Locus 3415

Sequence ID X_DroMel_CAF1
Location 9,129,221 – 9,129,399
Length 178
Max. P 0.959334
window5584 window5585 window5586 window5587 window5588

overview

Window 4

Location 9,129,221 – 9,129,319
Length 98
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 76.70
Mean single sequence MFE -32.04
Consensus MFE -24.77
Energy contribution -25.15
Covariance contribution 0.38
Combinations/Pair 1.08
Mean z-score -1.60
Structure conservation index 0.77
SVM decision value 0.70
SVM RNA-class probability 0.825372
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9129221 98 - 22224390
UCGCAUUUAAGCGCGCUCUCUUUAAUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUCAGCCGGGAAAUUUCGAAAAUAUUUAGG--------------------AGCUG
((((.(((((((((((((((...........)))))))))....)))))).)))).(((((((......((((....))))........))))--------------------))).. ( -30.84)
>DroSec_CAF1 5228 102 - 1
UCGCAGUUAAGCGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGUCGGGAAAUUUCGAAAAUAUU----------------UACUUAAUAACUG
...((((((..(((((((((..(.....)..))))))))).((((((((((((...)))))...)))))))..................----------------.......)))))) ( -33.70)
>DroSim_CAF1 3875 111 - 1
UCGC-------CGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGUCGGGAAAUUUCGAAAAUAUUUAAGAGUUUACCUUUUUACCUAAUAACUG
....-------(((((((((..(.....)..))))))))).((((((((((((...)))))...)))))))((((((((..((.....))..)))))).))................. ( -31.50)
>DroYak_CAF1 5175 115 - 1
UCGCAUACAA-CGCGCUCUCUUCAUUCAGCUGAGAGCGUGGCGACUUAAGAGCGGCGUUUUGGUCGAGCCGGGAAAUUUCGAAAAUAUUUAAGAGGCUUG--AGGAACUUAUUAUAUG
..((......-(((((((((..(.....)..)))))))))((.........)).))(((((..(((((((...((((.........))))....))))))--)))))).......... ( -32.10)
>consensus
UCGCAUUUAA_CGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGCCGGGAAAUUUCGAAAAUAUUUAAG____________UACUUAAUAACUG
(((........(((((((((...........))))))))).((((((((((((...)))))))...)))))........))).................................... (-24.77 = -25.15 +   0.38)

alignment

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secondary structure

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Window 5

Location 9,129,239 – 9,129,359
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.96
Mean single sequence MFE -42.08
Consensus MFE -31.75
Energy contribution -33.62
Covariance contribution 1.88
Combinations/Pair 1.08
Mean z-score -2.11
Structure conservation index 0.75
SVM decision value 0.53
SVM RNA-class probability 0.770717
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9129239 120 + 22224390
GAAAUUUCCCGGCUGAACAAGAGCGCCGCUCUUAAGUCGUCACGCUCUCAGCUGAUUAAAGAGAGCGCGCUUAAAUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGUGGUGGAUGAAAAU
......((((((((((((..((((((.((((((...(.((((.((.....)))))).)..)))))))))))).....((.((((....)))).))))).))))))).))........... ( -43.10)
>DroSec_CAF1 5250 120 + 1
GAAAUUUCCCGACUCAACAAGAGCGCCGCUCUUAAGUCGUCACGCUCUCAGCUGAAUGAAGAGAGCGCGCUUAACUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAU
...(((..((((((....((((((...)))))).))))(((.(((((((..(.....)..))))))).(((((((..(...(((....))).)..)))).))).)))))..)))...... ( -41.00)
>DroSim_CAF1 3913 113 + 1
GAAAUUUCCCGACUCAACAAGAGCGCCGCUCUUAAGUCGUCACGCUCUCAGCUGAAUGAAGAGAGCGCG-------GCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAU
....((((....(((.....)))(((((((......(((((.(((((((..(.....)..))))))).)-------))))((((....))))..(((....))))))))))...)))).. ( -40.00)
>DroYak_CAF1 5211 119 + 1
GAAAUUUCCCGGCUCGACCAAAACGCCGCUCUUAAGUCGCCACGCUCUCAGCUGAAUGAAGAGAGCGCG-UUGUAUGCGAUUCCAAUUGGAAGUGGUUGCAGUCGGCGGUGGUUGAAAAU
.............(((((((...(((((((.....((.(((((((((((..(.....)..))))))(((-(...))))..((((....))))))))).)))).))))).))))))).... ( -44.20)
>consensus
GAAAUUUCCCGACUCAACAAGAGCGCCGCUCUUAAGUCGUCACGCUCUCAGCUGAAUGAAGAGAGCGCG_UUAAAUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAU
......((((((((((((..((((((.((((((...((((((.((.....))))).))).)))))))))))).....((.((((....)))).)))))).)))))).))........... (-31.75 = -33.62 +   1.88)

