Locus 6652

Sequence ID 2L_DroMel_CAF1
Location 18,669,390 – 18,669,529
Length 139
Max. P 0.999840
window10611 window10612 window10613

overview

Window 1

Location 18,669,390 – 18,669,498
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.67
Mean single sequence MFE -34.24
Consensus MFE -21.21
Energy contribution -21.56
Covariance contribution 0.35
Combinations/Pair 1.16
Mean z-score -4.51
Structure conservation index 0.62
SVM decision value 2.98
SVM RNA-class probability 0.997986
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18669390 108 - 22407834
AAGUCCGAAAGGAUGUCGGAAAAAAAAUCAGAGAGGAA------------UUCCGAAAAUAAGAUAGGACGAAAAUCUGAAAGGCUUUCUGAGAGACGGUCUGAAAGAAAGUCCCGAAAU
..((((....)))).((((........(((((......------------.(((............)))......)))))..((((((((...((.....))...))))))))))))... ( -29.52)
>DroSec_CAF1 22094 120 - 1
AAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGCGAGGAUUUCCGAAAAUAAGAUAGCACGAAAAUCUGAAAGGCUUUCUGAGAGAAGGUCUGAAAGGAAGUCCCGAAAU
..........(((..(((.........(((((..((((((((....))))))))........(....).......))))).((((((((.....))))))))....)))..)))...... ( -36.50)
>DroSim_CAF1 23368 120 - 1
AAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGCGAGGAUUUCAGAAAAUAAGAUAGCACGAAAAUCUGAAAGGCUUUCUGAGAGAAGGUCUGAAAGGAAGUCCCGAAAU
..........(((..(((.........(((((...(((((((....))))))).........(....).......))))).((((((((.....))))))))....)))..)))...... ( -33.00)
>DroEre_CAF1 22378 120 - 1
AGUUCUGAGAGGAAGUCGCAGAGGAAGUCGCAGAGGAAGUCGCAGAGGAAGUCUGAUAAAAUGACAGGACGAAAGUCUGAAAGGCUUUCUGAGAGACGAUCUGAAAGAAAGUCCAGAAAU
...((((.((.....)).))))(((..((.((((....(((.(..(((((((((............((((....))))...)))))))))..).)))..))))...))...)))...... ( -35.76)
>DroYak_CAF1 22275 120 - 1
AAGUCUGAGAGGAAGACCGAGAGGAAGUCAGAAAGGAAGUCCGAGAGGAAGUCUGAUAGAAUGAUAGGACGAAAGUCUGAAAGGCUUUCUGAAAGACGGUCUGAAAGAAAGUCCAGAAAU
..((((...((((((.((........((((....(((..(((....)))..))).......)))).((((....))))....))))))))...))))((.((.......)).))...... ( -36.40)
>consensus
AAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGAGAGGAAUUCCGAAAAUAAGAUAGGACGAAAAUCUGAAAGGCUUUCUGAGAGACGGUCUGAAAGAAAGUCCCGAAAU
...(((....)))..............(((((..((((.(((....))).)))).....................)))))..((((((((...((.....))...))))))))....... (-21.21 = -21.56 +   0.35)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,669,430 – 18,669,529
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.76
Mean single sequence MFE -20.39
Consensus MFE -4.96
Energy contribution -5.99
Covariance contribution 1.03
Combinations/Pair 1.06
Mean z-score -2.10
Structure conservation index 0.24
SVM decision value 1.29
SVM RNA-class probability 0.938381
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18669430 99 + 22407834
UCAGAUUUUCGUCCUAUCUUAUUUUCGGAA------------UUCCUCUCUGAUUUUUUUUCCGACAUCCUUUCGGACUUUCUCUCGGAAUU---------UCGAACCGACUUCCUGGAC
..........((((.........(((((((------------((((.....((.......(((((.......)))))...))....))))))---------)))))..........)))) ( -21.41)
>DroSec_CAF1 22134 111 + 1
UCAGAUUUUCGUGCUAUCUUAUUUUCGGAAAUCCUCGCGGACUUCCUCUCUGACUUUCUCUCGGACUUCCUUUCGGACUUUCUCUCGGAAUU---------UCGAACCGACUUCCUGGAC
(((((.....(......)........((((.(((....))).))))..))))).....(((.(((..((..((((((.((((....)))).)---------)))))..))..))).))). ( -23.90)
>DroSim_CAF1 23408 111 + 1
