Locus 5724

Sequence ID X_DroMel_CAF1
Location 14,813,067 – 14,813,211
Length 144
Max. P 0.917157
window9287 window9288 window9289

overview

Window 7

Location 14,813,067 – 14,813,172
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.74
Mean single sequence MFE -36.50
Consensus MFE -23.33
Energy contribution -24.85
Covariance contribution 1.52
Combinations/Pair 1.07
Mean z-score -2.46
Structure conservation index 0.64
SVM decision value 0.54
SVM RNA-class probability 0.774985
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813067 105 + 22224390
------GUGUGCAACUAAAACUCGCUCUUGCACUUC-CAAACU----GGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGU--U-UGGACCGAGUUGAA-AGUUUACGCAAU
------(((((.((((..(((((((....))...((-(((((.----.(.(((((((.(((((.......)))))))))).)).)..))--)-))))..)))))...-)))))))))... ( -40.70)
>DroSec_CAF1 7015 106 + 1
------GUGUGGAACUAAAACUCGCUCUUGCACUUC-CAAACU----GGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGU--UUUGGACCGAGUUGAA-AGUUUACGCAAU
------(((((((.....(((((((....))...((-((((..----.(((((((((.....))))))))).(((((......).))))--))))))..)))))...-..)))))))... ( -37.20)
>DroSim_CAF1 6242 106 + 1
------GUGUGGAACUAAAACUCGCUCUUGCACUUC-CAAACU----GGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGU--UUUGGACCGAGUUGAA-AGUUUACGCAAU
------(((((((.....(((((((....))...((-((((..----.(((((((((.....))))))))).(((((......).))))--))))))..)))))...-..)))))))... ( -37.20)
>DroEre_CAF1 12259 111 + 1
GUUUGUGUGUGGAACUAAAACUCGCUCUUGCACUUC-CAAACU----GGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGCU--U-UGGUCCGAGUUGAA-AGUUUACGCAAU
.....((((((((.....((((((..((.(((.(..-((((.(----((((((((((.....))))))))...))).))))..).))).--.-.))..))))))...-..)))))))).. ( -36.10)
>DroAna_CAF1 35150 113 + 1
------GAGU-AAACUAAAACUCGCUGAUGCACUAGACAAGCGGGAGGGGGUAAAGGUGGUUGAUUUUCCCGGCGACUCUGUUGUUGGGCCUAUGGAUCCAGAUGAAUAGUUUAAGCAAU
------(..(-((((((..((((.((..(((.........)))..)).)))).....(((((.((...(((((((((...)))))))))...)).)).)))......)))))))..)... ( -31.30)
>consensus
______GUGUGGAACUAAAACUCGCUCUUGCACUUC_CAAACU____GGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGU__U_UGGACCGAGUUGAA_AGUUUACGCAAU
......((((.(((((..(((((((....)).................(((((((((.....)))))))))(((((.................))).)))))))....)))))))))... (-23.33 = -24.85 +   1.52)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,813,100 – 14,813,211
Length 111
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 97.01
Mean single sequence MFE -27.97
Consensus MFE -25.90
Energy contribution -26.40
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.93
SVM decision value 0.81
SVM RNA-class probability 0.857076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813100 111 + 22224390
ACUGGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGUU-UGGACCGAGUUGAAAGUUUACGCAAUCAACUUUUUCGCCAUUCUCUUUUUUUUUUUAUUUAUCAG
..(((((((((((((..(((.....(((((.((...)).)))))((-(.(((...))).)))......)))..)))))))))).)))......................... ( -28.10)
>DroSec_CAF1 7048 111 + 1
ACUGGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGUUUUGGACCGAGUUGAAAGUUUACGCAAUCAACUUUUUCGCCAUUCUCUUUUU-UUUUUAUUUAUCAG
..(((((((((((((..(((.....(((((.((...)).)))))((((.(((...))).)))).....)))..)))))))))).)))..........-.............. ( -28.50)
>DroSim_CAF1 6275 112 + 1
ACUGGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGUUUUGGACCGAGUUGAAAGUUUACGCAAUCAACUUUUUCGCCAUUCUCUUUUUUUUUUUAUUUAUCAG
..(((((((((((((..(((.....(((((.((...)).)))))((((.(((...))).)))).....)))..)))))))))).)))......................... ( -28.50)
>DroEre_CAF1 12298 110 + 1
ACUGGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGCUU-UGGUCCGAGUUGAAAGUUUACGCAAUCAACUUUUUCGCCAUUCCCUUCUU-UUUUUAUUUAUCAG
..(((((((((((((..((((((..(((((((....((....))..-))).))).)..))).(....))))..)))))))))).)))..........-.............. ( -26.80)
>consensus
ACUGGGGAAAAGUUGGCUGCUUUUCCCGGCCACUUUGUUGCUGGUU_UGGACCGAGUUGAAAGUUUACGCAAUCAACUUUUUCGCCAUUCUCUUUUU_UUUUUAUUUAUCAG
.((((((((((((.....)))))))))(((............(((.....)))(((((((..((....))..)))))))....))).......................))) (-25.90 = -26.40 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,813,100 – 14,813,211
Length 111
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 97.01
Mean single sequence MFE -24.52
Consensus MFE -23.81
Energy contribution -23.81
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.97
SVM decision value 1.11
SVM RNA-class probability 0.917157
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14813100 111 - 22224390
CUGAUAAAUAAAAAAAAAAAGAGAAUGGCGAAAAAGUUGAUUGCGUAAACUUUCAACUCGGUCCA-AACCAGCAACAAAGUGGCCGGGAAAAGCAGCCAACUUUUCCCCAGU
(((.......................(((.....((((((..(......)..)))))).(((...-.)))............)))((((((((.......))))))))))). ( -24.50)
>DroSec_CAF1 7048 111 - 1
CUGAUAAAUAAAAA-AAAAAGAGAAUGGCGAAAAAGUUGAUUGCGUAAACUUUCAACUCGGUCCAAAACCAGCAACAAAGUGGCCGGGAAAAGCAGCCAACUUUUCCCCAGU
(((...........-...........(((.....((((((..(......)..)))))).(((.....)))............)))((((((((.......))))))))))). ( -24.50)
>DroSim_CAF1 6275 112 - 1
CUGAUAAAUAAAAAAAAAAAGAGAAUGGCGAAAAAGUUGAUUGCGUAAACUUUCAACUCGGUCCAAAACCAGCAACAAAGUGGCCGGGAAAAGCAGCCAACUUUUCCCCAGU
(((.......................(((.....((((((..(......)..)))))).(((.....)))............)))((((((((.......))))))))))). ( -24.50)
>DroEre_CAF1 12298 110 - 1
CUGAUAAAUAAAAA-AAGAAGGGAAUGGCGAAAAAGUUGAUUGCGUAAACUUUCAACUCGGACCA-AAGCAGCAACAAAGUGGCCGGGAAAAGCAGCCAACUUUUCCCCAGU
(((...........-...........(((.(....((((.((((.......(((.....)))...-..))))))))....).)))((((((((.......))))))))))). ( -24.60)
>consensus
CUGAUAAAUAAAAA_AAAAAGAGAAUGGCGAAAAAGUUGAUUGCGUAAACUUUCAACUCGGUCCA_AACCAGCAACAAAGUGGCCGGGAAAAGCAGCCAACUUUUCCCCAGU
.........................(((.(.((((((((..((((........)..(((((.(((...............))))))))....)))..)))))))).)))).. (-23.81 = -23.81 +   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 11:54:52 2006