Locus 6655

Sequence ID 3L_DroMel_CAF1
Location 17,720,401 – 17,720,561
Length 160
Max. P 0.785442
window10821 window10822 window10823

overview

Window 1

Location 17,720,401 – 17,720,521
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.06
Mean single sequence MFE -41.80
Consensus MFE -30.61
Energy contribution -31.58
Covariance contribution 0.97
Combinations/Pair 1.22
Mean z-score -2.70
Structure conservation index 0.73
SVM decision value 0.57
SVM RNA-class probability 0.785442
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17720401 120 + 23771897
ACAUAAAAGUCGUCGGUCAGAGGGGCGGAGUUCCAGAAACACGGAUAGUCCGAACCAAUUACAAUUGGAAAUCCGGCGGCAAUCAAAUACGCCGCCGGAUGUUGACGAAAAUCGUUAAAG
.........(((((((.(...((..((((.((((........))).).))))..))..............((((((((((..........))))))))))))))))))............ ( -42.40)
>DroVir_CAF1 1971 120 + 1
ACAUAGAAAUCAUCGGUGAGCGGUGCCGCAUUCCAGAAAUAUGGAUAGUCCGAGCCAACAACGAUGGGAUAGCCAGCAGCAAUCAGAUACGCCGCCGGAUGUUGACUAAAAUCGUUCACA
...............(((((((((.......((((......))))(((((....(((.......)))((((.((.((.((..........)).)).)).)))))))))..))))))))). ( -30.10)
>DroPse_CAF1 4127 120 + 1
ACGUAGAAGUCGUCGGUGAGAGGGGCUGCGUCCCAGAAAUGGGGAUAAUCGGAGCCCAUAACGAUGGGGUAGCCUGCAGCUAGCAAAUACGCUGCCGGAUGCUCGCGGAAAUCUUGGAUA
..((..(((...((.(((((..(((((((.(((((....)))))..........(((((....))))))))))))(((((((.....)).)))))......))))).))...)))..)). ( -45.30)
>DroSim_CAF1 1667 120 + 1
ACAUAGAAGUCGUCGGUCAGAGGGGCGGAGUUCCAGAAACACGGAUAGUCCGACCCAAUUACAAUUGGAAAUCCGGCGGCAAUCAGAUACGCCGCCGGAUGUUGACGAAAAUCGUUAAAG
.....((..(((((((.(...(((.((((.((((........))).).)))).)))..............((((((((((..........))))))))))))))))))...))....... ( -44.60)
>DroEre_CAF1 16044 120 + 1
ACGUAGAAGUCGUCGGUCAGAGGGGCGGAGUUCCAGAAACACGGAUAAUCCGACCCAAUUACAAUUGGAAAACCGGCGGCAAUCAGAUACGCCGCCGGAUGUUGACGAAAGUCGUUAAAG
.....((..(((((((.((..(((.((((..(((........)))...)))).)))................((((((((..........)))))))).)))))))))...))....... ( -44.90)
>DroYak_CAF1 16350 120 + 1
ACAUAGAAGUCGUCGGUGAGAGGGGCGGAGUUCCAGAAACACGGAUAGUCCGACCCAAUUACAAUUGGAAAGCCGGCGGCAAUCAGAUACGCCGCCGGAUGUUGGCGGAAAUCGUUGAAG
.....((..((((((((((..(((.((((.((((........))).).)))).)))..))))..........((((((((..........))))))))....))))))...))....... ( -43.50)
>consensus
ACAUAGAAGUCGUCGGUCAGAGGGGCGGAGUUCCAGAAACACGGAUAGUCCGACCCAAUUACAAUUGGAAAGCCGGCGGCAAUCAGAUACGCCGCCGGAUGUUGACGAAAAUCGUUAAAG
.....((..(((((((.....(((.((((..(((........)))...)))).)))................((((((((..........))))))))...)))))))...))....... (-30.61 = -31.58 +   0.97)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,720,401 – 17,720,521
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.06
Mean single sequence MFE -37.59
Consensus MFE -25.70
Energy contribution -26.68
Covariance contribution 0.98
Combinations/Pair 1.31
Mean z-score -2.14
Structure conservation index 0.68
SVM decision value 0.03
SVM RNA-class probability 0.547952
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17720401 120 - 23771897
CUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUUUGAUUGCCGCCGGAUUUCCAAUUGUAAUUGGUUCGGACUAUCCGUGUUUCUGGAACUCCGCCCCUCUGACCGACGACUUUUAUGU
............(((((...(((((((((((........)))))))))))........((....((..((((...((((......))))..))))..))....)).)))))......... ( -40.30)
>DroVir_CAF1 1971 120 - 1
UGUGAACGAUUUUAGUCAACAUCCGGCGGCGUAUCUGAUUGCUGCUGGCUAUCCCAUCGUUGUUGGCUCGGACUAUCCAUAUUUCUGGAAUGCGGCACCGCUCACCGAUGAUUUCUAUGU
.......((..((((((((((.(((((((((........)))))))))............)))))))((((....((((......))))..(((....)))...)))))))..))..... ( -35.42)
>DroPse_CAF1 4127 120 - 1
UAUCCAAGAUUUCCGCGAGCAUCCGGCAGCGUAUUUGCUAGCUGCAGGCUACCCCAUCGUUAUGGGCUCCGAUUAUCCCCAUUUCUGGGACGCAGCCCCUCUCACCGACGACUUCUACGU
......(((..((..(((((...((((((((....)))).))))...))).............(((((.((....((((.......)))))).))))).......))..))..))).... ( -31.30)
