Locus 6706

Sequence ID 2L_DroMel_CAF1
Location 18,733,630 – 18,733,870
Length 240
Max. P 0.998154
window10708 window10709 window10710 window10711 window10712

overview

Window 8

Location 18,733,630 – 18,733,750
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -28.68
Consensus MFE -25.38
Energy contribution -25.82
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.27
Structure conservation index 0.88
SVM decision value 0.02
SVM RNA-class probability 0.542131
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18733630 120 - 22407834
AUAAUUAAAUAUGUAAGAGGCAAGAGCCCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGUUAAAAAUUUAAUAAUCGCCUGCGAGUAUAAGGCGGCCAGAUGCA
...........((((...((((((((....((((......))))(((........)))))))))))((((....(((((....)))))....((((.........))))))))...)))) ( -29.80)
>DroSec_CAF1 26155 120 - 1
AUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGCUGAAAAUUUAAUAAUCGCCUGCGAGUAUAAGGCGGCCAGAUGCA
...(((((((..(((((((((.(((......)))........(((......)))..)))))))))((((.....))))...)))))))..((((((.........))))))......... ( -29.00)
>DroSim_CAF1 24710 120 - 1
AUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGCUGAAAAUUUAAUAAUCGCCUGCGAGUACAAGGCGGCCAGAUGCA
...(((((((..(((((((((.(((......)))........(((......)))..)))))))))((((.....))))...)))))))..((((((.........))))))......... ( -29.00)
>DroEre_CAF1 26184 120 - 1
AUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGCUGAAAAUUUAAUAAUCGCCUGCGAGUACAAAGCGGCCAGUUGCA
...(((((((..(((((((((.(((......)))........(((......)))..)))))))))((((.....))))...)))))))....(((.((.........)))))........ ( -26.60)
>DroYak_CAF1 26257 120 - 1
AUAAUUAAAUAUGUAAGAGGCAAGCGACCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGCUGAAAAUUUAAUAAUCGCCUGCGAGCAUAAGGCGGCCAGAUGCA
...(((((((..(((((((((.(((......)))........(((......)))..)))))))))((((.....))))...)))))))..((((((.........))))))......... ( -29.00)
>consensus
AUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAACAGCUGCUACCACAGAAGCCUUUUGCCGGCCAAACGCUGAAAAUUUAAUAAUCGCCUGCGAGUAUAAGGCGGCCAGAUGCA
...(((((((..(((((((((.(((......)))........(((......)))..)))))))))((((.....))))...)))))))..((((((.........))))))......... (-25.38 = -25.82 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,733,710 – 18,733,830
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.66
Mean single sequence MFE -42.76
Consensus MFE -38.58
Energy contribution -38.98
Covariance contribution 0.40
Combinations/Pair 1.05
Mean z-score -2.28
Structure conservation index 0.90
SVM decision value 3.02
SVM RNA-class probability 0.998154
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18733710 120 + 22407834
GUUAUUAACUUGGGCUCUUGCCUCUUACAUAUUUAAUUAUUUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGG
.........((((((.............(((......))).(((((.((((..((((..(....)..))))((((((((...)))))))).........))))...)))))))))))... ( -42.40)
>DroSec_CAF1 26235 120 + 1
GUUAUUAACUUGGGCGCUUGCCUCUUACAUAUUUAAUUAUUUGGGCGGGCCAGGUCUUUAAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGA
.........((((((((((((((.......((((((..((((((.....))))))..))))))....)))))))).(((.....(((((.((....)).)))))...))).))))))... ( -43.50)
>DroSim_CAF1 24790 120 + 1
GUUAUUAACUUGGGCGCUUGCCUCUUACAUAUUUAAUUAUUUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGA
.........((((((((((((((.......((((((..((((((.....))))))..))))))....)))))))).(((.....(((((.((....)).)))))...))).))))))... ( -43.60)
>DroEre_CAF1 26264 118 + 1
GUUAUUAACUUGGGCGCUUGCCUCUUACAUAUUUAAUUAUUUGG--GGGCCAGGCCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUUGGCCACAGCCCAGCCCAAUGA
.........((((((((((((((((...(((......)))..))--))).)))))...........(((((((((((((...))))))))...((.....))....)))))))))))... ( -44.70)
>DroYak_CAF1 26337 118 + 1
GUUAUUAACUUGGUCGCUUGCCUCUUACAUAUUUAAUUAUUUGG--GGGCCAGGCCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUUGGCCACAGCCCAGCCCAAUGA
................((.((((((...(((......)))..))--)))).))((((..(....)..))))((((.(((.....(((((..........)))))...))).))))..... ( -39.60)
>consensus
GUUAUUAACUUGGGCGCUUGCCUCUUACAUAUUUAAUUAUUUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGA
.........((((((((((((((((((.(((......))).)))).))).)))))...........(((((.((((((((((.(......).)).))))))))...)))))))))))... (-38.58 = -38.98 +   0.40)

