Locus 1406

Sequence ID 2R_DroMel_CAF1
Location 5,439,510 – 5,439,645
Length 135
Max. P 0.957509
window2411 window2412 window2413

overview

Window 1

Location 5,439,510 – 5,439,616
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 91.31
Mean single sequence MFE -33.16
Consensus MFE -28.84
Energy contribution -29.68
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.87
SVM decision value 1.48
SVM RNA-class probability 0.957509
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5439510 106 - 20766785
GCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACGAUUACGGUCAUUCGGCAUUGCAGAGCCUAGAUAACGGGACCCCACCUCCGAUCACGUUCACGUUCGGACCA
(((((((......)))))))(((((........)))))..((((....(((........)))........((....)).....(((..(((....)))))))))). ( -34.30)
>DroSec_CAF1 28071 99 - 1
GCCGUGGACUUAGCCACGGCGAUCGCCGAUA-ACGAUAAAGGUCAUUCGGCAUUGCAGAGCCUAGAUAACGGGUCCCCACCUCCGAUCACGUUCACGAUC------
(((((((......)))))))(((((((((..-..(((....)))..)))))......((((...(((...((((....))))...)))..))))..))))------ ( -35.60)
>DroSim_CAF1 28147 100 - 1
GCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACGAUAACGGUCAUUCGGCAUUGCAGAGCCUAGAUAACGGGACCCCACCUCCGAUCACGUUCACGAUC------
(((((((......)))))))(((((((((....((....)).....)))))......((((...(((..((((........)))))))..))))..))))------ ( -34.90)
>DroEre_CAF1 28609 100 - 1
GCCGCGGACUUAGCCACGGCGAUCGCCGAUAAAUGAUAACGCCUAUUCGUCAAUGUAGAGCCUAGAUAACGGGACCCCACCUCCGAUCAUGUUCACGAUC------
((((.((......)).))))(((((..((...(((((...((((((........)))).))........((((........)))))))))..)).)))))------ ( -28.20)
>DroYak_CAF1 28968 100 - 1
GCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACGAUAACGUUUAUUCGUCAAUGCAGAGCCUAGAUAACGGGACCCCACCUCCGAUCACGUUCACGAUC------
(((((((......)))))))(((((.(((((((((....)))))).)))........((((...(((..((((........)))))))..)))).)))))------ ( -32.80)
>consensus
GCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACGAUAACGGUCAUUCGGCAUUGCAGAGCCUAGAUAACGGGACCCCACCUCCGAUCACGUUCACGAUC______
(((((((......)))))))(((((((((....((....)).....)))))......((((...(((...(((......)))...)))..))))..))))...... (-28.84 = -29.68 +   0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,439,550 – 5,439,645
Length 95
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -30.45
Consensus MFE -20.13
Energy contribution -20.85
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -1.74
Structure conservation index 0.66
SVM decision value 0.95
SVM RNA-class probability 0.887931
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5439550 95 + 20766785
UCUAGGCUCUGCAAUGCCGAAUGACCGU-----AAU-------CGUUUAUCGGCGAUCGCCGUGGCUAAGUCCACGGCAAAUCUGCGGUGAUUAUCGCCUUC-GAAUG
((.((((.(((((.((((((.(((.((.-----...-------)).)))))))))...(((((((......))))))).....))))).(.....)))))..-))... ( -33.70)
>DroSec_CAF1 28105 94 + 1
UCUAGGCUCUGCAAUGCCGAAUGACCUU-----UAU-------CGU-UAUCGGCGAUCGCCGUGGCUAAGUCCACGGCAAAUCUGCGGUGAUUAUCGCCAUC-GAAUG
....(((.(((((.((((((.((((...-----...-------.))-))))))))...(((((((......))))))).....))))).(.....))))...-..... ( -33.30)
>DroSim_CAF1 28181 95 + 1
UCUAGGCUCUGCAAUGCCGAAUGACCGU-----UAU-------CGUUUAUCGGCGAUCGCCGUGGCUAAGUCCACGGCAAAUCUGCGGUGAUUAUCGCCAUC-GAAUG
....(((.(((((.((((((.(((.((.-----...-------)).)))))))))...(((((((......))))))).....))))).(.....))))...-..... ( -33.30)
>DroEre_CAF1 28643 95 + 1
