Locus 5035

Sequence ID 3L_DroMel_CAF1
Location 13,795,461 – 13,795,674
Length 213
Max. P 0.967827
window7969 window7970 window7971 window7972 window7973 window7974

overview

Window 9

Location 13,795,461 – 13,795,581
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.92
Mean single sequence MFE -34.60
Consensus MFE -32.30
Energy contribution -32.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.93
SVM decision value 0.15
SVM RNA-class probability 0.609789
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795461 120 - 23771897
ACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGGCGACGAAGACUUAAAACGUCGUUCGACAUAAAUCCCACCC
.((((....)))).((((((............))))))....(((.((((....)))))))((((..((((....))))((((((...........))))))............)))).. ( -36.20)
>DroSec_CAF1 32516 120 - 1
ACUGCAUAAGCAGAAGUGCCCCUAUCUAAAUAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGGCGACGAAGACUUAAAACGUCGUUCGACAUAAAUCCCACCC
.((((....)))).((((((............))))))....(((.((((....)))))))((((..((((....))))((((((...........))))))............)))).. ( -36.20)
>DroSim_CAF1 28645 120 - 1
ACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGGCGACGAAGACUUAAAACGUCGUUCGACAUAAAUCCCACCC
.((((....)))).((((((............))))))....(((.((((....)))))))((((..((((....))))((((((...........))))))............)))).. ( -36.20)
>DroEre_CAF1 33564 120 - 1
ACUGCAUAAGCAGAAGUGCCCCUAUCUAAGCAGCCACUAUAUAGAAUUGGUAGCCGAGUCUGUGGAACAGCUGUUGCUGGCGACGAAGACUUAAAACGUCGUUCGACAUAAAUCCCACCC
.((((....))))...((((........((((((.....((((((.((((...)))).)))))).....))))))...)))).(((((((.......))).))))............... ( -29.80)
>consensus
ACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGGCGACGAAGACUUAAAACGUCGUUCGACAUAAAUCCCACCC
.((((....)))).((((((............)))))).........(((((.....(((.......((((....))))((((((...........))))))..))).....)))))... (-32.30 = -32.80 +   0.50)

alignment

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secondary structure

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Window 0

Location 13,795,501 – 13,795,594
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 97.31
Mean single sequence MFE -30.30
Consensus MFE -27.29
Energy contribution -27.60
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.90
SVM decision value 0.83
SVM RNA-class probability 0.861676
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795501 93 + 23771897
CCAGCAACAGCUGUUCCACAGACUGGGCUCCCAAUUCUAUAUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCG
.......((((((((.((.(((.(((....)))..)))....(((((((.(......).))))))).((((....)))).)).)))))))).. ( -31.50)
>DroSec_CAF1 32556 93 + 1
CCAGCAACAGCUGUUCCACAGACUGGGCUCCCAAUUCUAUAUAGUGCCUAUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCG
..((((.((((((.....))).))).(((((....((((.((((...)))).))))..))))).....))))...(((((((...))))))). ( -30.30)
>DroSim_CAF1 28685 93 + 1
CCAGCAACAGCUGUUCCACAGACUGGGCUCCCAAUUCUAUAUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCG
.......((((((((.((.(((.(((....)))..)))....(((((((.(......).))))))).((((....)))).)).)))))))).. ( -31.50)
>DroEre_CAF1 33604 93 + 1
CCAGCAACAGCUGUUCCACAGACUCGGCUACCAAUUCUAUAUAGUGGCUGCUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCG
.......((((((((((.......(((((((............))))))).........))(((...((((....)))).))))))))))).. ( -27.89)
>consensus
CCAGCAACAGCUGUUCCACAGACUGGGCUCCCAAUUCUAUAUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCG
.......((((((((.((........(((((....((((.((((...)))).))))..)))))....((((....)))).)).)))))))).. (-27.29 = -27.60 +   0.31)

alignment

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secondary structure

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Window 1

Location 13,795,501 – 13,795,594
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 97.31
Mean single sequence MFE -34.50
Consensus MFE -32.20
Energy contribution -32.70
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -3.02
Structure conservation index 0.93
SVM decision value 1.62
SVM RNA-class probability 0.967827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795501 93 - 23771897
CGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGG
.(((((((((.(..((((....)))).((((((............))))))..(((((.((((....)))))))))).)))))))))...... ( -36.20)
>DroSec_CAF1 32556 93 - 1
CGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAAUAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGG
.(((((((((.(..((((....)))).((((((............))))))..(((((.((((....)))))))))).)))))))))...... ( -36.20)
>DroSim_CAF1 28685 93 - 1
CGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGG
.(((((((((.(..((((....)))).((((((............))))))..(((((.((((....)))))))))).)))))))))...... ( -36.20)
>DroEre_CAF1 33604 93 - 1
CGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAGCAGCCACUAUAUAGAAUUGGUAGCCGAGUCUGUGGAACAGCUGUUGCUGG
.((((((((((((.((((....))))...)))(((...((..((.((((...........)))).))..))...).)))))))))))...... ( -29.40)
>consensus
CGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAUAUAGAAUUGGGAGCCCAGUCUGUGGAACAGCUGUUGCUGG
.(((((((((.(..((((....)))).((((((............))))))..(((((.((((....)))))))))).)))))))))...... (-32.20 = -32.70 +   0.50)