alignment

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secondary structure

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Window 0

Location 18,733,710 – 18,733,830
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -36.80
Consensus MFE -32.22
Energy contribution -32.82
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.88
SVM decision value 1.28
SVM RNA-class probability 0.940074
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18733710 120 - 22407834
CCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAAAUAAUUAAAUAUGUAAGAGGCAAGAGCCCAAGUUAAUAAC
...(((((((((((.(.(((((...(((((......)))))..))))))))))..............((.((((...((.((......)).))...).))).)))))))))......... ( -36.90)
>DroSec_CAF1 26235 120 - 1
UCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUUAAAGACCUGGCCCGCCCAAAUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAAC
...(((((((((((.(.(((((...(((((......)))))..)))))))))))................((..((((..(((........)))..).)))..))))))))......... ( -37.10)
>DroSim_CAF1 24790 120 - 1
UCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAAAUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAAC
...(((((((((((.(.(((((...(((((......)))))..)))))))))))................((..((((..(((........)))..).)))..))))))))......... ( -37.10)
>DroEre_CAF1 26264 118 - 1
UCAUUGGGCUGGGCUGUGGCCAAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGGCCUGGCCC--CCAAAUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAAC
((.((((((.(((((((((((..........))))).......)))))))))))))).......(((((.((((--....(((......)))....).))).)).)))............ ( -37.91)
>DroYak_CAF1 26337 118 - 1
UCAUUGGGCUGGGCUGUGGCCAAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGGCCUGGCCC--CCAAAUAAUUAAAUAUGUAAGAGGCAAGCGACCAAGUUAAUAAC
((.((((((.(((((((((((..........))))).......)))))))))))))).......(((((.((((--....(((......)))....).))).)).).))........... ( -35.01)
>consensus
UCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAAAUAAUUAAAUAUGUAAGAGGCAAGCGCCCAAGUUAAUAAC
...(((((((((((.(.(((((...(((((......)))))..))))))))))).............((.((((...((.((......)).))...).))).)).))))))......... (-32.22 = -32.82 +   0.60)

