Locus 5217

Sequence ID 3R_DroMel_CAF1
Location 13,660,322 – 13,660,532
Length 210
Max. P 0.996899
window8508 window8509 window8510 window8511 window8512

overview

Window 8

Location 13,660,322 – 13,660,426
Length 104
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 86.29
Mean single sequence MFE -38.52
Consensus MFE -27.27
Energy contribution -27.50
Covariance contribution 0.23
Combinations/Pair 1.24
Mean z-score -2.79
Structure conservation index 0.71
SVM decision value -0.04
SVM RNA-class probability 0.510964
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13660322 104 + 27905053
AGGACAACACCAGUCGAAGGAUUUGCCUUCGAAGCGAAACAAAUUGUUCUGGCGUGUGGAAAGUUUCCGGGUUGAAGAACUUUCCCACUUGCGGUGUGAUGUUG------
..(((((((((..(((((((.....))))))).(((((((.....))).....(((.(((((((((..........)))))))))))))))))))))..)))).------ ( -35.30)
>DroSec_CAF1 25489 104 + 1
AGGACAACACCAGUCGAAGGAUUUGCCUUCGAAGCGAAACAAAUUGUUCUGGCGUGUGGAAAGUUUCCGGGUUGUAGAACUUUCCCACUUGCGGUGUGGUGUUG------
....((((((((.(((((((.....))))))).(((((((.....))).....(((.(((((((((..........))))))))))))))))....))))))))------ ( -37.00)
>DroSim_CAF1 25355 104 + 1
AGGAAAACACCAGUCGAAGGAUUUGCCUUCGAAGCGAAACAAAUUGUUCUGGCGUGUGGAAAGUUUCCGGGUUGGAGAACUUUCCCACUUGCGGUGUGGUGUUG------
.....(((((((.(((((((.....))))))).(((((((.....))).....(((.(((((((((((.....)))).))))))))))))))....))))))).------ ( -38.30)
>DroEre_CAF1 29446 110 + 1
AGGACAACACCAGUCGAAGGAUUUGCCUUCGAAGCGAAACAAAUUGUUCUGGCGUGUGGAAAGUUUUCGGGGUGGAGAACUUUCCCACUUGCGGUGUGGUGUUGUACGUU
.(.(((((((((.(((((((.....))))))).(((((((.....))).....(((.(((((((((((......))))))))))))))))))....))))))))).)... ( -45.00)
>DroYak_CAF1 25877 103 + 1
AGGACAACACCAGUCGAAGGAUUUGCCUUCGAAGCUAAACAAAUUGUUCUGGCGUGUGGAAAGUUUCCGGGCUGGAGACCUUCCCCACUUGUGGUGUGGUAUU-------
...((.((((((.(((((((.....))))))).(((((((.....))).))))(((.((((.((((((.....)))))).)))).)))...)))))).))...------- ( -39.70)
>DroAna_CAF1 21116 104 + 1
AGGACCACUUCGACCCAAAGAUUUGUCUCUGAGUCGAAGCAAAUUGUUCGGGCGUGUGGAAAGUUUCUUCGGGAGAGAACUUUGCCACUUGAGGUGUGGUCGAG------
..((((((.(((.(((...((((((..((......))..))))))....))))..(((((((((((..((....))))))))).))))....)).))))))...------ ( -35.80)
>consensus
AGGACAACACCAGUCGAAGGAUUUGCCUUCGAAGCGAAACAAAUUGUUCUGGCGUGUGGAAAGUUUCCGGGUUGGAGAACUUUCCCACUUGCGGUGUGGUGUUG______
......(((((..(((((((.....))))))).(((((((.....))).....(((.((((((((((((...)))))).))))))))))))))))))............. (-27.27 = -27.50 +   0.23)

