Locus 7750

Sequence ID 3R_DroMel_CAF1
Location 20,788,724 – 20,789,032
Length 308
Max. P 0.988546
window12502 window12503 window12504 window12505 window12506 window12507

overview

Window 2

Location 20,788,724 – 20,788,844
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.06
Mean single sequence MFE -34.95
Consensus MFE -32.28
Energy contribution -32.15
Covariance contribution -0.13
Combinations/Pair 1.05
Mean z-score -1.41
Structure conservation index 0.92
SVM decision value 0.01
SVM RNA-class probability 0.538770
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788724 120 - 27905053
CGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAAAAUAUGUAUGUAUGUUUGGACGCUUCAUUCGGGUGUUGAAGAAGCUUUCACGCCGCCCAAAAAACAAAGACCCCAAAUCG
...((.(((((...(((....(((...(((((..(((..(((((((....)))))))....)))..)))))(((((.((((....))))))))))))......))).)))))))...... ( -32.00)
>DroSec_CAF1 4534 116 - 1
CGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAAAAUAUGU----AUGUUUGGCCGCUCCAUUCGGGCGAUGAAGAAGCUUUCACGCCGCCCAAAAAACAAAGACCCCAAAUCG
.(.((((((......(((((((.(((((..(((.(((((((......----...)))))))((((.....)))))))..)))))))))))))))))))...................... ( -35.10)
>DroSim_CAF1 4489 116 - 1
CGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAAAAUAUGU----AUGUUUGGCCGCUCCAUUCGGGCGGUGAAGAAGCUUUCACGCCGCCCAAAAAACAAAGACCCCAAAUCG
...((.(((((.((((.((..((((...((((...((........))----..))))))))..)))))).((((((((..((.....)).)))))))).........)))))))...... ( -37.60)
>DroEre_CAF1 1148 114 - 1
CGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAAAAUAUGU----AUGUUUGGCCGCUCCAUUCGGGCGAUGAAGAAGCUUUCACGCCGCCCAA--AACAAAGGCCCCAAAUCG
.(.((((((......(((((((.(((((..(((.(((((((......----...)))))))((((.....)))))))..)))))))))))))))))))..--.................. ( -35.10)
>consensus
CGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAAAAUAUGU____AUGUUUGGCCGCUCCAUUCGGGCGAUGAAGAAGCUUUCACGCCGCCCAAAAAACAAAGACCCCAAAUCG
...((.(((((...(((....(((...(((((.((((((((.(((......)))))))))))....)))))((((.(((((....))))))))))))......))).)))))))...... (-32.28 = -32.15 +  -0.13)

alignment

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secondary structure

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Window 3

Location 20,788,804 – 20,788,924
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -37.55
Consensus MFE -34.15
Energy contribution -34.65
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.91
SVM decision value 0.68
SVM RNA-class probability 0.819869
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788804 120 - 27905053
UAAGCCCAUAAGCCUUUUAGAUUUGCAAUUGUCCGCGAGCGUUUGAGCCCAAUUCUCCAGAGAUUCUGACAAAACAUCAGCGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAA
..((((((.((((((((((.(((((..((((((((((((...(((....)))..)))(((.....)))...........))).)))))).))))).)))))))))).)).....)))).. ( -36.70)
>DroSec_CAF1 4610 120 - 1
UAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGCGCUUGCGCCCAAUUCUCCAGAGAUUCUGACAAAACAUCAGCGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAA
..((((((.((((((((((((((((((((((..(((((....)))))..)))))...(((.....)))...........))))))).((....)).)))))))))).)).....)))).. ( -37.80)
>DroSim_CAF1 4565 120 - 1
UAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGCGCUUGCGCCCAAUUCUCCAGAGAUUCUGACAAAACAUCAGCGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAA
..((((((.((((((((((((((((((((((..(((((....)))))..)))))...(((.....)))...........))))))).((....)).)))))))))).)).....)))).. ( -37.80)
>DroEre_CAF1 1222 120 - 1
UAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGCGCUUGCGCCCAAUUCUCCAGAGAUUCUGACAAAACACUCGCGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAA
..((((((.((((((((((((((((((((((..(((((....)))))..)))))...(((.....)))...........))))))).((....)).)))))))))).)).....)))).. ( -37.90)
>consensus
UAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGCGCUUGCGCCCAAUUCUCCAGAGAUUCUGACAAAACAUCAGCGAGGCGGUCUAGAUGUGAAAGGCUUUUGAAUUUGGCUAA
..((((((.((((((((((((((((((((((..(((((....)))))..)))))...(((.....)))...........))))))).((....)).)))))))))).)).....)))).. (-34.15 = -34.65 +   0.50)