alignment

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secondary structure

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Window 1

Location 18,733,750 – 18,733,870
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.16
Mean single sequence MFE -43.14
Consensus MFE -39.46
Energy contribution -39.90
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 0.91
SVM decision value 1.51
SVM RNA-class probability 0.960181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18733750 120 + 22407834
UUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGGCCAACCUAUUGGCCUUAAUAUCUGCUGUCGAUCUGUCCAU
.(((((((((((((..........)))))((((((.(((.....(((((.((....)).)))))...))).))))...((((((....)))))).........))......)))))))). ( -48.10)
>DroSec_CAF1 26275 120 + 1
UUGGGCGGGCCAGGUCUUUAAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGACCAACCUAUUGGCCUUAAUAUCCGCUGUCGAUCUGUCCAU
.(((((((..(.((((.........((((((((((.((....))(((((.((....)).)))))..)))).)))))).))))..((....)).................)..))))))). ( -41.50)
>DroSim_CAF1 24830 120 + 1
UUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGACCAACCUAUUGGCCUUAAUAUCCGCUGUCGAUCUGUCCAU
.((((((((((((((((..(....)..))))((((.(((.....(((((.((....)).)))))...))).)))).............))))))).......((....))....))))). ( -42.90)
>DroEre_CAF1 26304 118 + 1
UUGG--GGGCCAGGCCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUUGGCCACAGCCCAGCCCAAUGACCAACCUAUUGGCCUUAAUAUCCGCUGUCGAUUCGUCCAU
.(((--(((((((((((..(....)..))))((((.(((.....(((((..........)))))...))).)))).............))))))).......((....))......))). ( -41.60)
>DroYak_CAF1 26377 118 + 1
UUGG--GGGCCAGGCCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUUGGCCACAGCCCAGCCCAAUGACCAACCUAUUGGCCUUAAUAUCCGCUGUCGAUUUGUCCAU
.(((--(((((((((((..(....)..))))((((.(((.....(((((..........)))))...))).)))).............))))))).......((....))......))). ( -41.60)
>consensus
UUGGGCGGGCCAGGUCUUUGAAUUCUUGGGCGGGCCGGGACACUUGGCCUAAUGCUUUCGGCCACAGCCCAGCCCAAUGACCAACCUAUUGGCCUUAAUAUCCGCUGUCGAUCUGUCCAU
.((((((((((((((((..(....)..))))((((.(((.....(((((.((....)).)))))...))).)))).............))))))........((....))...)))))). (-39.46 = -39.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,733,750 – 18,733,870
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.16
Mean single sequence MFE -43.93
Consensus MFE -42.67
Energy contribution -42.27
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.97
SVM decision value 2.82
SVM RNA-class probability 0.997239
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18733750 120 - 22407834
AUGGACAGAUCGACAGCAGAUAUUAAGGCCAAUAGGUUGGCCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAA
..((.(((.((...............((((((....)))))).((((((.(((((((((((..........))))).......)))))))))))).........)).)))..))...... ( -45.51)
>DroSec_CAF1 26275 120 - 1
AUGGACAGAUCGACAGCGGAUAUUAAGGCCAAUAGGUUGGUCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUUAAAGACCUGGCCCGCCCAA
.(((.(...(((....))).......(((((...((((..((.((((((.(((((((((((..........))))).......)))))))))))))).......))))))))).).))). ( -43.81)
>DroSim_CAF1 24830 120 - 1
AUGGACAGAUCGACAGCGGAUAUUAAGGCCAAUAGGUUGGUCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAA
.(((.(...(((....))).......(((((...((((.(...((((((.(((((((((((..........))))).......)))))))))))).....)...))))))))).).))). ( -43.81)
>DroEre_CAF1 26304 118 - 1
AUGGACGAAUCGACAGCGGAUAUUAAGGCCAAUAGGUUGGUCAUUGGGCUGGGCUGUGGCCAAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGGCCUGGCCC--CCAA
.(((..(((((....((.........((((((....))))))...(((((((((..(((((..........)))))...).))))))))))....).))))...(((...))).--))). ( -43.90)
>DroYak_CAF1 26377 118 - 1
AUGGACAAAUCGACAGCGGAUAUUAAGGCCAAUAGGUUGGUCAUUGGGCUGGGCUGUGGCCAAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGGCCUGGCCC--CCAA
.(((.....(((....))).......(((((.....((((...((((((.(((((((((((..........))))).......))))))))))))....)))).....))))).--))). ( -42.61)
>consensus
AUGGACAGAUCGACAGCGGAUAUUAAGGCCAAUAGGUUGGUCAUUGGGCUGGGCUGUGGCCGAAAGCAUUAGGCCAAGUGUCCCGGCCCGCCCAAGAAUUCAAAGACCUGGCCCGCCCAA
.(((....(((.......))).....(((((...((((.(...((((((.(((((((((((..........))))).......)))))))))))).....)...)))))))))...))). (-42.67 = -42.27 +  -0.40)

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 12:18:05 2006