Locus 1227

Sequence ID 2L_DroMel_CAF1
Location 3,265,744 – 3,265,887
Length 143
Max. P 0.999417
window2013 window2014 window2015

overview

Window 3

Location 3,265,744 – 3,265,847
Length 103
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 77.32
Mean single sequence MFE -33.00
Consensus MFE -24.30
Energy contribution -27.26
Covariance contribution 2.96
Combinations/Pair 1.04
Mean z-score -3.27
Structure conservation index 0.74
SVM decision value 3.58
SVM RNA-class probability 0.999417
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3265744 103 + 22407834
--AAUGU-AUCGCU-AAGGGAAAUUUUUCCGGGGAAAAGGUCGAAAGACCUCUCCCAACCGUGCAACACGUUCGCUGCAACAUGUUGCAUGGGGACACAUCCUUUUA
--.....-......-((((((......(((.((((..(((((....))))).))))..((((((((((.(((......))).)))))))))))))....)))))).. ( -40.90)
>DroSec_CAF1 92406 106 + 1
AUAAUGUAAUCGCU-AAGGGAAAUUUUUCCGGGGAAAAGGUCGAAAGACCUCUCCCAACCGUGCAACACGUUCGCUGCAACAUGUUGCAUGGGGACACAUCGUUUUA
...((((.......-...((((....)))).((((..(((((....))))).))))..((((((((((.(((......))).))))))))))....))))....... ( -37.70)
>DroSim_CAF1 95487 106 + 1
AUAAUGUAAUCGCU-AAGGGAAAUUUUUCCGGGGAAAAGGUCGAAAGACCUCUCCCAACCGUGCAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
....((((......-...((((....)))).((((..(((((....))))).)))).....)))).......................................... ( -21.60)
>DroEre_CAF1 89123 102 + 1
---AUGU-UUCGCA-AGGGGAAAUUUUUCCGAGGAAAAGGUUGAAAGACCUAUGCCAACCGUGCAACACGUUCGCUGCAACAUGUUGCAUGGGGACACAACCUUUUA
---...(-..(...-.)..).......(((..((...(((((....)))))...))..((((((((((.(((......))).)))))))))))))............ ( -33.70)
>DroYak_CAF1 88791 103 + 1
---AUGU-UUCGCAGAAGGGAAAUUUUUCCGAGGAAAAGAUUGAAAGACCUCUCCCAACCGUGCAACACGUUCGCUGCAACAUGUUGCAUGGGGACACAGUCUUUUA
---..((-(((.(....).)))))(((((....)))))...((((((((...((((...(((((((((.(((......))).)))))))))))))....)))))))) ( -31.10)
>consensus
__AAUGU_AUCGCU_AAGGGAAAUUUUUCCGGGGAAAAGGUCGAAAGACCUCUCCCAACCGUGCAACACGUUCGCUGCAACAUGUUGCAUGGGGACACAUCCUUUUA
.................((((...(((((....)))))((((....))))..))))..((((((((((.(((......))).))))))))))............... (-24.30 = -27.26 +   2.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,265,744 – 3,265,847
Length 103
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 77.32
Mean single sequence MFE -32.82
Consensus MFE -23.85
Energy contribution -26.34
Covariance contribution 2.49
Combinations/Pair 1.04
Mean z-score -3.06
Structure conservation index 0.73
SVM decision value 3.38
SVM RNA-class probability 0.999109
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3265744 103 - 22407834
UAAAAGGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCGACCUUUUCCCCGGAAAAAUUUCCCUU-AGCGAU-ACAUU--
......((((((((.((.(((((((((((......))))))))))).))..((((((((((....))))))))))..((((....))))...-...)))-)))))-- ( -41.60)
>DroSec_CAF1 92406 106 - 1
UAAAACGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCGACCUUUUCCCCGGAAAAAUUUCCCUU-AGCGAUUACAUUAU
......((((((((.((.(((((((((((......))))))))))).))..((((((((((....))))))))))..((((....))))...-...)).)))))).. ( -38.40)
>DroSim_CAF1 95487 106 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUUGCACGGUUGGGAGAGGUCUUUCGACCUUUUCCCCGGAAAAAUUUCCCUU-AGCGAUUACAUUAU
........................................(((((..((..((((((((((....))))))))))))((((....))))...-.)))))........ ( -23.10)
>DroEre_CAF1 89123 102 - 1
UAAAAGGUUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGCAUAGGUCUUUCAACCUUUUCCUCGGAAAAAUUUCCCCU-UGCGAA-ACAU---
.(((((((((((((.((.(((((((((((......))))))))))).))..)))).........)))))))))....((((....))))...-......-....--- ( -30.30)
>DroYak_CAF1 88791 103 - 1
UAAAAGACUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCAAUCUUUUCCUCGGAAAAAUUUCCCUUCUGCGAA-ACAU---
..(((((((...(((((.(((((((((((......))))))))))).))..)))...))))))).....(((((....))))).((((.(....).)))-)...--- ( -30.70)
>consensus
UAAAAGGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCGACCUUUUCCCCGGAAAAAUUUCCCUU_AGCGAU_ACAUU__
...............((.(((((((((((......))))))))))).))..((((((((((....))))))))))..((((....)))).................. (-23.85 = -26.34 +   2.49)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,265,780 – 3,265,887
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 93.93
Mean single sequence MFE -31.81
Consensus MFE -25.73
Energy contribution -25.72
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.81
SVM decision value 0.07
SVM RNA-class probability 0.566316
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3265780 107 - 22407834
CCGUGGAUCUGUGACAAGUUCCACACAAUGCGUAAACAAAUAAAAGGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCGA
..(((((.((......)).)))))...................((((((.(.(((((.(((((((((((......))))))))))).)...)))).).))))))... ( -35.90)
>DroSec_CAF1 92445 103 - 1
---UGGAUCUGUGACAAG-UCCACACAAUGCGUAAACAAAUAAAACGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCGA
---.((((((.(..(((.-...(((((...(((...........))).)))))..((.(((((((((((......))))))))))).)))))..).))))))..... ( -30.90)
>DroEre_CAF1 89158 107 - 1
CAGUGAAUCUGUGACAAGUUCCACACAAUGCGUAAACAAAUAAAAGGUUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGCAUAGGUCUUUCAA
...((((((((((.(((.....(((((((.................)))))))..((.(((((((((((......))))))))))).))))).)))))))...))). ( -29.93)
>DroYak_CAF1 88827 107 - 1
CAGUGAAUCUGUGACAAGUUCCACACAAUGCGUAAACAAAUAAAAGACUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCAA
..(((...((......))...)))..................(((((((...(((((.(((((((((((......))))))))))).))..)))...)))))))... ( -30.50)
>consensus
CAGUGAAUCUGUGACAAGUUCCACACAAUGCGUAAACAAAUAAAAGGAUGUGUCCCCAUGCAACAUGUUGCAGCGAACGUGUUGCACGGUUGGGAGAGGUCUUUCAA
...((((.....(((...(((((((((.....................)))))..((.(((((((((((......))))))))))).))..))))...))).)))). (-25.73 = -25.72 +  -0.00)

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 09:57:14 2006