Locus 4652

Sequence ID 2L_DroMel_CAF1
Location 13,331,519 – 13,331,663
Length 144
Max. P 0.922029
window7350 window7351 window7352

overview

Window 0

Location 13,331,519 – 13,331,636
Length 117
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.06
Mean single sequence MFE -34.06
Consensus MFE -24.90
Energy contribution -25.10
Covariance contribution 0.20
Combinations/Pair 1.30
Mean z-score -2.16
Structure conservation index 0.73
SVM decision value 1.15
SVM RNA-class probability 0.922029
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13331519 117 + 22407834
ACAAAUGAUGGAUGAAUCAUUUGUCGGUGG--CGGGUAUUUUGCGCGAAUUGCCGAAAAUCGAUUCAGGGCGGCAUACCGAAAAGGAUGGAGACCUCAAUUGAUUUUGAGGUGUUUUGA
.((((((((......))))))))(((((((--((.(.....).)))....(((((....((......)).))))))))))).......(((.(((((((......))))))).)))... ( -38.20)
>DroPse_CAF1 57903 96 + 1
AUAAAUGAUGGAUGAAUCAUUAGUCAGAAAUGAAGGCCUGCCGUGCCAAAUGCUGCAAAUCGAUUAAAG-UUCCAUACAAAACGUGGUGAUGGCUUU----------------------
...((((((......))))))..(((....)))((((((((.((.......)).)))...........(-((((((.......)))).)))))))).---------------------- ( -17.40)
>DroSec_CAF1 44113 117 + 1
ACAAAUGAUGGAUGAAUCAUUUGUCGGUGG--CGGGUAUUUCGCGCGAAUUGCCGAAAAUCGAUUCGGGGCGGCAUUCCGAAAAGGAUGGAGACCUCAAUUGAUUUUGAGGUGUUUUGA
.((((((((......))))))))((((..(--((.(.....).)))....(((((....(((...)))..)))))..)))).......(((.(((((((......))))))).)))... ( -36.40)
>DroSim_CAF1 43418 117 + 1
ACAAAUGAUGGAUGAAUCAUUUGUCGGUGG--CGGGUAUUUCGCGCGAAUUGCCGAAAAUCGAUUCAGGGCGGCAUACCGAAAAGGAUGGAGACCUCAAUUGAUUUUGAGGUGUUUUGA
.((((((((......))))))))(((((((--((.(.....).)))....(((((....((......)).))))))))))).......(((.(((((((......))))))).)))... ( -39.30)
>DroEre_CAF1 45003 117 + 1
ACAAAUGAUGGAUGAAUCAUUUGUCGGUGG--CGGGUAUUUCGCGCGAAUUGCCGAAAAUCGAUUCAGGGCGGCAUACUGAAAUGGAUAGAGACCUCAAUUGAUUUUGAGGUGUUUCAA
.((((((((......))))))))(((((((--((.(.....).)))....(((((....((......)).))))))))))).......(((.(((((((......))))))).)))... ( -37.20)
>DroYak_CAF1 44045 117 + 1
ACAAGUGAUGGAUGAAUCAUUUGUCGGUGG--CGGGUAUUUUGUGCGAAUUGCCGAAAAUCGAUUCAGGGCGGCAUACUGAAAGGGAUAGAGACCUCAAUUGAUUUUGAGGUGAUUCAA
(((((((((......))))))))).....(--((.(.....).)))((((..((.((((((((((.(((........((....))........))).))))))))))..))..)))).. ( -35.89)
>consensus
ACAAAUGAUGGAUGAAUCAUUUGUCGGUGG__CGGGUAUUUCGCGCGAAUUGCCGAAAAUCGAUUCAGGGCGGCAUACCGAAAAGGAUGGAGACCUCAAUUGAUUUUGAGGUGUUUUGA
.((((((((......))))))))((((..(..((.((.....)).))..)..))))...((.((((....(((....)))....)))).)).(((((((......)))))))....... (-24.90 = -25.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,331,519 – 13,331,636
Length 117
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.06
Mean single sequence MFE -23.70
Consensus MFE -13.79
Energy contribution -15.43
Covariance contribution 1.64
Combinations/Pair 1.04
Mean z-score -1.99
Structure conservation index 0.58
SVM decision value 0.44
SVM RNA-class probability 0.735731
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13331519 117 - 22407834
UCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCAAAAUACCCG--CCACCGACAAAUGAUUCAUCCAUCAUUUGU
.......(((((((......)))))))...........(((((.(((((....(((.....))))))))....(((.........))--).)))))((((((((......)))))))). ( -27.20)
>DroPse_CAF1 57903 96 - 1
----------------------AAAGCCAUCACCACGUUUUGUAUGGAA-CUUUAAUCGAUUUGCAGCAUUUGGCACGGCAGGCCUUCAUUUCUGACUAAUGAUUCAUCCAUCAUUUAU
----------------------...(((....(((.((.((((((.((.-......)).))..)))).)).)))...))).((...(((((.......))))).....))......... ( -12.90)
