Locus 6181

Sequence ID X_DroMel_CAF1
Location 15,771,806 – 15,772,006
Length 200
Max. P 0.955396
window10071 window10072 window10073 window10074

overview

Window 1

Location 15,771,806 – 15,771,926
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.94
Mean single sequence MFE -27.91
Consensus MFE -20.66
Energy contribution -22.73
Covariance contribution 2.06
Combinations/Pair 1.09
Mean z-score -3.30
Structure conservation index 0.74
SVM decision value 1.19
SVM RNA-class probability 0.928752
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15771806 120 + 22224390
GAUGAUAGCUAGCGAAAGUGUGUUAAAACACAACAAAAUAAUAAUGAAAAGGUGGUAACUUUGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUA
.(((((((((.(((...((((......)))).............((....((((..((((((((....))))))))....))))....))................))).))))))))). ( -30.60)
>DroSec_CAF1 2390 120 + 1
GAUGAUAGCUAGCGAAAUUGUGUUAUAACACAAAAAAAUAAUAAUGAAAAGGUGGUAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGGAAAGAAAAAGUGCAGUUUGUUAUA
....(((((.(((....((((((....)))))).................((((..(((((.((....)).)))))....))))..((((.((..........)).))))))).))))). ( -23.50)
>DroEre_CAF1 2542 116 + 1
GAUGAUAGCUAGCACAAGCGUGUUAUAACAGAA-AAAAUAAUAACGAAAAGG---UAACUUUGGCGAGCCAAAGUUCAAGUACCGAUGCAGUUAAAAAUGAAAAAGUGCAGGUUGUUAUA
.(((((((((.((((..(((((((((.......-......))))).....((---(((((((((....))))))).....)))).)))).........(....).)))).))))))))). ( -30.42)
>DroYak_CAF1 2519 116 + 1
GUUGAUAGCUAGCAAAAGCGUGUUAUAACACAA-AAAAUAAUAACGAAAAGG---UAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGCCUUA
((((...(((......)))((((....))))..-.......))))...((((---(((((((((.((((....)))).....))))((((.((..........)).))))))))))))). ( -27.10)
>consensus
GAUGAUAGCUAGCAAAAGCGUGUUAUAACACAA_AAAAUAAUAACGAAAAGG___UAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUA
.(((((((((.(((.....((((....))))..........((((.....((((..((((((((....))))))))....))))......))))............))).))))))))). (-20.66 = -22.73 +   2.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,771,806 – 15,771,926
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.94
Mean single sequence MFE -20.18
Consensus MFE -16.02
Energy contribution -16.40
Covariance contribution 0.38
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.79
SVM decision value 0.80
SVM RNA-class probability 0.852926
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15771806 120 - 22224390
UAUAACAACCUGCACUUUUUCUUUUCUAACUGCAUCGGUAUUUGAACUUUGGCUCGCCAAAGUUACCACCUUUUCAUUAUUAUUUUGUUGUGUUUUAACACACUUUCGCUAGCUAUCAUC
((((((((..((((.((..........)).))))..(((.....((((((((....))))))))...)))..............))))))))............................ ( -19.10)
>DroSec_CAF1 2390 120 - 1
UAUAACAAACUGCACUUUUUCUUUCCUAACUGCAUCGGUAUUUGAACUUUGGCUCGCCGAAGUUACCACCUUUUCAUUAUUAUUUUUUUGUGUUAUAACACAAUUUCGCUAGCUAUCAUC
.............................((((...(((.....((((((((....))))))))...))).................((((((....))))))....)).))........ ( -18.90)
>DroEre_CAF1 2542 116 - 1
UAUAACAACCUGCACUUUUUCAUUUUUAACUGCAUCGGUACUUGAACUUUGGCUCGCCAAAGUUA---CCUUUUCGUUAUUAUUUU-UUCUGUUAUAACACGCUUGUGCUAGCUAUCAUC
((((((((((((((.((..........)).))))..))).....((((((((....)))))))).---..................-...)))))))....(((......)))....... ( -21.00)
>DroYak_CAF1 2519 116 - 1
UAAGGCAACCUGCACUUUUUCUUUUCUAACUGCAUCGGUAUUUGAACUUUGGCUCGCCGAAGUUA---CCUUUUCGUUAUUAUUUU-UUGUGUUAUAACACGCUUUUGCUAGCUAUCAAC
...(((((...((.......................((((.....(((((((....)))))))))---))................-..((((....))))))..))))).......... ( -21.70)
>consensus
UAUAACAACCUGCACUUUUUCUUUUCUAACUGCAUCGGUAUUUGAACUUUGGCUCGCCAAAGUUA___CCUUUUCAUUAUUAUUUU_UUGUGUUAUAACACACUUUCGCUAGCUAUCAUC
(((((((...((((.((..........)).))))..(((.....((((((((....))))))))...)))....................)))))))....................... (-16.02 = -16.40 +   0.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,771,846 – 15,771,966
