Locus 3287

Sequence ID 3L_DroMel_CAF1
Location 9,642,819 – 9,642,979
Length 160
Max. P 0.996394
window5111 window5112 window5113 window5114

overview

Window 1

Location 9,642,819 – 9,642,939
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.78
Mean single sequence MFE -39.78
Consensus MFE -32.28
Energy contribution -32.28
Covariance contribution 0.00
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.81
SVM decision value 0.01
SVM RNA-class probability 0.536821
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9642819 120 + 23771897
GUUGAGGAAAGUGAACAGGAUGCGCGUGCAGUUCUCCAGCAGCUGCGGAUAGGUGUCGGUGACGUCGCGCACCAGAAACUGAGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGGAA
((((..(((.(....)....(((....))).)))..)))).....(((((.((((((((.((.((((.((((.....((.....))....)))).)))).)))))))))).))))).... ( -44.80)
>DroVir_CAF1 40578 120 + 1
GUUUAGAAAGACAAACAAGAUGCGCGUGCAGUUCUCCAACAAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAA
(((.((((............(((....))).))))..)))..((.(((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))).)). ( -35.92)
>DroGri_CAF1 36506 120 + 1
GUUUAGGAAGACAAACAAGAUGCGCGUGCAGUUCUCCAACAAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAA
.....(((..((........(((....)))))..))).....((.(((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))).)). ( -39.20)
>DroWil_CAF1 58614 120 + 1
AUUUAAAAAUACAAACAAUAUACGCGUACAAUUCUCCAAUAAUUGCGGAUAGGUGUCGGUGACAUCGCGCACUAGAAACUGUGUGUAACCGUGCACAACAUCCUGACGCCAAUCCGGAAA
..........................................((.(((((.((((((((.((....((((((........))))))....((.....)).)))))))))).))))).)). ( -31.10)
>DroMoj_CAF1 40559 120 + 1
GGUUAGGAGAACAAACAAGAUGCGCGUACAGUUCUCCAACAAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAA
.(((.(((((((..................))))))))))..((.(((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))).)). ( -44.17)
>DroAna_CAF1 51045 120 + 1
GUUGAGAAAGUUGAACAAGAUACGCGUGCAGUUCUCCAGGAGUUGCGGAUAGGUGUCGGUGACGUCGCGCACCAGAAACUGGGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAA
...(((((...((.((.........)).)).)))))......((.(((((.((((((((.((.((((.(((((((...)))((.....)))))).)))).)))))))))).))))).)). ( -43.50)
>consensus
GUUUAGAAAGACAAACAAGAUGCGCGUGCAGUUCUCCAACAAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAA
...........................((((((.......))))))((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))..... (-32.28 = -32.28 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,642,819 – 9,642,939
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.78
Mean single sequence MFE -41.70
Consensus MFE -37.65
Energy contribution -36.10
Covariance contribution -1.55
Combinations/Pair 1.22
Mean z-score -2.35
Structure conservation index 0.90
SVM decision value 2.36
SVM RNA-class probability 0.992974
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9642819 120 - 23771897
UUCCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACUCAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAGCUGCUGGAGAACUGCACGCGCAUCCUGUUCACUUUCCUCAAC
.(((.((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).))))((....)).)))(((((((....)))....))))............ ( -44.60)
>DroVir_CAF1 40578 120 - 1
UUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUUGUUGGAGAACUGCACGCGCAUCUUGUUUGUCUUUCUAAAC
....(((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))......(((((((...(((.(((.....))).))).))))))).. ( -41.10)
>DroGri_CAF1 36506 120 - 1
UUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUUGUUGGAGAACUGCACGCGCAUCUUGUUUGUCUUCCUAAAC
....(((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))......((((.(((..(((.(((.....))).))).))))))).. ( -40.00)
>DroWil_CAF1 58614 120 - 1
UUUCCGGAUUGGCGUCAGGAUGUUGUGCACGGUUACACACAGUUUCUAGUGCGCGAUGUCACCGACACCUAUCCGCAAUUAUUGGAGAAUUGUACGCGUAUAUUGUUUGUAUUUUUAAAU
.....((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).))))((((((.......))))))....(((((.....)))))........ ( -35.00)
>DroMoj_CAF1 40559 120 - 1
UUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUUGUUGGAGAACUGUACGCGCAUCUUGUUUGUUCUCCUAACC
....(((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).))))).....((((((((((...(((.......)))..))))))).))). ( -46.80)
>DroAna_CAF1 51045 120 - 1
UUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACCCAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAACUCCUGGAGAACUGCACGCGUAUCUUGUUCAACUUUCUCAAC
....(((((.((.(((.(((((((((((((((.....))(((...))))))))))))))).).))).)).))))).........(((((......(((.....)))......)))))... ( -42.70)
>consensus
UUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUUGUUGGAGAACUGCACGCGCAUCUUGUUUGUCUUCCUAAAC
....(((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))........((((((((((....)))....))))....)))..... (-37.65 = -36.10 +  -1.55)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,642,859 – 9,642,979
