Locus 4253

Sequence ID 3R_DroMel_CAF1
Location 11,388,051 – 11,388,243
Length 192
Max. P 0.999046
window6903 window6904 window6905 window6906

overview

Window 3

Location 11,388,051 – 11,388,171
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -26.05
Consensus MFE -23.08
Energy contribution -23.48
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.89
SVM decision value 0.64
SVM RNA-class probability 0.807070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11388051 120 + 27905053
GUUCCACAAACUCUCAACUUUCUUCAUCAGAUAUUUGCCACCUAAUUGUUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGC
...((.((((.((..........((((..(((((((......(((((((....)))))))........)))))))..))))(((((((((....))))))))).)).))))..))..... ( -24.54)
>DroSec_CAF1 135826 120 + 1
GUUCCAGAAACUUUCAACUUUCUUCAUCAGCGAUGUGCCACCUAAUUGUUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGC
....(((.................((((...)))).(((.((.(((((.(((((((.((((....))))..)))))))...(((((((((....))))))))))))))..)).)))))). ( -26.60)
>DroSim_CAF1 126925 120 + 1
GUUCCAGAAACUUUCAACUUUCUUCAUCAGCGAUUUGCCACCUAAUUGCUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGC
(((((((((..............((((.(((((((........)))))))((((((.((((....))))..))))))))))(((((((((....)))))))))...)))))).))).... ( -25.80)
>DroEre_CAF1 124310 119 + 1
GCUCCAGAAACUCUCAACUUUCUUCAUCAGCGAUUUGCCACCUAAUUGUUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGA-ACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCCGC
.....(((((........)))))......(((..((((((...(((((.(((((((.((((....))))..)))))))...(((-(((((....)))))))).))))).))))))..))) ( -23.90)
>DroYak_CAF1 126560 120 + 1
GUGCCAGAGACUCUCAACUUUCUUCAUCAGCGAUUUGCCACCUAAUUGUUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGAAACAAGUUCUUUUGUUUCCCGACUUUGGCGGCCUGC
.((((((((..............((((.(((((((........)))))))((((((.((((....))))..))))))))))(((((((((....)))))))))...))))))))...... ( -29.40)
>consensus
GUUCCAGAAACUCUCAACUUUCUUCAUCAGCGAUUUGCCACCUAAUUGUUUGGACAAUUAAAUCAUUAAAAUGUUCAAUGAGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGC
....................................(((.((.(((((.(((((((.((((....))))..)))))))...(((((((((....))))))))))))))..)).))).... (-23.08 = -23.48 +   0.40)

alignment

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secondary structure

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Window 4

Location 11,388,051 – 11,388,171
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -31.28
Consensus MFE -29.16
Energy contribution -29.24
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.13
Structure conservation index 0.93
SVM decision value 3.34
SVM RNA-class probability 0.999046
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11388051 120 - 27905053
GCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGGUGGCAAAUAUCUGAUGAAGAAAGUUGAGAGUUUGUGGAAC
((((((((((.......((((((((......))))))))(((((((.....)))))))..(((((((....))))))))))))).....(((.....)))...........))))..... ( -31.00)
>DroSec_CAF1 135826 120 - 1
GCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGGUGGCACAUCGCUGAUGAAGAAAGUUGAAAGUUUCUGGAAC
.(((((((((.......((((((((......))))))))(((((((.....)))))))..(((((((....))))))))))))).((((...)))).................))).... ( -32.80)
>DroSim_CAF1 126925 120 - 1
GCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAGCAAUUAGGUGGCAAAUCGCUGAUGAAGAAAGUUGAAAGUUUCUGGAAC
.(((((((((.......((((((((......))))))))(((((((.....)))))))..(((((((....)))))))))))))...(((((.........)).)))......))).... ( -31.80)
>DroEre_CAF1 124310 119 - 1
GCGGGCCGCCAAAAUCGGGAAACAAAAGAACUUGU-UCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGGUGGCAAAUCGCUGAUGAAGAAAGUUGAGAGUUUCUGGAGC
((((((((((.......((((.(((......))))-)))(((((((.....)))))))..(((((((....)))))))))))))...))))......(((((.(....).)))))..... ( -29.30)
>DroYak_CAF1 126560 120 - 1
GCAGGCCGCCAAAGUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGGUGGCAAAUCGCUGAUGAAGAAAGUUGAGAGUCUCUGGCAC
.(((((((((.......((((((((......))))))))(((((((.....)))))))..(((((((....)))))))))))))...(((((.........)).)))......))).... ( -31.50)
>consensus
GCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGGUGGCAAAUCGCUGAUGAAGAAAGUUGAGAGUUUCUGGAAC
.(((((((((.......((((((((......))))))))(((((((.....)))))))..(((((((....)))))))))))))......((.....))..............))).... (-29.16 = -29.24 +   0.08)

