Locus 3105

Sequence ID 2L_DroMel_CAF1
Location 8,823,530 – 8,823,659
Length 129
Max. P 0.992906
window4939 window4940 window4941

overview

Window 9

Location 8,823,530 – 8,823,625
Length 95
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 75.29
Mean single sequence MFE -27.38
Consensus MFE -15.97
Energy contribution -16.93
Covariance contribution 0.96
Combinations/Pair 1.14
Mean z-score -2.64
Structure conservation index 0.58
SVM decision value 2.36
SVM RNA-class probability 0.992906
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8823530 95 + 22407834
---AAAAUACAAAACACAA-------AUAGCAGCAACAAAGC--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAG------------AAUCGGAGUCAGAAUCAGAAU
---................-------...((.((......))--.)).((((((.(.....).))))))(((((..(((((.....------------..)))))..)))))....... ( -21.60)
>DroSec_CAF1 33316 107 + 1
---AAAAUACAAAACACAA-------AUAGCAGCAACAAAGA--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAAACUGAUUCAGAAUCGGAGUCAGAAUCGGAAU
---................-------..............((--(...((((((.(.....).)))))).(((((.((.(((((((...))))))).)).))))))))........... ( -24.50)
>DroSim_CAF1 31523 107 + 1
---AAAAUACAAAACACAA-------AUAGCAGCAACAAAGA--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAAUCGGAUUCAGAAUCGGAGUCAGAAUCAGAAU
---................-------................--..(((((...(((((((..((...(((((((((((((.......))))))))))))))))))).))).))))).. ( -29.60)
>DroEre_CAF1 36187 91 + 1
---GGAACACAAGA-ACAAA-CU----------CAAC-------CGUCUGAGUGGCUACUCGUCGCUCAUUCUGGAUCCGAAUCGGAC------UCCGAAUCGGAUUCAGAAUCGGAAU
---...........-.....-..----------...(-------((...(((((((.....)))))))(((((((((((((.((((..------.)))).))))))))))))))))... ( -36.90)
>DroYak_CAF1 34419 110 + 1
---AAAAUACAAAACACAAAACACCAAUAGCAGCAACAAUGCCAUGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCCGAA------UCAGAAUCGGAUUCAGAAUCGGAAU
---....................((....(((.......)))......((((((.(.....).))))))((((((((((((.((....------...)).))))))))))))..))... ( -28.90)
>DroAna_CAF1 33641 97 + 1
GCAGAAAUACAUAGUACAG---------AGCGGCAACAAAGC--CGUCUGAGUGUCUACUCGUCUCUGAUUCUCAUUCCGCAUCCGAU------UCCGAAUCCGAGUCUGGGCC-----
((.(((......(((.(((---------((((((......))--))...((((....))))..))))))))....))).)).((((((------((.......))))).)))..----- ( -22.80)
>consensus
___AAAAUACAAAACACAA_______AUAGCAGCAACAAAGC__CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAA______UCAGAAUCGGAGUCAGAAUCGGAAU
................................................((((((.(.....).))))))((((((.(((((.((.((.......)).)).))))).))))))....... (-15.97 = -16.93 +   0.96)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,823,530 – 8,823,625
Length 95
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 75.29
Mean single sequence MFE -30.33
Consensus MFE -15.55
Energy contribution -17.62
Covariance contribution 2.07
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.51
SVM decision value 0.96
SVM RNA-class probability 0.890295
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8823530 95 - 22407834
AUUCUGAUUCUGACUCCGAUU------------CUGAUUCGGAUCCAGAAUGAGCGACGAGUAGACACUCAGACG--GCUUUGUUGCUGCUAU-------UUGUGUUUUGUAUUUU---
...((.((((((..(((((..------------.....)))))..)))))).))..((((...(((((..((.((--((......))))))..-------..))))))))).....--- ( -27.10)
>DroSec_CAF1 33316 107 - 1
AUUCCGAUUCUGACUCCGAUUCUGAAUCAGUUUCUGAUUCGGAUCCAGAAUGAGCGACGAGUAGACACUCAGACG--UCUUUGUUGCUGCUAU-------UUGUGUUUUGUAUUUU---
......((((((..(((((.((.(((.....))).)).)))))..)))))).((((((((..((((........)--))))))))))).....-------................--- ( -30.30)
>DroSim_CAF1 31523 107 - 1
AUUCUGAUUCUGACUCCGAUUCUGAAUCCGAUUCUGAUUCGGAUCCAGAAUGAGCGACGAGUAGACACUCAGACG--UCUUUGUUGCUGCUAU-------UUGUGUUUUGUAUUUU---
