Locus 7709

Sequence ID 3L_DroMel_CAF1
Location 20,609,491 – 20,609,645
Length 154
Max. P 0.999341
window12539 window12540 window12541 window12542

overview

Window 9

Location 20,609,491 – 20,609,605
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.36
Mean single sequence MFE -34.72
Consensus MFE -28.90
Energy contribution -29.58
Covariance contribution 0.68
Combinations/Pair 1.03
Mean z-score -2.57
Structure conservation index 0.83
SVM decision value 2.42
SVM RNA-class probability 0.993729
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20609491 114 + 23771897
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCG------AGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGAAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGA
....................(.((((((.((------(.(((((..((((((((((((((.........)))))..((......))....)))))))))..))))).))).)))))).). ( -34.20)
>DroSec_CAF1 54350 114 + 1
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCG------AGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGA
....................(.((((((.((------(.(((((..((((((((((((((.........)))))..(((....)))....)))))))))..))))).))).)))))).). ( -36.90)
>DroAna_CAF1 76164 120 + 1
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCGUCUGGUAGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGCCUGUAACUAAUUAAAUGCACUUGCAAAUUGCCGGCAACGA
.............................(((((((((((((((..(((((((((...(((.....)))..(((....))).........)))))))))..))).)))))))))..))). ( -32.70)
>DroSim_CAF1 49180 114 + 1
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCG------AGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGACAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGA
....................(.((((((.((------(.(((((..((((((((((((((((.((......)).....)))))..)))...))))))))..))))).))).)))))).). ( -32.30)
>DroEre_CAF1 46835 114 + 1
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCG------AGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGGCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGA
....................(.((((((.((------(.(((((..((((((((((((((.........)))))...((((....)))).)))))))))..))))).))).)))))).). ( -37.50)
>consensus
AAUAUGAUAUUAAAAUUGAACUUUGCCGCCG______AGUUGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGA
......................(((.(((((........(((((..((((((((((((((.........)))))..(((....)))....)))))))))..))))).....))))).))) (-28.90 = -29.58 +   0.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,609,491 – 20,609,605
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.36
Mean single sequence MFE -36.38
Consensus MFE -32.96
Energy contribution -32.88
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -2.36
Structure conservation index 0.91
SVM decision value 3.53
SVM RNA-class probability 0.999341
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20609491 114 - 23771897
UCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUUCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACU------CGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..((((((((....(((((..(((((((((((..(....)..))))(((.(((......))))))..)))))))..))))).)------)))))))........................ ( -36.40)
>DroSec_CAF1 54350 114 - 1
UCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACU------CGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..((((((((....(((((..(((((((....(((((....)))))(((.(((......))))))..)))))))..))))).)------)))))))........................ ( -37.80)
>DroAna_CAF1 76164 120 - 1
UCGUUGCCGGCAAUUUGCAAGUGCAUUUAAUUAGUUACAGGCAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACUACCAGACGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..(((((((.....(((((..(((((((....((((...(((....)))..(((.....))))))).)))))))..)))))........)))))))........................ ( -33.52)
>DroSim_CAF1 49180 114 - 1
UCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGUCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACU------CGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..((((((((....(((((..(((((((....((((...(((....)))..(((.....))))))).)))))))..))))).)------)))))))........................ ( -36.40)
>DroEre_CAF1 46835 114 - 1
UCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGCCAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACU------CGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..((((((((....(((((..(((((((....((((..(((.....)))..(((.....))))))).)))))))..))))).)------)))))))........................ ( -37.80)
>consensus
UCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCAACU______CGGCGGCAAAGUUCAAUUUUAAUAUCAUAUU