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.05
Mean single sequence MFE -27.98
Consensus MFE -22.51
Energy contribution -23.70
Covariance contribution 1.19
Combinations/Pair 1.09
Mean z-score -1.75
Structure conservation index 0.80
SVM decision value 0.33
SVM RNA-class probability 0.691154
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15771846 120 + 22224390
AUAAUGAAAAGGUGGUAACUUUGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUAGUCGUUCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAA
....((....((((..((((((((....))))))))....))))....)).((((..((((.....((((((((((...((((....)))).....)))))))))).))))...)))).. ( -31.10)
>DroSec_CAF1 2430 120 + 1
AUAAUGAAAAGGUGGUAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGGAAAGAAAAAGUGCAGUUUGUUAUAGUCGUUCGAUUUUCCCACAAAUUGCAAUCUUGUCCUAAAA
....((....((((..(((((.((....)).)))))....))))....)).((((((((((.....((((((((((...((((....)))).....)))))))))).)))).)))))).. ( -32.10)
>DroEre_CAF1 2581 117 + 1
AUAACGAAAAGG---UAACUUUGGCGAGCCAAAGUUCAAGUACCGAUGCAGUUAAAAAUGAAAAAGUGCAGGUUGUUAUAAUCGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAA
.((((.....((---(((((((((....))))))).....))))......)))).....((.....((((((((((...((((....)))).....))))))))))......))...... ( -27.20)
>DroYak_CAF1 2558 117 + 1
AUAACGAAAAGG---UAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGCCUUAGACGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAA
........((((---(((((((((.((((....)))).....))))((((.((..........)).))))))))))))).((((...((((..............)))).))))...... ( -21.54)
>consensus
AUAACGAAAAGG___UAACUUCGGCGAGCCAAAGUUCAAAUACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUAGUCGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAA
.((((.....((((..((((((((....))))))))....))))......)))).....((.....((((((((((...((((....)))).....))))))))))......))...... (-22.51 = -23.70 +   1.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,771,886 – 15,772,006
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.90
Mean single sequence MFE -29.55
Consensus MFE -25.04
Energy contribution -26.72
Covariance contribution 1.69
Combinations/Pair 1.06
Mean z-score -2.50
Structure conservation index 0.85
SVM decision value 1.45
SVM RNA-class probability 0.955396
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15771886 120 + 22224390
UACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUAGUCGUUCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAAUCGCCCUGAAAAUUCCCAUAUAAUAUAUGGGCAACGGAAA
..(((.(((..((((..((((.....((((((((((...((((....)))).....)))))))))).))))...)))).................((((((...))))))))).)))... ( -29.20)
>DroSec_CAF1 2470 120 + 1
UACCGAUGCAGUUAGGAAAGAAAAAGUGCAGUUUGUUAUAGUCGUUCGAUUUUCCCACAAAUUGCAAUCUUGUCCUAAAAUCGCCCUGAAAAUUCCCAUAUAAUAUAUGGGCAUCGGAAA
..(((((((..((((((((((.....((((((((((...((((....)))).....)))))))))).)))).)))))).................((((((...)))))))))))))... ( -38.90)
>DroEre_CAF1 2618 118 + 1
UACCGAUGCAGUUAAAAAUGAAAAAGUGCAGGUUGUUAUAAUCGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAAUCGGUCUGAAAAUUCCCAUAUAAUAUA--GGCAUCGGAAA
..(((((((.................((((((((((...((((....)))).....)))))))))).((..(.((.......)).).))..................--.)))))))... ( -27.30)
>DroYak_CAF1 2595 118 + 1
UACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGCCUUAGACGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAAUCGCCCUGAAAAUUCCCAUAUAAUAUA--GGCAUCGGAAA
..(((((((..((((..((((.....(((((((((....((((....).))).....))))))))).))))...))))..((.....))..................--.)))))))... ( -22.80)
>consensus
UACCGAUGCAGUUAGAAAAGAAAAAGUGCAGGUUGUUAUAGUCGUCCGAUUUUCCCACAAUUUGCAAUCUUGUCCUAAAAUCGCCCUGAAAAUUCCCAUAUAAUAUA__GGCAUCGGAAA
..(((((((..((((..((((.....((((((((((...((((....)))).....)))))))))).))))...)))).................((((((...)))))))))))))... (-25.04 = -26.72 +   1.69)

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 12:06:38 2006