92
Covariance contribution -0.30
Combinations/Pair 1.28
Mean z-score -2.33
Structure conservation index 0.63
SVM decision value 1.30
SVM RNA-class probability 0.938925
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20699358 111 - 22407834
AAGUCGGUUAG----CCACUUGUUAGCCGCUUCUUAAGCGACUGUAUUUUGCGGCUAAC---UUAGCGCCCAUUAAGUGUUUCC--CAGCAAUCAGCUUUUAAGCACUCUGCGGUUAGCG
......(((((----((....(((((((((....................)))))))))---.....((......(((((((..--.(((.....)))...)))))))..))))))))). ( -33.65)
>DroSec_CAF1 22311 111 - 1
AAGUCGGUUAG----CCACUUGUUAGCCGCUUCUUAAGCGACUGUAUUUUGCGGCUAAC---UUAGCGCCCAUUAAGUGUUUCG--CAGCAAUCAGCUUUUAAGCACUCUGCGGUUAGUG
.((((((((((----(.....)))))))(((.....)))))))..........((((((---..(((((.......))))).((--(((......(((....)))...))))))))))). ( -30.60)
>DroSim_CAF1 13294 111 - 1
AAGUCGGUUAG----CCACUUGUUAGCCGCUUCUUAAGCGACUGUAUUUUGCGGCUAAC---UUAGCGCCCAUUAAGUGUUUCG--CAGCAAUCAGCUUUUAAGCACUCUGCGGUUAGCG
((((.((....----))))))(((((((((..((((((.(.(((.(((((((((...((---((((......))))))...)))--))).))))))).))))))......))))))))). ( -34.40)
>DroEre_CAF1 19403 113 - 1
AAGUCGGUUAGCCAGCCACUUGUUAGCCGCUUCCCAAGCGUUCGUACUUUGCGGCUAAC---UUGGCGGCCAUUAAGUGUUGCC--CAGCACUUGGCU--UAAACACUCUGUGGCUAGCA
......((((((((((((...(((((((((.......((....)).....)))))))))---.))))(((((...((((((...--.)))))))))))--...........)))))))). ( -46.80)
>DroYak_CAF1 22611 111 - 1
AAGUUGGUUAG----CCACUUGUUAGCCGCUUCUUAAGAGUCUGUGUUUUGCAGCUAAC---UUAGCGCCCAUUAAUUGUUUCC--AAGCACUCGGCUUUUAAACACUCUGUGGCUAGCA
((((.((....----))))))(((((((((...(((((((((.((((((.((.((((..---.)))))).((.....)).....--))))))..))))))))).......))))))))). ( -32.80)
>DroAna_CAF1 24513 104 - 1
AAAUCGGUUAC----CGAGUUGUUAGCCGCUUCUUAAGC------------CGGCCAGCUAGUUAGCGGUUAUUGAGUGUUUUCGUUAGUAGUUGGCCAUUUAAUACGGUGUGGUUAGUU
...((((...)----)))....((((((((.(((((((.------------.(((((((((.(((((((..((.....))..)))))))))))))))).)))))...)).)))))))).. ( -34.30)
>consensus
AAGUCGGUUAG____CCACUUGUUAGCCGCUUCUUAAGCGACUGUAUUUUGCGGCUAAC___UUAGCGCCCAUUAAGUGUUUCC__CAGCAAUCAGCUUUUAAACACUCUGCGGUUAGCG
((((.((........))))))(((((((((.......................(((((....))))).........((((((.....(((.....)))...))))))...))))))))). (-22.22 = -21.92 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,699,433 – 20,699,523
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -30.19
Consensus MFE -17.38
Energy contribution -17.97
Covariance contribution 0.59
Combinations/Pair 1.09
Mean z-score -3.09
Structure conservation index 0.58
SVM decision value 0.20
SVM RNA-class probability 0.630762
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20699433 90 + 22407834
CGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUUU-GCCGCAGCGAAUGAAUUGGCAAAGCCUUUCAAGCCGUU------------------------UAGUAAGCCCAAUAA-
.(((((..((((((((.....((((----(...........-)))))......((((..(((...))).)))))))))))------------------------)..))))).......- ( -32.30)
>DroSec_CAF1 22386 90 + 1
CGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUUU-GCCGCAGCGAAUGAAUUGGCAAAGCCUUUCAAGCCGUU------------------------UAGUAAGCCCAAUAA-
.(((((..((((((((.....((((----(...........-)))))......((((..(((...))).)))))))))))------------------------)..))))).......- ( -32.30)
>DroSim_CAF1 13369 90 + 1
CGCUUAAGAAGCGGCUAACAAGUGG----CUAACCGACUUU-GCCGCAGCGAAUGAAUUGGCAAAGCCUUUCAAGCCGUU------------------------UAGUAAGCCCAAUAA-
.(((((..((((((((.....((((----(...........-)))))......((((..(((...))).)))))))))))------------------------)..))))).......- ( -32.30)
>DroEre_CAF1 19476 94 + 1
CGCUUGGGAAGCGGCUAACAAGUGGCUGGCUAACCGACUUU-GCCGCAGCAAAUGAAUUGGCAAAGCCUUUCAAGCCGUU------------------------UAGUAAGCUCAAUAA-
.(((((..((((((((.....((((((((....))).....-)))))......((((..(((...))).)))))))))))------------------------)..))))).......- ( -32.20)
>DroYak_CAF1 22686 90 + 1
CUCUUAAGAAGCGGCUAACAAGUGG----CUAACCAACUUU-GCCGCAGCAAAUGAAUUGGCAAAGCCUUUCAAGGCGUU------------------------UAGUAAGCUCAAUAA-
..((((..(((((.((.....((((----(...........-)))))......((((..(((...))).)))))).))))------------------------)..))))........- ( -23.70)
>DroAna_CAF1 24582 115 + 1
-GCUUAAGAAGCGGCUAACAACUCG----GUAACCGAUUUUGGCCACAACAAAUGAAUUGGCAAAGCCUUUCAAGCCGUUACCAAUUCCACACCAACGGCGAUUAAGAAGGCUCAAUAAA
-(((.....)))((((((....(((----(...))))..))))))...........((((....(((((((...((((((..............))))))......)))))))))))... ( -28.34)
>consensus
CGCUUAAGAAGCGGCUAACAAGUGG____CUAACCGACUUU_GCCGCAGCAAAUGAAUUGGCAAAGCCUUUCAAGCCGUU________________________UAGUAAGCCCAAUAA_
.(((((....(((((....((((((........)).))))..)))))......((((..(((...))).))))..................................)))))........ (-17.38 = -17.97 +   0.59)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:24 2006