alignment

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secondary structure

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Window 5

Location 11,388,091 – 11,388,210
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -26.71
Consensus MFE -23.14
Energy contribution -23.22
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.33
Structure conservation index 0.87
SVM decision value 0.36
SVM RNA-class probability 0.702668
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11388091 119 - 27905053
-CCCAGCCCAAAGUCGCCAGCCAAAUAAUUGAUGAAAGUGGCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGG
-...........((.(((.((((.....((.....)).)))).))).))........((((((((......))))))))(((((((.....))))))).((((((((....)))))))). ( -27.20)
>DroSec_CAF1 135866 119 - 1
-CCCAGCCCAAAGUCGCCGGCUAAAUAAUUGAUGAAAGUGGCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGG
-...((((..........)))).......((((....((((....))))....))))((((((((......))))))))(((((((.....))))))).((((((((....)))))))). ( -28.10)
>DroSim_CAF1 126965 119 - 1
-CCCAGCCCAAAGUCGCCGGCUAAAUAAUUGAUGAAAGUGGCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAGCAAUUAGG
-...((((..........)))).......((((....((((....))))....))))((((((((......))))))))(((((((.....))))))).((((((((....)))))))). ( -28.40)
>DroEre_CAF1 124350 117 - 1
-UCUAGCCCAAAGUCCGCAGC-AAAUAAUUGAUGAAAGUAGCGGGCCGCCAAAAUCGGGAAACAAAAGAACUUGU-UCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGG
-...........((((((.((-...............)).))))))...........((((.(((......))))-)))(((((((.....))))))).((((((((....)))))))). ( -22.26)
>DroYak_CAF1 126600 119 - 1
CUCUGGCCCAAAGUCCCCGGC-AAAUAAUUGAUGAAAGUGGCAGGCCGCCAAAGUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGG
.....(((..........)))-..........(((...((((.....))))...)))((((((((......))))))))(((((((.....))))))).((((((((....)))))))). ( -27.60)
>consensus
_CCCAGCCCAAAGUCGCCGGC_AAAUAAUUGAUGAAAGUGGCAGGCCGCCAAAAUCGGGAAACAAAAGAACUUGUUUCCUCAUUGAACAUUUUAAUGAUUUAAUUGUCCAAACAAUUAGG
.............................((((....((((....))))....))))((((((((......))))))))(((((((.....))))))).((((((((....)))))))). (-23.14 = -23.22 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,388,131 – 11,388,243
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.01
Mean single sequence MFE -33.91
Consensus MFE -29.12
Energy contribution -29.16
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -1.26
Structure conservation index 0.86
SVM decision value 0.13
SVM RNA-class probability 0.599497
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11388131 112 + 27905053
AGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGCCACUUUCAUCAAUUAUUUGGCUGGCGACUUUGGGCUGGG--------GCUUUGCGGGAAAUUCCUUGUUUGUCCGCAAAC
.(((((((((....)))))))))(((..(((.(((((.....................))))).)))..)))(((....--------)))(((((((((((.....)))).))))))).. ( -34.10)
>DroSec_CAF1 135906 112 + 1
AGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGCCACUUUCAUCAAUUAUUUAGCCGGCGACUUUGGGCUGGG--------GCUUUGCGGGAAAUUCCUUGUUUGUCCGCAAAC
.(((((((((....))))))))).((...((((.....))))...)).............(((((........))))).--------..((((((((((((.....)))).)))))))). ( -34.00)
>DroSim_CAF1 127005 112 + 1
AGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGCCACUUUCAUCAAUUAUUUAGCCGGCGACUUUGGGCUGGG--------GCUUUGCGGGAAAUUCCUUGUUUGUCCGCAAAC
.(((((((((....))))))))).((...((((.....))))...)).............(((((........))))).--------..((((((((((((.....)))).)))))))). ( -34.00)
>DroEre_CAF1 124390 110 + 1
AGGA-ACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCCGCUACUUUCAUCAAUUAUUU-GCUGCGGACUUUGGGCUAGA--------GCUUUGCGGCAAAUUCCUUGUUUGUCCGCAAAC
.(((-(((((....))))))))((((..((.(((((......................-))))).))..))))((....--------))((((((((((((.....))))).))))))). ( -32.15)
>DroYak_CAF1 126640 119 + 1
AGGAAACAAGUUCUUUUGUUUCCCGACUUUGGCGGCCUGCCACUUUCAUCAAUUAUUU-GCCGGGGACUUUGGGCCAGAGAAAUGGGGCUUUGCGGGAAAUUCCUUGUUUGUCCGCAAAC
.(((((((((....)))))))))...(((((((((....)).................-.(((....)...)))))))))...((((((...(((((......)))))..)))).))... ( -35.30)
>consensus
AGGAAACAAGUUCUUUUGUUUCCCGAUUUUGGCGGCCUGCCACUUUCAUCAAUUAUUU_GCCGGCGACUUUGGGCUGGG________GCUUUGCGGGAAAUUCCUUGUUUGUCCGCAAAC
.(((((((((....))))))))).((...((((.....))))...))........(((((((.(......).)))))))..........((((((((((((.....)))).)))))))). (-29.12 = -29.16 +   0.04)

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 11:23:39 2006