>DroSec_CAF1 44113 117 - 1
UCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGAAUGCCGCCCCGAAUCGAUUUUCGGCAAUUCGCGCGAAAUACCCG--CCACCGACAAAUGAUUCAUCCAUCAUUUGU
.......(((((((......)))))))...........((((...((....(((((......)))))......))(((.......))--)..))))((((((((......)))))))). ( -28.30)
>DroSim_CAF1 43418 117 - 1
UCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAAAUACCCG--CCACCGACAAAUGAUUCAUCCAUCAUUUGU
.......(((((((......)))))))...........(((((.(((((....(((.....))))))))....(.(((.......))--)))))))((((((((......)))))))). ( -28.90)
>DroEre_CAF1 45003 117 - 1
UUGAAACACCUCAAAAUCAAUUGAGGUCUCUAUCCAUUUCAGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAAAUACCCG--CCACCGACAAAUGAUUCAUCCAUCAUUUGU
((((...(((((((......)))))))..........(((((.........))))))))).(((((((.....)).)))))......--......(((((((((......))))))))) ( -24.50)
>DroYak_CAF1 44045 117 - 1
UUGAAUCACCUCAAAAUCAAUUGAGGUCUCUAUCCCUUUCAGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCACAAAAUACCCG--CCACCGACAAAUGAUUCAUCCAUCACUUGU
.(((((((.(((((......)))))(((...(((...(((((.........)))))..)))....(((..................)--))...)))...)))))))............ ( -20.37)
>consensus
UCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAAAUACCCG__CCACCGACAAAUGAUUCAUCCAUCAUUUGU
.......(((((((......))))))).................(((((....(((.....))))))))..........................(((((((((......))))))))) (-13.79 = -15.43 +   1.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,331,556 – 13,331,663
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 89.16
Mean single sequence MFE -23.00
Consensus MFE -17.52
Energy contribution -17.36
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.76
SVM decision value -0.03
SVM RNA-class probability 0.520732
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13331556 107 - 22407834
GAAUUGGAUUACAAAAUCUCUUGUUCUUCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCAAA
((((((((..((((......))))...))......((..((((((.(((.(((.(..(((((.....)).)))..).))).))).)))))).))))))))....... ( -21.80)
>DroSec_CAF1 44150 107 - 1
GAAUUGGAUUACAAAAUCUCCCGUUCUUCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGAAUGCCGCCCCGAAUCGAUUUUCGGCAAUUCGCGCGAA
((((((((((....))))..(((....((.....(((((((......)))))))..........(((((.........)))))..))....)))))))))....... ( -23.30)
>DroSim_CAF1 43455 107 - 1
GAAUUGGAUUAUAAAAUCUCCCGUUCUUCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAA
((((((((((....))))..(((....((.....(((((((......)))))))............(((....))).........))....)))))))))....... ( -21.70)
>DroEre_CAF1 45040 105 - 1
GAAUUGA-UUAUUGAAACUGUCGAU-UUUGAAACACCUCAAAAUCAAUUGAGGUCUCUAUCCAUUUCAGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAA
((((((.-.((((((((.((..(((-...((...(((((((......))))))).)).))))))))))))).......(((((......)))))))))))....... ( -23.20)
>DroYak_CAF1 44082 107 - 1
GAAUUGAAUUAUUUAAUCUGUGGUUUUUUGAAUCACCUCAAAAUCAAUUGAGGUCUCUAUCCCUUUCAGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCACAAA
((((((.............(((((...(((((..(((((((......)))))))..........)))))...))))).(((((......)))))))))))....... ( -25.00)
>consensus
GAAUUGGAUUAUAAAAUCUCUCGUUCUUCAAAACACCUCAAAAUCAAUUGAGGUCUCCAUCCUUUUCGGUAUGCCGCCCUGAAUCGAUUUUCGGCAAUUCGCGCGAA
((((((............................(((((((......)))))))........................(((((......)))))))))))....... (-17.52 = -17.36 +  -0.16)

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 11:23:41 2006