Locus 3987

Sequence ID 3L_DroMel_CAF1
Location 11,608,202 – 11,608,345
Length 143
Max. P 0.993879
window6208 window6209 window6210 window6211

overview

Window 8

Location 11,608,202 – 11,608,322
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.07
Mean single sequence MFE -33.03
Consensus MFE -20.63
Energy contribution -20.51
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -3.07
Structure conservation index 0.62
SVM decision value 1.84
SVM RNA-class probability 0.979715
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11608202 120 + 23771897
UCUUGACUUUUACGUUUGGCGUAUGGAUUCUGUGGGUCGUCGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAAAUCACCGCAAUUAGCAUACAAUUCAAGUUCAAGUUCAAACU
.............((((((........(((....((((..(.....)..))))....)))..(((((((((((((..........((.....))......))))))))))))))))))). ( -27.89)
>DroSec_CAF1 101819 105 + 1
-------AUUUACGAUUGGC--------UCUGCGGGUCGUCGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACU
-------((((.((((((((--------...(((((((...)))))))..))))))))))))(((((((((((((.........(((.....))).....)))))))))))))....... ( -35.34)
>DroSim_CAF1 102305 112 + 1
UCUUGACUUUUACGAUUGGC--------UCUGCGGGUCGUCGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUGCAAUUCAAGUUCAAGUUUAAACU
............((((((((--------...(((((((...)))))))..))))))))....(((((((((((((......((.(((.....)))))...)))))))))))))....... ( -36.30)
>DroEre_CAF1 92628 118 + 1
GCUUGACUUUUACGAUUGCUAUAUGG-CUCUGUAGGUCAUCGAUCUGGUGGGUAAUUGAAAUACCUGAUCUUGAAAAAGAUCGCUGGUAUUAGCAUACAAU-CAAGUUCAAGUUUAAGCU
(((((((((..(((((((...(((((-(((..((((((...))))))..))))......(((((((((((((....)))))))..))))))..))))))))-)..))..))).)))))). ( -34.50)
>DroYak_CAF1 107065 119 + 1
UCCUGACUUUUACGAUUGGUAUAUGG-CUCUGUGGGUCGUCGAUCUGGUGGGUAAUUGAAAAACUUGAACUUGAAAAAGAUCGCUUGUAUUAGCAUACAAUUCAAGUUCAAGUUAAAACU
..((.(((.....(((((....((((-((.....))))))))))).))).)).........((((((((((((((....((.(((......)))))....))))))))))))))...... ( -31.10)
>consensus
UCUUGACUUUUACGAUUGGC_UAUGG__UCUGUGGGUCGUCGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACU
............((((((((............((((((...))))))...))))))))....(((((((((((((.........................)))))))))))))....... (-20.63 = -20.51 +  -0.12)

