Locus 335

Sequence ID 2L_DroMel_CAF1
Location 1,010,247 – 1,010,429
Length 182
Max. P 0.990986
window531 window532 window533 window534

overview

Window 1

Location 1,010,247 – 1,010,353
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 99.37
Mean single sequence MFE -20.23
Consensus MFE -19.69
Energy contribution -19.47
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.88
Structure conservation index 0.97
SVM decision value 0.67
SVM RNA-class probability 0.818651
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010247 106 + 22407834
GCUUGAUUUAUUUUCAGUAAUCAUUUAAGUUCCUUUUUGAUUUAUCAGUUUAGUACAUUUAGAUAUUAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACC
.............(((.((((.((((((((..((..((((....))))...))...)))))))))))).)))....((((((((........))))))))...... ( -20.30)
>DroSec_CAF1 121975 106 + 1
GCUUGAUUUAUUUUCAGUAAUCAUUUAAGUUCCCUUUUGAUUUAUCAGUUUAGUACAUUUAGAUAUUAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACC
.............(((.((((.((((((((...((.((((....))))...))...)))))))))))).)))....((((((((........))))))))...... ( -20.20)
>DroSim_CAF1 122539 106 + 1
GCUUGAUUUAUUUUCAGUAAUCAUUUAAGUUCCCUUUUGAUUUAUCAGUUUAGUACAUUUAGAUAUUAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACC
.............(((.((((.((((((((...((.((((....))))...))...)))))))))))).)))....((((((((........))))))))...... ( -20.20)
>consensus
GCUUGAUUUAUUUUCAGUAAUCAUUUAAGUUCCCUUUUGAUUUAUCAGUUUAGUACAUUUAGAUAUUAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACC
.............(((.((((.((((((((...((.((((....))))...))...)))))))))))).)))....((((((((........))))))))...... (-19.69 = -19.47 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,010,247 – 1,010,353
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 99.37
Mean single sequence MFE -16.79
Consensus MFE -15.43
Energy contribution -15.76
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.92
SVM decision value 0.02
SVM RNA-class probability 0.545887
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010247 106 - 22407834
GGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUAAUAUCUAAAUGUACUAAACUGAUAAAUCAAAAAGGAACUUAAAUGAUUACUGAAAAUAAAUCAAGC
(((.....((((((........)))))).....))).....((((...............))))...................(((((..(....)..)))))... ( -14.86)
>DroSec_CAF1 121975 106 - 1
GGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUAAUAUCUAAAUGUACUAAACUGAUAAAUCAAAAGGGAACUUAAAUGAUUACUGAAAAUAAAUCAAGC
(((.....((((((........)))))).....))).....((((...............))))(((((.(((....)))...))))).................. ( -17.76)
>DroSim_CAF1 122539 106 - 1
GGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUAAUAUCUAAAUGUACUAAACUGAUAAAUCAAAAGGGAACUUAAAUGAUUACUGAAAAUAAAUCAAGC
(((.....((((((........)))))).....))).....((((...............))))(((((.(((....)))...))))).................. ( -17.76)
>consensus
GGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUAAUAUCUAAAUGUACUAAACUGAUAAAUCAAAAGGGAACUUAAAUGAUUACUGAAAAUAAAUCAAGC
(((.....((((((........)))))).....))).....((((...............))))(((((.(((....)))...))))).................. (-15.43 = -15.76 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,010,313 – 1,010,429
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -18.30
Consensus MFE -16.42
Energy contribution -16.43
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.90
SVM decision value 0.83
SVM RNA-class probability 0.862207
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010313 116 + 22407834
UAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACCUUUUUUUUUGGAUUUUGGAUUUCUCAUCGGUUUUUUCGUCUUU----UUCAUCUUUGCUUAAUAACACAAAUCUUUGCCA
...((((...((((((((........))))))))...............((((((((((....))..(((.....))).....----..................)).))))))..)))) ( -18.70)
>DroSec_CAF1 122041 115 + 1
UAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACCUUUU-UUUUGGAUUUUGGAUUUCUCAUUGGUUUUUUCGUCUUU---UUUCAUCU-UGCUUAAUAACACAAAUCUUUGCCA
...((((...((((((((........))))))))..........-....((((...(((..((.....))..)))..))))..---........-.....................)))) ( -18.00)
>DroSim_CAF1 122605 113 + 1
UAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACCUUUU-UUUUGGAUUUUGGAUUU--CAUUGGUUUUUUCGUCUUU---UUUCAUCU-UGCUUAAUAACACAAAUCUUUGCCA
...((((...((((((((........))))))))....((....-....)).....((((((--.....(((.((..((....---........-.))..)).)))..))))))..)))) ( -18.02)
>DroYak_CAF1 129254 112 + 1
UAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACCUUUU-UUUUGG-------GUUUCUUAUUAGUUUUUUCAUUUUUGCUUUUCAUCUUUGCUUAAUAACACAAAUCUUUGCCA
...((((...((((((((........))))))))...((((...-....))-------))........................................................)))) ( -18.50)
>consensus
UAGUGGCCUCAGCCAGCAUAAUUUUUUGCUGGUUUUUACCUUUU_UUUUGGAUUUUGGAUUUCUCAUUGGUUUUUUCGUCUUU___UUUCAUCU_UGCUUAAUAACACAAAUCUUUGCCA
...((((...((((((((........))))))))....((.........)).................................................................)))) (-16.42 = -16.43 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,010,313 – 1,010,429
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.95
Mean single sequence MFE -18.32
Consensus MFE -17.40
Energy contribution -17.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.95
SVM decision value 2.24
SVM RNA-class probability 0.990986
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1010313 116 - 22407834
UGGCAAAGAUUUGUGUUAUUAAGCAAAGAUGAA----AAAGACGAAAAAACCGAUGAGAAAUCCAAAAUCCAAAAAAAAAGGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUA
((((...(((((.((((....))))........----..................((....))..)))))..................((((((........)))))).....))))... ( -18.00)
>DroSec_CAF1 122041 115 - 1
UGGCAAAGAUUUGUGUUAUUAAGCA-AGAUGAAA---AAAGACGAAAAAACCAAUGAGAAAUCCAAAAUCCAAAA-AAAAGGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUA
((((...(((((.((((....))))-........---..................((....))..))))).....-............((((((........)))))).....))))... ( -18.00)
>DroSim_CAF1 122605 113 - 1
UGGCAAAGAUUUGUGUUAUUAAGCA-AGAUGAAA---AAAGACGAAAAAACCAAUG--AAAUCCAAAAUCCAAAA-AAAAGGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUA
((((..((.(((((........)))-))......---...................--.................-............((((((........))))))))...))))... ( -17.30)
>DroYak_CAF1 129254 112 - 1
UGGCAAAGAUUUGUGUUAUUAAGCAAAGAUGAAAAGCAAAAAUGAAAAAACUAAUAAGAAAC-------CCAAAA-AAAAGGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUA
((((..((.(((((.(((((.......)))))...)))))....................((-------(.....-....))).....((((((........))))))))...))))... ( -20.00)
>consensus
UGGCAAAGAUUUGUGUUAUUAAGCA_AGAUGAAA___AAAGACGAAAAAACCAAUGAGAAAUCCAAAAUCCAAAA_AAAAGGUAAAAACCAGCAAAAAAUUAUGCUGGCUGAGGCCACUA
((((..((((((.((((....)))).))))..........................................................((((((........))))))))...))))... (-17.40 = -17.40 +   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 09:33:19 2006