alignment

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secondary structure

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Window 9

Location 13,660,322 – 13,660,426
Length 104
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 86.29
Mean single sequence MFE -36.98
Consensus MFE -26.98
Energy contribution -27.68
Covariance contribution 0.70
Combinations/Pair 1.29
Mean z-score -4.84
Structure conservation index 0.73
SVM decision value 1.74
SVM RNA-class probability 0.974963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13660322 104 - 27905053
------CAACAUCACACCGCAAGUGGGAAAGUUCUUCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCGCUUCGAAGGCAAAUCCUUCGACUGGUGUUGUCCU
------((((((((....((..(((((((((((.(((.....))))))))))).)))....((((.....)))).)).(((((((.....))))))).)))))))).... ( -34.00)
>DroSec_CAF1 25489 104 - 1
------CAACACCACACCGCAAGUGGGAAAGUUCUACAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCGCUUCGAAGGCAAAUCCUUCGACUGGUGUUGUCCU
------((((((((....((..(((((((((((((.......)).)))))))).)))....((((.....)))).)).(((((((.....))))))).)))))))).... ( -35.90)
>DroSim_CAF1 25355 104 - 1
------CAACACCACACCGCAAGUGGGAAAGUUCUCCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCGCUUCGAAGGCAAAUCCUUCGACUGGUGUUUUCCU
------.(((((((....((..(((((((((((.(((.....))))))))))).)))....((((.....)))).)).(((((((.....))))))).)))))))..... ( -36.70)
>DroEre_CAF1 29446 110 - 1
AACGUACAACACCACACCGCAAGUGGGAAAGUUCUCCACCCCGAAAACUUUCCACACGCCAGAACAAUUUGUUUCGCUUCGAAGGCAAAUCCUUCGACUGGUGUUGUCCU
...(.(((((((((....((..(((((((((((.((......)).)))))))).)))....((((.....)))).)).(((((((.....))))))).))))))))).). ( -39.00)
>DroYak_CAF1 25877 103 - 1
-------AAUACCACACCACAAGUGGGGAAGGUCUCCAGCCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUAGCUUCGAAGGCAAAUCCUUCGACUGGUGUUGUCCU
-------....((((.......))))(((((((.(((.....))).)))))))((((((((((((.....))).....(((((((.....))))))))))))).)))... ( -37.00)
>DroAna_CAF1 21116 104 - 1
------CUCGACCACACCUCAAGUGGCAAAGUUCUCUCCCGAAGAAACUUUCCACACGCCCGAACAAUUUGCUUCGACUCAGAGACAAAUCUUUGGGUCGAAGUGGUCCU
------...((((.........((((.((((((.(((.....)))))))))))))...............(((((((((((((((....))))))))))))))))))).. ( -39.30)
>consensus
______CAACACCACACCGCAAGUGGGAAAGUUCUCCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCGCUUCGAAGGCAAAUCCUUCGACUGGUGUUGUCCU
......(((((((.....((..(((((((((((.(((.....))))))))))).)))....((((.....)))).)).(((((((.....)))))))..))))))).... (-26.98 = -27.68 +   0.70)