..(((((((.....(((((..(((((((....(((((....)))))(((.(((......))))))..)))))))..)))))........)))))))........................ (-32.96 = -32.88 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,609,525 – 20,609,645
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -31.22
Consensus MFE -28.72
Energy contribution -29.04
Covariance contribution 0.32
Combinations/Pair 1.06
Mean z-score -1.34
Structure conservation index 0.92
SVM decision value 0.70
SVM RNA-class probability 0.826453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20609525 120 + 23771897
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGAAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGAAUCAUUUAUUGAGUUAUUCAAAUGAAAUGCCAGCUAUGUG
((((..((((((((((((((.........)))))..((......))....)))))))))..))))....((.((((.....(((.....)))....(((....))).)))).))...... ( -29.70)
>DroSec_CAF1 54384 120 + 1
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGAAUCAUUUAUUGAGUUAUUCAAAUGAAAUGCCAGCUAUGUG
((((..((((((((((((((.........)))))..(((....)))....)))))))))..))))....((.((((.....(((.....)))....(((....))).)))).))...... ( -32.40)
>DroAna_CAF1 76204 120 + 1
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGCCUGUAACUAAUUAAAUGCACUUGCAAAUUGCCGGCAACGAAUCACUUAUUGAGUUAUUCAAAUGAAAUGCCAGCAAUGCG
((((..(((((((((...(((.....)))..(((....))).........)))))))))..)))).(((((.((((..((((.((((...)))).))))........)))).)))))... ( -33.20)
>DroSim_CAF1 49214 120 + 1
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGACAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGAAUCAUUUAUUGAGUUAUUCAAAUGAAAUGCCAGCUAUGUG
((((..((((((((((((((((.((......)).....)))))..)))...))))))))..))))....((.((((.....(((.....)))....(((....))).)))).))...... ( -27.80)
>DroEre_CAF1 46869 120 + 1
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGGCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGAAUCAUUUAUUGAGUUAUUCAAAUGAAAUGCCAGCUAUGUG
((((..((((((((((((((.........)))))...((((....)))).)))))))))..))))....((.((((.....(((.....)))....(((....))).)))).))...... ( -33.00)
>consensus
UGCACUUGCAUUUGAGCCGGAUCUCUUCCCUGGCAACUGUCCGCAGCUAAUUAAAUGCACUUGCAAAUUGCCGGCGACGAAUCAUUUAUUGAGUUAUUCAAAUGAAAUGCCAGCUAUGUG
((((..((((((((((((((.........)))))..(((....)))....)))))))))..))))....((.((((.....(((.....)))....(((....))).)))).))...... (-28.72 = -29.04 +   0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,609,525 – 20,609,645
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -35.82
Consensus MFE -32.94
Energy contribution -32.86
Covariance contribution -0.08
Combinations/Pair 1.08
Mean z-score -2.12
Structure conservation index 0.92
SVM decision value 3.01
SVM RNA-class probability 0.998109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20609525 120 - 23771897
CACAUAGCUGGCAUUUCAUUUGAAUAACUCAAUAAAUGAUUCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUUCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
......((((((((.(((((((..........)))))))...)).))))))....((((..(((((((((((..(....)..))))(((.(((......))))))..)))))))..)))) ( -34.40)
>DroSec_CAF1 54384 120 - 1
CACAUAGCUGGCAUUUCAUUUGAAUAACUCAAUAAAUGAUUCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
......((((((((.(((((((..........)))))))...)).))))))....((((..(((((((....(((((....)))))(((.(((......))))))..)))))))..)))) ( -35.80)
>DroAna_CAF1 76204 120 - 1
CGCAUUGCUGGCAUUUCAUUUGAAUAACUCAAUAAGUGAUUCGUUGCCGGCAAUUUGCAAGUGCAUUUAAUUAGUUACAGGCAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
...((((((((((..((((((((.....))))...)))).....)))))))))).((((..(((((((....((((...(((....)))..(((.....))))))).)))))))..)))) ( -38.70)
>DroSim_CAF1 49214 120 - 1
CACAUAGCUGGCAUUUCAUUUGAAUAACUCAAUAAAUGAUUCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGUCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
......((((((((.(((((((..........)))))))...)).))))))....((((..(((((((....((((...(((....)))..(((.....))))))).)))))))..)))) ( -34.40)
>DroEre_CAF1 46869 120 - 1
CACAUAGCUGGCAUUUCAUUUGAAUAACUCAAUAAAUGAUUCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGCCAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
......((((((((.(((((((..........)))))))...)).))))))....((((..(((((((....((((..(((.....)))..(((.....))))))).)))))))..)))) ( -35.80)
>consensus
CACAUAGCUGGCAUUUCAUUUGAAUAACUCAAUAAAUGAUUCGUCGCCGGCAAUUUGCAAGUGCAUUUAAUUAGCUGCGGACAGUUGCCAGGGAAGAGAUCCGGCUCAAAUGCAAGUGCA
......((((((((.((((((((.....))))...))))...)).))))))....((((..(((((((....(((((....)))))(((.(((......))))))..)))))))..)))) (-32.94 = -32.86 +  -0.08)

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 12:54:38 2006