alignment

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secondary structure

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Window 9

Location 11,608,202 – 11,608,322
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.07
Mean single sequence MFE -25.17
Consensus MFE -17.04
Energy contribution -17.84
Covariance contribution 0.80
Combinations/Pair 1.14
Mean z-score -1.65
Structure conservation index 0.68
SVM decision value 0.02
SVM RNA-class probability 0.542411
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11608202 120 - 23771897
AGUUUGAACUUGAACUUGAAUUGUAUGCUAAUUGCGGUGAUUUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCGACGACCCACAGAAUCCAUACGCCAAACGUAAAAGUCAAGA
..((((((((((((((((((..((.(((.....)))...))....))))))))))))).......(((((.....((((...........).))).....))))).........))))). ( -27.30)
>DroSec_CAF1 101819 105 - 1
AGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCGACGACCCGCAGA--------GCCAAUCGUAAAU-------
.......(((((((((((((..(..(((.....))).....)...)))))))))))))(((((.((((((.......((..((...))..))--------)))))).).))))------- ( -24.71)
>DroSim_CAF1 102305 112 - 1
AGUUUAAACUUGAACUUGAAUUGCAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCGACGACCCGCAGA--------GCCAAUCGUAAAAGUCAAGA
.......((((((((((((((..(.(((.....))))..)).....))))))))))))......((((((.......((..((...))..))--------)))))).............. ( -26.11)
>DroEre_CAF1 92628 118 - 1
AGCUUAAACUUGAACUUG-AUUGUAUGCUAAUACCAGCGAUCUUUUUCAAGAUCAGGUAUUUCAAUUACCCACCAGAUCGAUGACCUACAGAG-CCAUAUAGCAAUCGUAAAAGUCAAGC
.((((..((((.....((-(((((..(((......)))((((((....))))))((((...((.(((........))).))..))))......-.......)))))))...)))).)))) ( -23.30)
>DroYak_CAF1 107065 119 - 1
AGUUUUAACUUGAACUUGAAUUGUAUGCUAAUACAAGCGAUCUUUUUCAAGUUCAAGUUUUUCAAUUACCCACCAGAUCGACGACCCACAGAG-CCAUAUACCAAUCGUAAAAGUCAGGA
.(....((((((((((((((..(..((((......))))..)...))))))))))))))...).........((.(((..((((.........-...........))))....))).)). ( -24.45)
>consensus
AGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCGACGACCCACAGA__CCAUA_GCCAAUCGUAAAAGUCAAGA
.......(((((((((((((.....((((......))))......))))))))))))).((((.((((((.......((...........))........)))))).).)))........ (-17.04 = -17.84 +   0.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,608,242 – 11,608,345
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.88
Mean single sequence MFE -25.11
Consensus MFE -14.11
Energy contribution -15.51
Covariance contribution 1.40
Combinations/Pair 1.12
Mean z-score -2.50
Structure conservation index 0.56
SVM decision value 1.76
SVM RNA-class probability 0.975915
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11608242 103 + 23771897
CGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAAAUCACCGCAAUUAGCAUACAAUUCAAGUUCAAGUUCAAACUCUAUUAGAAGAGCUAACUGGUAA-----------------
...((((((((....((((...(((((((((((((..........((.....))......)))))))))))))))))...))))))))...............----------------- ( -23.69)
>DroSec_CAF1 101844 115 + 1
CGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACUCUAUUUGAAGAGCUAACUGGUACUGCAACAAUAU-----A
.....(((.(((((.(((....(((((((((((((.........(((.....))).....))))))))))))).....((((......)))).))).)))))..))).......-----. ( -25.84)
>DroSim_CAF1 102337 115 + 1
CGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUGCAAUUCAAGUUCAAGUUUAAACUUUACCAGAAGAGCUAACUGGUACUGCAACAAUAU-----A
.....((((.((..........(((((((((((((......((.(((.....)))))...)))))))))))))........((((((.........))))))..))))))....-----. ( -26.60)
>DroEre_CAF1 92667 119 + 1
CGAUCUGGUGGGUAAUUGAAAUACCUGAUCUUGAAAAAGAUCGCUGGUAUUAGCAUACAAU-CAAGUUCAAGUUUAAGCUUUAUCAGAAGAGCUAAUUGGUACUGCAUGAAUAUUCUAUA
.......(((((..(((.((((((((((((((....)))))))..)))))).((((((...-..(((((((((....))))........))))).....))).))).).)))..))))). ( -24.90)
>DroYak_CAF1 107104 104 + 1
CGAUCUGGUGGGUAAUUGAAAAACUUGAACUUGAAAAAGAUCGCUUGUAUUAGCAUACAAUUCAAGUUCAAGUUAAAACUUUCUUAGAAUAUU-AUAUCAUAAAG---------------
.(((.(((((.......((((((((((((((((((....((.(((......)))))....)))))))))))))).....))))......))))-).)))......--------------- ( -24.52)
>consensus
CGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACUUUAUUAGAAGAGCUAACUGGUACUGCA__AAUAU_____A
...((((((((....((((...(((((((((((((.........................)))))))))))))))))...))))))))................................ (-14.11 = -15.51 +   1.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,608,242 – 11,608,345
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.88
Mean single sequence MFE -26.80
Consensus MFE -16.88
Energy contribution -16.72
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -2.72
Structure conservation index 0.63
SVM decision value 2.43
SVM RNA-class probability 0.993879
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11608242 103 - 23771897
-----------------UUACCAGUUAGCUCUUCUAAUAGAGUUUGAACUUGAACUUGAAUUGUAUGCUAAUUGCGGUGAUUUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCG
-----------------...((((((((((((......))))))...(((((((((((((..((.(((.....)))...))....))))))))))))).....))))))........... ( -29.40)
>DroSec_CAF1 101844 115 - 1
U-----AUAUUGUUGCAGUACCAGUUAGCUCUUCAAAUAGAGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCG
.-----...(((((......((((((((((((......))))))...(((((((((((((..(..(((.....))).....)...))))))))))))).....))))))..))))).... ( -31.00)
>DroSim_CAF1 102337 115 - 1
U-----AUAUUGUUGCAGUACCAGUUAGCUCUUCUGGUAAAGUUUAAACUUGAACUUGAAUUGCAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCG
.-----...(((((((..((((((.........))))))........((((((((((((((..(.(((.....))))..)).....))))))))))))..........)).))))).... ( -32.80)
>DroEre_CAF1 92667 119 - 1
UAUAGAAUAUUCAUGCAGUACCAAUUAGCUCUUCUGAUAAAGCUUAAACUUGAACUUG-AUUGUAUGCUAAUACCAGCGAUCUUUUUCAAGAUCAGGUAUUUCAAUUACCCACCAGAUCG
.............((.((((((....((((..........))))....((((((...(-(((((............))))))...))))))....)))))).))................ ( -19.30)
>DroYak_CAF1 107104 104 - 1
---------------CUUUAUGAUAU-AAUAUUCUAAGAAAGUUUUAACUUGAACUUGAAUUGUAUGCUAAUACAAGCGAUCUUUUUCAAGUUCAAGUUUUUCAAUUACCCACCAGAUCG
---------------...........-..........((((.....((((((((((((((..(..((((......))))..)...))))))))))))))))))................. ( -21.50)
>consensus
U_____AUAUU__UGCAGUACCAGUUAGCUCUUCUAAUAAAGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCG
...............................................(((((((((((((.....((((......))))......)))))))))))))...................... (-16.88 = -16.72 +  -0.16)

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 11:11:44 2006