alignment

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secondary structure

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Window 6

Location 9,129,239 – 9,129,359
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.96
Mean single sequence MFE -40.08
Consensus MFE -33.69
Energy contribution -33.50
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.84
SVM decision value 1.50
SVM RNA-class probability 0.959334
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9129239 120 - 22224390
AUUUUCAUCCACCACCGGCUGCAACCACUUCCAAUUGGAAUCGCAUUUAAGCGCGCUCUCUUUAAUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUCAGCCGGGAAAUUUC
..............(((((((.(((...((((....))))((((.(((((((((((((((...........)))))))))....)))))).)))).......))))))))))........ ( -42.10)
>DroSec_CAF1 5250 120 - 1
AUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGCAGUUAAGCGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGUCGGGAAAUUUC
.......(((......((((((......((((....))))..))))))...(((((((((..(.....)..))))))))).((((((((((((...)))))...))))))))))...... ( -40.80)
>DroSim_CAF1 3913 113 - 1
AUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGC-------CGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGUCGGGAAAUUUC
..............((((((.((((...((((....))))(((.-------(((((((((..(.....)..))))))))).)))...((((((...))))))))))))))))........ ( -40.50)
>DroYak_CAF1 5211 119 - 1
AUUUUCAACCACCGCCGACUGCAACCACUUCCAAUUGGAAUCGCAUACAA-CGCGCUCUCUUCAUUCAGCUGAGAGCGUGGCGACUUAAGAGCGGCGUUUUGGUCGAGCCGGGAAAUUUC
...(((.((((.(((((.((........((((....))))((((......-(((((((((..(.....)..)))))))))))))......)))))))...)))).)))............ ( -36.90)
>consensus
AUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGCAUUUAA_CGCGCUCUCUUCAUUCAGCUGAGAGCGUGACGACUUAAGAGCGGCGCUCUUGUUGAGCCGGGAAAUUUC
..............((((((........((((....))))...........(((((((((...........))))))))).((((...(((((...))))).))))))))))........ (-33.69 = -33.50 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,129,279 – 9,129,399
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.60
Mean single sequence MFE -43.95
Consensus MFE -38.70
Energy contribution -39.08
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.84
Structure conservation index 0.88
SVM decision value 0.79
SVM RNA-class probability 0.851860
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9129279 120 + 22224390
CACGCUCUCAGCUGAUUAAAGAGAGCGCGCUUAAAUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGUGGUGGAUGAAAAUGUGUCCACCAAUGGCGCGCCUCAAAUGCCAUGUCCACCUG
..(((((((...........)))))))(((......)))........((((.((((((((.((((.((((((((........)))))))).)))))))........))))).)))).... ( -45.90)
>DroSec_CAF1 5290 120 + 1
CACGCUCUCAGCUGAAUGAAGAGAGCGCGCUUAACUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAUGUGUCCACCAAUGGCGCGCCUCAAAUGCCAUGUCCACCUG