>DroSim_CAF1 1667 120 - 1
CUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGAUUUCCAAUUGUAAUUGGGUCGGACUAUCCGUGUUUCUGGAACUCCGCCCCUCUGACCGACGACUUCUAUGU
.......((...(((((...(((((((((((........)))))))))))........((....(((.((((...((((......))))..)))).)))....)).)))))..))..... ( -43.90)
>DroEre_CAF1 16044 120 - 1
CUUUAACGACUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGUUUUCCAAUUGUAAUUGGGUCGGAUUAUCCGUGUUUCUGGAACUCCGCCCCUCUGACCGACGACUUCUACGU
............(((((.....(((((((((........)))))))))..........((....(((.((((...((((......))))..)))).)))....)).)))))......... ( -40.50)
>DroYak_CAF1 16350 120 - 1
CUUCAACGAUUUCCGCCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGCUUUCCAAUUGUAAUUGGGUCGGACUAUCCGUGUUUCUGGAACUCCGCCCCUCUCACCGACGACUUCUAUGU
.......((..((.........(((((((((........)))))))))................(((.((((...((((......))))..)))).)))..........))..))..... ( -34.10)
>consensus
CUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGCUUUCCAAUUGUAAUUGGGUCGGACUAUCCGUGUUUCUGGAACUCCGCCCCUCUCACCGACGACUUCUAUGU
.......((...(((((.....(((((((((........)))))))))....(((((....)))))..((((...((((......))))..))))...........)))))..))..... (-25.70 = -26.68 +   0.98)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,720,441 – 17,720,561
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.89
Mean single sequence MFE -36.38
Consensus MFE -26.33
Energy contribution -26.28
Covariance contribution -0.05
Combinations/Pair 1.29
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.05
SVM RNA-class probability 0.556969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17720441 120 - 23771897
CCGUGGAGAUCUGUCCGCUGUCCAACCAUUAUCUGCAAUACUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUUUGAUUGCCGCCGGAUUUCCAAUUGUAAUUGGUUCGGACUAUCCGU
..(((((......))))).(((((((((.....((((((......(((.....)))....(((((((((((........))))))))))).....))))))..))))).))))....... ( -43.70)
>DroVir_CAF1 2011 120 - 1
CCGCCGAGGUGUGUCCACUGUCCAAUUAUUAUCUGCAGUAUGUGAACGAUUUUAGUCAACAUCCGGCGGCGUAUCUGAUUGCUGCUGGCUAUCCCAUCGUUGUUGGCUCGGACUAUCCAU
.......((...(((((((((.............)))))..............((((((((.(((((((((........)))))))))............)))))))).))))...)).. ( -33.94)
>DroPse_CAF1 4167 120 - 1
CCGUAGAGUUGUGUCCGCUCUCUAACCACUAUAUGCAGUAUAUCCAAGAUUUCCGCGAGCAUCCGGCAGCGUAUUUGCUAGCUGCAGGCUACCCCAUCGUUAUGGGCUCCGAUUAUCCCC
...(((((..((....)).))))).......................(((...((.((((..((.(((((..........))))).)).....((((....))))))))))...)))... ( -27.30)
>DroSim_CAF1 1707 120 - 1
CCGUGGAGAUCUGUCCCCUGUCCAACCAUUAUCUGCAAUACUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGAUUUCCAAUUGUAAUUGGGUCGGACUAUCCGU
....(((..((((.(((.((......)).....((((((......(((.....)))....(((((((((((........))))))))))).....))))))...))).))))...))).. ( -38.80)
>DroEre_CAF1 16084 120 - 1
CCGUGGAGAUCUGUCCGCUGUCCAACCAUUAUCUGCAAUACUUUAACGACUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGUUUUCCAAUUGUAAUUGGGUCGGAUUAUCCGU
..(((((......))))).((((.(((...((.((((((........(((....))).....(((((((((........))))))))).......))))))))..))).))))....... ( -39.20)
>DroYak_CAF1 16390 120 - 1
CCGUGGAGAUCUGUCCCCUGUCCAACCAUUAUCUGCAAUACUUCAACGAUUUCCGCCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGCUUUCCAAUUGUAAUUGGGUCGGACUAUCCGU
..(((((((((....................................)))))))))......(((((((((........)))))))))...((((((....)))))).(((.....))). ( -35.32)
>consensus
CCGUGGAGAUCUGUCCGCUGUCCAACCAUUAUCUGCAAUACUUUAACGAUUUUCGUCAACAUCCGGCGGCGUAUCUGAUUGCCGCCGGCUUUCCAAUUGUAAUUGGGUCGGACUAUCCGU
....(((.....((((..............................................(((((((((........)))))))))....(((((....)))))...))))..))).. (-26.33 = -26.28 +  -0.05)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:39 2006