UCUAGGCUCUACAUUGACGAAUAGGCGU-----UAU-------CAUUUAUCGGCGAUCGCCGUGGCUAAGUCCGCGGCAAAUCUGCGCUGAUUAUCGCCUUC-GAAUG
.................(((..(((((.-----...-------.....(((((((...(((((((......))))))).......)))))))...)))))))-).... ( -29.60)
>DroYak_CAF1 29002 95 + 1
UCUAGGCUCUGCAUUGACGAAUAAACGU-----UAU-------CGUUUAUCGGCGAUCGCCGUGGCUAAGUCCACGGCAAAUCUGCGGUGAUUAUCGCCUUG-GAAUA
(((((((.((((((((.(((.((((((.-----...-------))))))))).)))..(((((((......))))))).....))))).(.....)))).))-))... ( -33.40)
>DroAna_CAF1 23724 97 + 1
-----------GAGGUCCGAAUUAUCGCCAAGCUAUCUCAAGCUAUUUUUCGAUAAUCGCAGUGGCCAAGUCCAAAGCAAAUCUAUCCCGAUUACGGCGAUCUGAAUU
-----------............((((((.((((......)))).......(.((((((..((((....((.....))....))))..)))))))))))))....... ( -19.40)
>consensus
UCUAGGCUCUGCAAUGCCGAAUGACCGU_____UAU_______CGUUUAUCGGCGAUCGCCGUGGCUAAGUCCACGGCAAAUCUGCGGUGAUUAUCGCCAUC_GAAUG
...................................................((((((.(((((((......))))))).((((......))))))))))......... (-20.13 = -20.85 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,439,550 – 5,439,645
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -30.80
Consensus MFE -20.33
Energy contribution -21.05
Covariance contribution 0.72
Combinations/Pair 1.11
Mean z-score -1.92
Structure conservation index 0.66
SVM decision value 1.19
SVM RNA-class probability 0.928700
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5439550 95 - 20766785
CAUUC-GAAGGCGAUAAUCACCGCAGAUUUGCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACG-------AUU-----ACGGUCAUUCGGCAUUGCAGAGCCUAGA
.....-..(((((.....)...(((((((.(((((((......)))))))))))(((((....((-------...-----.)).....)))))..)))...))))... ( -35.00)
>DroSec_CAF1 28105 94 - 1
CAUUC-GAUGGCGAUAAUCACCGCAGAUUUGCCGUGGACUUAGCCACGGCGAUCGCCGAUA-ACG-------AUA-----AAGGUCAUUCGGCAUUGCAGAGCCUAGA
...((-...((((.....)...(((((((.(((((((......)))))))))))(((((..-..(-------((.-----...)))..)))))..)))...)))..)) ( -33.70)
>DroSim_CAF1 28181 95 - 1
CAUUC-GAUGGCGAUAAUCACCGCAGAUUUGCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACG-------AUA-----ACGGUCAUUCGGCAUUGCAGAGCCUAGA
...((-...((((.....)...(((((((.(((((((......)))))))))))(((((....((-------...-----.)).....)))))..)))...)))..)) ( -34.00)
>DroEre_CAF1 28643 95 - 1
CAUUC-GAAGGCGAUAAUCAGCGCAGAUUUGCCGCGGACUUAGCCACGGCGAUCGCCGAUAAAUG-------AUA-----ACGCCUAUUCGUCAAUGUAGAGCCUAGA
((((.-...((((((((((......))))(((((.((......)).)))))))))))....))))-------...-----..((((((........)))).))..... ( -26.80)
>DroYak_CAF1 29002 95 - 1
UAUUC-CAAGGCGAUAAUCACCGCAGAUUUGCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACG-------AUA-----ACGUUUAUUCGUCAAUGCAGAGCCUAGA
.....-..(((((.....)...(((((((.(((((((......)))))))))))((.((((((((-------...-----.)))))))).))...)))...))))... ( -32.40)
>DroAna_CAF1 23724 97 - 1
AAUUCAGAUCGCCGUAAUCGGGAUAGAUUUGCUUUGGACUUGGCCACUGCGAUUAUCGAAAAAUAGCUUGAGAUAGCUUGGCGAUAAUUCGGACCUC-----------
.......(((((((.......(((((..((((..(((......)))..))))))))).......((((......)))))))))))............----------- ( -22.90)
>consensus
CAUUC_GAAGGCGAUAAUCACCGCAGAUUUGCCGUGGACUUAGCCACGGCGAUCGCCGAUAAACG_______AUA_____ACGGUCAUUCGGCAUUGCAGAGCCUAGA
.........((((((((((......))))((((((((......))))))))))))))................................................... (-20.33 = -21.05 +   0.72)

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 10:04:07 2006