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.44
Mean single sequence MFE -45.37
Consensus MFE -36.48
Energy contribution -36.23
Covariance contribution -0.25
Combinations/Pair 1.09
Mean z-score -2.34
Structure conservation index 0.80
SVM decision value 0.31
SVM RNA-class probability 0.681086
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9642859 120 + 23771897
AGCUGCGGAUAGGUGUCGGUGACGUCGCGCACCAGAAACUGAGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGGAAAUCUAUGACCAAAGUCGUAAGCGACUGGUGGGUUAGAAUU
.....(((((.((((((((.((.((((.((((.....((.....))....)))).)))).)))))))))).))))).....((((...(((.(((((....)))))..)))..))))... ( -50.20)
>DroVir_CAF1 40618 120 + 1
AAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAAGUCUAUGACCAGCGUCUGCAGCGAUUGAUGCGUCAAUAUG
..((.(((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))).))......((((..(((((..........)))))))))..... ( -42.00)
>DroWil_CAF1 58654 120 + 1
AAUUGCGGAUAGGUGUCGGUGACAUCGCGCACUAGAAACUGUGUGUAACCGUGCACAACAUCCUGACGCCAAUCCGGAAAAUCAAUGACCAGCGUCUGCAGCGAUUGAUGCGUCAAUAUG
..((.(((((.((((((((.((....((((((........))))))....((.....)).)))))))))).))))).))......((((..(((((..........)))))))))..... ( -39.70)
>DroMoj_CAF1 40599 120 + 1
AAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAAGUCUUUGACCAGCGUCUGCAGCGAUUGAUACGUCAGUAUG
((((((((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))...........(((....)))....)))))).((((....)))). ( -39.00)
>DroAna_CAF1 51085 120 + 1
AGUUGCGGAUAGGUGUCGGUGACGUCGCGCACCAGAAACUGGGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAAGUCAAUCACCAGCGUGGUCAGCGAUUGGUGCGUCAAAAUG
..((.(((((.((((((((.((.((((.(((((((...)))((.....)))))).)))).)))))))))).))))).)).......(((((((((.....))).)))))).......... ( -49.20)
>DroPer_CAF1 39635 120 + 1
AGCUGCGGAUAGGUGUCGGUGACGUCGCGCACCAGAAACUGGGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGGAAGUCAAUGACCAGCGUCUGCAGCGACUGGUGCGUCAGUAUG
.(((((((((.((((((((.((.((((.(((((((...)))((.....)))))).)))).)))))))))).....((..(.....)..))...))))))))).(((((....)))))... ( -52.10)
>consensus
AAUUGCGGAUAGGUGUCGGUGACAUCGCGCACCAGAAACUGUGUGUAACCGUGCACGACAUCCUGACGCCAAUCCGGAAAGUCAAUGACCAGCGUCUGCAGCGAUUGAUGCGUCAAUAUG
((((((((((.((((((((.((..(((.((((.....((.....))....)))).)))..)))))))))).))))...........(((....)))....)))))).............. (-36.48 = -36.23 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,642,859 – 9,642,979
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.44
Mean single sequence MFE -44.90
Consensus MFE -40.18
Energy contribution -39.52
Covariance contribution -0.67
Combinations/Pair 1.10
Mean z-score -2.74
Structure conservation index 0.89
SVM decision value 2.69
SVM RNA-class probability 0.996394
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9642859 120 - 23771897
AAUUCUAACCCACCAGUCGCUUACGACUUUGGUCAUAGAUUUCCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACUCAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAGCU
...((((..(((..(((((....))))).)))...)))).....(((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))..... ( -46.90)
>DroVir_CAF1 40618 120 - 1
CAUAUUGACGCAUCAAUCGCUGCAGACGCUGGUCAUAGACUUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUU
...(((((....)))))...(((.(((....)))...........((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))))... ( -40.50)
>DroWil_CAF1 58654 120 - 1
CAUAUUGACGCAUCAAUCGCUGCAGACGCUGGUCAUUGAUUUUCCGGAUUGGCGUCAGGAUGUUGUGCACGGUUACACACAGUUUCUAGUGCGCGAUGUCACCGACACCUAUCCGCAAUU
.........((((((((.(((((....)).))).)))))).....((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))).... ( -41.90)
>DroMoj_CAF1 40599 120 - 1
CAUACUGACGUAUCAAUCGCUGCAGACGCUGGUCAAAGACUUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGAUGUCACCGACACCUAUCCGCAAUU
.((((....)))).......(((.(((....)))...........((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))))... ( -40.00)
>DroAna_CAF1 51085 120 - 1
CAUUUUGACGCACCAAUCGCUGACCACGCUGGUGAUUGACUUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACCCAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAACU
.........((..((((((((.........)))))))).......((((.((.(((.(((((((((((((((.....))(((...))))))))))))))).).))).)).)))))).... ( -47.80)
>DroPer_CAF1 39635 120 - 1
CAUACUGACGCACCAGUCGCUGCAGACGCUGGUCAUUGACUUCCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACCCAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAGCU
......(((......)))(((((.(((....)))...........((((.((.(((.(((((((((((((((.....))(((...))))))))))))))).).))).)).))))))))). ( -52.30)
>consensus
CAUACUGACGCACCAAUCGCUGCAGACGCUGGUCAUAGACUUUCCGGAUUGGCGUCAGGAUGUCGUGCACGGUUACACACAGUUUCUGGUGCGCGACGUCACCGACACCUAUCCGCAACU
..................((....(((....)))...........((((.((.(((.(((((((((((((((..((.....))..)).)))))))))))).).))).)).)))))).... (-40.18 = -39.52 +  -0.67)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:59 2006