alignment

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secondary structure

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Window 4

Location 20,788,884 – 20,788,992
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.52
Mean single sequence MFE -43.23
Consensus MFE -38.77
Energy contribution -39.27
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.90
SVM decision value 2.12
SVM RNA-class probability 0.988546
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788884 108 + 27905053
GCUCGCGGACAAUUGCAAAUCUAAAAGGCUUAUGGGCUUAUGGACCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAG
....((((((....((...........))..((((((....((.(..(.((((((------------(((((((....))))).)))))))))..)))...)))))).).)))))..... ( -40.00)
>DroSec_CAF1 4690 108 + 1
GCUCGCGGACAAUUGCAAAGCUAAAAGGCUUAUGGGCUUAUGGAUCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAG
....(((((.....((.(((((....)))))((((((....((......((((((------------(((((((....))))).))))))))....))...)))))).)))))))..... ( -44.50)
>DroSim_CAF1 4645 108 + 1
GCUCGCGGACAAUUGCAAAGCUAAAAGGCUUAUGGGCUUAUGGAUCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAG
....(((((.....((.(((((....)))))((((((....((......((((((------------(((((((....))))).))))))))....))...)))))).)))))))..... ( -44.50)
>DroEre_CAF1 1302 120 + 1
GCUCGCGGACAAUUGCAAAGCUAAAAGGCUUAUGGGCUUACGGACCGAUGGUUCCAUAGCUCCAUGGCUCCAUAGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAG
....(((((.....((.(((((....)))))((((((....(((.(.((((..((((......))))..)))).).)))...((((((.......)))))))))))).)))))))..... ( -43.90)
>consensus
GCUCGCGGACAAUUGCAAAGCUAAAAGGCUUAUGGGCUUAUGGACCGAUGGUCGC____________UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAG
....(((((.....((.(((((....)))))((((((.((((((.(.((((..................)))).).))))))((((((.......)))))))))))).)))))))..... (-38.77 = -39.27 +   0.50)