......((((((..(((((.((.((((...)))).)).)))))..)))))).((((((((..((((........)--))))))))))).....-------................--- ( -29.70)
>DroEre_CAF1 36187 91 - 1
AUUCCGAUUCUGAAUCCGAUUCGGA------GUCCGAUUCGGAUCCAGAAUGAGCGACGAGUAGCCACUCAGACG-------GUUG----------AG-UUUGU-UCUUGUGUUCC---
......((((((.((((((.((((.------..)))).)))))).))))))((((.(((((.(((.((((((...-------.)))----------))-)..))-)))))))))).--- ( -35.30)
>DroYak_CAF1 34419 110 - 1
AUUCCGAUUCUGAAUCCGAUUCUGA------UUCGGAUUCGGAUCCAGAAUGAGCGACGAGUAGACACUCAGACAUGGCAUUGUUGCUGCUAUUGGUGUUUUGUGUUUUGUAUUUU---
.....(..(((((((((((......------.)))))))))))..)((((((...((((...((((((.(((...(((((....)))))...)))))))))..))))...))))))--- ( -32.70)
>DroAna_CAF1 33641 97 - 1
-----GGCCCAGACUCGGAUUCGGA------AUCGGAUGCGGAAUGAGAAUCAGAGACGAGUAGACACUCAGACG--GCUUUGUUGCCGCU---------CUGUACUAUGUAUUUCUGC
-----....((...(((.(((((..------..))))).)))..)).....((((((...((((.....((((((--((......)))).)---------)))..))))...)))))). ( -26.90)
>consensus
AUUCCGAUUCUGACUCCGAUUCUGA______UUCUGAUUCGGAUCCAGAAUGAGCGACGAGUAGACACUCAGACG__GCUUUGUUGCUGCUAU_______UUGUGUUUUGUAUUUU___
......((((((..(((((.((.((.......)).)).)))))..)))))).((((((((((....)))).(......)...))))))............................... (-15.55 = -17.62 +   2.07)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,823,559 – 8,823,659
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.62
Mean single sequence MFE -34.25
Consensus MFE -15.35
Energy contribution -16.78
Covariance contribution 1.43
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.45
SVM decision value -0.05
SVM RNA-class probability 0.506133
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8823559 100 + 22407834
AGC--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAG------------AAUCGGAGUCAGAAUCAGAAUCGCAAUCCGAGUAUGAGUCUG------AGUAUAAGUCUGG
..(--((..((((((.(.....).))))))..).))........(((------------(.....(.(((((.(((...(((.....)))...))).))))------).).....)))). ( -26.60)
>DroSec_CAF1 33345 112 + 1
AGA--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAAACUGAUUCAGAAUCGGAGUCAGAAUCGGAAUCGCAAUUCUAGUAUGAGUCUG------AGUAUAAGUCUGU
(((--((.(.....).)((((((..((((((.(((((..(((.((.((..(((((((.......)))))))..)).)).)))....))))).)))))).))------))))...)))).. ( -34.60)
>DroSim_CAF1 31552 112 + 1
AGA--CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAAUCGGAUUCAGAAUCGGAGUCAGAAUCAGAAUCGCAAUUCGAGUAUGAGGCUG------AGUUUAAGUCUGU
(((--(...((((((.(.....).))))))((((((((((((.......))))))))))))(..((.((((..(((...(((.....)))...)))..)))------).))..))))).. ( -40.60)
>DroEre_CAF1 36209 109 + 1
-----CGUCUGAGUGGCUACUCGUCGCUCAUUCUGGAUCCGAAUCGGAC------UCCGAAUCGGAUUCAGAAUCGGAAUCAGAAUCCGAAUCGGAGUCUGAGUCUGAGUUUAAGUCUGG
-----....((((((((.....))))))))((((((((((((.((((..------.)))).))))))))))))(((((.(((((.((((...)))).))))).)))))............ ( -50.40)
>DroYak_CAF1 34455 108 + 1
UGCCAUGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCCGAA------UCAGAAUCGGAUUCAGAAUCGGAAUCGCAAUCUGCAUCGGAGUCUG------AGUAUAAGUCUGG
..(((.(.(((((((.(.....).))))).((((((((((((.((....------...)).))))))))))))(((((.((((.....))....)).))))------).....)).)))) ( -32.50)
>DroPer_CAF1 50675 90 + 1
AGC--CGUCUGAGUGUCUACUCGUCUCUGAGUCUGAAUCUGAAUCUGAA------UC-----CCGAGUCUGAGUC-----------UCGAGUCUGGGUCUG------CUUCUGCGUCUGG
((.--(((..(((((.(((((((.(((.((.((.((.((.......)).------))-----..)).)).)))..-----------.)))))...)).).)------)))..))).)).. ( -20.80)
>consensus
AGC__CGUCUGAGUGUCUACUCGUCGCUCAUUCUGGAUCCGAAUCAGAA______UCAGAAUCGGAGUCAGAAUCGGAAUCGCAAUCCGAGUAUGAGUCUG______AGUAUAAGUCUGG
......(.(((((((.(.....).)))))(((((((.(((((.((.((.......)).)).))))).))))))).....................)).)..................... (-15.35 = -16.78 +   1.43)

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 10:44:29 2006