Locus 2941

Sequence ID 3L_DroMel_CAF1
Location 8,398,207 – 8,398,457
Length 250
Max. P 0.963890
window4598 window4599 window4600 window4601 window4602

overview

Window 8

Location 8,398,207 – 8,398,297
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 85.34
Mean single sequence MFE -25.90
Consensus MFE -16.76
Energy contribution -18.64
Covariance contribution 1.88
Combinations/Pair 1.08
Mean z-score -2.59
Structure conservation index 0.65
SVM decision value 0.83
SVM RNA-class probability 0.861038
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8398207 90 - 23771897
CAUAUAAUUUCCGCCGUUUAUCGGCCGAUCCAGCAUGCCGGGCAUUAUUUAUAUAAUACUCGCACUGGUUUUGGUUGGCGAUCGGGAAAA
.......(((((((((.....))))(((((((((..((((((((((((....)))))....)).)))))....)))))..))))))))). ( -29.80)
>DroSec_CAF1 5500 90 - 1
CAUAUAAUUUCCGCCGUUUAUCGGCCGAUCCAUCAUGCCGGGCAUUAUUUAUAUAAUACUCGCACUGGUUUUGGUUGGCGAGCGGGUAAA
.............((((((..(((((((.(((...(((.(((.(((((....))))).)))))).)))..)))))))..))))))..... ( -28.10)
>DroSim_CAF1 5500 90 - 1
CAUAUAAUUUCCGCCGUUUAUCGGCCGAUCCAGCAUGCCGGGCAUUAUUUAUAUAAUACUCGCACUGGUUUUGGUUGGCGAGCGGGUAAA
.............((((((..(((((((.((((..(((.(((.(((((....))))).))))))))))..)))))))..))))))..... ( -31.00)
>DroEre_CAF1 3452 77 - 1
CAUAUAAUUUCCGCCGUUUAUCCAGCGAUCC------------AUUAUUUAUAUAAUACUCGCACUGGUU-UGCUUGGCGAGCGGGAAAA
.......(((((((((((...(((((((...------------(((((....)))))..))))..)))..-.....)))).))))))).. ( -20.70)
>DroYak_CAF1 3731 77 - 1
CAUAUAAUUUCCGCCGUUUAUCCAGCGAUCC------------AUUAUUUAUAUAAUACUCGCACUGGUU-UGCUAGUUGAGCGGGAAAG
.......(((((((((........((((...------------(((((....)))))..))))(((((..-..))))))).))))))).. ( -19.90)
>consensus
CAUAUAAUUUCCGCCGUUUAUCGGCCGAUCCA_CAUGCCGGGCAUUAUUUAUAUAAUACUCGCACUGGUUUUGGUUGGCGAGCGGGAAAA
.............((((((..((((((..(((......((((.(((((....))))).))))...)))...))))))..))))))..... (-16.76 = -18.64 +   1.88)

alignment

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secondary structure

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Window 9

Location 8,398,297 – 8,398,417
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -34.27
Consensus MFE -27.69
Energy contribution -28.13
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.62
Structure conservation index 0.81
SVM decision value 0.37
SVM RNA-class probability 0.709760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8398297 120 + 23771897
GCAAGGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAAAGUAUAUCCUCAAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUCCAACACAAGUCGCAUUUAAGGCGAUA
(((.((((...(....).))))))).(((((.((.(((.((((((((((((.((((....)))).....))))))))))))))).))...))))).......(((((.......))))). ( -36.30)
>DroSec_CAF1 5590 120 + 1
GCAAGGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACAUCCCCGAAAGGAAACAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCCCAUUUAAGGCGAUA
(((((..(((....)(((((((.....))...........((((((((((.....((....)).......))))))))))))))).))..))))).......(((((......)).))). ( -32.20)
>DroSim_CAF1 5590 120 + 1
GCAAGGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACUUCCCUGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUA
(((((..(((....)(((((((.....))...........((((((((((.(((.((....))...))).))))))))))))))).))..))))).......(((((.......))))). ( -34.30)
>consensus
GCAAGGGGAGAGUUCGCGCCUCUGCAGGAAAAAUACGUACAUACAGAGUACAUCCCCGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUA
(((((..(((....)(((((((.....))...........((((((((((..(((......)))......))))))))))))))).))..))))).......(((((.......))))). (-27.69 = -28.13 +   0.45)