alignment

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secondary structure

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Window 5

Location 20,788,884 – 20,788,992
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.52
Mean single sequence MFE -43.33
Consensus MFE -35.98
Energy contribution -36.05
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.58
Structure conservation index 0.83
SVM decision value 1.54
SVM RNA-class probability 0.962733
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788884 108 - 27905053
CUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGGUCCAUAAGCCCAUAAGCCUUUUAGAUUUGCAAUUGUCCGCGAGC
.....(((((.((((..(((((....((((((((((.(((((....)))))))------------)))......(((......))).....))))).....))))).))))))))).... ( -40.30)
>DroSec_CAF1 4690 108 - 1
CUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGAUCCAUAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGC
.....(((((.((((((((....))......(((((.(((((....)))))))------------))).))))))........((....((((......)))).)).....))))).... ( -42.00)
>DroSim_CAF1 4645 108 - 1
CUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGAUCCAUAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGC
.....(((((.((((((((....))......(((((.(((((....)))))))------------))).))))))........((....((((......)))).)).....))))).... ( -42.00)
>DroEre_CAF1 1302 120 - 1
CUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCUAUGGAGCCAUGGAGCUAUGGAACCAUCGGUCCGUAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGC
.....(((((.((((..((.(((((((((((.....(((((((..(....)..)))))))((((((((.((...))))))).)))......))))..))))))))).))))))))).... ( -49.00)
>consensus
CUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA____________GCGACCAUCGAUCCAUAAGCCCAUAAGCCUUUUAGCUUUGCAAUUGUCCGCGAGC
.....((((((((((((((((((((.......)))))).(((((.(.((((..................)))).).)))))..))))))((((......))))))).....))))).... (-35.98 = -36.05 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,788,924 – 20,789,032
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.50
Mean single sequence MFE -37.70
Consensus MFE -29.16
Energy contribution -28.85
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.740088
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788924 108 + 27905053
UGGACCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAGGUCGAAUUUCUUUUGUGUUGAACUCCCAUAGAGAAUGAUC
..((((...((((((------------(((((((....))))).))))))))(((((....((.....))...))))).))))....((((((.(((.........)))))))))..... ( -35.80)
>DroSec_CAF1 4730 108 + 1
UGGAUCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAGGUCGAAUUUCUUUUGUGUUGAACCUCCAUGGAGAAUGAUC
..(((((((((((((------------(((((((....))))).))))))))...((....))..))).(((((.((.(((((((....(....)..))).)))).)))))))...)))) ( -38.90)
>DroSim_CAF1 4685 108 + 1
UGGAUCGAUGGUCGC------------UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAGGUCGAAUUUCUUUUGUGUUGAACUUCCAUGGAGAAUGAUC
..(((((((((((((------------(((((((....))))).))))))))...((....))..))).(((((..((((.((((....(....)..)))).))))..)))))...)))) ( -39.00)
>DroEre_CAF1 1342 120 + 1
CGGACCGAUGGUUCCAUAGCUCCAUGGCUCCAUAGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAGGUCGAAUUUCUUUUGUGUUGAACUCCCAUGGAGAAUGAUC
.(((((...)))))(((..((((((((.....((((.(...(((((.((((((((((....((.....))...)))).))))))..)))))...).)))).....)))))))).)))... ( -37.10)
>consensus
UGGACCGAUGGUCGC____________UUCCAUGGCUCCAUGGAAAGCGGCCUUAGCUUUCGCCCAUCGCUCCGCUGAAGGUCGAAUUUCUUUUGUGUUGAACUCCCAUGGAGAAUGAUC
((((.((((((.(.................((((....))))((((((.......))))))).)))))).)))).....(((((...((((((.(((.........)))))))))))))) (-29.16 = -28.85 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,788,924 – 20,789,032
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.50
Mean single sequence MFE -41.66
Consensus MFE -34.22
Energy contribution -33.34
Covariance contribution -0.88
Combinations/Pair 1.13
Mean z-score -3.29
Structure conservation index 0.82
SVM decision value 1.94
SVM RNA-class probability 0.983451
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20788924 108 - 27905053
GAUCAUUCUCUAUGGGAGUUCAACACAAAAGAAAUUCGACCUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGGUCCA
((..(((((.....))))))).........(((........)))...(((.((((((((....))......(((((.(((((....)))))))------------))).)))))).))). ( -39.10)
>DroSec_CAF1 4730 108 - 1
GAUCAUUCUCCAUGGAGGUUCAACACAAAAGAAAUUCGACCUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGAUCCA
((((...((((.((((((((.................))))))))..)))).(((((((....))......(((((.(((((....)))))))------------))).))))))))).. ( -44.83)
>DroSim_CAF1 4685 108 - 1
GAUCAUUCUCCAUGGAAGUUCAACACAAAAGAAAUUCGACCUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA------------GCGACCAUCGAUCCA
((((...((((...((((.((................)).))))...)))).(((((((....))......(((((.(((((....)))))))------------))).))))))))).. ( -39.69)
>DroEre_CAF1 1342 120 - 1
GAUCAUUCUCCAUGGGAGUUCAACACAAAAGAAAUUCGACCUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCUAUGGAGCCAUGGAGCUAUGGAACCAUCGGUCCG
((..(((((.....))))))).........(((........)))..((((.((((((((....))..........((((((((..(((((....)))))..)))))))))))))).)))) ( -43.00)
>consensus
GAUCAUUCUCCAUGGAAGUUCAACACAAAAGAAAUUCGACCUUCAGCGGAGCGAUGGGCGAAAGCUAAGGCCGCUUUCCAUGGAGCCAUGGAA____________GCGACCAUCGAUCCA
((((...((((((((((.............(((........)))(((((..(....(((....)))..).)))))))))))))))..((((..................)))).)))).. (-34.22 = -33.34 +  -0.88)

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 12:53:52 2006