alignment

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secondary structure

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Window 2

Location 13,795,541 – 13,795,634
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 97.85
Mean single sequence MFE -35.45
Consensus MFE -32.05
Energy contribution -32.55
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -3.80
Structure conservation index 0.90
SVM decision value 0.97
SVM RNA-class probability 0.892497
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795541 93 + 23771897
AUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGG
..(((((((.(......).)))))))...((..(((((((.((....(((((((........)))))))......)).)))))))..)).... ( -35.70)
>DroSec_CAF1 32596 93 + 1
AUAGUGCCUAUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGG
..(((((((..........)))))))...((..(((((((.((....(((((((........)))))))......)).)))))))..)).... ( -34.00)
>DroSim_CAF1 28725 93 + 1
AUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGG
..(((((((.(......).)))))))...((..(((((((.((....(((((((........)))))))......)).)))))))..)).... ( -35.70)
>DroEre_CAF1 33644 93 + 1
AUAGUGGCUGCUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCCGCUUGG
..(((((.(((...(((.(..(((...((((....)))).)))..).(((((((........)))))))......)))...))).)))))... ( -36.40)
>consensus
AUAGUGCCUGUUUAGAUAGGGGCACUUCUGCUUAUGCAGUUGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGG
..(((((((.(......).)))))))...((..(((((((.((....(((((((........)))))))......)).)))))))..)).... (-32.05 = -32.55 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,795,541 – 13,795,634
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 97.85
Mean single sequence MFE -34.27
Consensus MFE -33.39
Energy contribution -33.45
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -3.99
Structure conservation index 0.97
SVM decision value 1.51
SVM RNA-class probability 0.960392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795541 93 - 23771897
CCAAGCAGAUGCAAUGACUUUAUGGCUGCGCAUUUGUAAGCGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAU
....((((.((((((........((((((((........)))))))))))))).)))).........((((((............)))))).. ( -35.30)
>DroSec_CAF1 32596 93 - 1
CCAAGCAGAUGCAAUGACUUUAUGGCUGCGCAUUUGUAAGCGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAAUAGGCACUAU
....((((.((((((........((((((((........)))))))))))))).)))).........((((((............)))))).. ( -35.30)
>DroSim_CAF1 28725 93 - 1
CCAAGCAGAUGCAAUGACUUUAUGGCUGCGCAUUUGUAAGCGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAU
....((((.((((((........((((((((........)))))))))))))).)))).........((((((............)))))).. ( -35.30)
>DroEre_CAF1 33644 93 - 1
CCAAGCGGAUGCAAUGACUUUAUGGCUGCGCAUUUGUAAGCGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAGCAGCCACUAU
...((.((.(((.........((((((((((........)))))))))).(((.((((....))))...)))..........))).)).)).. ( -31.20)
>consensus
CCAAGCAGAUGCAAUGACUUUAUGGCUGCGCAUUUGUAAGCGCAGCUGUUGCAACUGCAUAAGCAGAAGUGCCCCUAUCUAAACAGGCACUAU
....((((.((((((........((((((((........)))))))))))))).)))).........((((((............)))))).. (-33.39 = -33.45 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,795,581 – 13,795,674
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 99.46
Mean single sequence MFE -22.03
Consensus MFE -22.02
Energy contribution -22.02
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 1.00
SVM decision value -0.01
SVM RNA-class probability 0.526459
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13795581 93 + 23771897
UGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGGCCAGCAUAUUUGAAAUAAUUCUUUCUAAGCUCAUCUGGUU
(((....(((((((........)))))))......((((..((....)).))))..))).....((((......))))............... ( -22.10)
>DroSec_CAF1 32636 93 + 1
UGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGGCCAGCAUAUUUGAAAUAAUUCUUUCUAAGCUCAUCUGGUU
(((....(((((((........)))))))......((((..((....)).))))..))).....((((......))))............... ( -22.10)
>DroSim_CAF1 28765 93 + 1
UGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGGCCAGCAUAUUUGAAAUAAUUCUUUCUAAGCUCAUCUGGUU
(((....(((((((........)))))))......((((..((....)).))))..))).....((((......))))............... ( -22.10)
>DroEre_CAF1 33684 93 + 1
UGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCCGCUUGGCCAGCAUAUUUGAAAUAAUUCUUUCUAAGCUCAUCUGGUU
(((....(((((((........)))))))......((((..((....)).))))..))).....((((......))))............... ( -21.80)
>consensus
UGCAACAGCUGCGCUUACAAAUGCGCAGCCAUAAAGUCAUUGCAUCUGCUUGGCCAGCAUAUUUGAAAUAAUUCUUUCUAAGCUCAUCUGGUU
(((....(((((((........)))))))......((((..((....)).))))..))).....((((......))))............... (-22.02 = -22.02 +   0.00)

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 11:40:16 2006