alignment

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secondary structure

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Window 0

Location 13,660,356 – 13,660,455
Length 99
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 72.86
Mean single sequence MFE -19.40
Consensus MFE -12.58
Energy contribution -12.75
Covariance contribution 0.17
Combinations/Pair 1.21
Mean z-score -2.96
Structure conservation index 0.65
SVM decision value 2.77
SVM RNA-class probability 0.996899
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13660356 99 - 27905053
CCAGCACACAUACACAU---ACUUGCAACAUA--------------CAACAUCACACCGCAAGUGGGAAAGUUCUUCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCG
...((...........(---((((((......--------------............)))))))((((((((.(((.....)))))))))))....))..((((.....)))).. ( -19.17)
>DroSec_CAF1 25523 102 - 1
CCAGCACACACACACUUGCAACAUACAACAUA--------------CAACACCACACCGCAAGUGGGAAAGUUCUACAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCG
...((.......(((((((.............--------------............)))))))((((((((((.......)).))))))))....))..((((.....)))).. ( -20.41)
>DroSim_CAF1 25389 102 - 1
CCAGCACACACACACUUGCAACAUACAACAUA--------------CAACACCACACCGCAAGUGGGAAAGUUCUCCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCG
...((.......(((((((.............--------------............)))))))((((((((.(((.....)))))))))))....))..((((.....)))).. ( -24.01)
>DroEre_CAF1 29480 116 - 1
UCGGCAGACAUACACAUACAACAUACAACAUACAACAUACAACGUACAACACCACACCGCAAGUGGGAAAGUUCUCCACCCCGAAAACUUUCCACACGCCAGAACAAUUUGUUUCG
..(((......................................((........)).......(((((((((((.((......)).)))))))).)))))).((((.....)))).. ( -20.10)
>DroYak_CAF1 25911 88 - 1
CCUGCAUAUAUACACAUAC----------------------------AAUACCACACCACAAGUGGGGAAGGUCUCCAGCCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUAG
...((..............----------------------------....((((.......))))(((((((.(((.....))).)))))))....))..((((.....)))).. ( -20.80)
>DroAna_CAF1 21150 75 - 1
---------------------------UCAUC--------------CUCGACCACACCUCAAGUGGCAAAGUUCUCUCCCGAAGAAACUUUCCACACGCCCGAACAAUUUGCUUCG
---------------------------.....--------------................((((.((((((.(((.....))))))))))))).....((((........)))) ( -11.90)
>consensus
CCAGCACACAUACACAU_C_ACAUACAACAUA______________CAACACCACACCGCAAGUGGGAAAGUUCUCCAACCCGGAAACUUUCCACACGCCAGAACAAUUUGUUUCG
..............................................................(((((((((((.(((.....))))))))))).)))................... (-12.58 = -12.75 +   0.17)

alignment

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secondary structure

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Window 1

Location 13,660,426 – 13,660,532
Length 106
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.18
Mean single sequence MFE -35.72
Consensus MFE -20.06
Energy contribution -19.70
Covariance contribution -0.36
Combinations/Pair 1.27
Mean z-score -2.22
Structure conservation index 0.56
SVM decision value 0.86
SVM RNA-class probability 0.869104
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13660426 106 + 27905053
--------UAUGUUGCAAGU---AUGUGUAUGUGUGCUGGAUGUGCUGGGUUGGGAAGGUGGGUCCUUCAGCUGGCUGUUCCAGUGUGACAAGCCACUGAGGUGGCAUAUUUGACAA
--------....((((((((---((.....((((..(((((...((..(.....(((((.....)))))..)..))...)))))..).))).(((((....)))))))))))).))) ( -38.50)
>DroSec_CAF1 25593 109 + 1
--------UAUGUUGUAUGUUGCAAGUGUGUGUGUGCUGGAUGUGCUGGGUUGGGUAGGUGGGUCCUUCAGCUGGCUGUUCCAGUGUGACAAGCCACUGAGGUGGCAUAUUUGACAA
--------..((((((((((..(.((((..((((..(((((...((..(.((((..(((.....))))))))..))...)))))..).)))...))))...)..))))))..)))). ( -39.60)
>DroSim_CAF1 25459 109 + 1
--------UAUGUUGUAUGUUGCAAGUGUGUGUGUGCUGGAUGUGCUGGGUUGGGGAGGUGGGUCCUUCAGCUGGCUGUUCCAGUGUGACAAGCCACUGAGGUGGCAUAUUUGACAA
--------..((((((((((..(.((((..((((..(((((...((..(.(..((((......))))..).)..))...)))))..).)))...))))...)..))))))..)))). ( -41.80)
>DroEre_CAF1 29556 116 + 1
GUAUGUUGUAUGUUGUAUGUUGUAUGUGUAUGUCUGCCGAAUGUGCUGUGU-GCGGAUGUAGGUGCUUCAGCUGGCGGUUCCAGUGUGACAAGCCUCUGAGGUGCCAUAUUUGACAA
...(((((((..(.(((((((...((.(((....)))))))))))).)..)-))((((((.((..((((((..(((...((......))...))).))))))..)))))))))))). ( -33.00)
>DroYak_CAF1 25980 95 + 1
---------------------GUAUGUGUAUAUAUGCAGGAUAGGCUGGAU-GAGGAUGUGGGUGCUUUAGCUGGCGGUUCCGAUGUGUCAAGCCUCUGAGGUGGCAUAUUUGACAA
---------------------.....(((..((((((.....(((((.(((-(.((((((.(((......))).)))..)))....)))).)))))........))))))...))). ( -25.72)
>consensus
________UAUGUUGUAUGUUGCAUGUGUAUGUGUGCUGGAUGUGCUGGGUUGGGGAGGUGGGUCCUUCAGCUGGCUGUUCCAGUGUGACAAGCCACUGAGGUGGCAUAUUUGACAA
..........................(((..(((((((...((..(((((.......(((.(((......))).)))..)))))..))....(((.....))))))))))...))). (-20.06 = -19.70 +  -0.36)