UCAGAUUUUCGUGCUAUCUUAUUUUCUGAAAUCCUCGCGGACUUCCUCUCUGACUUUCUCUCGGACUUCCUUUCGGACUUUCUCUCGGAAUU---------UCGAACCGACUUCCUGGAC
(((((.....(......).........(((.(((....))).)))...))))).....(((.(((..((..((((((.((((....)))).)---------)))))..))..))).))). ( -19.90)
>DroEre_CAF1 22418 108 + 1
UCAGACUUUCGUCCUGUCAUUUUAUCAGACUUCCUCUGCGACUUCCUCUGCGACUUCCUCUGCGACUUCCUCUCAGAACUUCUG---GA---------UAUUCUUACCGACCUCCUGGAC
(((((.....(((..(((.........))).......(((........))))))....((((.((.....)).))))...))))---).---------........(((......))).. ( -14.30)
>DroYak_CAF1 22315 120 + 1
UCAGACUUUCGUCCUAUCAUUCUAUCAGACUUCCUCUCGGACUUCCUUUCUGACUUCCUCUCGGUCUUCCUCUCAGACUUUCUCUCAGAAAUUUGAGAUAUUCUUACCGACCUCCUGGAU
(((((.....((((........................))))......)))))..(((..(((((.....(((((((.((((.....))))))))))).......)))))......))). ( -22.46)
>consensus
UCAGAUUUUCGUCCUAUCUUAUUUUCAGAAAUCCUCGCGGACUUCCUCUCUGACUUUCUCUCGGACUUCCUUUCGGACUUUCUCUCGGAAUU_________UCGAACCGACUUCCUGGAC
((((....(((................(((.(((....))).)))...(((((...................)))))..............................)))....)))).. ( -4.96 =  -5.99 +   1.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,669,430 – 18,669,529
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.76
Mean single sequence MFE -30.54
Consensus MFE -17.41
Energy contribution -17.84
Covariance contribution 0.43
Combinations/Pair 1.18
Mean z-score -3.49
Structure conservation index 0.57
SVM decision value 4.22
SVM RNA-class probability 0.999840
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18669430 99 - 22407834
GUCCAGGAAGUCGGUUCGA---------AAUUCCGAGAGAAAGUCCGAAAGGAUGUCGGAAAAAAAAUCAGAGAGGAA------------UUCCGAAAAUAAGAUAGGACGAAAAUCUGA
((((.....(((..((((.---------((((((........((((....)))).((.((.......)).))..))))------------)).)))).....))).)))).......... ( -23.50)
>DroSec_CAF1 22134 111 - 1
GUCCAGGAAGUCGGUUCGA---------AAUUCCGAGAGAAAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGCGAGGAUUUCCGAAAAUAAGAUAGCACGAAAAUCUGA
...((((...(((((((((---------..((((..(.((...(((....)))..)))..).)))..)).....((((((((....))))))))........))..)).)))...)))). ( -34.90)
>DroSim_CAF1 23408 111 - 1
GUCCAGGAAGUCGGUUCGA---------AAUUCCGAGAGAAAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGCGAGGAUUUCAGAAAAUAAGAUAGCACGAAAAUCUGA
...((((...(((((((((---------..((((..(.((...(((....)))..)))..).)))..))......(((((((....))))))).........))..)).)))...)))). ( -31.40)
>DroEre_CAF1 22418 108 - 1
GUCCAGGAGGUCGGUAAGAAUA---------UC---CAGAAGUUCUGAGAGGAAGUCGCAGAGGAAGUCGCAGAGGAAGUCGCAGAGGAAGUCUGAUAAAAUGACAGGACGAAAGUCUGA
.(((.(((..((.....))...---------))---).((..((((....)))).)).....))).((((....(((..((......))..))).......)))).((((....)))).. ( -26.80)
>DroYak_CAF1 22315 120 - 1
AUCCAGGAGGUCGGUAAGAAUAUCUCAAAUUUCUGAGAGAAAGUCUGAGAGGAAGACCGAGAGGAAGUCAGAAAGGAAGUCCGAGAGGAAGUCUGAUAGAAUGAUAGGACGAAAGUCUGA
.(((....((((..........(((((......))))).....(((....))).))))....))).((((....(((..(((....)))..))).......)))).((((....)))).. ( -36.10)
>consensus
GUCCAGGAAGUCGGUUCGA_________AAUUCCGAGAGAAAGUCCGAAAGGAAGUCCGAGAGAAAGUCAGAGAGGAAGUCCGAGAGGAAUUCCGAAAAUAAGAUAGGACGAAAAUCUGA
...((((...(((.........................((...(((....)))..)).........(((.....((((.(((....))).))))........)))....)))...)))). (-17.41 = -17.84 +   0.43)

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 12:16:32 2006