..(((((((..(.....)..)))))))(((......)))........((((.((((((((.((((..(((((((........)))))))..)))))))........))))).)))).... ( -45.50)
>DroSim_CAF1 3953 113 + 1
CACGCUCUCAGCUGAAUGAAGAGAGCGCG-------GCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAUGUGUCCACCAAUGGCGCGCCUCAAAUGCCAUGUCCACCUG
..(((((((..(.....)..))))))).(-------(((.((((....))))(.(((.((.((((..(((((((........)))))))..))))))))).)...))))........... ( -45.60)
>DroYak_CAF1 5251 119 + 1
CACGCUCUCAGCUGAAUGAAGAGAGCGCG-UUGUAUGCGAUUCCAAUUGGAAGUGGUUGCAGUCGGCGGUGGUUGAAAAUGUGUCCACCAAUGGCGCGCCUCAAAUGCCGUGUCCACCUG
..(((((((..(.....)..))))))).(-(((..(((((((((....)))....))))))..))))(((((............)))))..(((((((.(......).)))).))).... ( -38.80)
>consensus
CACGCUCUCAGCUGAAUGAAGAGAGCGCG_UUAAAUGCGAUUCCAAUUGGAAGUGGUUGCAGCCGGCGGUGGAUGAAAAUGUGUCCACCAAUGGCGCGCCUCAAAUGCCAUGUCCACCUG
..(((((((...........)))))))(((......)))........((((..(((((((.((((..(((((((........)))))))..)))))))........))))..)))).... (-38.70 = -39.08 +   0.37)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,129,279 – 9,129,399
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -41.08
Consensus MFE -38.29
Energy contribution -38.35
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 0.93
SVM decision value 0.63
SVM RNA-class probability 0.804385
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9129279 120 - 22224390
CAGGUGGACAUGGCAUUUGAGGCGCGCCAUUGGUGGACACAUUUUCAUCCACCACCGGCUGCAACCACUUCCAAUUGGAAUCGCAUUUAAGCGCGCUCUCUUUAAUCAGCUGAGAGCGUG
..(((((.....((.......))(((((..(((((((..........)))))))..))).))..)))))(((....)))...((......))((((((((...........)))))))). ( -41.90)
>DroSec_CAF1 5290 120 - 1
CAGGUGGACAUGGCAUUUGAGGCGCGCCAUUGGUGGACACAUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGCAGUUAAGCGCGCUCUCUUCAUUCAGCUGAGAGCGUG
..(((((.....((.......))(((((..(((((((..........)))))))..))).))..)))))(((....)))...((......))((((((((..(.....)..)))))))). ( -41.40)
>DroSim_CAF1 3953 113 - 1
CAGGUGGACAUGGCAUUUGAGGCGCGCCAUUGGUGGACACAUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGC-------CGCGCUCUCUUCAUUCAGCUGAGAGCGUG
((((((.......)))))).((((((((..(((((((..........)))))))..))).))......((((....))))..))-------)((((((((..(.....)..)))))))). ( -42.60)
>DroYak_CAF1 5251 119 - 1
CAGGUGGACACGGCAUUUGAGGCGCGCCAUUGGUGGACACAUUUUCAACCACCGCCGACUGCAACCACUUCCAAUUGGAAUCGCAUACAA-CGCGCUCUCUUCAUUCAGCUGAGAGCGUG
..(((((.((((((......((....))...(((((............)))))))))..))...)))))(((....)))...........-(((((((((..(.....)..))))))))) ( -38.40)
>consensus
CAGGUGGACAUGGCAUUUGAGGCGCGCCAUUGGUGGACACAUUUUCAUCCACCGCCGGCUGCAACCACUUCCAAUUGGAAUCGCAUUUAA_CGCGCUCUCUUCAUUCAGCUGAGAGCGUG
..(((((.....((.......))(((((..((((((............))))))..))).))..)))))(((....)))............(((((((((...........))))))))) (-38.29 = -38.35 +   0.06)

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 10:58:49 2006