alignment

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secondary structure

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Window 2

Location 13,660,426 – 13,660,532
Length 106
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 80.18
Mean single sequence MFE -19.45
Consensus MFE -9.78
Energy contribution -10.30
Covariance contribution 0.52
Combinations/Pair 1.19
Mean z-score -2.05
Structure conservation index 0.50
SVM decision value 0.24
SVM RNA-class probability 0.649597
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13660426 106 - 27905053
UUGUCAAAUAUGCCACCUCAGUGGCUUGUCACACUGGAACAGCCAGCUGAAGGACCCACCUUCCCAACCCAGCACAUCCAGCACACAUACACAU---ACUUGCAACAUA--------
(((.(((.((((((((....))))).(((....(((((...((.....(((((.....)))))........))...)))))...))).....))---).))))))....-------- ( -21.52)
>DroSec_CAF1 25593 109 - 1
UUGUCAAAUAUGCCACCUCAGUGGCUUGUCACACUGGAACAGCCAGCUGAAGGACCCACCUACCCAACCCAGCACAUCCAGCACACACACACUUGCAACAUACAACAUA--------
(((.(((....(((((....))))).(((....(((((.(((....))).(((.....)))...............)))))...))).....))))))...........-------- ( -20.00)
>DroSim_CAF1 25459 109 - 1
UUGUCAAAUAUGCCACCUCAGUGGCUUGUCACACUGGAACAGCCAGCUGAAGGACCCACCUCCCCAACCCAGCACAUCCAGCACACACACACUUGCAACAUACAACAUA--------
(((.(((....(((((....))))).(((....(((((.(((....)))..(((......))).............)))))...))).....))))))...........-------- ( -20.10)
>DroEre_CAF1 29556 116 - 1
UUGUCAAAUAUGGCACCUCAGAGGCUUGUCACACUGGAACCGCCAGCUGAAGCACCUACAUCCGC-ACACAGCACAUUCGGCAGACAUACACAUACAACAUACAACAUACAACAUAC
.((((.....((((...((((.(........).))))....))))(((((((......)....((-.....))...)))))).)))).............................. ( -19.40)
>DroYak_CAF1 25980 95 - 1
UUGUCAAAUAUGCCACCUCAGAGGCUUGACACAUCGGAACCGCCAGCUAAAGCACCCACAUCCUC-AUCCAGCCUAUCCUGCAUAUAUACACAUAC---------------------
.(((...((((((........(((((.((......((.....)).((....))............-.)).))))).....))))))..))).....--------------------- ( -16.22)
>consensus
UUGUCAAAUAUGCCACCUCAGUGGCUUGUCACACUGGAACAGCCAGCUGAAGGACCCACCUCCCCAACCCAGCACAUCCAGCACACAUACACAUACAACAUACAACAUA________
.((.(((....(((((....)))))))).))..(((((.......((((..((..........))....))))...))))).................................... ( -9.78 = -10.30 +   0.52)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:19 2006