alignment

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secondary structure

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Window 0

Location 8,398,297 – 8,398,417
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -37.40
Consensus MFE -30.54
Energy contribution -30.77
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -3.20
Structure conservation index 0.82
SVM decision value 0.82
SVM RNA-class probability 0.859145
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8398297 120 - 23771897
UAUCGCCUUAAAUGCGACUUGUGUUGGAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUUGAGGAUAUACUUUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCCUUGC
............((((.(((.(((.(((((..((((((.((((((((((((.(((((......))))).))))))))))))..))))))))))).))).))))))).............. ( -40.30)
>DroSec_CAF1 5590 120 - 1
UAUCGCCUUAAAUGGGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUGUUUCCUUUCGGGGAUGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCCUUGC
.............((((.((((((((((....((((((.((((((.(((((..((..((....))..))))))).))))))..)))))).....))))...))))))....))))..... ( -34.10)
>DroSim_CAF1 5590 120 - 1
UAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCAGGGAAGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCCUUGC
...((((((...((((((....))))))....((((((.((((((.(((((((((((......))))))))))).))))))..)))))).........))))))................ ( -37.80)
>consensus
UAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCGGGGAUGUACUCUGUAUGUACGUAUUUUUCCUGCAGAGGCGCGAACUCUCCCCUUGC
...((((((...((((((....))))))....((((((.((((((.(((((.....((((....)))).))))).))))))..)))))).........))))))................ (-30.54 = -30.77 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,398,337 – 8,398,457
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -30.07
Consensus MFE -25.66
Energy contribution -25.67
Covariance contribution 0.01
Combinations/Pair 1.08
Mean z-score -3.50
Structure conservation index 0.85
SVM decision value 1.56
SVM RNA-class probability 0.963890
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8398337 120 + 23771897
AUACAAAGUAUAUCCUCAAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUCCAACACAAGUCGCAUUUAAGGCGAUAGUUGAUCGAUCAUCUAAGACUUAAAAUUAAGUUGAUGUAU
(((((((((((.((((....)))).....)))))))))))...((((((((((.......(((((((.......))..(((.(((....))).))).)))))......)))))))))).. ( -30.22)
>DroSec_CAF1 5630 116 + 1
AUACAGAGUACAUCCCCGAAAGGAAACAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCCCAUUUAAGGCGAUAGUU----GAUCAUCAAAGACUUUAAAUUAAAUUGAUGUAU
((((((((((.....((....)).......))))))))))...(((((((((((......(((((((......)).(((....----.)))......))))).....))))))))))).. ( -28.50)
>DroSim_CAF1 5630 116 + 1
AUACAGAGUACUUCCCUGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUC----GAUCAUCUAAGACUUUAAAUUAAAUUGAUGUAU
((((((((((.(((.((....))...))).))))))))))...(((((((((((........(((((.......)))))((((----..........))))......))))))))))).. ( -31.50)
>consensus
AUACAGAGUACAUCCCCGAAAGGAAAGAAAUACUUUGUAUGGCGCAUCAAUUUGCAACACAAGUCGCAUUUAAGGCGAUAGUU____GAUCAUCUAAGACUUUAAAUUAAAUUGAUGUAU
((((((((((..(((......)))......))))))))))...(((((((((((......(((((((.......))(((.(((....))).)))...))))).....))))))))))).. (-25.66 = -25.67 +   0.01)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,398,337 – 8,398,457
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -29.70
Consensus MFE -20.99
Energy contribution -21.22
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 0.27
SVM RNA-class probability 0.663608
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8398337 120 - 23771897
AUACAUCAACUUAAUUUUAAGUCUUAGAUGAUCGAUCAACUAUCGCCUUAAAUGCGACUUGUGUUGGAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUUGAGGAUAUACUUUGUAU
...((((((.(((((..((((((.(((.(((....))).)))..((.......)))))))).)))))...))))))....(((((((((((.(((((......))))).))))))))))) ( -28.60)
>DroSec_CAF1 5630 116 - 1
AUACAUCAAUUUAAUUUAAAGUCUUUGAUGAUC----AACUAUCGCCUUAAAUGGGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUGUUUCCUUUCGGGGAUGUACUCUGUAU
...((((((((((((...(((((...((((...----...)))).((......)))))))..))))..))))))))....(((((.(((((..((..((....))..))))))).))))) ( -28.00)
>DroSim_CAF1 5630 116 - 1
AUACAUCAAUUUAAUUUAAAGUCUUAGAUGAUC----GACUAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCAGGGAAGUACUCUGUAU
...(((((((((.((((((.((..(((......----..)))..)).))))))(((((....))))))))))))))....(((((.(((((((((((......))))))))))).))))) ( -32.50)
>consensus
AUACAUCAAUUUAAUUUAAAGUCUUAGAUGAUC____AACUAUCGCCUUAAAUGCGACUUGUGUUGCAAAUUGAUGCGCCAUACAAAGUAUUUCUUUCCUUUCGGGGAUGUACUCUGUAU
...(((((((((......(((((...((((..........))))((.......))))))).......)))))))))....(((((.(((((.....((((....)))).))))).))))) (-20.99 = -21.22 +   0.23)

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 10:45:45 2006